Vasconcelos Duarte
email: duartenvg@gmail.com

Gonçalves

Fernando Martínez-Freiría

Pierre-André Crochet

Philippe Geniez

Salvador Carranza

José Carlos Brito

The role of climatic cycles and trans-Saharan migration corridors in species diversification: biogeography of Psammophis schokari group in North Africa

Keywords: climatic cycles, ecological niche-based modelling, paleoclimate, phylogeography, snakes, vicariance

Highlands, hydrographic systems and coastal areas have been hypothesised to form corridors across the hyperarid Sahara desert in North Africa, allowing dispersal and gene flow for nonxeric species. Here we aim to provide a genetic test for the trans-Saharan corridor model, and predict the location and stability of ecological-corridors, by combining phylogeography and palaeoclimatic modelling. The model was the Psammophis schokari (Schokari sand racer) group, fast-moving and widely distributed generalist colubrids occurring mostly in arid and semiarid scrublands. We combined dated phylogenies of mitochondrial and nuclear markers with palaeoclimatic modelling. For the phylogeographic analysis, we used 75 samples of P. schokari and P. aegyptius, and Bayesian and Maximum-Likelihood methods. For the ecological models, we used Maxent over the distribution of P. schokari and West African lineages.

Models were projected to past conditions (mid Holocene, Last Glacial Maximum and Last Inter-

Glacial) to infer climatic stable areas. Climatic stability was predicted to be mostly restricted to coastal areas and not spatially continuous. A putative temporary trans-Saharan corridor was identified in Eastern Sahara, with a more stable one along the Atlantic coast. Six parapatric lineages were identified within P. schokari, four occurring in North Africa. These likely diverged during the Pliocene. The Tamanraset River might have been a vicariant agent. African lineages may have experienced further subsequent diversification during the late Pleistocene. The main P.schokari refugia were probably located along the northern margins of the Sahara, allowing its North-to-South colonisation. Trans-Saharan corridors seem to have played a role in P. schokari biogeography, allowing colonization of central Saharan mountains and Sahel. Some might have worked as refugia, and even the most stable corridors may have sections working as filters, depending on each climatic phase. We expect the use of trans-Saharan corridors to decrease for more mesic species or with less dispersal capabilities.

Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009

Introduction

Numerous geological and climatic events have affected the geographic and biological diversity of North Africa in the last few million years [START_REF] Houérou | Climate, flora and fauna changes in the Sahara over the past 500 million years[END_REF][START_REF] Fabre | Géologie du Sahara occidental et central[END_REF]. Geological events include the opening of the Mediterranean to the Atlantic 7-9 million years ago (Ma), the subsequent closure 6 Ma and re-opening 5.3 Ma (MSC, [START_REF] Krijgsman | Chronology, causes and progression of the Messinian salinity crisis[END_REF], recurrent episodes of desiccation and refilling in the Red Sea area [START_REF] Girdler | The Afro-Arabian rift system -an overview[END_REF][START_REF] Bosworth | The Red Sea and Gulf of Aden Basins[END_REF], marine transgressions [START_REF] Tawadros | Geology of North Africa[END_REF], or the Atlas mountains uplift [START_REF] De | In search of historical biogeographic patterns in the western Mediterranean terrestrial fauna[END_REF]. These had climatic repercussions, but the most wide-ranging climatic event was a shift from tropical to arid environments around mid-Miocene (Zachos et al., 2001) that eventually led to the appearance of the Sahara desert between 7 Ma and 2.5 Ma [START_REF] Schuster | The age of the Sahara desert[END_REF][START_REF] Swezey | Cenozoic stratigraphy of the Sahara, Northern Africa[END_REF]. Arid and humid conditions then alternated during the last few million years, causing a series of expansions and contractions of climatic zones [START_REF] Houérou | Outline of the biological history of the Sahara[END_REF][START_REF] Swezey | Cenozoic stratigraphy of the Sahara, Northern Africa[END_REF]) that largely determined current biodiversity patterns [START_REF] Brito | Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel[END_REF].

Diversification due to humid-arid cycles has been explained through genome rearrangements [START_REF] Dobigny | Recent radiation in West African Taterillus (Rodentia, Gerbillinae): the concerted role of chromosome and climatic changes[END_REF], adaptation to novel habitats (Boratyński et al., 2012;[START_REF] Carranza | Relationships and evolution of the North African geckos, Geckonia and Tarentola (Reptilia: Gekkonidae), based on mithochondrial and nuclear DNA sequences[END_REF][START_REF] Guillaumet | Climate-driven diversification in two widespread Galerida larks[END_REF] or, most commonly, divergence in allopatry [START_REF] Brito | Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel[END_REF].

