Philippe Rinaudo

Yann Ponty

Dominique Barth

Alain Denise

Tree decomposition and parameterized algorithms

Introduction

The RNA structure-sequence comparison problem arises in two main kinds of applications: searching for a given structured RNA in a long sequence or a set of sequences, and three-dimensional modeling by homology. In [START_REF] Jiang | A general edit distance between RNA structures[END_REF], Jiang and al. addressed the problem of pairwise comparison of RNA structures in its full generality. They defined the edit distance problem on RNA structures represented as graphs, using a set of atomic edition operations. Notably, they gave a dynamic programming algorithm in O(nm 3 ) time complexity for comparing a sequence to a nested structure where n is the length of the sequence with known structure and m the length of the sequence of unknown structure. They also established that computing the edit distance between a sequence and a structure is a Max-SNP-hard problem if the structure contains pseudoknots.

Meanwhile, consiodering all the known interactions in RNAs including non-canonical ones [START_REF] Leontis | Geometric nomenclature and classification of RNA base pairs[END_REF] and pseudoknots is crucial for precise structure-sequence alignment. In [START_REF] Jiang | A general edit distance between RNA structures[END_REF], a polynomial algorithm was developed for pseudoknotted structures, but it involves constraints on the costs of the edition operations. It has been observed that the so-called H-type and kissing-hairpin pseudoknots represent more than 80% of the pseudoknots in known structures [START_REF] Rødland | Pseudoknots in RNA secondary structures: representation, enumeration, and prevalence[END_REF]. If the structure contains only only H-Type pseudoknots, the alignment problem can be solved in O(nm 3 ) [START_REF] Han | Structural alignment of pseudoknotted RNA[END_REF][START_REF] Wong | Structural alignment of RNA with complex pseudoknot structure[END_REF]. Moreover, in [START_REF] Han | Structural alignment of pseudoknotted RNA[END_REF] these two classes of pseudoknots where embedded into a more general class, the standard pseudoknots. Two O(nm k ) and O(nm k+1 ) algorithms, respectively for a single standard pseudoknot, and for a standard pseudoknot which is embedded inside a nested structure were developed, where k is the so-called degree of the pseudoknot. Recently, the more general class of simple non-standard pseudoknots was defined, and an algorithm was given in O(nm k+1 ) if alone, or in O(nm k+2 ) for a simple recursion [START_REF] Wong | Structural alignment of RNA with complex pseudoknot structure[END_REF].

In the present paper, we give a general setting for sequence-structure comparison in a large class of RNA structures that unifies and generalizes all the above families of structures. Notably, we handle structures where every nucleotide can be paired to any number of other nucleotides, thus considering all kinds of non-canonical interactions [START_REF] Leontis | Geometric nomenclature and classification of RNA base pairs[END_REF]. Our approach is based on tree decomposition of structures and gives rises to a general parameterized algorithm, where the exponential part of the complexity depends on the family of structures. For each of the previously studied families, our algorithm has the same complexity as the specific algorithm that had been given before. Table 1 give a summary of the previous works that are generalized by our approaches, and the time complexity of our algorithm for each of the classes.

O(nm k+2 ) O(nm 3 ) O(nm k+1 ) O(nm k ) O(nm k ) O(nm k+2 ) O(nm k+1 ) O(nm k+1 ) O(nm 3 ) O(nm 3 ) √ √ √ √ √ - [6] [5] [5] - - [11] - [11] [10]
Table 1. Summary of existing algorithms for structure-sequence alignment. Our approach unifies all these algorithms and, for each class of structures captured by pre-existing works, specializes into time complexities that matches previous efforts: the tree structure represents an inclusion relation. Hence the root class RCS includes all other classes. Notation: k is the degree of the pseudoknot/(simple) standard structure.

Sequence-Structure Alignment

At first let us state some definitions, starting with the concept of arc-annotated sequence, which will be used as an abstract representation for RNA structure.

Definition 1 (Arc-annotated sequence). An arc-annotated sequence is a pair (S, P ), where S is a sequence over an alphabet Σ and P is a set of unordered pairs of positions in S.

For RNA structures, obviously S is the nucleotide sequence and P the set of the interactions over S, as illustrated by Figure 2 (Upper part). Here Σ = {A, U, G, C}, and any (i, j) ∈ P represents an interaction between the nucleotides at position i and j. The nucleotides are numbered from 1 to n (where n is the sequence length), follow a 5' to 3' order, and S[i] denotes the nucleotide number i. One should notice that, unlike most definitions, a position i can be involved in multiple interactions, allowing for the representation of tertiary structures. In the following, we sometimes refer to such an arc-annotated sequence as an RNA graph interaction structure or, in short, an RNA graph.

There exists several equivalent ways to define a structure-sequence alignment, that is an alignment between an arc-annotated sequence and a (plain) sequence. We choose to abstract an alignment as a mapping, i.e. we represent an alignment as a partial mapping between positions in the arc-annotated sequence and positions in the plain sequence, as shown in Figure 2.

Definition 2 (Structure-Sequence Alignment). A structure-sequence alignment between an arcannotated sequence A = (S A , P A ) of size n and a plain sequence

B = (S B , ∅) of size m is a partial mapping µ from [1, n] to [1, m + 1] such that:
µ is injective.

µ preserves the order: µ(i) < µ(j) ⇒ i < j.

We write F (A, B) (or F when there is no ambiguity) for the set of all possible alignments between A and B.

Remark that some positions in the arc-annotated sequence may be without a corresponding position in the plain sequence. We note µ(i) =⊥ if position i does not have an image by µ, and qualify it as unmatched. Consecutive sequences of unmatched positions in the structure (µ(i) =⊥) or in the sequence (µ -1 (i) =⊥) are usually grouped and scored together. A (composite) gap is then the maximum set of consecutive positions (i, . . . , j) that are either unmatched or do no have an antecedent by µ. The length |g| of a gap g is simply the number of positions it contains. By grouping unmatched positions within gaps, one can handle affine penalty functions in the cost function. Let us now define the cost of an alignment, which captures the level of similarity between two RNAs, and needs account both for structure and sequence elements.

Definition 3 (Cost of a Sequence-Structure Alignment). The cost of a structure-sequence alignment µ between an arc-annotated sequence A = (S A , P A ) of size n and a plain sequence B = (S B , ∅) is defined by:

Cost(µ) = i∈[1,n],µ(i) =⊥ γ(i, µ(i)) + gap g⊂A λ A (|g|) + gap g⊂B λ B (|g|) + (i,j)∈PA ϕ(i, j, µ(i), µ(j)) (1)
where γ(i, µ(i)) is the cost of a base substitution between position i in A and position

µ(i) in B. -λ Y (x) = α Y • x + β Y ,
is the affine cost penalty for a gap of length x in a sequence Y .

ϕ(i, j, µ(i), µ(j)) is the cost of an arc removing (µ(i) = µ(j) =⊥), arc altering (µ(i) or µ(j) =⊥) or arc substitution involving paired positions i and j in A.

Note that unlike the score functions defined in [START_REF] Han | Structural alignment of pseudoknotted RNA[END_REF][START_REF] Wong | Structural alignment of RNA with complex pseudoknot structure[END_REF], our formulation captures arc-alterations and arc-breakings as atomic operations on their interactions (as in [START_REF] Jiang | A general edit distance between RNA structures[END_REF]), allowing for general cost schemes.

Definition 4 (Structure-Sequence Alignment Problem). Given an arc-annotated sequences A and a plain sequence B = (S B , ∅), the structure-sequence alignment problem is to find an alignment between A and B having the minimum cost.

As stated in [START_REF] Zhang | Computing similarity between rna structures[END_REF][START_REF] Blin | Alignment of RNA structures[END_REF] the problem is already NP-Hard if we consider Crossing interactions (i.e. pseudoknots, without multiple pairings). In the following, we will use a parameterized approach to handle general structures including unrestricted crossing interactions and multiple interactions per position, assuming that the total number of interactions per position is bounded by a constant.

Tree Decomposition and Alignment Algorithm

As previously sketched, our alignment algorithm relies on tree decomposition of an arc-annotated sequence. Tree decompositions are usually defined on graphs rather than on arc-annotated sequences.

Here we give a straightforward adaptation that preserves all the properties of the standard tree decompositions.

Definitions

Definition 5 (Tree Decomposition of an arc-annotated sequence). Given an arc-annotated sequence A = (S, P ), a tree decomposition of A is a pair (X, T ) where X = {X 1 , . . . , X N } is a family of subsets of positions {i, i ∈ [1, n]}, n = length(S), and T is a tree whose nodes are the subsets X l (called bags), satisfying the following properties: Fig. 2. An arc-annotated sequence and an associated tree decomposition. Each bag contains three positions, so the tree width of this tree decomposition is 2. As there is only one bag which does not respect the smooth property (the one with two children), the tree decomposition is 1-weakly-smooth.

Each position belongs to a bag

: l∈[1,N ] X l = [1, n].
2. Both ends of an interaction are present in a bag:

∀(i, j) ∈ P , ∃l ∈ [1, N ], {i, j} ⊂ X l . 3. Consecutive positions are both present in a bag: ∀i ∈ [1, n -1], ∃l ∈ [1, N ], {i, i + 1} ⊂ X l . 4. For every X l and X s , l, s ∈ [1, N ], X l ∩ X s ⊂ X r
for all X r on the path between X l and X s .

Figure 2 illustrates the tree decomposition of an arc-annotated sequence.

Definition 6 (Treewidth). The width of a tree decomposition (X, T ) is the size of its largest set X l minus one. The treewidth t w (A) of an arc-annotated sequence A is the minimum width among all possible tree decompositions of A.

In general, tree decomposition are not rooted. Nevertheless, for the sake of clarity, we will arbitrarily choose a root X 0 in our decompositions. Additionally, we use the following notation: for any two bags X l and X r in X, we write X l,r as shorthand for X l ∩ X r .

The process of assigning consecutive positions can be simplified by the affine gap penalties, using the general idea of Gotoh's algorithm [START_REF] Gotoh | An improved algorithm for matching biological sequences[END_REF]. Let us then define the notion of smooth bag, that will help us take advantage of this optimization.

Definition 7 (Smooth Bag of a Tree Decomposition). Let X l ∈ X be a bag in a tree decomposition (X, T ) for an arc-annotated sequence A = (S, P ). If X l = X 0 , then let X r be its father. X l is then smooth iff there exist two consecutive positions i and j such that i ∈ X l -X r , j ∈ X l,r , j is not in one of the child of X l , and there is no i ′ ∈ X l -X r such that (i ′ , j) ∈ P or i ′ (except i) consecutive to j. The root X 0 is smooth iff (1) there exist two consecutive positions i, j ∈ X 0 such that j is not in any child of X 0 and (i, j) / ∈ P , or (2) iff the size of the root is strictly smaller than the size of one of its children.

Definition 8 ((Weakly-)Smooth Tree Decomposition).

A tree decomposition (X, T ) for an arc-annotated sequence A = (S, P ) is smooth iff every bag X l ∈ X are smooth. A tree decomposition (X, T ) is k-Weakly-Smooth iff at most k of its bags are not smooth.

