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1.
Ecol Evol ; 14(5): e11229, 2024 May.
Article in English | MEDLINE | ID: mdl-38751825

ABSTRACT

Predator-prey interaction is a major force driving natural selection. Yet, the identification of species preying on, or consuming, aposematic species is largely unknown. Here, I conduct a study evaluating the role of the exotic Rattus rattus as a consumer and possible predator of the aposematic and toxic Salamandra salamandra. I used camera traps to investigate the response of R. rattus towards S. salamandra carcasses in two insular populations, Ons and San Martiño (NW Spain), which show remarkable contrasting behaviour (nocturnal vs. diurnal activity) and demographic and phenotypic differences. This study unveils R. rattus consumes S. salamandra despite its aposematic colour pattern and toxicity. The high number of salamander carcasses consumed or taken by rats throughout each island (90%-100%) and the lack of other possible predator-prey interactions points to R. rattus as an efficient consumer of S. salamandra in these insular environments, which might exert a high predation pressure on both islands. Yet, the drivers underlying the behavioural and phenotypic differences in these insular populations should be further investigated.

2.
Mol Biol Rep ; 51(1): 294, 2024 Feb 09.
Article in English | MEDLINE | ID: mdl-38334910

ABSTRACT

BACKGROUND: European vipers (genus Vipera) are a well-studied taxonomic group, but the low resolution of nuclear sanger-sequenced regions has precluded thorough studies at systematic, ecological, evolutionary and conservation levels. In this study, we developed novel microsatellite markers for the three Iberian vipers, Vipera aspis, V. latastei and V. seoanei, and assessed their polymorphism in north-central Iberian populations. METHODS AND RESULTS: Genomic libraries were developed for each species using an Illumina Miseq sequencing approach. From the 70 primer pairs initially tested, 48 amplified reliably and were polymorphic within species. Cross-species transferability was achieved for 31 microsatellites loci in the three target species and four additional loci that were transferable to one species only. The 48 loci amplified in average seven alleles, and detected average expected and observed heterozygosities of 0.7 and 0.55, in the three genotyped populations/species (26 V. aspis, 20 V. latastei and 10 V. seoanei). CONCLUSIONS: Our study provides a selection of 48 polymorphic microsatellite markers that will contribute significantly to current knowledge on genetic diversity, gene flow, population structure, demographic dynamics, systematics, reproduction and heritability in these species, and potentially in other congeneric taxa.


Subject(s)
Vipera , Viperidae , Animals , Polymorphism, Genetic , Viperidae/genetics , Biological Evolution , Microsatellite Repeats/genetics
3.
Mol Phylogenet Evol ; 191: 107979, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38040070

ABSTRACT

The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.


Subject(s)
Cerastes , Viperidae , Animals , Phylogeny , Viperidae/genetics , Tunisia , Vipera
4.
Ecol Evol ; 13(1): e9666, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36620407

ABSTRACT

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study. Our main hypothesis assumes that topography along with contemporary and historical climate are drivers of phylogenetic diversity and endemism, but that the strength of these predictors may be weaker at the regional scale than it tends to be at the global scale. We mapped spatial patterns of Iberian amphibians' phylogenetic diversity and endemism, using previously published phylogenetic and distribution data. Furthermore, we compiled spatial data on topographic and climatic variables related to the water-energy availability, topography, and historical climatic instability hypotheses. To test our hypotheses, we used Spatial Autoregressive Models and selected the best model to explain diversity patterns based on Akaike Information Criterion. Our results show that, out of the variables tested in our study, water-energy availability and historical climate instability are the most important drivers of amphibian diversity in Iberia. However, as predicted, the strength of these predictors in our case study is weaker than it tends to be at global scales. Thus, additional drivers should also be investigated and we suggest caution when interpreting these predictors as surrogates for different components of diversity.