While during humid phases, the hyper-arid regions were reduced and probably isolated, in arid phases the mesic species were pushed towards coastal areas and mountains [START_REF] Houérou | Outline of the biological history of the Sahara[END_REF][START_REF] Messerli | Climate, Environmental Change, and Resources of the African Mountains from the Mediterranean to the Equator[END_REF]. This resulted in disjoint distributions and allopatric diversification, currently best observed in mesic species, for example Mediterranean-Sahel separations (e.g. [START_REF] Gonçalves | Phylogeny of North African Agama lizards (Reptilia: Agamidae) and the role of the Sahara desert in vertebrate speciation[END_REF][START_REF] Guillaumet | Climate-driven diversification in two widespread Galerida larks[END_REF], isolated populations in highlands [START_REF] Geniez | A new species of Semaphore gecko Pristurus (Squamata: Gekkonidae) from Mauretania, represents a 4700km range extension for genus[END_REF][START_REF] Metallinou | Species on the rocks: Systematics and biogeography of the[END_REF], rock pools (Brito et al., 2011a;[START_REF] Vale | Overlooked mountain rock pools in deserts are critical local hotspots of biodiversity[END_REF] or desert-border refugia [START_REF] Dobigny | Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (murinae) and sub-saharan open habitats pleistocene history[END_REF]. Arid phases conversely allowed range expansions of xeric taxa [START_REF] Arnold | Systematics, biogeography and evolution of the endemic Hemidactylus geckos (Reptilia, Squamata, Gekkonidae) of the Cape Verde Islands: based on morphology and mitochondrial and nuclear DNA sequences[END_REF][START_REF] Kissling | Historical colonization and dispersal limitation supplement climate and topography in shaping species richness of African lizards (Reptilia: Agaminae)[END_REF][START_REF] Leaché | Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae)[END_REF]Pook et al., 2009), later broken during humid phases [START_REF] Metallinou | Species on the rocks: Systematics and biogeography of the[END_REF][START_REF] Wüster | Molecular Phylogenetics and Evolution A nesting of vipers : Phylogeny and historical biogeography of the Viperidae ( Squamata : Comment citer ce document[END_REF] Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito Landscape features modulate gene flow [START_REF] Brown | Biogeography[END_REF]. Depending on climaticcycle phase and species' ecological requirements, a geographic feature can constitute a barrier to gene flow, an ecological corridor (connecting two larger similar areas), a filter bridge (or barrier, a more selective connection), or a refugium (where a species survives during unfavourable periods). Lake Chad, for instance, has been identified as a refugium [START_REF] Granjon | The importance of cytotaxonomy in understanding the biogeography of African rodents: Lake Chad murids as an example[END_REF] or a corridor connecting the Sahel to the Tibesti [START_REF] Drake | Ancient watercourses and biogeography of the Sahara explain the peopling of the desert[END_REF][START_REF] Dumont | Relict distribution patterns of aquatic animals: another tool in evaluating Late Pleistocene climate changes in the Sahara and Sahel[END_REF] for mesic taxa and a vicariant barrier for xeric ones (Pook et al., 2009;[START_REF] Metallinou | Species on the rocks: Systematics and biogeography of the[END_REF]. Mountains, presently working as biodiversity hotspots and refugia for mesic species [START_REF] Brito | Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel[END_REF](Brito et al., , 2011a;;[START_REF] Vale | Overlooked mountain rock pools in deserts are critical local hotspots of biodiversity[END_REF], likely constitute barriers for lowland or xeric species. Lastly, mountains, coastal areas and hydrographic systems can be linked, forming ecological corridors for mesic species. Several areas likely to constitute North-South oriented ecological corridors have been proposed [START_REF] Dumont | Relict distribution patterns of aquatic animals: another tool in evaluating Late Pleistocene climate changes in the Sahara and Sahel[END_REF]; these geographic features are hereby referred to as trans-Saharan corridors (tS-corridors), to avoid confusion with the ecological corridor feature. They include the more transitory river drainages from central Sahara Mountains [START_REF] Drake | Ancient watercourses and biogeography of the Sahara explain the peopling of the desert[END_REF], or the more stable (thus possibly refugia for some species) Red Sea, Nile River or Atlantic Sahara [START_REF] Brito | Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel[END_REF]. However, these have been proposed

based on ecological/geological data and species' distributions, and no genetic-level assessments have been conducted so far.

Our goal is to provide a genetic assessment of the validity of the tS-corridor model. For that, since most speciation events far predate the last humid/arid shift, data on the distribution of intraspecific genetic variability is required. While many mesic taxa may use the corridors during the humid phases, only those with high mobility and more adaptations to xeric environments are expected to do so during arid phases. Mesic-xeric species with broad ecological spectrum are thus expected to make more use of tS-corridors. We have selected the

6

Psammophis schokari (Schokari sand racer) group in North Africa as a model since it is widely distributed in North Africa, occurring mostly in arid and semiarid habitats; it presents a continuous distribution along the Atlantic coast, thus apparently making use of this tS-corridor (Fig. 1). These snakes are large and mobile animals with likely good dispersal abilities. Thus, we do not expect limited dispersal or narrow distribution to restrict its use of ecologically suitable corridors. Previous work on P. schokari (Rato et al., 2007) identified several lineages but no conclusions were drawn regarding trans-Saharan dispersal.

Here we propose to model the species' potential distribution in different climatic phases to assess the suitability of candidate tS-corridors as ecological corridors for Psammophis, thus allowing us to build clear hypothesis on the persistence of gene flow along tS-corridors for mesic species during the past climatic cycles. The general aim of this study is to assess the role of corridors in trans-Saharan dispersal, with particular focus on the Atlantic Sahara tS-corridor, in an integrative framework joining phylogeography and palaeoclimatic modelling. Using P.

schokari, we aim to answer the questions: 1) where are the areas with higher climatic stability throughout the species range and particularly West Africa and where are the potential dispersal routes across the Sahara?; 2) how is the genetic variability spatially structured?. By combining results from these two sections, we expect to find phylogeographic patterns coherent with refugia close to the Mediterranean coast and in the Saharan mountains, and tScorridors connecting them.

Material and methods

Sampling and study areas

The snake genus Psammophis includes 34 diurnal fast-moving species occurring mostly throughout tropical Africa, with some species reaching the Middle East and South-Central Asia (Sindaco et al., 2013, Uetz and[START_REF] Uetz | The Reptile Database[END_REF] India (Fig. 1), mostly in desert and xeric scrublands, marginally in sandy habitats in dry Mediterranean zones [START_REF] Kelly | The snake family Psammophiidae (Reptilia: Serpentes): phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera[END_REF][START_REF] Schleich | Amphibians and reptiles of North Africa: biology, systematics, field guide[END_REF][START_REF] Sindaco | The Reptiles of the Western Palearctic, Volume 2: Annotated Checklist and Distributional Atlas of the Snakes of Europe, North Africa, Middle East and Central Asia, with an Update to[END_REF]. Its sister species Psammophis aegyptius MARX, 1958, commonly known as Egyptian sand snake, is a typical Saharan species renowned for inhabiting even the driest areas of the eastern Sahara [START_REF] El Din | A Guide to the Reptiles and Amphibians of Egypt[END_REF].