As stated in [START_REF] Bodlaender | Treewidth: Algorithmic techniques and results[END_REF], a tree decomposition can always be converted into a binary tree in linear time. Moreover, this transformation can be done without breaking the smoothness of the tree decomposition. Therefore, we will limit, without loss of generality, the scope of our algorithm and analysis to binary tree decompositions. At last, if the tree decomposition is smooth and root X 0 is smooth by condition (1), then the tree can made smooth by condition (2) by creating a new root composed of the positions of the old one except the position i (with i as in the definition above) and add it as the father of X 0 . In the following we will only consider case (2) for the alignment algorithms.

An Alignment Algorithm based on Tree Decomposition

Let us describe an algorithm that computes the minimum cost alignment of an arc-annotated sequence A and a (flat) sequence B (P B = ∅). This algorithm implements a dynamic programming strategy, based on a k-Weakly-Smooth tree decomposition of A. An alternative internal representation for alignments. The recursive step in our scheme consists in extending a partial alignment, assigning positions that are proper to the bag (i.e. not

A G C G C C A A U C A A G G U 2 1
3 4 5 6 7 8 9 10 11 12 13 14 15

A G C G C C A A U C A A G G U 2 1
3 4 5 6 7 8 9 10 11 12 13 14 15 16

Fig. 3. Internal representation of alignments as a pair f = (µ, δ), used within our dynamic programming algorithm. A function µ defines a complete mapping, while δ discriminates matched positions (solid stroke) from unmatched ones (dashed stroke). Additionally, unmatched positions are forced to aggregate to their nearest matched neighbor to their right, and we create an additional virtual position (16 here) to provide an image to trailing unmatched positions in the structure.

present in the bag's father). One of the main challenge is to preserve the sequential order. Indeed, only consecutive positions (i, i + 1) are guaranteed to be simultaneously present in a bag, allowing for a direct control over the sequential ordering (µ(i) < µ(i + 1)) at the time of an assignment. Intuitively, this property may extend transitively over µ, since µ(i) < µ(i + 1) and µ(i + 1) < µ(i + 2) implies µ(i) < µ(i + 2). However, this property no longer holds when a position is unmatched, as µ(i + 1) is then undefined and cannot serve as a reference point for the relative positioning of µ(i) and µ(i + 2).

To work around this issue, we identify, in the description of our algorithm, an alignment with a pair f = (µ, δ), where µ :

[1, n] → [1, m + 1] is a full ordered mapping (µ(•) =⊥) and δ : [1, n] → [0, 1]
distinguishes between matched (δ(i) = 1) and unmatched positions (δ(i) = 0). As illustrated by Figure 3, this new representation aggregates consecutive unmatched positions in A to their nearest rightward position that is matched in the alignment. A virtual position m + 1 is then added to B to serve as an image for the unmatched positions appearing at the end of A.

Dynamic programming recursion. Our dynamic programming algorithm assigns positions in B to the elements of a bag, proceeding to a recursive call that assigns the positions found further down in the tree decomposition. This requires a few additional notions and definitions.

Let (S, P ) be an arc-annotated sequence, and S ′ be a subset of S. The arc-annotated subsequence induced by S ′ is the pair (S ′ , P ′ ) such that P ′ is the subset of arcs in P whose both extremities are in S ′ . Let X l be a bag in the tree-decomposition of A. The descending subsequence of X l is the subset of positions appearing in the descendants of X l in the tree. The descending arc-annotated subsequence of X l is the arc-annotated subsequence induced by its descending subsequence. The notion of alignment between A and B naturally extends to alignments involving a sub-arc-annotated structure of A, and we denote by F | S ′ the set of all possible alignments between the arc-annotated subsequence induced by S ′ , and B.

Let X l be a bag having father X r (X r := X l when l = 0), let f ∈ F | X l,r be an alignment for the common positions of X l and X r to B. Let us denote by C l f the cost of the best alignment between the descending arc-annotated subsequence of X l and B, which matches f on X l,r . It can be shown that C l f obeys

C l f = min f ′ =(µ ′ ,δ ′ )∈F |X l f ′ (i)=f (i),∀i∈X l,r    LCost(X l , f ′ ) + s∈sons(l) C s f ′ |X s,l    . (2)
Moreover, the local contribution LCost(X l , f ) of a bag X l to an alignment f = (µ, δ) is

LCost(X l , f ) = i∈X l -Xr δ(i)=1
γ(i, µ(i)) + i,j∈X l s.t. i or j∈X l -Xr and (i,j)∈PA ϕ(i, j, f (i), f (j))

// Bases and interactions + i,i+1∈X l s.t. i or i+1∈X l -Xr and µ(i+1)>µ(i)

α B • (µ(i + 1) -µ(i)) + β B , // Gaps in sequence B + i,i+1∈X l s.t. i or i+1∈X l -Xr δ(i)=1 and δ(i+1)=0 β A + i∈X l -Xr s.t. δ(i)=0 α A , // Gaps in sequence A assuming a gentle abuse of notation, in which f (i) = {µ(i) if δ(i) = 1, or ⊥ otherwise}.
A dynamic programming algorithm follows from this general recurrence equation, in a standard way. The cost of the best alignment is given by min{C

0 f | f ∈ F | X0 }.
A simple backtrack procedure gives the best alignment between A and B. The following theorem gives the worst-case complexity of the algorithm.

Theorem 1. Let A and B be two arc-annotated sequences (P B = ∅), and let (X, T ) be a tree decomposition of A. The structure-sequence alignment of A and B can be computed in Θ(N • m t+1 ) time and Θ(N • m t ) in space, where N = |X|, t is the tree-width of (X, T ), and m = |B|. This complexity can be further improved when the tree decomposition is smooth (or even only kweakly smooth), by taking advantage of the affine nature of gap penalty functions. To that purpose, one uses the general principle underlying Gotoh's algorithm [START_REF] Gotoh | An improved algorithm for matching biological sequences[END_REF], and introduce a secondary matrix to distinguish gap openings from gap-extensions. We obtain the dynamic programming equation summarized in Figure 4 Theorem 2. If the tree decomposition of A is k-weakly smooth, then the sequence-structure alignment of A and B, can be computed in Θ(k

• m t+1 + (N -k) • m t ) time.
Corollary 1. Let A and B be as before. If the tree decomposition (X, T ) of A is smooth and has width t, then time complexity of the structure-sequence alignment algorithm is in Θ(N • m t ).

Tree Decomposition and Sequence Structure Alignment of RNA Structures

In its full generality, the problem of computing a tree decomposition of minimum width for an arc-annotated sequence is NP-Hard [START_REF] Arnborg | Complexity of finding embeddings in a k-tree[END_REF]. However, by restricting the problem to some specific RNA structure families, one can obtain a tree decomposition with a small width in reasonable time. The key idea relies on a total ordering of the positions in the arc-annotated sequence, as shown in the following. For the sake of clarity, we suppose at first that there is no unpaired position in the structure.

Definition 9. A wave embedding W of an arc-annotated sequence A = (S, P ) is defined by an increasing sequence of pivot positions y = {y i } k i=0 , such that y 0 := 1 and y k := n (Figure 5). The degree of a Wave Embedding is its number of pivots minus one. Now, a total ordering on the interactions can be inferred from a wave embedding, in which case the wave embedding is said to be ordering. Let us now give a sufficient condition for a given embedding to be ordering. To that purpose, we introduce the upward graph, and show that its acyclicity is a sufficient condition for the embedding to be ordering.

C

l f = min                                  A If δ(i -1) = 0: Aggregate i on i -1 (µ ′ (i) = µ(i -1)). B If δ(i -1) = 1: i is either next to i -1 (µ ′ (i) = µ(i -1) + 1, no gap). . . min f ′ =(µ ′ ,δ ′ )∈F | X l s.t.f ′ =f on X l,r ∆ l (f ′ )
C . . . or further away: Open a gap and shift i-1 to avoid testing every position for i. (µ ′′ (i -1) = µ(i -1) + 1, and

f ′′ = f otherwise) αB + βB + D l f ′′ D l f = min                        D Found a position for i (µ ′ (i) = µ(i - 1) + 1). min f ′ =(µ ′ ,δ ′ )∈F | X l s.t.f ′ =f on X l,r ∆ l (f ′ )
E Look one step further for a suitable position for i (δ(i -1) = 1, µ ′′ (i -1) = µ(i -1) + 1)

αB + D l f ′′ 2. C l f = min                                  A' If δ ′ (i) = 0: Aggregate i on i + 1 (µ ′ (i) = µ(i + 1)). B' If δ ′ (i) = 1: i can be right before i + 1 (no gap). . . min f ′ =(µ ′ ,δ ′ )∈F | X l s.t.f ′ =f on X l,r ∆ l (f ′ )
C' . . . or further away: Open a gap and virtually shift i+1 to avoid testing every candidate position for i. (µ ′′ (i + 1) = µ(i + 1) -1, and

f ′′ = f otherwise) αB + βB + D l f ′′ D l f = min                            D' If δ ′ (i) = 1: Found position for i (µ ′ (i) = µ(i + 1) -1) ⇒ No added gap min f ′ =(µ ′ ,δ ′ )∈F | X l s.t.f ′ =f on X l,r ∆ l (f ′ ) E' If δ(i + 1) = 1, µ ′′ (i + 1) = µ(i + 1)
-1, and f ′′ = f otherwise: Virtually shifting i + 1 to avoid testing every candidate position for i.

αB + D l f ′′ ∆ l (f ) := LCost(X l , f ) + s∈sons(l) C s f | X s,l
Fig. 4. Dynamic programming equation for aligning a smooth bag X l , whose father Xr has previously been assigned. Case 1. and 2. above apply respectively to smooth bags such that i -1 ∈ Xr or i + 1 ∈ Xr (note that these two cases are mutually exclusive from the definition of smoothness).

Given a wave embedding W of an arc-annotated sequence A = (S, P ), we call intervals of W the half open intervals: I t = [y t , y t+1 [ for t ∈ [1, k -2] and the interval I k = [y k-1 , y k ]. Now, let us start by defining a partial order • ≺ • on the positions of a single interval, as follows: for any i, j ∈ I t , one has i ≺ j if either i < j and t is odd, or i > j and t is even. This relation can be used to define the position directly below i, i.e. the closest position i -to i such that i -≺ j. In other words, one has i -= i -1 if i, i -1 belong to an odd interval, and i -1 ∈ I t or i -= i + 1 if i, i + 1 belongs to an even interval. In the absence of such a position, we set i -= 0. The highest position of an interval I t is the position i ∈ I t such that there is no position j in I t with i ≺ j. Now we can define the upward graph: Definition 10. Given a wave embedding W of an arc-annotated sequence A = (S, P ), the upward graph of A associated to W is the directed graph G = (V G , A G ) such that V G = P , and A G is the set of arcs ((i, j) → (i ′ , j ′ )) such that i or j is directly below i ′ or j ′ in W . A wave embedding of an arc-annotated sequence A = (S, P ) is ordering if its upward graph is acyclic.

Algorithm 1 takes as input an upward graph, supposed to be acyclic, and assigns a level for each vertex, thus a level for each interaction of the associated arc-annotated sequence . This algorithm is a straightforward modification of Kahn's topological ordering algorithm [START_REF] Kahn | Topological sorting of large networks[END_REF], illustrated in Figure 6.

Now we define the level of any position as the minimum level of all interactions in which the position is implicated, as illustrated in Figure 6.