5.
Sci Data ; 9(1): 459, 2022 08 01.
Article in English | MEDLINE | ID: mdl-35915106

ABSTRACT

DNA barcode reference libraries are now continuously produced for the tree of life, which are essential pillars for the study of biological diversity. Yet, our knowledge about global diversity is largely limited in undersampled regions such as the largest warm desert, the Sahara-Sahel. This dataset provides a DNA barcode reference library for the reptiles of the Western Sahara-Sahel (WSS) and neighbouring countries across this region. It includes 760 barcodes from 133 reptile taxa, distributed in 23 families, and covering the intraspecific diversity of some species. A total of 84 species were collected in the WSS (83% of the total reptile species richness) over 18 overland field expeditions conducted since 2003. DNA barcodes resulted in a high success rate (95%) of species identification and barcoding gap analysis highlighted the effectiveness of the COI fragment as a barcode marker for the WSS reptiles. This dataset represents a comprehensive and reliable DNA reference library for the WSS, filling an important biodiversity gap across a remote and hard-to-sample region.


Subject(s)
DNA Barcoding, Taxonomic , Reptiles , Africa, Northern , Animals , Biodiversity , Gene Library , Phylogeny , Reptiles/genetics
7.
Syst Parasitol ; 99(3): 367-373, 2022 06.
Article in English | MEDLINE | ID: mdl-35312903

ABSTRACT

Molecular tools have revolutionized assessments of blood parasites in freshwater turtles. In the Iberian Peninsula and North Africa, two native species of terrapins occur, Emys orbicularis (Linnaeus) and Mauremys leprosa (Schweigger). Both have been identified as hosts for the blood parasite Haemogregarina stepanowi Danilewsky, 1885, which has also been found in related species. However, recent assessments of M. leprosa have identified several distinct genetic lineages of these parasites in this host, while only three haemogregarine lineages were identified in E. orbicularis in Tunisia. Here, we screened 215 individuals of E. orbicularis from the Iberian Peninsula, Menorca Island and Morocco for haemogregarine parasites using partial 18S rRNA gene sequences to estimate relationships. Three unrelated lineages of parasites were detected, one presumed H. stepanowi and two lineages previously known from M. leprosa. A considerable undescribed diversity of parasites exists within these vertebrate host species, while mixed infection and host-sharing is also widespread. Considering that E. orbicularis is near threatened in this region, it is of great importance to identify the parasites infecting it, and to further assess the potential deleterious impact of these diverse parasites on their hosts.


Subject(s)
Apicomplexa , Eucoccidiida , Parasites , Turtles , Animals , Species Specificity , Turtles/parasitology
8.
Mol Phylogenet Evol ; 167: 107347, 2022 02.
Article in English | MEDLINE | ID: mdl-34763070

ABSTRACT

The ability to bear live offspring, viviparity, has evolved multiple times across the tree of life and is a remarkable adaptation with profound life-history and ecological implications. Within amphibians the ancestral reproductive mode is oviparity followed by a larval life stage, but viviparity has evolved independently in all three amphibian orders. Two types of viviparous reproduction can be distinguished in amphibians; larviparity and pueriparity. Larviparous amphibians deliver larvae into nearby ponds and streams, while pueriparous amphibians deliver fully developed juveniles and thus do not require waterbodies for reproduction. Among amphibians, the salamander genus Salamandra is remarkable as it exhibits both inter- and intraspecific variation in the occurrence of larviparity and pueriparity. While the evolutionary relationships among Salamandra lineages have been the focus of several recent studies, our understanding of how often and when transitions between modes occurred is still incomplete. Furthermore, in species with intraspecific variation, the reproductive mode of a given population can only be confirmed by direct observation of births and thus the prevalence of pueriparous populations is also incompletely documented. We used sequence capture to obtain 1,326 loci from 94 individuals from across the geographic range of the genus, focusing on potential reproductive mode transition zones. We also report additional direct observations of pueriparous births for 20 new locations and multiple lineages. We identify at least five independent transitions from the ancestral mode of larviparity to pueriparity among and within species, occurring at different evolutionary timescales ranging from the Pliocene to the Holocene. Four of these transitions occurred within species. Based on a distinct set of markers and analyses, we also confirm previous findings of introgression between species and the need for taxonomic revisions in the genus. We discuss the implications of our findings with respect to the evolution of this complex trait, and the potential of using five independent convergent transitions for further studies on the ecological context in which pueriparity evolves and the genetic architecture of this specialized reproductive mode.