We used 68 samples of P. schokari covering a representative part of the species distribution, particularly in West Africa (Table A.1; Fig. 1). Seven samples of P. aegyptius were also included.

For the phylogenetic analyses (see below), outgroups and other species of Psammophis were selected based mostly on [START_REF] Kelly | The snake family Psammophiidae (Reptilia: Serpentes): phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera[END_REF] 2).

Climatic variables

Nineteen variables for current climatic conditions at 30 arc-second resolution (~1x1 km) were downloaded from WorldClim (www.worldclim.org; [START_REF] Hijmans | Very high resolution interpolated climate surfaces for global land areas[END_REF]. Variables were clipped to each study area (Global and Regional) and, for the Global dataset, upscaled to five arc-minutes (~10x10 km). After visual inspection, five variables were excluded due to the presence of spatial artefacts. The remaining 14 variables (Table A.2) were considered for ecological models. Bivariate correlations among the 14 variables were tested within Global and Regional datasets. We retained the same five slightly correlated (R<0.7) variables in both datasets (BIO 4,10,12,14,19;Table A.2), which are commonly used in ecological niche-based modelling approaches developed for other snake species (e.g. [START_REF] Martínez-Freiría | Trapped by climate: interglacial refuge and recent population expansion in the endemic Iberian adder Vipera seoanei[END_REF]Brito et al., 2011b).

For past conditions, the same five variables were downloaded from WorldClim for the Last 9 upscaled to 5 arc-minute resolution for Global models and kept at original pixel size for Regional models.

DNA extraction and amplification

DNA was extracted from ethanol-preserved tissue using DNeasy Blood & Tissue Kit (Qiagen) as per manufacturer's instructions. Amplifications were performed using MyTaq™ Mix. To benefit from sequence data available from GenBank [START_REF] Kelly | The snake family Psammophiidae (Reptilia: Serpentes): phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera[END_REF]Rato et al., 2007), specimens were bi-directionally sequenced for two mitochondrial (NADH dehydrogenase subunit 4, ND4;

cytochrome b, CYTB) and two nuclear (oocyte maturation factor MOS, c-mos; Recombination activating gene 2, RAG2) gene fragments. ND4, CYTB, c-mos and RAG2 were amplified using primers from [START_REF] Arevalo | Mitochondrial DNA Sequence Divergence and Phylogenetic Relationships among Eight Chromosome Races of the Sceloporus Grammicus Complex (Phrynosomatidae) in Central Mexico[END_REF][START_REF] De Queiroz | Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough?[END_REF], [START_REF] Saint | C-mos, a nuclear marker useful for squamate phylogenetic analysis[END_REF][START_REF] Vidal | The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes[END_REF][START_REF] Vidal | The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes[END_REF], respectively. PCR conditions were: pre-denaturation at 94ºC (15'); 40 cycles with 92ºC (30") denaturing, 50ºC (45") annealing and 72ºC (45") extension; final extension at 60ºC (15'). Some samples required repeating the reactions with annealing temperatures in the 48-52ºC range.

Phylogenetic analyses

Sequences were aligned using MAFFT v7 [START_REF] Katoh | MAFFT multiple sequence alignment software version 7: Improvements in performance and usability[END_REF], with Auto option, then proofread by eye. No stop codons were found in coding genes. Each marker was individually analysed inferring independent ML trees in RAXML v8.1.21 [START_REF] Stamatakis | RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies[END_REF], in order to detect topological incongruences suggesting sample curation errors.

For both sequence datasets, the best-fit partitioning scheme and models of molecular evolution were selected using PARTITIONFINDER v.1.1.1 [START_REF] Lanfear | PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses[END_REF] [START_REF] Ronquist | MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space[END_REF] and BEAST v1.8.3 [START_REF] Drummond | Bayesian Phylogenetics with BEAUti and the BEAST 1.7[END_REF].

MRBAYES was run for 10 7 generations in two independent runs sampling every 1000 generations. Parameters of sequence evolution (statefreq, revmat, shape, pinvar) were unlinked for all partitions and the overall rate (ratepr) variable among them. BEAST was run in CIPRES gateway (Miller et al., 2010) in three independent runs of 5x10 7 generations, sampling at every 5000, with unlinked substitution and clock models, under an uncorrelated lognormal relaxed clock [START_REF] Drummond | Relaxed phylogenetics and dating with confidence[END_REF], and considering ambiguities in nuclear sequences (manually editing the xml file to UseAmbiguities=true). A constant population size coalescent tree prior [START_REF] Kingman | The coalescent[END_REF] was used for dataset 1, and a Yule speciation tree prior (Yule 1925;

Gernhard 2008) for dataset 2. Burn-in was determined using Tracer v1.6 (Rambaut et al., 2014), upon stabilisation of log likelihood, average standard deviation of split frequencies, and ESS for all parameters. For BEAST analysis, runs were combined with LogCombiner and a maximum credibility tree was generated with TREEANNOTATOR (both in the BEAST package).

Burn-in was determined using TRACER v1.6 (Rambaut et al., 2014). ML analyses were performed in RAXML v8.1.21 [START_REF] Stamatakis | RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies[END_REF]) through RAXMLGUI 1.5b1 [START_REF] Silvestro | RaxmlGUI: A graphical front-end for RAxML[END_REF], with partition schemes as above and GTR+G model of sequence evolution. The program was set to perform 10 ML searches and 1000 thorough bootstrapping replicates. To test the paraphyly against the monophyly of African populations, the best tree in which Algerian/Tunisian populations are sister taxa to the rest of African and Middle East populations was compared with the alternative constrained topology in which Africa was forced monophyletic. Per-site log likelihoods were obtained with RAxML, then used to run the Shimodaira-Hasegawa (SH) [START_REF] Shimodaira | Letter to the Editor Multiple Comparisons of Log-Comment citer ce document[END_REF] and Approximately-Unbiased (AU) [START_REF] Shimodaira | An Approximately Unbiased Test of Phylogenetic Tree Selection[END_REF] topology tests in CONSEL [START_REF] Shimodaira | CONSEL: for assessing the confidence of phylogenetic tree selection[END_REF].