Algorithm 1: Level Algorithm

Input : a directed acyclic graph G = (VG, AG) Output: Assign a level for each vertex

-L = {v ∈ VG, d -(v) = 0} -For each v ∈ L, level(v) = 1 -While L = ∅: • pop front v from L. • For each v ′ such that (v, v ′ ) ∈ AG: * remove (v, v ′ ) from AG * If d -(v ′ ) = 0: • push back v ′ into L • level(v ′ ) = level(v) + 1
Definition 11 (Level of a position). Given an ordering wave embedding W of an arc-annotated sequence A = (S, P ), the level of a position i defined by: level(i) = min (i,j)∈P (level((i, j))). We define a total order on S through: i j iff either level(i) < level(j), or level(i) = level(j) and i < j.

Then, we introduce Algorithm 2 which, starting from an ordering wave embedding, decomposes any arc-annotated sequence. The key idea is to create a root which contains the highest position in each interval. The successor of a bag is then obtained by changing the highest level position into the position directly below it (Figure 6). Theorem 3. Given an ordering wave embedding of degree k for an arc-annotated sequence A, then a tree decomposition of A having width k can always be computed in time O(k • n).

Corollary 2. Let A and B be two arc-annotated sequences with P B = ∅. Given an ordering wave embedding of degree k of A, the structure-sequence alignment of A and B can be computed in O(n•m k ).

Application to three general classes of structures

In this section, we define three new structure classes, which respectively generalize the standard pseudoknots [START_REF] Han | Structural alignment of pseudoknotted RNA[END_REF], the simple non-standard pseudoknots [START_REF] Wong | Structural alignment of RNA with complex pseudoknot structure[END_REF] and the standard triple helices [START_REF] Wong | Structural alignment of RNA with triple helix structure[END_REF]. For each of them, a natural ordering wave embedding can be found, such that our general alignment algorithm has the same complexity as its, previously introduced, ad hoc alternatives.

Algorithm 2: Chaining Algorithm

Input : an arc-annotated sequence A and an ordering wave embedding of degree k Output: A tree decomposition of A -Assign a level for each interaction using Algorithm 1, and map level to each position -X = ∅ and T is an empty tree -Create a node X0 composed of the highest position of each interval and set X0 as the root of T l = 0 -While there is a position i ∈ X l such that i -= 0 • Search the position p ∈ X l with the highest level and such that p -= 0

• Add p -to X l • Add X l to X • If l > 0, set X l as the son of X l-1 • Set l = l + 1 and X l = X l-1 -{p} -Return (X, T )

Standard Structures

Here we define and describe the alignment of standard structures, a natural generalization of the standard pseudoknots defined by Han et al [START_REF] Han | Structural alignment of pseudoknotted RNA[END_REF]. The main specificity of this class is that bases can interact with several other bases. This allows the consideration oft multiple non-canonical interactions (e.g. base triples) in RNA structures (see Figure 7.A).

Definition 12 (Standard Structure

). An arc-annotated sequence A = (S, P ) is a standard structure if there exists an ordering wave embedding, based on a pivot list y = {y i } k i=0 , k > 1, such that the extremities of any interaction (i, j) ∈ P are separated by exactly one pivot.

The ordering wave embedding can then be used by Algorithm 2 to yield a smooth tree decomposition of width k, therefore the complexity of the structure-sequence alignment is O(n • m k ).

Simple Non-Standard Structures

In [START_REF] Wong | Structural alignment of RNA with complex pseudoknot structure[END_REF], the algorithm of [START_REF] Han | Structural alignment of pseudoknotted RNA[END_REF] is extended to capture the so-called simple non-standard pseudoknots. Briefly, a simple non-standard pseudoknot contains a standard pseudoknot, and defines a special region from which interactions may initiate, possibly crossing interactions in the standard pseudoknot. We extend this class in order to capture multiple interactions, as illustrated by Figure 7.B. Definition 13 (Simple Non-Standard Structure). An arc-annotated sequence A = (S, P ) is a simple non-standard structure (Type I) if there exist an ordering wave embedding, based on a pivot list y

= {y i } k i=0 , k > 1 and τ ∈ [1, k -k ′ -1], k ′ ∈ {1, 2}
, such that the extremities of any interaction (i, j) ∈ P with j < y k-k ′ are separated by exactly one pivot and the others interactions (i, j) ∈ P with y k-k ′ ≤ j are such that y τ -1 i < y τ .

As in [START_REF] Wong | Structural alignment of RNA with complex pseudoknot structure[END_REF], Type II simple non-standard structures are symmetric to Type I: the special region lies on the beginning of the sequence. To be coherent with the definition of simple non-standard pseudoknots given in [START_REF] Wong | Structural alignment of RNA with complex pseudoknot structure[END_REF], we define the degree of a standard structure as it number of pivots in its ordering wave embedding. Therefore, the treewidth of a simple non-standard structure of degree k + 1 is at most k + 1 and, given its pivots sequence, we can build a smooth tree decomposition of width k + 1. Hence the complexity of the structure-sequence alignment is O(n • m k+1 ).

Extended Standard Triple Helices

To our knowledge, the standard triple helices [START_REF] Wong | Structural alignment of RNA with triple helix structure[END_REF] constitute the first attempt to handle base triples in sequence/structure alignments. A standard triple helix is a kind of standard pseudoknot of degree 3 where some positions are allowed to be involved in multiple base pairs. We define the extended standard triple helix as the structures admitting an ordering wave embedding of degree 3 (Figure 7.C). This new class strictly includes standard triple helices. Furthermore, each such structure can be represented by a tree-decomposition which is smooth and has width at most 3. This gives an algorithm in O(n • m 3 ) for the structure-sequence alignment.

Recursive Structures

Now we consider much more general RNA structures, where different kinds of pseudoknots can occur anywhere. As will be seen below, such structures can be decomposed into primitives, and from the tree-decomposition of each primitive a global tree-decomposition of the structure can be built. The set of primitive sub-arc-annotated subsequences (primitives for short) of an arc-annotated sequence is the set of all sub-arc-annotated sequences induced by the connected components of its conflict graph, which is defined as follows. The conflict graph G = (V, E) of an arc-annotated sequence A = (S, P ) is the graph such that:

-V = P (the nodes of G are the interactions of A).

-(v 1 , v 2 ) ∈ E with v 1 = (i 1 , j 1 ) and v 2 = (i 2 , j 2 ) (i 1 < i 2 ) iff i 1 < i 2 < j 1 < j 2 (interactions cross).
Algorithm 3: Recursive Algorithm -Compute a tree decomposition for all primitive extensions using Algorithm 2.

-For each primitive A0 of depth 0:

• Create a bag χ containing the right boundary of A0 and the left boundary of its next primitive A ′ 0 . • Let (X 0 , T 0 ) be the tree decomposition of the extension of A0 and (X ′0 , T ′0 ) the one of the extension of A ′ 0 . • Add to χ the position i of the root of (X ′0 , T ′0 ) such that i -1 or i + 1 belongs to the root too.

• Connect the leaf of (X 0 , T 0 ) to χ and connect χ to the root of (X ′0 , T ′0 ).

-For each possible depth i > 0 in increasing order:

• For each primitive A of depth i: * Let (X, T ) be the tree decomposition of the extension of A and (X ′ , T ′ ) the one of the extension of the arc-annotated sequence A ′ in which A is encapsulated. * Find a bag χ in (X ′ , T ′ ) such that χ contains the boundaries of A. * Connect (X, T ) to (X ′ , T ′ ) by connecting the root of (X, T ) to χ. * Add the right-most boundary of A in (X, T ) to all bags from the root to the first bag containing it.

The boundaries of a primitive are its left-most and right-most positions. Let A and A ′ be two primitives of an arc-annotated sequence, and let i ′ and j ′ be the boundaries of A ′ (i ′ < j ′ ). We say that A is encapsulated in A ′ iff for any position i ∈ A, one has i ′ ≤ i ≤ j ′ , and there exists at least one position j ∈ A such that i ′ < j < j ′ . The depth of a primitive of an arc-annotated sequence is the number of primitives which encapsulate it. We say that A is directly encapsulated in A ′ if A is encapsulated in A ′ and depth(A) = depth(A ′ ) + 1.

The extension of a primitive A of depth i is the arc-annotated subsequence consisting of: the primitive A; the boundaries of any primitive that is directly encapsulated in A; and the unpaired positions that are directly encapsulated in A.

Given a primitive A 0 of depth 0 of an arc-annotated sequence A, the next primitive of A 0 is the following primitive of level 0 in the sequential order (note that they can share a boundary). Theorem 4. Let A be an arc-annotated sequence of size n. If there exist an ordering wave embeddings of degree at most k for each extension of its primitives, then the treewidth of A is at most k + 1, and a κ-weakly smooth tree decomposition of A can be built in O(k • n) time, where κ is the number of primitives of odd degree, whose level is greater or equal to 1. Corollary 3. Let A and B be two arc-annotated sequences with P B = ∅. Given an ordering wave embedding of degree k (at most) for each extension of the primitives of A, the structure-sequence alignment of A and B can be computed in O(κ • m k+1 + n • m k ) (with κ defined in Theorem 4).

Conclusion

We have given a general parameterized dynamic programming scheme for sequence-structure comparison in a large class of RNA structures, which unifies and generalizes several families of structures that have been independently considered by previous works. Notably, we can handle structures where each nucleotide can be paired to any number of other nucleotides, thus cqpturing any type of non-canonical interactions. Our approach relies on a tree decomposition approach of arc-annotated sequences represented as wave embeddings, and the treewidth of the decomposition is then equal to the degree of the wave embedding. Computing a wave embedding of small degree is easy for all classes of pseudoknotted structures considered in this paper. However, the problem of finding a minimum degree wave embedding for any kind of pseudoknotted structure remains open.

Fig. 1 .

 1 Fig. 1. A representation of a partial mapping between an arc-annotated sequence (upper part) and a (plain) sequence (lower part).

Fig. 5 .

 5 Fig. 5. A: An arc-annotated sequence with its pivots. B: An embedding wave representation of the same arc-annotated sequence. C: The associated (acyclic) upward graph (interactions are rank by their level).

Fig. 6 .

 6 Fig. 6. A: Arc-annotated sequence and its pivots. B: Ranking of the positions by decreasing for the level. C: Tree decomposition obtained with Algorithm 2. The highlighted position in each bag is the position denoted as position p within Algorithm 2. The last position in each bag is the position p -.

Fig. 7 .

 7 Fig. 7. A: A standard structure and one of its ordering wave embedding representation. B: A simple Non-Standard structure and one of its ordering wave embedding representation (k ′ = 2). C: An extended triple helix and one of its ordering wave embedding representation.

Fig. 8 .

 8 Fig. 8. (A) An arc-annotated sequence and (B) a representation of the tree decomposition given by Algorithm 3. Each box correspond to an extension of a primitive and its associated tree decomposition. Dashed links correspond to the connections made by Algorithm 3. The Dashed bag (top of B) correspond to the bag χ added to connect two consecutive primitive of level 0. The position 8 in a dashed box illustrates the case where the right boundary of a primitive need to be added in its tree decomposition.