Subject(s)
Salamandra , Animals , Biological Evolution , Humans , Oviparity/genetics , Phylogeny , Urodela/genetics , Viviparity, Nonmammalian/genetics
9.
J Fungi (Basel) ; 7(8)2021 Aug 07.
Article in English | MEDLINE | ID: mdl-34436183

ABSTRACT

The recent introduction of the chytrid fungus Batrachochytrium salamandrivorans into northeastern Spain threatens salamander diversity on the Iberian Peninsula. We assessed the current epidemiological situation with extensive field sampling of urodele populations. We then sought to delineate priority regions and identify conservation units for the Iberian Peninsula by estimating the susceptibility of Iberian urodeles using laboratory experiments, evidence from mortality events in nature and captivity and inference from phylogeny. None of the 1395 field samples, collected between 2015 and 2021 were positive for Bsal and no Bsal-associated mortality events were recorded, in contrast to the confirmed occurrence of Bsal outbreak previously described in 2018. We classified five of eleven Iberian urodele species as highly susceptible, predicting elevated mortality and population declines following potential Bsal emergence in the wild, five species as intermediately susceptible with variable disease outcomes and one species as resistant to disease and mortality. We identified the six conservation units (i.e., species or lineages within species) at highest risk and propose priority areas for active disease surveillance and field biosecurity measures. The magnitude of the disease threat identified here emphasizes the need for region-tailored disease abatement plans that couple active disease surveillance to rapid and drastic actions.

11.
Sci Rep ; 11(1): 9259, 2021 04 29.
Article in English | MEDLINE | ID: mdl-33927228

ABSTRACT

Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.


Subject(s)
Reproductive Isolation , Urodela/physiology , Animals , Evolution, Molecular , Gene Flow , Genetic Variation , Genetics, Population , Hybridization, Genetic , Phenotype , Phylogeography , Urodela/genetics
12.
Mol Phylogenet Evol ; 157: 107063, 2021 04.
Article in English | MEDLINE | ID: mdl-33387650

ABSTRACT

The salamander genus Salamandra is widespread across Europe, North Africa, and the Near East and is renowned for its conspicuous and polymorphic colouration and diversity of reproductive modes. The phylogenetic relationships within the genus, and especially in the highly polymorphic species S. salamandra, have been very challenging to elucidate, leaving its real evolutionary history and classification at species and subspecies levels a topic of debate and contention. However, the distribution of diversity and species delimitation within the genus are critically important for identifying evolutionarily significant units for conservation and management, especially in light of threats posed by the pathogenic chytrid fungus Batrachochytrium salamandrivorans that is causing massive declines of S. salamandra populations in central Europe. Here, we conducted a phylogenomic analysis from across the taxonomic and geographic breadth of the genus Salamandra in its entire range. Bayesian, maximum likelihood and network-based phylogenetic analyses of up to 4905 ddRADseq-loci (294,300 nucleotides of sequence) supported the distinctiveness of all currently recognised species (Salamandra algira, S. atra, S. corsica, S. infraimmaculata, S. lanzai, and S. salamandra), and all five species for which we have multiple exemplars were confirmed as monophyletic. Within S. salamandra, two main clades can be distinguished: one clade with the Apenninic subspecies S. s. gigliolii nested within the Iberian S. s. bernardezi/fastuosa; and a second clade comprising all other Iberian, Central and East European subspecies. Our analyses revealed that some of the currently recognized subspecies of S. salamandra are paraphyletic and may require taxonomic revision, with the Central- and Eastern-European subspecies all being poorly differentiated at the analysed genomic markers. Salamandra s. longirostris - sometimes considered a separate species - was nested within S. salamandra, consistent with its subspecies status. The relationships identified within and between Salamandra species provide valuable context for future systematic and biogeographic studies, and help elucidate critical evolutionary units for conservation and taxonomy.


Subject(s)
Phylogeny , Urodela/classification , Urodela/genetics , Animals , Bayes Theorem , Biodiversity , Genotype , Geography , Principal Component Analysis , Species Specificity
13.
Conserv Biol ; 35(2): 634-642, 2021 04.
Article in English | MEDLINE | ID: mdl-32761662

ABSTRACT

Protected-area systems should conserve intraspecific genetic diversity. Because genetic data require resources to obtain, several approaches have been proposed for generating plans for protected-area systems (prioritizations) when genetic data are not available. Yet such surrogate-based approaches remain poorly tested. We evaluated the effectiveness of potential surrogate-based approaches based on microsatellite genetic data collected across the Iberian Peninsula for 7 amphibian and 3 reptilian species. Long-term environmental suitability did not effectively represent sites containing high genetic diversity (allelic richness). Prioritizations based on long-term environmental suitability had similar performance to random prioritizations. Geographic distances and resistance distances based on contemporary environmental suitability were not always effective surrogates for identification of combinations of sites that contain individuals with different genetic compositions. Our results demonstrate that population genetic data based on commonly used neutral markers can inform prioritizations, and we could not find an adequate substitute. Conservation planners need to weigh the potential benefits of genetic data against their acquisition costs.