MEGA6 [START_REF] Tamura | MEGA6: Molecular evolutionary genetics analysis version 6.0[END_REF] groups of samples for each mitochondrial marker in dataset 1. DNASP v.5.10.1 [START_REF] Librado | DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[END_REF] was used to calculate sequence and nucleotide diversity measures. The PHASE 2.1 algorithm [START_REF] Stephens | A new statistical method for haplotype reconstruction from population data[END_REF] implemented in DNASP was used to infer haplotypes for nuclear sequences. The software was run for 10 4 iterations with a thinning interval of five and a burn-in value of 1000, and repeated three times. Consistency was checked across runs by analysing haplotype frequency estimates and goodness-of-fit measures. Haplotypes were used to produce haplotype networks using NETWORK 5.0 (Fluxus-engineering.com) with medianjoining algorithm and default parameters [START_REF] Bandelt | Median-joining networks for inferring intraspecific phylogenies[END_REF].

Time calibration

No calibration constraints are available within the genus Psammophis or the family Psammophiidae. Therefore, to obtain estimates of the divergence times among P. schokari lineages, the dataset was expanded to span the superfamily Colubroidea plus Achrochordus, and thus make use of the calibration scheme used by [START_REF] Wüster | Molecular Phylogenetics and Evolution A nesting of vipers : Phylogeny and historical biogeography of the Viperidae ( Squamata : Comment citer ce document[END_REF] and Pook et al. (2009). Other authors have used a slightly different prior set [START_REF] Sanders | Molecular evidence for a rapid late-Miocene radiation of Australasian venomous snakes (Elapidae, Colubroidea)[END_REF][START_REF] Kelly | Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene[END_REF], so we also dated the phylogeny according to the revised version by [START_REF] Sanders | Phylogeny and divergence times of filesnakes (Acrochordus): Inferences from morphology, fossils and three molecular loci[END_REF]. RAG2 was excluded given that it was not available for most of the dataset.

Palaeoclimate modelling

Palaeoclimate models were computed at a Global scale, which includes the whole species distribution and aims at a species-wide average niche, and at a Regional scale, including just the West African populations and targeting local environmental species preferences. Models were generated using the maximum entropy approach with MAXENT v3.3.k (Phillips et al., 2006). This algorithm requires only presence data, performs well comparing to other methods [START_REF] Elith | Novel methods improve prediction of species' distributions from occurrence data[END_REF], and has been used successfully in modelling snake species distributions (e.g. Brito et al., 2011b;[START_REF] Martínez-Freiría | Trapped by climate: interglacial refuge and recent population expansion in the endemic Iberian adder Vipera seoanei[END_REF]. Thirty replicates were run with random seed and 70%/30% training/testing partition and using bootstrap with replacement. Models were 12 run with auto-features, and the area-under-the-curve (AUC) of the receiver-operating characteristics (ROC) plots was taken as measure of individual model fit [START_REF] Fielding | A review of methods for the assessment of prediction errors in conservation presence/absence models[END_REF]. The importance of climatic variables in explaining the species' distribution was determined by their mean percentage contribution to the models.

The individual model replicates were used to generate a mean forecast of probability of species occurrence under current conditions [START_REF] Marmion | Evaluation of consensus methods in predictive species distribution modelling[END_REF]. Standard deviation was used as indication of prediction uncertainty (e.g. Brito et al., 2011b;[START_REF] Martínez-Freiría | Trapped by climate: interglacial refuge and recent population expansion in the endemic Iberian adder Vipera seoanei[END_REF]. Individual model replicates were projected to past climatic conditions (midHol, LGM and LIG) and subjected to the same procedure. Stable climatic areas, i.e. stable potential areas of occurrence that could serve as refugia in different time periods [START_REF] Carnaval | Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot[END_REF], were calculated by averaging the probability of occurrence across all time phases.

Niche overlap test

In order to assess the potential role of ecological processes in the evolutionary history of the lineages along the Atlantic corridor, we tested niche overlap, equivalency and similarity between regional lineages (see [START_REF] Warren | Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution[END_REF]. Tests were based on a 2D representation of climatic space of lineages (retrieved using 14 climatic variables; Table A.2), represented by the first two components of a Principal Component Analysis (PCA). We used the PCA-env ordination approach developed by [START_REF] Broennimann | Measuring ecological niche overlap from occurrence and spatial environmental data[END_REF] in R (R Core Team 2016). This approach uses Gaussian functions to smooth densities of records and background climate and measures overlap through Schoener's D metric. The significance of equivalency and similarity tests is approached via randomization; we used 100 repetitions.

Results

Phylogenetic relationships

Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza 1.

Genetic identity of specimens was coherent with prior morphology-based species assignment:

specimens identified as Psammophis schokari and P. aegyptius formed two reciprocally monophyletic groups in the concatenated phylogenetic ML and BI trees (Fig. 2). The nuclear DNA did not exhibit a clear separation in the network analysis, with a shared basal haplotype in c-mos, and some RAG2 schokari haplotypes being closer to aegyptius haplotypes than to the remaining schokari alleles (Fig. 2). Six monophyletic lineages of P. schokari were found, three occurring in Northwest Africa with apparently parapatric distributions, one in NE Africa and the Middle East, one in Iran, and one in SE Arabian Peninsula (Oman). ML and BI supported substructuring was found within all four lineages occurring in Africa. Except for the earliestsplitting Oman lineage, relationships among lineages were not resolved. Monophyly of the NW African lineages was recovered in some analysis, but the topology test was inconclusive (Table A.4). A "Middle East" lineage, spreading from Egypt to the Persian Gulf, and a Mauritanian lineage occurring throughout the country were identified. The later apparently contacts with the Moroccan one. Most nuclear haplotypes of the Mauritanian lineage are shared by Moroccan populations (Fig. 2).