  Recursive Classical Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . PKF -Secondary Structures (Pseudoknot-free) . . . . . . . . . . . . . . . ESP -Embedded Standard Pseudoknots . . . . . . . . . . . . . . . . . . . . . . SST -Standard Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . SPK -Standard Pseudoknots. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2RP -2-Level Recursive Simple Non-Standard Pseudoknots . . . SNS -Simple Non-Standard Structures . . . . . . . . . . . . . . . . . . . . . . . SNP -Simple Non-Standard Pseudoknots . . . . . . . . . . . . . . . . . ETH -Extended Triple Helices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . STH -Triple Helices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

	Class of Structures	Time comp.	Multiple interactions	Ref.
	RCS -

  ✁ 2 ✁ 6 ✁ 7 2 ✁ 5 ✁ 6 ✁ 7 9 ✱ 10 ✱ 12 10 ✱ 11 ✱ 12 14 ✱ 15 ✱ 17 15 ✱ 16 ✱ 17 2 ✁ 5 ✁ 4 ✁ 7 2 ✁ 3 ✁ 4 ✁ 7 2 ✁ 3 ✁ 7 ✁ 8

	1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 1 B	1 ✱ 8 ✱ 13 8 ✱ 9 ✱ 13 9 ✱ 12 ✱ 13	1	13 ✱ 14 8 9	12 13	14 15 16 17 15 16	15 ✱ 16
	1 2 3 4 5 6 7 8	8	8	8	8
					10 ✱ 11
				10 11
								9 10 11 12

Acknowledgments

This work was supported by the DIGITEO RNAOmics project (AD, PR and YP), the ANR AMIS ARN project (ANR-09-BLAN-0160, AD and PR) and the ANR MAGNUM project (ANR-2010-BLAN-0204, YP).


Carlson Tuttle

Carlos Agudelo

Remerciements Biographie

AGRADECIMIENTOS / Biografia

Y Prefacio/ Biography

PRÉSENTATION

En Amérique, les garifuna 1 possèdent des singularités qui les distinguent des autres populations d'origine africaine (sub-saharienne) ou que l'on appelle également populations noires, afro-américaines (avec ses variantes nationales du type afrocolombiennes, afro-brésiliennes, afro-cubaines, etc.) ou plus récemment les afrodescendants. Issue d'un métissage entre Africains et indiens caraïbes et arawaks dans les Antilles mineures durant la période coloniale (au XVI e et au XVIII e siècle), leur spécificité repose bien sur l'histoire de leur origine. Vers la fin du XVIII e siècle, les garifuna sont déportés par les Anglais en Amérique centrale. Depuis leur premier peuplement sur le continent à Trujillo, Honduras, le peuple garifuna commence à s'installer de manière, que l'on dirait aujourd'hui, transnationale sur les côtes caraïbes du Honduras, Guatemala, Belize et Nicaragua. C'est ainsi qu'est déclenché le processus d'identification multiple entre l'identité nationale, transnationale, noire y indienne. À partir du milieu du XX e siècle, les garifuna commencent à migrer en grand nombre aux États-Unis. Malgré ces dynamiques de mobilité et de peuplement dans des contextes nationaux et linguistiques très divers, ils préservent, certaines caractéristiques culturelles comme la langue, la religiosité, la musique, la danse et les traditions alimentaires.

La publication de cette compilation bibliographique sur les garifuna s'inscrit dans le cadre des travaux de recherche, de documentation et de diffusion des programmes AFRODESC et EURESCL2 . Une partie de ces travaux a été réalisée en Amérique centrale et d'autres projets sur les garifuna sont toujours en cours. L'auteur de ce travail est Carlson Tuttle, documentaliste et spécialiste des questions socio-culturelles garifuna. Installé au Belize depuis plus de 30 ans, Carlson Tuttle a réalisé une compilation de références multidisciplinaires qu'il a commencé en 1985, comme lui-même le décrit ci-dessous. Ce travail de longue haleine possède à nos yeux une valeur inestimable pour les spécialistes et les personnes intéressées par le sujet.

Odile Hoffmann, chercheure pour les programmes AFRODESC et EURESCL, et moi-même avons eu la chance de rencontrer Carlson Tuttle grâce à notre collègue anthropologue garifuna belizéen, Joseph Palacio. Nous lui avons rendu visite à Barranco, Belize, dans sa maison-bibliothèque où il nous a montré une partie de son travail documentaire qui, à cette époque (2009), comprenait divers formats (papier, listes variées d'archives informatisés etc.).

Nous avions déjà publié, dans le cadre des programmes AFRODESC-EURESCL, des compilations bibliographiques et des anthologies de travaux peu diffusés sur des 1 Le mot garifuna désignant les individus ou la population vient du terme karina en langue arawak qui signifie « mangeurs de manioc ». Quelques auteurs différencient l'usage du mot garifuna au singulier pour désigner les individus et la langue, de l'usage du mot garinagu ou garifunas au pluriel pour parler de la population. On remarquera que dans les références de la compilation, toutes ces différentes formes sont utilisées, tout comme l'expression « Caraïbes noirs »". populations d'origine africaine au Mexique et en Amérique centrale. Face à la valeur d'un tel travail, nous avons proposé à Carlson de systématiser sa compilation d'informations documentaires et bibliographiques afin de l'éditer et de la rendre accessible aussi bien aux chercheurs qu'aux propres garifunas. Carlson a accepté notre proposition et nous avons dès lors commencé la réalisation de ce projet.

La compilation est composée de 888 titres, publiés entre 1665 et 2012 et classés par Carlson Tuttle dans les domaines suivants : histoire, ethnohistoire, anthropologie, linguistique, spiritualité, musique danse et arts, littérature, santé et médecine, éducation et tourisme. Parmi ces titres, 331 correspondent à des livres et 102 à des travaux universitaires (essentiellement des thèses doctorales). On y trouve également 455 articles de publications périodiques (revues scientifiques) et autres documents difficilement accessibles (actes de colloques, rapports divers, communications).

En observant les références bibliographiques, plusieurs conclusions peuvent être tirées. Dès leur « naissance » en tant que peuple sur l'île de Saint Vincent, les garifuna ont suscité un vif intérêt chez les missionnaires, voyageurs et fonctionnaires coloniaux. Au XVII e siècle, l'existence des garifuna est évoquée pour la première fois dans des chroniques d'auteurs anglais et français. Parmi ces oeuvres, on distingue les chroniques et travaux de linguistique du Père Raymond Breton (Dictionnaire Caraïbe-Français et Grammaire Caraïbe). Au XIX e siècle, les récits de voyages, études linguistiques et rapports coloniaux mentionnent aussi bien les garifuna vivant dans les Antilles mineures que ceux installés dans les nouveaux lieux de peuplement en Amérique centrale. Durant ce même siècle, les travaux d'histoire sont majoritairement écrits par les Anglais. C'est également à cette époque qu'apparaissent les premières références d'auteurs étatsuniens. À la fin du XIX e siècle, les premiers écrits d'anthropologie sont rédigés.

Il faut souligner que les frontières qui séparent les catégories élaborées pour cette bibliographie, sont extrêmement poreuses et que, notamment pour les documents publiés entre le XVIIe et le XIXe siècle, plusieurs travaux peuvent être considérés comme appartenant aussi bien à l'histoire qu'à l'anthropologie, l'ethnohistoire ou la géographie.

Parmi les 590 références de la compilation publiées au XX e siècle, seules 40 datent de la première moitié du siècle alors que 550 correspondent aux travaux réalisés après 1950. C'est dans les années 1950 que l'on voit apparaître les premières thèses doctorales sur les garifuna, parmi lesquelles se distinguent celle de l'anthropologue nord-américaine Nancie Gonzalez (une des auteures les plus prolifiques sur le sujet), The Consanguineal Household among the Black Carib of Central America, et celle de l'anthropologue brésilien Ruy Galvao de Andrade Cohelo, The Black Carib of Honduras. En 1951, le linguiste et anthropologue anglais Douglas MacRae Taylor écrit l'une des principales oeuvres de référence sur les garifuna, The Black Caribs of British Honduras. La première édition de l'oeuvre de Palacio (1973) et de l'intellectuel et dirigeant politique Roy [START_REF] Cayetano | Garifuna Songs of Mourning[END_REF], tous deux Belizéens, ainsi que la publication d'un dictionnaire garifuna-espagnol par l'essayiste hondurien Humberto Rivera y Morillo (1977).

Dans les années 1980, la tendance ne faiblit pas avec des publications et des travaux universitaires (masters et thèses doctorales principalement d'universités nordaméricaines). Les problématiques culturelles « indiennes » obtiennent plus de crédibilité au sein de la communauté internationale et les études sur des aspects spécifiques de la culture garifuna tels que la langue ou la religiosité ne cessent de se multiplier. En 1985, l'anthropologue guatémaltèque Alfonso Arrivillaga publie son premier ouvrage sur la culture garifuna au Guatemala. À partir de la fin des années 1980 et du début des années 1990, un processus de visibilisation des problématiques des populations noires en Amérique latine se met en place, dans un contexte de changements institutionnels en matière de reconnaissance de la diversité ethnoraciale dans plusieurs pays de la région. C'est effectivement à cette époque que surgissent les politiques multiculturelles et de reconnaissance. Ce processus aura un impact direct sur le nombre de publications sur les garifuna.

Entre 1990 et la fin de la compilation (2012), le nombre de références double encore par rapport aux deux décennies précédentes. L'établissement en 2001 par l'Unesco de la culture garifuna comme patrimoine intangible de l'humanité sera un autre facteur qui a stimulé la réalisation des recherches et des publications sur le sujet. En effet, près d'un quart des références de cette compilation correspond à la période 2000-2012.

Durant cette période, les études anthropologiques et linguistiques restent les plus nombreuses et la langue garifuna est un aspect de la culture qui a suscité un grand intérêt. Après l'oeuvre pionnière du Père Breton et celle de Taylor, l'ouvrage de la linguiste française Sybille de Pury Toumi est publié dans les années 1990. En anthropologie, l'anthropologue garifuna bélizéen Joseph Palacio, publie en 2005, l' Finalement, lorsque l'on observe la répartition par domaine des références de la compilation de Carlson Tuttle, on constate que la moitié appartient au domaine de l'anthropologie. Si l'on y additionne l'ethnohistoire, la linguistique, la spiritualité, la musique, danse et arts, la littérature ainsi que l'éducation et le tourisme sans oublier la santé et la médecine (généralement un lien entre l'anthropologie, les sciences médicales et la biologie), on constate que l'intérêt suscité par la culture de ces populations est considérable. Les références restantes, soit 10% de la compilation, correspondent à des travaux d'histoire dont la plupart sont extrêmement liés à la culture. Il faut également souligner que plusieurs travaux portant sur des problématiques contemporaines pourraient appartenir également à la sociologie ou aux sciences politiques.

Des 331 livres de la compilation, 155 (47%) ont été publiés aux États-Unis alors que les 54% restants conrrespondent à des publications en Amérique latine (40%) et en Europe (13%). En ce qui concerne les travaux universitaires, sur un ensemble de 192 références, 62 sont des thèses doctorales ; 37 des masters et licences ; 90% de ces documents proviennent d'universités aux États-Unis. Pour les articles de revues et autres références (455), l'anglais est la langue principale de publication (85%).

En matière de travaux universitaires, on note la prédominance des éditions universitaires des États-Unis. Néanmoins, les références commencent progressivement à se diversifier à partir des années 1980, notamment avec l'apparition de publications réalisées dans les pays d'Amérique centrale ayant une population garifuna (principalement au Belize et au Honduras).