Evaluación de los Sustitutos de la Diversidad Genética para la Planeación de la Conservación Resumen Los sistemas de áreas protegidas deberían conservar la diversidad genética intraespecífica. Ya que para obtener datos genéticos se requieren recursos, se han propuesto distintas estrategias para generar los planes para los sistemas de áreas protegidas (priorizaciones) cuando los datos genéticos no están disponibles. A pesar de lo anterior, dichas estrategias basadas en sustitutos han sido poco evaluadas. Evaluamos la efectividad del potencial de las estrategias basadas en sustitutos cuya base son los datos genéticos de microsatélites obtenidos en toda la Península Ibérica y correspondientes a siete especies de anfibios y a tres de reptiles. La idoneidad ambiental a largo plazo no representó efectivamente los sitios que contienen una diversidad genética alta (riqueza de alelos). Las priorizaciones basadas en la idoneidad ambiental a largo plazo tuvieron un desempeño similar a las priorizaciones aleatorias. Las distancias geográficas y las distancias de resistencia basadas en la idoneidad ambiental contemporánea no siempre fueron sustitutos efectivos para la identificación de las combinaciones de sitios que contienen individuos con composiciones genéticas diferentes. Nuestros resultados demuestran que los datos genéticos de una población basados en marcadores neutrales de uso común pueden informar a las priorizaciones y que no pudimos encontrar un sustituto adecuado. Los planificadores de la conservación necesitan sopesar los beneficios potenciales de los datos genéticos contra sus costos de adquisición.


Subject(s)
Biodiversity , Conservation of Natural Resources , Ecosystem , Europe , Genetic Variation
14.
Ecol Evol ; 10(19): 10353-10363, 2020 Oct.
Article in English | MEDLINE | ID: mdl-33072264

ABSTRACT

Reduced representation genome sequencing has popularized the application of single nucleotide polymorphisms (SNPs) to address evolutionary and conservation questions in nonmodel organisms. Patterns of genetic structure and diversity based on SNPs often diverge from those obtained with microsatellites to different degrees, but few studies have explicitly compared their performance under similar sampling regimes in a shared analytical framework. We compared range-wide patterns of genetic structure and diversity in two amphibians endemic to the Iberian Peninsula: Hyla molleri and Pelobates cultripes, based on microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci) datasets of comparable sample size and spatial extent. Model-based clustering analyses with STRUCTURE revealed minor differences in genetic structure between marker types, but inconsistent values of the optimal number of populations (K) inferred. SNPs yielded more repeatable and less admixed ancestries with increasing K compared to microsatellites. Genetic diversity was weakly correlated between marker types, with SNPs providing a better representation of southern refugia and of gradients of genetic diversity congruent with the demographic history of both species. Our results suggest that the larger number of loci in a SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset, at least at the spatial and temporal scales investigated.

15.
Sci Rep ; 10(1): 14744, 2020 09 08.
Article in English | MEDLINE | ID: mdl-32901062

ABSTRACT

The reduction in fecundity associated with the evolution of viviparity may have far-reaching implications for the ecology, demography, and evolution of populations. The evolution of a polygamous behaviour (e.g. polyandry) may counteract some of the effects underlying a lower fecundity, such as the reduction in genetic diversity. Comparing patterns of multiple paternity between reproductive modes allows us to understand how viviparity accounts for the trade-off between offspring quality and quantity. We analysed genetic patterns of paternity and offspring genetic diversity across 42 families from two modes of viviparity in a reproductive polymorphic species, Salamandra salamandra. This species shows an ancestral (larviparity: large clutches of free aquatic larvae), and a derived reproductive mode (pueriparity: smaller clutches of larger terrestrial juveniles). Our results confirm the existence of multiple paternity in pueriparous salamanders. Furthermore, we show the evolution of pueriparity maintains, and even increases, the occurrence of multiple paternity and the number of sires compared to larviparity, though we did not find a clear effect on genetic diversity. High incidence of multiple paternity in pueriparous populations might arise as a mechanism to avoid fertilization failures and to ensure reproductive success, and thus has important implications in highly isolated populations with small broods.