Time calibration

Dataset 2 resulted in an alignment of 2379 positions (Table A. Psammophis schokari and P. aegyptius separation was dated at 9.93 Ma (7.85 -12.07), while their estimated crown ages are 6.17 My (4.89-7.5) and 0.78 My (0.41-1.21), respectively.

Divergence events among the major lineages of P. schokari were all placed in the Pliocene.

African P. schokari lineages and P. aegyptius may have suffered roughly contemporaneous 14 internal divergence events during the late Pleistocene.

Palaeoclimate models

Predictions of ecological models were robust (Table 2), identifying most of the species' occurrence with high probability (Figs. A.3-A.6). Accuracy was lower in the most arid parts of the Algerian Sahara and in portions of the Asian range. Contribution of variables changed according to modelling approach (Table 2).

The major areas predicted with climatic stability (potential refugia) in the Global model were mostly restricted to coastal areas and were not spatially continuous (Fig. 4A). In the Regional model, climatic stability was predicted to restricted areas of the West Sahara and in few patches across north-eastern and central Morocco and central and south-western Mauritania (Fig. 4B). When comparing the Moroccan and Mauritanian models, climatic stability mostly corresponded to allopatric areas (Fig. 4C-D). In comparison to predictions for the current time, there was a general trend for an increase of available suitable climatic areas in the LGM scenarios and the opposite trend for the mid Holocene and LIG scenarios (Figs. A.3-A.6).

Niche overlap

Niche overlap between Moroccan/Mauritanian lineages is extremely reduced (D = 0.036; Fig.

Discussion

The history of North Africa is rich in climatic and geological changes with significant impact on local biodiversity, making it hard to link timing of diversification with particular past events.

Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza should also be a reasonable surrogate for past habitat changes, as the distribution of desert species (particularly ectotherms) is strongly dependent on temperature and rainfall [START_REF] Ward | The Biology of Deserts[END_REF]. Although geological features (e.g. soil type) also determine habitat and species distributions, we did not include such data in the models, as the large fluctuation in aeolian sand deposition regimes and scarce paleontological data caused by study area remoteness and stratigraphic discontinuities caused by erosion hamper predictions about past land-cover or soil types. Also, our paleoclimatic reconstructions are referent to the Pleistocene. During

Pliocene, similar cycles seem to have occurred both globally [START_REF] Lisiecki | A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records[END_REF] and in North Africa (Rohling et al., 2015), but uncertainties regarding the climatic conditions at the time and out-of-pleistocene-bounds temperature variation [START_REF] Snyder | Evolution of global temperature over the past two million years[END_REF] limit the extrapolations of the models beyond the Pleistocene.

Migration corridors across the Sahara

Trans-Saharan corridors (tS-corridors) can be more or less permanent (i.e. active ecological corridors), with the coastal ones expected to be more permanent [START_REF] Brito | Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel[END_REF]. The climatically stable areas mostly fit this prediction, with the Atlantic Sahara suggested even as potential refugium area. In a simple scenario, stronger gene flow along the Atlantic than from the coast to the Algerian Mountains would then be expected, but the distribution of genetic variability seems to indicate the opposite.

The same mitochondrial haplotype was found in E-Tunisia and Hoggar (Figs. 2,4). This contrasts with the genetic differentiation commonly observed in populations from Saharan mountains, illustrated by the high rate of endemism (more than half of Sahara-Sahel et al., 2015). The species' broad niche can partly explain it, and this shows that the predicted level of connection of northern areas with south Algeria Mountains seems therefore sufficient to allow the species' dispersal.

According to the ecological models, the link is more likely to occur under current conditions, which suggests a very recent (re-) colonization or secondary contact. The most probable path to southern Algerian mountains seems to be through Fezzan region in Libya, but a tS-corridor from there to the Sahel seems unlikely. A putative tS-corridor seems more likely in Eastern Sahara, active under LGM-like conditions (CCSM and MIROC,Fig. A.3), linking the Mediterranean to Gilf Kebir, Jebel Uweinat, Ennedi/Borkou, and possibly Tibesti and Marra mountains. However, identification of suitable areas in the Eastern Sahara is affected by the low availability of precise observational data (Fig. 1), resulting in less clear distribution patterns.

The Atlantic coast was the sole permanent tS-corridor for mesic species well supported and it seems to have been the most climatically stable dispersal path across the Sahara. The split of the Moroccan and Mauritanian lineages seems to contradict this pattern, but these lineages might have been separated by the Tamanrasset palaeoriver basin, which opened on the Atlantic coast in the north of present-day Mauritania (Fig. 4; [START_REF] Skonieczny | African humid periods triggered the reactivation of a large river system in Western Sahara[END_REF]. This river system was activated in the humid periods of the Sahara, which seem to have occurred cyclically since before the Pliocene (Rohling et al., 2015). With a drainage area comparable to the ones of Niger or Zambezi rivers [START_REF] Vorosmarty | Geomorphometric attributes of the global system of rivers at 30-minute spatial resolution[END_REF], it could represent a barrier during humid phases, as well as constitute an unsuitable sandy expanse during warm ones.

Phylogenetic relationships

The status of sister species is supported for P. schokari and P. aegyptius, in agreement with Rato et al. ( 2007), although differentiation in the nuclear markers was not complete (Fig. 2).