Cette compilation de travaux réalisés au fil des siècles (du XVII e au XXI e siècle), dans divers espaces géographiques et sous de multiples formats permet de constater l'existence d'une production bibliographique considérable, mais dispersée et partiellement connue des spécialistes et autres personnes interessées sur le sujet ; sans parler des personnes qui s'intéressent aux populations noires d'autres régions du monde et qui ne connaissent pas l'existence des garifuna. C'est pourquoi les programmes AFRODESC -EURESCL, fidèles à leurs objectifs, se réjouissent de contribuer à l'édition et à la diffusion du travail de Carlson Tuttle. En tant que coordinateur de ce travail d'édition, je ne peux conclure cette présentation sans mentionner le soutien et la participation d'Odile Hoffmann qui furent cruciaux pour sa finalisation. Je remercie également ma fille Mayra Agudelo pour la traduction français-espagnol-anglais de cette présentation ainsi que de celle de Carlson Tuttle.

Carlos Agudelo

Sociologue-Chercheur AFRODESC-EURESCL

Chercheur associé URMIS Unité de Recherche Migrations et Société www.unice.fr/urmis/

PRESENTACIÓN

En América, entre los grupos humanos de origen africano (sub-sahariano) o también llamados poblaciones negras, afroamericanas (con sus declinaciones nacionalesafrocolombianos, afrobrasileños, afrocubanos, etc. etc.) o más recientemente afrodescendientes, los garífuna 3 tienen connotaciones especiales. En su historia y devenir actual llama la atención su origen en el mestizaje entre africanos e indígenas caribes y arawaks en las Antillas menores durante el periodo colonial (siglos XVI al XVIII). Los garifuna son deportados por los ingleses hacia América Central a finales del siglo XVIII. Desde su asentamiento inicial en Trujillo, Honduras, esta población inicia su asentamiento, que actualmente llamariamos transnacional, en las costas caribes de lo que hoy son Honduras, Guatemala, Belice y Nicaragua. Ellos van construyendo un 3 La palabra garífuna con la cual se puede nombrar a los individuos o al grupo de población viene del término Karina en lengua arawak que significaría "comedores de yuca". Algunos autores diferencian la palabra garífuna en singular para nombrar los individuos y la lengua mientras que el grupo de población se le llama garinagu o garífunas en plural. En las referencias de la presente compilación se usan las diferentes formas así como la apelación de "caribes negros". proceso de identificación múltiple entre lo nacional, lo transnacional, lo negro y lo indígena. A partir de mediados del siglo XX los garífuna inician una importante migración hacia los Estados Unidos. En medio de estas dinámicas de movilidad y poblamiento, en contaxtos nacionales y liguisticos diversos, ellos mantienen en un proceso complejo y dinámico ciertas características culturales tales como su lengua, su religiosidad, la música, la danza y sus tradiciones alimentarias.

La publicación de la presente compilación bibliográfica sobre los garífuna se inscribe en el marco de los trabajos de investigación, documentación y difusión realizados por los programas AFRODESC y EURESCL4 . Una parte de este trabajo se ha realizado en América Central y el interés por los pueblos garífuna hace parte de investigaciones que aun están en curso.

El autor de este trabajo, Carlson Tuttle es especialista y documentalista de las problemáticas sociales y culturales de los Garifuna. Radicado en Belice desde hace más de treinta años, Carlson ha realizado esta recopilación de referencias multidisciplinarias desde 1985, como él mismo lo describe en su prefacio. Ha sido un trabajo de largo aliento que consideramos será de gran valor para los especialistas e interesados en el tema.

Con Odile Hoffmann, investigadora de AFRODESC y EURESCL, tuvimos la oportunidad de conocer personalmente a Carlson, a través de nuestro colega, el antropólogo garífuna de Belice, Joseph Palacio. Lo visitamos en Barranco -Belice, en su casa-biblioteca donde nos mostró parte de su trabajo documental que en ese momento ( 2009) se encontraba disperso en varios formatos (impresos, listas varias en archivos informatizados, etc.).

En los programas AFRODESC-EURESCL teníamos ya antecedentes de publicaciones de compilaciones bibliográficas y antologías de trabajos poco difundidos sobre estudios de poblaciones de origen africano en México y América Central. Ante la relevancia del trabajo que de forma empírica venía realizando Carlson, le propusimos efectuar una sistematización de sus recopilaciones de información documental y bibliográfica para editarla difundirla y volverla accesible tanto a los investigadores como a los propios garífuna. Carlson aceptó nuestra propuesta y a partir de esta fecha, el trabajo comenzó a realizarse gradualmente.

La compilación está compuesta por 888 entradas y registra trabajos desde 1665 a 2012 clasificados en las siguientes disciplinas: historia, etnohistoria, antropología, lingüística, espiritualidad, música danza y artes, literatura, salud y medicina, educación y turismo. 331 entradas corresponden a libros, 102 a trabajos universitarios, mayoritariamente tesis de doctorado y 455 son artículos en publicaciones periódicas (revistas científicas) et otros documentos difícilmente accesibles (actas de coloquios, informes, ponencias, y otros formatos).

Una mirada a estas referencias bibliográficas permite inferir algunas reflexiones. Desde su proceso de gestación como pueblo en la isla de San Vicente, los garífuna despertaron el interés de misioneros, viajeros, funcionarios coloniales. Las primeras referencias francesas e inglesas datan del siglo XVII. Se distinguen las crónicas y trabajos de lingüística del abad Raymond Breton (Dictionnaire Caraïbe-Français et Grammaire Caraïbe). Para el siglo XIX siguen sobresaliendo las narraciones de viaje, los estudios de la lengua y los informes coloniales que se refieren tanto a las Antillas menores como a los nuevos asentamientos en América Central. En este siglo predominan los trabajos de historia realizados por ingleses y surgen las primeras referencias de autores estadounidenses. A finales de este siglo XIX aparecen los primeros escritos de antropología.

Hay que señalar que aunque en la presente compilación se realizó una clasificación por disciplinas, las fronteras entre ellas, en particular entre los siglos XVII y XIX son bastante porosas y varios de los trabajos podrían considerarse tanto de historia como de antropología, etnohistoria o geografía. [START_REF] Cayetano | Garifuna Songs of Mourning[END_REF], ambos beliceños, y la publicación de un diccionario garífunaespañol por el ensayista hondureño Humberto Rivera y Morillo (1977).

En los años 1980 continua una tendencia al aumento de publicaciones y la realización de trabajos universitarios (masters y doctorados, principalmente de universidades norteamericanas). Las problemáticas indígenas adquieren más relevancia en la opinión pública internacional y los estudios sobre aspectos específicos de la cultura garífuna, tales como su lengua y su religiosidad siguen incrementándose. En 1985 el antropólogo guatemalteco Alfonso Arrivillaga hace su primera publicación sobre la cultura garífuna en Guatemala. A finales de esta década y principios de los años 1990 se va gestar un proceso de visibilización de las problemáticas de los pueblos negros en América latina en el marco de los cambios institucionales en materia de reconocimiento de la diversidad etnoracial que se produce en varios países de la región. Es la llegada de las llamadas políticas multiculturales o de reconocimiento. Este proceso va a influir directamente en un nuevo aumento de publicaciones sobre los garífuna.

Entre 1990 y la finalización de esta recopilación (2012) se doblaron el número de referencias con respecto a las dos décadas anteriores. La declaración en 2001 de la cultura garífuna como patrimonio intangible de la humanidad por parte de la Unesco será otro factor que estimula la realización de investigaciones y de publicaciones sobre este tema. Prácticamente un cuarto de las referencias de esta compilación corresponde al periodo 2000-2012.

Durante estos años han continuado predominando los estudios antropológicos y de lingüística. En efecto, la lengua garífuna ha despertado un interés relevante entre los aspectos de la cultura de este grupo de población. Ya mencionábamos la obra pionera del abad Breton y los trabajos de Nancie González habla justamente de la transformación entre los garífuna de su forma de auto representación, considerando el tránsito de « Caribes negros » a « Garífunas » como un proceso de etnicización que correspondía a transformaciones en los procesos de politización de la identidad influenciada por la experiencia del movimiento indígena pero igualmente del movimiento negro en Estados Unidos. Hay pues una confluencia en el proceso de transformación en los términos de apelación entre los estudios científicos y las autorepresentaciones de estas poblaciones. Esta tendencia se reforzará en los años 1990 con el advenimiento de las políticas de reconocimiento y el papel protagónico que van jugar las poblaciones negras o de origen africano, entre ellas, los garífuna.

Finalmente, a propósito de la distribución por disciplinas realizada por Carlson Tuttle en esta compilación, cerca de la mitad conciernen a la antropología. Si a dichos registros le agregamos las correspondientes a Etnohistoria, Lingüística, Espiritualidad, Música danza y artes, Literatura y Educación y Turismo, más las de Salud y Medicina (que presentan en general una relación entre antropología, ciencias médicas y biológicas), se evidencia el peso de lo cultural en el interés que ha despertado siempre el estudio de estas poblaciones. El resto de referencias, el 10% de la compilación corresponde a trabajos de Historia, muchos de los cuales también presentan conexiones muy fuertes con la cultura. Hay que señalar que igualmente varios trabajos sobre problemáticas contemporáneas podrían clasificarse también como pertenecientes a la sociología o a las ciencias políticas.

De 331 libros registrados 155 (47%) son publicados en los Estados Unidos, mientras que el 53% restante corresponde a publicaciones en América latina (40 %) y Europa (13%). En cuanto a los trabajos universitarios, de 102 referencias registradas en la compilación, hay 65 tesis doctorales y 37 master y licenciaturas. De estos trabajos el 90% han sido realizados en universidades de los Estados Unidos. Para los artículos de revistas y demás referencias (455) se evidencia la predominancia del inglés como lengua de publicación (85%).

En materia de trabajos universitarios es muy fuerte la supremacía de las universidades de los Estados Unidos. Sin embrago, las referencias comienzan gradualmente a diversificarse a partir de los años 1980, en particular con el surgimiento de publicaciones realizadas en los países centroamericanos con población garífuna (principalmente Honduras y Belice).

Esta compilación, a través del tiempo (publicaciones desde el siglo XVII al XXI), de los múltiples espacios geográficos donde han surgido y de la diversidad de formatos permite observar la existencia de una producción bibliográfica importante pero dispersa y parcialmente conocida aun por los especialistas y otros interesados en el tema. Qué no decir de parte del público que se interesa en las poblaciones negras de otras regiones del mundo y que en múltiples casos desconocen hasta la existencia de los garífuna. Es por esto que los programas AFRODESC -EURESCL, fiel a sus objetivos se complace en poder hacer este aporte de edición y difusión del trabajo de Carlson Tuttle.

Esta compilación está disponible en formato PDF en el sitio http://www.ird.fr/afrodesc/ Las personas interesadas en recibirla en forma de base de datos (lo que les permitirá revisar las referencias en orden alfabético de autores, en orden cronológico, por lugar de edición -para libros y tesis-, etc. podrán hacer una solicitud a ceagarifuna@gmail.com y se les hará un envío del archivo a la dirección e-mail indicada.

Finalmente, como coordinador de este trabajo de edición no puedo terminar esta presentación sin señalar que el apoyo y participación de Odile Hoffmann, fue determinante para su finalización. Agradezco igualmente a mi hija Mayra Agudelo el trabajo de traducción francés-español-inglés de la presente introducción y la presentación de Carlson Tuttle.

Carlos Agudelo

Sociólogo-Investigador AFRODESC-EURESCL

Investigador asociado URMIS Unidad de Investigación Migrations et Société www.unice.fr/urmis/

PRESENTATION

In America, the Garifuna5 have specificities which differentiate them from other populations of African heritage (sub-Saharian) which are also called black populations, Afro-Americans (with its national variations as Afro-Colombians, Afro-Brazilians, Afro-Cubans etc.) or other recent Afro-descendents. In their history and current situation, what draws attention is their origin: a mix of African and Carib and Arawak Indians in the Lesser Antilles during the colonial period (from 16 th to 18 th century). The English sent the Garifuna to Central America by the end of the 18 th century. Since their first settlement in Trujillo, Honduras, the Garifuna started to settle transnationally, as we would say nowadays, on the coasts of Honduras, Guatemala, Belize and Nicaragua. This is how they have been creating a multifaceted identification process between the national, transnational, black and indigenous identities. From the middle of the 20 th century, the Garifuna started to migrate to the United States. Despite these vast changes in settlement, and their diverse national and linguistics contexts, the Garifuna have preserve some cultural traditions such as their language, religiosity, music, dance and nutritional habits.

The publication of this bibliographical collection on the Garifuna is part of research, documentation and dissemination works of the AFRODESC and EURESCL programs. Part of the work was done in Central America and some is still ongoing due to the extreme interest in the Garifuna culture.

The author of this work is Carlson Tuttle, an expert and documentalist on social and cultural issues of the Garifuna. Based in Belize for more than 30 years, Carlson Tuttle has compiled references from various disciplines since 1985, as he describes below. We believe that this long and difficult task is extremely valuable for experts and others interested in the subject.

Odile Offmann, researcher for AFRODESC-EURESCL6 , and myself, had the opportunity to personally meet Carlson. He was introduced to us by Joseph Palacio, our garifuna colleague from Belize, who happens to be an expert anthropologist on the Garifuna. We visited him in Barranco, in his house-library, where he showed us a part of his documentary work, which was by that time (2009), composed documents of diverse formats (printed, various lists of computerized archives and so on).

As part of the AFRODESC-EURESCL programs, we had already published bibliographical collections and anthologies of works poorly disseminated on studies of African descendants in Mexico and Central America, as well as Belize. Due to the relevance of the empirical work of Carlson, we proposed the systematization of his collection of documentary and bibliographical data in order to publish and make it accessible for researchers and the Garifuna people. Carlson accepted and from this moment we gradually started working on the project.

The collection is composed of 888 entries of documents published between 1665 and 2012, classified by Carlson Tuttle within the following disciplines: history, ethnohistory, anthropology, linguistics, spirituality, music dance and arts, literature, health and medicine, education and tourism. There are 331 entries of books, 102 university works, especially doctoral theses and 452 periodical articles (scientific journals), and other documents poorly accessible (conference proceedings, diverse reports and releases).

By analyzing the bibliographical references, we can draw several conclusions. Since its period of gestation as a people on the island of Saint Vincent, the Garifuna strongly attracted the attention from missionaries, travelers and colonial officials. The first references of the Garifuna people can be seen in the seventeenth century from the French and British. Among these references we find the chronicles and linguistics studies of the abbot Raymond Breton (Dictionnaire Caraïbe-Français et Grammaire Caraïbe). During the 19 th century, the Garifuna people are also mentioned in the travel writings, linguistics studies and colonial reports, not only from the Lesser Antilles but also from the new settlements in Central America. During the same century, history works were mostly written by the English and first references by authors from the United States are being published. By the end of the 19 th century, the first writings of anthropology were published.

It is to point out that despite the classification by discipline of this collection, the frontier that separates them are extremely porous between the 17 th and the 19 th century and that several works could be considered as part of history but also of anthropology, ethnohistory or geography.

Of the 590 references published in the 20 th century, only 40 are from the first half while the other 550 works were published after 1950. The fifties is the decade where the first doctoral theses about the Garifuna is witnessed, in particular the doctoral thesis of the North-American anthropologist Nancie Gonzalez (one of the most prolific authors on the subject), The Consanguineal Household among the Black Carib of Central America, and the work of the Brazilian anthropologist Ruy Galvao de Andrade Cohelo, The Black Carib of Honduras. in 1951, the English linguist and anthropologist Douglas MacRae Taylor wrote one of the major works on Garifuna, The Black Caribs of British Honduras. The first edition of Taylor's masterpiece was in 1935 and the last in 1988. His work is mainly composed of articles from scientific publications of anthropology and linguistics.

Until the seventies, there were very few references from Central American authors and the few registered publications in Spanish are translations of works of North American and European authors. This is probably due to the poor development of social sciencesin the academic communities of Central American countries at this time. Between 1970 and1980, the number of publications doubled compared to the previous decade, changing from 46 to 105. During this period, we distinguish the work of the anthropologist Joseph Palacio (1973) and the intellectual and political leader Roy [START_REF] Cayetano | Garifuna Songs of Mourning[END_REF], both Belizeans, as well as the publication of a Garifuna-Spanish dictionary by the Honduran essayist Humberto Rivera y Morillo (1977).

During the eighties, the publications kept increasing and more university works (masters and doctoral theses mainly from universitiesin the United States) were published. The indigenous cultural matters got more credibility with in the international community and the studies of specific aspects of the Garifuna culture, as their language and religiosity keep increasing. In 1985, the Guatemalan anthropologist Alfonso Arrivillaga published his first work on the Garifuna culture in Guatemala. From the end of the eighties to the beginning of the nineties, a process of visibility of the issues of the black population from Latin America was put in place, in the framework of the institutional changes for the recognition of the ethno racial diversity in several countries of the region. This is the beginning of the so-called multicultural or recognition policies. This process has a direct impact on the number of works published on the Garifuna.

Between 1990 and the end of the compilation ( 2012), the number of references doubled compared to the previous two decades. The establishing in 2001 by Unesco of the Garifuna culture as the intangible heritage of humanity was another contributing factor in the stimulus for starting research and publishing more works on the subject. About 25% of the collection is from the period 2000-2012.

From this period, the anthropologic and linguistic works outnumber the rest. Indeed, among the cultural aspects of the Garifuna people, their language has aroused most attention. After referring to the pioneering masterpieces of the abbot Raymond (2000). This period is also marked by the publication of works written by intellectuals and political activists. After mentioning the Belizeans Roy Cayetano and Justo Flores, we can add the Hondureans Salvador Suazo, Crisanto Meléndez, Santos Centeno and Virgilio López García as well as the Guatemalan Mario Ellington. Honduran Historians Darío Euraque and Jorge Amaya can also be noted in this period of great publications.

By observing the references of this collection we see another interesting fact: the titles of the works from the collection reveal data on the changes of identification and representation forms of the Garifuna. The first references (from the 16 th to the beginning of the 20 th century) use the generic denomination Caribs. The first appearance of Black Caribs is in the work of Eduard Conzemus in 1928. He also uses in parentheses the term "Garif". in his numerous and relevant works, Taylor strictly uses the term Black Caribs, as did Cohelo or Nancie Gonzalez if there is to mention some of the greatest authors. In 1974, the term garifuna is used for the first time (yet along with "Black Caribs" in parentheses) in the writings of geographer William Davidson, who strictly used in his last works the term garifuna. By the end of the 1980s, the use of « black Caribs » had almost disappeared. One of the exceptions is the doctoral thesis of the French Nicolas Rey, Quand la Révolution, aux Amériques, était Nègre… Caraïbes Noirs, Negros Franceses et autres «Oubliés» de l'Histoire published in 2005. in an article published in 1976, Nancie Gonzalez discussed indeed the change of self-representation of the Garifuna and stated the transformation from « black Caribs » to « Garifuna » as a process of ethnicization corresponding to a change of the processes of politization of the identity, influenced by the experience of the indigenous movement and the black movement in the United States. Thus there is a confluence in the process of transformation in terms of denomination between the scientific studies and the selfrepresentations of these populations. This was reinforced in the nineties with the entry of recognition policies and the main role the black or Afro-descendent populations, such as the Garifuna played.

Finally, when we look at the distribution of the references by discipline of Carlson's collection, we notice that half of it is classified as belonging to anthropology. If we add to it ethnohistory, linguistics, spirituality, music, dance and arts, literature as well as education and tourism and mention those of health and medicine (generally linked to anthropology, medical and biological sciences), we realize how much attention the culture of these populations attracted. The rest of the references, that is 10% of the collection, are history works which are extremely linked to culture. There is also to mention that most the works on contemporary issues could be classified in sociology or political sciences.

Among the 331 registered books, 155 (47%) were published in the United States while the other 54% were published in Latin America (40%) and Europe (13%). Within the university works, for a total of 192, 62 are doctoral theses and 37 are Masters or Bachelors). 90% of these documents were published in the United States. To periodical articles and other references (455) the vast majority of these works were published in English (85%).

The universities of the United States are the predominant publishers. However, the academic reference started gradually to diversify from the 1980s onwards, especially with the publications of Central American countries with a Garifuna population (mainly in Belize and Honduras).

This collection of works published throughout the years (from the 17 th to the 21 st century) in different geographical places and under distinct formats allow us to confirm the existence of a great bibliographical production that is essentially different and little known by experts and other persons interested by the subject; let alone the persons interested in black populations who ignore the existence of the Garifuna. That is why the programs AFRODESC-EURESCL are glad to help to publish and disseminate the work of Carlson Tuttle.

The collection is avalaible in a PDF format on the website http://www.ird.fr/afrodesc/.

Anyone interested in receiving the collection in a database format (which will arrange the references alphabetically by author, chronologically or by place of publicationbooks and PhDs-), please ask so by email to ceagarifuna@gmail.com indicating the email address to be used for delivery.

As coordinator of this editorial work, I cannot conclude without expressing my gratitude to Odile Hoffmann for her vital support and participation. I would also like to thank my daughter Mayra Agudelo for her translation in French, English and Spanish of this presentation as well as Carlson Tuttle's.

Carlos Agudelo

Sociologist

AGRADECIMIENTOS Y PREFACIO DE CARLSON TUTTLE

Quiero agradecer primero a los ancestros por haberme transmitido sus conocimientos y su experiencia para que yo sea quien soy. Agradezco igualmente a Odile Hoffmann y a Carlos Agudelo por haberme propuesto la realización de este proyecto, haber tenido confianza en mí y animarme a hacerlo. Un gran agradecimiento al Dr. Joseph Palacio por su apoyo y por las respuestas a mis numerosas preguntas así como a Judy Lumb por su ayuda con la relectura y la edición de la base de datos Excel. Debo agradecer calurosamente a todos les bibliotecarios y archivistas que me han ayudado, muy numerosos para nombrarlos. Mis últimos agradecimientos se dirigen a los Baranguna (habitantes de Barranco) que me han inspirado y estimulado durante todos estos años.