Although c-mos exhibits a typical pattern of shared ancestral polymorphism where the most common haplotype in the two species is still the ancestral haplotype, RAG2 exhibits clear separation between species, so the nuclear data do not contradict reproductive isolation between these two species. The genetic distance found between the five P. schokari mtDNA lineages, compared in Table 1, was substantial (4.5-7.1%), and while not uncommon in reptiles, similarly deep evolutionary lineages were used to request taxonomy revisions in other species (e.g. Vipera latastei; Velo-Antón et al., 2012). Still, higher resolution nuclear markers or increased genomic coverage (e.g. [START_REF] Velo-Antón | Should I stay or should I go? Comment citer ce document[END_REF] would be needed to support it and to resolve the phylogenetic relations among lineages. Additional sampling would also be necessary to define lineage distributional limits and assess gene flow in contact zones.

Biogeography and diversification

Psammophis schokari and P. aegyptius seem to have diverged around 10 Ma (Fig. 3). The latter exists only in Africa, but P. schokari ranges from the Atlantic coast to India, and the earliestsplitting lineage identified here is found in Oman. If the African diversity is indeed embedded within Asian diversity, an Asian origin of P. schokari, for instance through vicariance from African populations (the ancestor of P. aegyptius), is plausible. However, clarification is dependent on covering sampling gaps, since an Oman lineage migration across the Red Sea cannot be ruled out, as exemplified by other faunal exchanges between Africa and Arabia during the progressive aridification of late Miocene [START_REF] Metallinou | Conquering the Sahara and Arabian deserts: Systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae)[END_REF][START_REF] Smíd | Out of Arabia: a complex biogeographic history of multiple vicariance and dispersal events in the gecko genus Hemidactylus (Reptilia: Gekkonidae)[END_REF]Tamar et al., 2016a). Ecological divergence into new more arid habitats could also have been involved, as suggested for other reptiles [START_REF] Carranza | Radiation, multiple dispersal and parallelism in the skinks, Chalcides and Sphenops (Squamata: Scincidae), with comments on Scincus and Scincopus and the age of the Sahara Desert[END_REF][START_REF] Carranza | Relationships and evolution of the North African geckos, Geckonia and Tarentola (Reptilia: Gekkonidae), based on mithochondrial and nuclear DNA sequences[END_REF][START_REF] Metallinou | Conquering the Sahara and Arabian deserts: Systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae)[END_REF]Pook et al., 2009;Tamar et al., 2016b).

The successive divergences among major lineages after the Messinian Salinity Crisis (Fig. 3) mirror the same diversification patterns in the Late Miocene and Pliocene found in many vertebrate and reptile groups [START_REF] Carranza | Radiation, multiple dispersal and parallelism in the skinks, Chalcides and Sphenops (Squamata: Scincidae), with comments on Scincus and Scincopus and the age of the Sahara Desert[END_REF][START_REF] Geniez | A new species of Semaphore gecko Pristurus (Squamata: Gekkonidae) from Mauretania, represents a 4700km range extension for genus[END_REF][START_REF] Gonçalves | Phylogeny of North African Agama lizards (Reptilia: Agamidae) and the role of the Sahara desert in vertebrate speciation[END_REF][START_REF] Wagner | Opening a box of cryptic taxa -the first review of the North African desert lizards in the Trapelus mutabilis Merrem, 1820 complex (Squamata: Agamidae) with descriptions of new taxa[END_REF], and have been associated with the original onset of the Sahara desert. Lineage distributions are broadly coherent with the predicted climatically stable areas, which could suggest a vicariant effect of climate (Fig. 4). However, our models are based on Pleistocene conditions and do not cover the Pliocene. Still, dust flux records indicate that notwithstanding a slight increase in the last Ma, humid-arid cycles have been occurring

similarly since 5 Ma [START_REF] Trauth | Trends, rhythms and events in Plio-Pleistocene African climate[END_REF].

The roughly contemporaneous and independent divergences of North African sub-lineages after mid-Pleistocene (Fig. 3) may be linked to persistence and subsequent isolation in Quaternary climate refugia during humid-dry cycles. In Morocco for example, the sub-lineages are separated by mountain ranges (Fig. 2), which agrees with a break in climatically stable areas found in Global, Regional, and Moroccan models (Figs. 4;). This suggests a role for climate in the group diversification and matches the refugia patterns identified in the region [START_REF] Husemann | Palaearctic biogeography revisited: Evidence for the existence of a North African refugium for Western Palaearctic biota[END_REF][START_REF] Martínez-Freiría | Integrative phylogeographical and ecological analysis reveals multiple Pleistocene refugia for Mediterranean Daboia vipers in north-west Africa[END_REF]. Similarly, the decreased suitability predicted for north-eastern Algeria/Tunisia could be linked with the divergence of the two sub-lineages, a pattern also found in other taxa [START_REF] Guiller | Historical biogeography of the land snail Cornu aspersum: a new scenario inferred from haplotype distribution in the Western Mediterranean basin[END_REF][START_REF] Husemann | Palaearctic biogeography revisited: Evidence for the existence of a North African refugium for Western Palaearctic biota[END_REF]Nicolas et al., 2015). In Mauritania, sporadic decreases in climatic connectivity or disruptive effects of rivers during humid phases (e.g. [START_REF] Dobigny | Recent radiation in West African Taterillus (Rodentia, Gerbillinae): the concerted role of chromosome and climatic changes[END_REF] could help explain the distribution of the sub-lineages. However, given most of the phylogenetic signal is from mtDNA, effects of coalescence cannot be ruled out without employing multiple nuclear markers. The observed haplogroups in P. aegyptius are probably due to considerable geographic distance (isolation by distance) between sample clusters (Egypt and Niger).