Desde mi primera visita a la Graduate Library de la Universidad de Michigan durante el mes de agosto de 1962, me enamore de esos estantes. Allí pasé maravillosos momentos a los largo de los años. En 1985, mientras hacia investigaciones sobre la fabricación tradicional de la escoba en Belice, encontré la obra de Douglas Taylor, The Black Caribs of British Honduras. Es a partir de este escrito que la constitución de la bibliografía comenzó. En 1989 luego de haber reunido numerosos artículos y obras sobre la cultura garífuna, creé oficialmente Tuani Garifuna Tuba Liburu, una biblioteca de investigación antropológica, en mi pueblo garífuna de residencia, Barranco.

A lo largo de los años visité numerosas bibliotecas y centros de archivos con el objetivo de realizar mis investigaciones y reunir artículos y obras sobre la cultura garífuna. Varios autores me han obsequiado sus libros y artículos y la adquisición en 1995 de la biblioteca de Emory Whipple gracias a la donación de la viuda de Emory Whipple contribuyó mucho a la constitución de la colección. Otros documentos han sido reunidos a partir de fuentes diversas como los registros de escuelas y de iglesias, correspondencia de iglesias, censos, registros de inmigración, de nacimiento, de matrimonio y de fallecimientos, registros catastrales y cartografía, minutas gubernamentales y cartas personales.

Es a partir de esta plétora de documentos que la bibliografía nació. Ella contiene principalmente obras y artículos académicos, dándole la prioridad a material impreso. Ella incluye igualmente obras populares como novelas y libros para niños. La mayor parte de documentos están en inglés pero se encuentran también numerosas obras en francés y en español. Cierto número de trabajos que datan de los últimos veinte años han sido escritos en alemán. La compilación bibliográfica incluye muchas obras en otras lenguas. Además, en los últimos cuarenta años un importante número de trabajos tanto académicos como populares han sido escritos por Garífunas.

Estoy convencido que he dejado de citar muchas contribuciones importantes y les pido mis excusas pero tenia que para en algún momento.

Para tomar contacto con el autor escribir a carlsontuttle@gmail.com BIOGRAPHY and editing the manuscript (Excel Database). And, especially, I want to thank all the librarians and archivists who have assisted me over the years, who are too numerous to name. Lastly thanks to the Baranguna (Barranco's people) who have nurtured and encouraged me over the years.

Since my first visit to the Graduate Library at the University of Michigan in August of 1962 I have had a love affair with its stacks. Over the years I have spent many wonderful hours there. In 1985 while doing research on broom making in Belize, I found and read Douglas Taylor's The Black Caribs of British Honduras. This began the making of this bibliography. In 1989, after gathering numerous papers and books on Garifuna culture, I formally established Tuani Garifuna Tuba Liburu, an anthropological research library, in the Garifuna village of Barranco in which I am a resident.

Over the years I have visited many libraries and archives doing research and collecting material on Garifuna culture. Many authors have contributed papers and books, the Emory Whipple Library that was contributed by Emory's widow was a major addition in 1995. Over the years material has been collected from many disparate sources, school attendance records, government census records, church sacramental records, church correspondences, immigration records, government birth, marriage and death records, government land records and maps, government minute papers, and personal letters.

From this plethora of material this bibliography comes. The material include in this work is mainly academic books, papers and theses with an emphasis on printed material. There are some popular works including novels and children's books. English language works are the majority with a large number in French and Spanish. In the last twenty years a number of works have been published in the German language. There is also a scattering of publications in other languages. Over the past forty years an increasing number of works have been authored by Garinagu, both academic and popular.

I am sure that I have missed some important citations, for which I apologize, but I need to stop somewhere and this is where it is.

To communicate with the author write carlsontuttle@gmail.com

ANTHROPOLOGY / ANTHROPOLOGIE/ ANTROPOLOGÍA

Acosta Saignes, Miguel (1950). Tlacaxipeualiztli, Un Complejo Mesoamericano Entre los Caribes. Caracas: Instituto de Antropología y Geografía, Facultad de Filosofía y Letras, Universidad Central. Adams, Richard N. (1956). «Cultural Components of Central America». American Anthropologist, 58, 881-907. Adams, Sharon Wilcox (2001). The Garifuna of Belize: Strategies of Representation. B.A. Honors Thesis, Mary Washington College. Adams, Sharon Wilcox (2006) Allaire, Louis (1980). «On the Historicity of Carib Migration in the Lesser Antilles». American Antiquity, 45 (2), 238-245. Allaire, Louis (1997). «The Island Caribs of the Lesser Antilles» in Samuel M. Wilson (ed.) The Indigenous People of the Caribbean. Gainesville: University Press of Florida, pp. 177-185. Álvarez Sambulá, Francisco (2008). Alternabilidad en el Poder como Mecanismo para la Consolidación de la Democracia en Centro América, Factor Básico para la Vigencia del Tratado Marco de Seguridad Democrática. Tegucigalpa: Centro de Cultura Garífuna.

  Tuttle, Carlson (2012), Compilation bibliographique sur le peuple garifuna/ Compilación bibliográfica sobre el pueblo garífuna/ Bibliographical collection on the garifuna people. Carlos Agudelo (Ed.) Document de travail/Cuaderno de trabajo/ Working Paper 15. AFRODESC -EURESCL. http://www.ird.fr/afrodesc/

  www.ird.fr/afrodesc/Les personnes souhaitant recevoir la compilation sous un format de base de données (par exemple pour classer les références par ordre alphabétique des auteurs, par ordre chronologique ou par lieu d'édition -livres et thèses -) devront en faire la demande à ceagarifuna@gmail.com en indiquant le courrier électronique par lequel elles désirent recevoir le fichier.

  Taylor date de 1935 et la dernière de 1988. Son oeuvre est composée principalement d'articles de publications scientifiques d'anthropologie et de linguistique. Jusqu'aux années 1970, on ne trouve que très peu de références d'auteurs d'Amérique centrale et les rares publications en espagnol sont des traductions des travaux d'auteurs nord-américains et européens. Ceci est probablement dû au faible développement des sciences sociales dans les milieux universitaires des pays d'Amérique centrale jusqu'à cette époque. Entre 1970 et 1980, le nombre de publications double par rapport à la décennie précédente et passe de 46 à 105. Durant cette période on distingue les travaux de l'anthropologue Joseph

  un des travaux collectifs les plus importants sur le sujet : The Garıfuna, a Nation Across Borders: Essays in Social Anthropology. Le Guatémaltèque Alfonso Arrivillaga publie également la plupart de ses ouvrages durant cette période. Les travaux des Étatsuniens Mark Anderson et Sarah England sont à citer également, notamment deux de leurs principales études respectives : Black and Indigenous. Garifuna activism and Consumer Culture in 'observation des références de cette compilation met en exergue une autre donnée intéressante. En effet, les titres des travaux que contient la compilation dévoilent les transformations des formes d'identification et de représentation des garifuna. Les premières réferences (du XVI e siècle au début du XX e ) utilisent la dénomination générique Caraïbes. En 1928, le terme Caraïbes noirs apparaît pour la première fois dans l'oeuvre d'Eduard Conzemius qui utilise également entre parenthèses le terme «Garif ». Dans ses nombreux et importants travaux, Doublas MacRaeTaylor utilise uniquement le terme Caraïbes noirs, comme le fait Ruy Galvao de Andrade Cohelo ou Nancie González pour ne mentionner que certains grands auteurs. En 1974, le terme garifuna est utilisé pour la première fois (bien qu'accompagné de « Caraïbes noirs » entre parenthèses)

	dans l'oeuvre du géographe William Davidson, qui optera exclusivement dans ses
	derniers travaux pour le terme garifuna. Vers la fin des années 1980, l'usage de
	"Caraïbes noirs" a pratiquement disparu. Une des exceptions notables est la publication
	en 2005 de la thèse doctorale du Français Nicolas Rey, Quand la Révolution, aux
	Amériques, était Nègre… Caraïbes Noirs, Negros Franceses et autres « Oubliés » de
	l'Histoire. Dans un article publié en 1976, Nancie González parle justement de la
	transformation de la forme d'auto-représentation chez les garifuna et considère le
	passage de "Caraïbes noirs" à "Garifunas" comme un processus d'ethnicisation qui
	correspondrait à une politisation de l'identité, influencée par l'expérience du
	mouvement indien ainsi que du mouvement noir aux États-Unis. Il y a donc une
	confluence dans le processus de transformation en termes de dénomination entre les
	études scientifiques et les auto-représentations de ces populations. Cette tendance sera
	confirmée dans les années 1990 avec l'avènement des politiques de reconnaissance et le
	rôle principal qu'y joueront les populations noires ou d'origine africaine, et parmi elles
	les garifuna.
	Honduras (2009) et Creating a Global Garífuna Nation. The Transnationalization of Race,
	Class, Gender and Politics in the Garífuna Diaspora (2000). Cette période est également
	marquée par la publication d'oeuvres d'intellectuels et d'activistes garifuna. Si l'on
	évoque la contribution des Bélizéens Roy Cayetano et de Justo Flores, on peut
	mentionner également Salvador Suazo, Crisanto Meléndez, Santos Centeno et Virgilio
	López García, tous Honduriens ainsi que le Guatémaltèque Mario Ellington. Pendant ces
	années, on remarque également les travaux des historiens honduriens Darío Euraque et
	Jorge Amaya.

L

  Taylor, en los años 1990 se distingue la obra de la lingüista francesa Sybille de Pury Toumi. En antropología se afianza la obra del antropólogo garífuna de Belice Joseph Palacio quien edita en 2005 uno de los trabajos colectivos más importantes sobre este tema, The Garıfuna, a Nation Across Borders: Essays in Social Anthropology. El guatemalteco Alfonso Arrivillaga también produce la mayor parte de su obra en estos años. Igualmente se distinguen los trabajos de los estadounidenses Mark Anderson y Sarah England. Dos de sus trabajos más importantes son respectivamente Black and Indigenous. Garifuna activism and Consumer Culture in Honduras (2009) y Creating a Global Garífuna Nation. The Transnationalization of Race,Class, Gender and Politics in the Garífuna Diaspora (2000). Otro elemento que se puede resaltar para este periodo es la publicación de obras de intelectuales y activistas garífunas. Además de los trabajos de Roy Cayetano y Justo Flores en Belice, podemos mencionar a Salvador Suazo, Crisanto Meléndez, Santos Centeno y Virgilio López García de Honduras y Mario Ellington de Guatemala. Se destacan igualmente los trabajos de los historiadores hondureños Darío Euraque y Jorge Amaya.Un aspecto general interesante que se puede observar en las referencias de esta compilación es el hecho de que los títulos de los trabajos registrados muestran igualmente las transformaciones en la forma de identificación y de representación de los garífuna. Las primeras referencias (siglos XVI a principios del XX) utilizan la denominación genérica de Caribes. La primera referencia a Caribes negros se encuentra en el trabajo de Eduard Conzemius en 1928, quien también coloca entre paréntesis el termino « Garif ». Los numerosos e importantes trabajos de Taylor van utilizar solamente la denominación de Caribes negros, igualmente es el caso de Cohelo o de Nancie González para mencionar solo algunos de los autores más relevantes. En 1974 aparece la primera referencia con el termino « garífuna » (pero acompañado de « Caribes negros» entre paréntesis) en la obra del geógrafo William Davidson quien en sus últimos trabajos opta por el uso exclusivo del termino garífuna. Hacia finales de los años 1980 el uso de « Caribes negros » había prácticamente desaparecido. Una de las excepciones notables a esta desaparición es la publicación en 2005 de la Tesis doctoral del francés Nicolás Rey, Quand la Révolution, aux Amériques, était Nègre… Caraïbes Noirs, Negros Franceses et autres «Oubliés» de l'Histoire. En un artículo aparecido en 1976

  Breton and Taylor, we have to mention the French linguist Sybille de Pury Toumi who published one of her studies in the nineties. As in anthropology, the work of the Belizean Garifuna anthropologist Joseph Palacio published in 2005, The Garıfuna, a Nation Across Borders: Essays in Social Anthropology, is one of the greatest collective works on this subject. The Guatemalan Alfonso Arrivillaga also published most of his works during this period. The works of the Americans Mark Anderson and Sarah England are also to be

mentioned, especially for their respective ma in studies: Black and Indigenous. Garifuna activism and Consumer Culture in Honduras (2009) et Creating a Global Garífuna Nation. The Transnationalization of Race, Class, Gender and Politics in the Garífuna Diaspora

  BIOGRAPHIECarlson John Tuttle est né en Amérique du Nord.En 1967, il est diplômé de l'Université de Windsor dans le Windsor, en Ontario. C.Tuttle a également fréquenté l'Université d'Etat du Wayne, l'Université d'Etat du Michigan et l'Université de l'Ouest de l'Ontario ainsi que d'autre universités de l'Etat du Michigan. Carlson John Tuttle est membre de la Southern Highland Craft Guild depuis 1983 et enseigne à la John C. Campbell Folk School depuis 1988. Actuellement, il est le seul au Belize à pratiquer encore certaines techniques de vannerie traditionnelle garifuna comme la fabrication de la ruguma (presse à manioc). En 1986, il s'installe à Barranco, dans le sud de Belize, où il fonde trois ans plus tard la Tuani Garifuna Tuba Liburu, une bibliothèque de recherche en anthropologie sur la culture garifuna. Depuis sa création, Carlson y tient le rôle de bibliothécaire de recherche. En 2011, il coécrit avec Joseph Palacio et Judith Lumb Garifuna Continuity in Land: Barranco Settlement and Land Use 1862 to 2000. Je souhaite d'abord remercier les ancêtres pour m'avoir transmis leurs connaissances et leur expérience afinde devenir qui je suis. Je remercie également Odile Hoffman et Carlos Agudelo de m'avoir proposé la réalisation de ce projet, de m'avoir accordé leur confiance et encouragé. Un grand merci au Dr Joseph Palacio pour son soutien et pour ses réponses à mes nombreuses questions ainsi qu'à Judy Lumb pour son aide dans la relecture et l'édition du manuscrit (basse de donnes Excel). Je tiens à remercier chaleureusement tous les bibliothécaires et les archivistes qui m'ont aidé, trop nombreux pour être tous nommés. Mes derniers remerciements s'adressent aux Baranguna, (habitants de Barranco) qui m'ont inspiré et encouragé durant toutes ces années.Dès ma première visite à la Graduate Library de l'Université du Michigan durant le mois d'août 1962, je suis tombé amoureux de ses rayons. J'y ai passé de merveilleux moments au fil des ans. En 1985, alors que je menais des recherches sur la fabrication traditionnelle de balai au Bélize, j'ai trouvé et lu l'ouvrage de Douglas Taylor The Black Caribs of British Honduras. C'est à partir de cet écrit que la constitution de la bibliographie a commencé. En 1989, après avoir réuni de nombreux articles et ouvrages sur la culture garifuna, j'ai officiellement créé Tuani Garifuna Tuba Liburu, une bibliothèque de recherche anthropologique, dans mon village garifuna de résidence, Barranco. 'est à partir de cette pléthore de documents que la bibliographie est née. Elle contient principalement des ouvrages et des articles académiques, la priorité ayant été donnée au matériel imprimé. Elle comprend également des oeuvres populaires comme des romans et des livres pour enfants. La plupart des documents sont en anglais mais l'on y trouve également de nombreuses oeuvres publiées en français et en espagnol. Un certain nombre d'ouvrages datant de ces vingt dernières années a été publié en allemand. La compilation bibliographique liste un grand nombre d'ouvrages dans d'autres langues. De plus, ces quarante dernières années, un nombre grandissant d'ouvrages aussi bien académiques que populaires a été écrit par des Garifunas.Carlson John Tuttle nació en América del norte. En 1967 es diplomado de la universidad de Windsor en Ontario. C. Tuttle ha igualmente frecuentado las universidades estatales de Wayne, de Michigan y la Universidad de Ouest en Ontario así como otras universidades de Michigan.Carlson John Tuttle es miembro de la Southern Highland Craft Guild desde 1983 y enseña en la John C. Campbell Folk School desde 1988. Actualmente es la única persona en Belice que practica todavía ciertas técnicas de cestería tradicional garífuna como la fabricación de la ruguma ((para exprimir la yuca). En 1986, Carlson Tuttle se radica en Barranco -sur de Belice-donde funda tres años después la Tuani Garífuna Tuba Liburu, una biblioteca de investigación antropológica sobre la cultura garífuna. Desde su creación Carlson se desempeña como bibliotecario de investigación. En 2011 participa, con Joeph Palacio y Judith Lumb, en la publicación del libro Garífuna Continuity in Land: Barranco Settlement and Land Use 1862 to 2000.

	Je suis convaincu que j'ai oublié de citer bien d'autres contributions encore et je m'en
	excuse mais il fallait bien m'arrêter.
	Pour contacter l'auteur, écrire à : carlsontuttle@gmail.co
	REMERCIEMENTS ET PREFACE DE CARLSON TUTTLE BIOGRAFÍA
	-Researcher AFRODESC-EURESCL
	Associated Member URMIS
	Migrations and Society Research Unit
	www.unice.fr/urmis/
	Au fil des ans, je me suis rendu dans de nombreuses bibliothèques et centres d'archives
	dans le but de mener mes recherches et rassembler des articles et ouvrages sur la
	culture garifuna. De nombreux auteurs m'ont fait don de livres et d'articles et
	l'acquisition en 1995 de la bibliothèque d'Emory Whipple grâce au don la veuve d'Emory
	Whipple a contribué grandement à la constitution de la collection. D'autres documents
	ont été rassemblés à partir de sources variées comme le gouvernement (registres
	d'écoles et d'églises, recensements, registres d'immigration, de naissance, de mariage et
	de décès, cartographie étatique et des communiqués aux citoyens) ainsi que des lettres
	personnelles.

C

  Carlson John Tuttle is of North American heritage. In 1967, he graduated from the University of Windsor in Windsor, Ontario. Carlson also attended Wayne State University, Michigan State University, the University of Western Ontario and various campuses of The University of Michigan. Carlson has been a member of the Southern Highland Craft Guild since 1983. He teaches at the John C. Campbell Folk School since 1988. Carlson is the only person who still makes ruguma (cassava squeezer) and other traditional Garifuna basketry in Belize. In 1986 Carlson moved to Barranco where he founded three years later the Tuani Garifuna Tuba Liburu, an anthropology research library on the Garifuna culture. From its founding, Carlson has been the reseach librarian of this library. in 2011, Carlson co-authored Garifuna Continuity in Land: Barranco Settlement and Land Use 1862 to 2000.

  . Reconstructing Identity: Representational Strategies in the Garifuna Community of Dangriga, Belize. M. A. Thesis, University of Texas, Austin. Agudelo, Carlos (2012). "Qu'est-ce qui vient après la reconnaissance ? Multiculturalisme et populations noires en Amérique latine» in Christian Gros et David Dumoulin Kervran (eds.) Le multiculturalisme au concret. Un modèle latino américain?. Paris: Presses Sorbonne Nouvelle, pp. 267-277. Agudelo, Carlos (2012). «The afro-guatemalan Political Mobilization: Between Identity, Construction Process, Global Influences and Institutionalization» in Jean Rahier (ed) Black Social Movements in Latin America. From Monocultural Mestizaje to Multiculturalism. Miami: Palgrave Macmillan. Agudelo, Carlos (2012). "Los garifunas, identidades y reivindicaciones de un pueblo afrodescendiente de América Central" in CINU-Centro de información de las Naciones Unidas (ed.) Afrodescendencia: aproximaciones contemporáneas desde América Latina y el Caribe, pp. 59-66. http://www.cinu.mx/AFRODESCENDENCIA.pdf viewed 06.04.2012. Agudelo, Carlos (2010). "Génesis de redes transnacionales. Movimientos afrolatinoamericanos en América Central» in Odile Hoffmann (ed.) Política e Identidad. Afrodescendientes en México y América Central. México: INAH, UNAM, CEMCA, IRD, pp. 65-92. Agudelo, Carlos (2011). "Les Garifuna. Transnationalité territoriale, construction d'identités et action politique». REMI, Revue Européenne des Migrations Internationales, 27 (1), 47-70. Agudelo, Carlos (2011). «Os garífunas: transnacionalidade territorial, construção de identidades et ação política». Desigualdade & Diversidade. Revista de Ciências Sociais da PUC Rio, 8 (jun/jul), 51-76. http://publique.rdc.puc-rio.br/desigualdadediversidade/ viewed 06.12.2011.

AFRODESC-EURESCL -Afro-descendants et esclavages : domination, identification et héritages dans les Amériques, programme de l'Agence Nationale de Recherche -ANR de France www.ird.fr/afrodesc/. EURESCL -Slave, Trade, Slavery, Abolitions and their legacies in European Histories and Identities, programme de l'Union européenne www.eurescl.eu/.

AFRODESC-Afrodescendientes y esclavitudes: dominación, identificación y herencias en las Américas, programa de la Agencia Nacional de Investigación -ANR de Francia www.ird.fr/afrodesc/. EURESCL-Slave Trade, Slavery, Abolitions and their Legacies in European Histories and Identities, programa de la Union europea www.eurescl.eu/

The word garifuna which designates the individuals and the population comes from Karina in Arawak language which means "yucca eaters". Some authors differentiated the word garifuna in singular to designate the individuals and the language, and the term garinagu or garifunas in plural to designate the population. We notice in the references of this collection, the different forms are used as well as the expression "black Caribs".

AFRODESC -Afro-descendants et esclavages : domination, identification et héritages dans les Amériques, program of the National Research Agency -ANR of France www.ird.fr/afrodesc/. EURESCL -Slave Trade, Slavery, Abolitions and their Legacies in European Histories and Identities, program of the European Union www.eurescl.eu/

ACKNOWLEDGEMENTS AND PREFACE OF CARSLON TUTTLE

I wish to first thank the ancestors for passing on their knowledge and experience which has allowed me to become who I am. Thanks to Odille Hoffman and Carlos Agudelo for suggesting this project, for their confidence in my ability to carry it out, and for their encouragement. I want to thank Dr. Joseph Palacio for his encouragement and for answering my many questions. I am grateful to Judy Lumb for her help in proofreading

AFRODESC/EURESCL -Document de travail/Cuaderno de trabajo/ Working Paper 15 Potter, Robert B. (1992). «Demographic Change in a Small Island State: St. Vincent and the Grenadines, 1980-1991». Geography, 77 (pt.,4, No. 337), 374-376. Reclus, Elisee (1891). The Earth and its Inhabitants. North America. Vol II. New York: D. Appleton and Co.