Conclusions and future research

The work here presented contributes to a better understanding of how Saharan mesic [START_REF] Carranza | Relationships and evolution of the North African geckos, Geckonia and Tarentola (Reptilia: Gekkonidae), based on mithochondrial and nuclear DNA sequences[END_REF] or habitat specialization (e.g. sympatric speciation in Jaculus; [START_REF] Boratyński | Large spatial scale of the phenotype-environment color matching in two cryptic species of African desert jerboas (Dipodidae: Jaculus)[END_REF] can also lead to species diversification. We contributed to a better understanding of the history of P. schokari in North Africa, but still further sampling and additional nuclear markers are needed to understand the history of the species along its full distribution. Of particular importance are the role of the interplay of Arabia Peninsula and Africa, and the possibilities of secondary contacts between species and lineages, as well as their evolutionary and taxonomic status.

Acknowledgements

Authors acknowledge BIODESERTS group members for their assistance during fieldwork. P.

  , J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09

  Interglacial (LIG; ~120,000-140,000 years BP;Otto-Bliesner et al., 2006), Last Glacial Maximum (LGM; ~21,000 years BP; Paleoclimate Modelling Intercomparison Project Phase III -PMIP3-CMIP5) and middle Holocene (midHol; 6000 years BP; PMIP3-CMIP5) periods. These periods are generally accepted as qualitatively representative of previous cycles during the Pleistocene (e.g.[START_REF] Martínez-Freiría | Integrative phylogeographical and ecological analysis reveals multiple Pleistocene refugia for Mediterranean Daboia vipers in north-west Africa[END_REF], in spite of variations in duration and intensity, since later cycles had the largest amplitude[START_REF] Snyder | Evolution of global temperature over the past two million years[END_REF]. LIG and midHol variables were at 30 arcsecond resolution. The corresponding Global Circulation Models (GCM) were the NCAR-CCSM and CCSM4, respectively. LGM variables were at 2.5 arc-minute resolution (~5 x 5 km) and were retrieved for three GCMs: CCSM4, MIROC-ESM and MPI-ESM-P. Past variables were also Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009

  3). Using the alternative calibration scheme by Sanders et al. (2010) produced very similar results (Fig. A.2a).

A

  .7). Their niches are not equivalent (Equivalency test, p < 0.05; Fig. A.7) although a similar pattern of habitat selection between lineages cannot be rejected (Similarity test, p > 0.05; Fig. A.7).

  However, it is still possible the observed pattern is a coincidence, thus phylogeographic studies with other taxa are needed to verify this hypothesis. Continued isolation may have subsequently led to some niche divergence among lineages, although the observed pattern could not be dissociated from the differences in local climatic conditions(Fig. A.7). Predicted climatic connectivity may have decreased periodically(Figs. A.3, A.4), but the fact that present conditions predict the narrowest suitable area and still allow species persistence along the coast seems to indicate that, at least climatically, some gene flow is always possible. Individual Moroccan-Mauritanian models predicted that lineage contact is most likely under LGM-like conditions (Figs.A.5, A.6), similar to the Eastern Sahara corridor. The Red Sea coast was expected to be clearly represented in the palaeomodels, given that the topography allows altitudinal range shifts according to climate fluctuations[START_REF] Messerli | Climate, Environmental Change, and Resources of the African Mountains from the Mediterranean to the Equator[END_REF]. Contrary to previously hypothesised, the Red Sea tS-corridor seems not permanent for mesic species, especially during hot and dry phases similar to LIG (Fig.A.3). Nevertheless, pixel size could be constraining model sensibility.All considered, it seems that the Atlantic coast works as a corridor when considering the climatic cycles altogether, but certain portions (e.g. Tamanrasset river basin) may work as filters depending on the climatic phase. For example, the predicted climatic suitability of northern costal Mauritania was not mirrored by availability of observations/samples, despite considerable local sampling efforts during the last decade[START_REF] Sow | Atlas of the distribution of reptiles in the Parc National du Banc d'Arguin[END_REF], and is probably related to the unsuitable character of the wide sandy habitats present along the coast and Azeffâl dunes, in the Tamanrasset palaeoriver basin. However, Contact between Mauritanian and Moroccan populations could also be allowed through the Adrar Atar in Mauritania and Adrar Souttouf in Morocco. Assessing the detailed location of the corridors and the role of the landscape in gene-flow would however need further studies with fast-evolving markers (e.g.[START_REF] Velo-Antón | Should I stay or should I go? Comment citer ce document[END_REF] and more taxa. Still, the likelihood of a climatic corridor along the Atlantic coast is shown, and we thus expect similar genetic structure patterns to occur in other species with likely similar dispersal capabilities, like the Moila Snake (Malpolon moilensis) orSaw-scaled Viper (Echis pyramidum;[START_REF] Wüster | Molecular Phylogenetics and Evolution A nesting of vipers : Phylogeny and historical biogeography of the Viperidae ( Squamata : Comment citer ce document[END_REF]. Stronger structuring is expected for more mesic species or with less dispersal capabilities.

  to an interplay of climatic fluctuations and geographic variability, and lays the ground for further hypothesis testing. Still, assessing how the shifts in the climatic conditions affect gene flow and evolution in other taxa is necessary to complete our understanding about the trans-Saharan corridor dynamics. Assessing the role of climate and landscape in gene-flow dynamics at local scales is also crucial. In addition to vicariance, ecological adaptation to different gradients of aridity (e.g. Tarentola along the Atlantic coast;

Figure 1 Figure 2 Figure 3

 123 Figure 1 Ranges and sample localities of P. schokari and P. aegyptius. Ranges were drawn based on distribution data from Sindaco et al. (2013), presence records collected for this study, and suitable areas predicted by ecological modelling. Letters mark mountain ranges mentioned in the text (A: Adrar Souttouf; B: Adrar Atar; C: Hoggar, Mouydir and Tassili n'Ajjer; D: Fezzan; E: Tibesti-Dohone; F: Ennedi-Borkou and Marra; G: Uweinat-Gilf Kebir).

Figure 4

 4 Figure 4 Stable climatic areas for P. schokari derived from four modelling frameworks: (A) Global, all the species range; (B) Regional, the NW-African lineages; (C) Moroccan lineage only; and (D) Mauritanian lineage only. Warmer colours depict areas with higher stability. Tamanrasset paleoriver (Skonieczny et al., 2015) is depicted in B-D.

  Most samples were successfully sequenced for all markers(Table A.1). Dataset 1 resulted in an alignment of 3111 positions (TableA.3). Uncorrected p-distances and diversity measures for the mitochondrial markers of P. schokari and P. aegyptius lineages can be found in Table

, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009 13

  combining geological/climatic knowledge and phylogenetic data, it is possible to approximate the processes that shaped Sahara colonization and the diversity of species in and around it. The models here presented include only climatic conditions, as no accurate geological data are available to past conditions for such large area. However, climatic variables

, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009 15 Nevertheless, by

  Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C.(2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009

  Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S.,Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009 Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009 Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. Ptyodactylus geckos (Squamata: Phyllodactylidae) in North Africa and Arabia.Mol. Phylogenet. Evol. 85, 208-220. doi:10.1016/j.ympev.2015.02.010 Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for Serpentes ).Mol. Phylogenet. Evol. 49, 445-459. doi:10.1016/j.ympev.2008.08.019 Yule, G.U., 1925. A Mathematical Theory of Evolution based on the Conclusions of Dr. J.C. Willis, F.R.S. J. R.Stat. Soc. 88, 433-436. doi:10.1098/rstb.1925.0002

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	(Squamata: Serpentes: Viperidae). Mol. Phylogenet. Evol. 53, 792-807.
	Lymberakis and A. Ohler provided access to samples; P. Campbell and R. Sindaco provided doi:10.1016/j.ympev.2009.08.002
	presence records for P. schokari. This work was funded by National Geographic Society (CRE R Core Team, 2016. R: A Language and Environment for Statistical Computing.
	7629-04/8412-08), Mohamed bin Zayed Species Conservation Fund (11052709, 11052707,
	Rambaut, A., Suchard, M., Xie, D., Drummond, A., 2014. Tracer v1.6.
	11052499), Fundação para a Ciência e a Tecnologia (PTDC/BIA-BEC/099934/2008 and
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	Competitiveness Factors -COMPETE (FCOMP-01-0124-FEDER-008917/028276). Individual and genetic diversity of Psammophis schokari (Serpentes) in North Africa based on
	support was given by FCT (contract IF/01425/2014, and grants SFRH/BD/78402/2011, mitochondrial DNA sequences. African Zool. 42, 112-117.
	SFRH/BPD/69857/2010) within QREN-POPH-T4.1 funded by ESF and Portuguese MEC. Logistic
	support for fieldwork was given by Pedro Santos Lda (Trimble GPS), Off Road Power Shop, P.N.

(2018)

. The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009 Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009 rock-dwelling Phillips, S.J., Anderson, R.P., Schapire, R.E., 2006. Maximum entropy modeling of species geographic distributions. Ecol. Modell. 190, 231-259. Rohling, E.J., Marino, G., Grant, K.M., 2015. Mediterranean climate and oceanography, and the periodic development of anoxic events (sapropels). Earth-Science Rev. 143, 62-97. Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009 Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C. (2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009

Table 2

 2 Number of samples, evaluation, and variable contribution for models. Top: number of samples and area-under-the-curve (AUC) average (and standard deviation) for training and testing, and AUC standard deviation for the four distinct approaches (Global, Regional, Morocco and Mauritania). Bottom: average (and standard deviation) contribution of each variable to the respective model.

	metric / variable	Global	Regional	Morocco	Mauritania
	N training / test samples	265 / 113	157 / 66	139 / 59	19 / 7
	Training AUC	0.891 (0.007) 0.9333 (0.005) 0.927 (0.007) 0.931 (0.022)
	Test AUC	0.842 (0.017) 0.882 (0.018) 0.899 (0.011) 0.901 (0.05)
	AUC Standard Deviation	0.0163	0.016	0.012	0.036
	BIO 4	27.889 (2.658) 9.075 (2.36) 4.015 (1.366) 53.255 (8.985)
	BIO 10	19.061 (4.26) 49.594 (6.96) 36.785 (6.935) 1.946 (2.59)
	BIO 12	9.861 (2.011) 16.35 (3.965) 5.712 (3.178) 25.476 (7.31)
	BIO 14	2.32 (1.138)	3.804 (1.55)	3.591 (1.22) 3.611 (3.024)
	BIO 19	40.871 (2.7) 21.175 (7.04) 49.896 (6.614) 15.711 (5.59)

Comment citer ce document : Gonçalves, D. V., Martínez-Freiría, Crochet, P.-A., Geniez, P., Carranza, S., Brito, J. C.

(2018). The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa. Molecular Phylogenetics and Evolution, 118, 64-74. DOI : 10.1016/j.ympev.2017.09.009

Table 1

Uncorrected p-distances among lineages, and indexes of genetic diversity for Dataset 1. Values above in regular font correspond to cytochrome b (CYTB), and in bold below correspond to NADH dehydrogenase subunit 4 (ND4). N = number of samples; h = number of haplotypes; Hd = haplotype diversity; π = nucleotide diversity. 5.8+-0.9 7.1+-0.9 6.1+-0.9 6+-0.8 0.2+-0.1 3 3 1.000+-0.272 0.00192+-0.00064

Highlights

Testing trans-Saharan mesic corridors model and predict their location and stability.

We combined phylogeography and palaeoclimate modelling of P. schokari in North Africa.

Atlantic corridor predicted to be permanent, others sporadically active.

Six parapatric lineages identified, four in North Africa. Divergence in Pliocene.

Lineages divergence attributed to climate cycles and possibly Tamanrasset palaeo-river basin.