Subject(s)
Biological Evolution , Paternity , Reproduction , Urodela/physiology , Viviparity, Nonmammalian , Animals , Behavior, Animal , Female , Male , Microsatellite Repeats , Sexual Behavior, Animal , Urodela/genetics
16.
Mol Ecol ; 28(20): 4573-4591, 2019 10.
Article in English | MEDLINE | ID: mdl-31541595

ABSTRACT

Evolutionary changes in reproductive mode may affect co-evolving traits, such as dispersal, although this subject remains largely underexplored. The shift from aquatic oviparous or larviparous reproduction to terrestrial viviparous reproduction in some amphibians entails skipping the aquatic larval stage and, thus, greater independence from water. Accordingly, amphibians exhibiting terrestrial viviparous reproduction may potentially disperse across a wider variety of suboptimal habitats and increase population connectivity in fragmented landscapes compared to aquatic-breeding species. We investigated this hypothesis in the fire salamander (Salamandra salamandra), which exhibits both aquatic- (larviparity) and terrestrial-breeding (viviparity) strategies. We genotyped 426 larviparous and 360 viviparous adult salamanders for 13 microsatellite loci and sequenced a mitochondrial marker for 133 larviparous and 119 viviparous individuals to compare population connectivity and landscape resistance to gene flow within a landscape genetics framework. Contrary to our predictions, viviparous populations exhibited greater differentiation and reduced genetic connectivity compared to larviparous populations. Landscape genetic analyses indicate viviparity may be partially responsible for this pattern, as water courses comprised a significant barrier only in viviparous salamanders, probably due to their fully terrestrial life cycle. Agricultural areas and, to a lesser extent, topography also decreased genetic connectivity in both larviparous and viviparous populations. This study is one of very few to explicitly demonstrate the evolution of a derived reproductive mode affects patterns of genetic connectivity. Our findings open avenues for future research to better understand the eco-evolutionary implications underlying the emergence of terrestrial reproduction in amphibians.


Subject(s)
Genetic Variation/genetics , Oviparity/genetics , Salamandra/embryology , Salamandra/genetics , Viviparity, Nonmammalian/genetics , Animals , Biological Evolution , DNA, Mitochondrial/genetics , Evolution, Molecular , Female , Gene Flow/genetics , Genetics, Population , Microsatellite Repeats/genetics
17.
Glob Chang Biol ; 25(12): 4034-4047, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31230387

ABSTRACT

Ongoing global warming is disrupting several ecological and evolutionary processes, spanning different levels of biological organization. Species are expected to shift their ranges as a response to climate change, with relevant implications to peripheral populations at the trailing and leading edges. Several studies have analyzed the exposure of species to climate change but few have explored exposure at the intraspecific level. We introduce a framework to forecast exposure to climate change at the intraspecific level. We build on existing methods by combining correlative species distribution models, a model of species range dynamics, and a model of phylogeographic interpolation. We demonstrate the framework by applying it to 20 Iberian amphibian and reptile species. Our aims were to: (a) identify which species and intraspecific lineages will be most exposed to future climate change; (b) test if nucleotide diversity at the edges of species ranges are significantly higher or lower than on the overall range; and (c) analyze if areas of higher species gain, loss, and turnover coincide with those predicted for lineages richness and nucleotide diversity. We found that about 80% of the studied species are predicted to contract their range. Within each species, some lineages were predicted to contract their range, while others were predicted to maintain or expand it. Therefore, estimating the impacts of climate change at the species level only can underestimate losses at the intraspecific level. Some species had significant high amount of nucleotide at the trailing or leading edge, or both, but we did not find a consistent pattern across species. Spatial patterns of species richness, gain, loss, and turnover were fairly concurrent with lineages richness and nucleotide diversity. Our results support the need for increased attention to intraspecific diversity regarding monitoring and conservation strategies under climate change.


Subject(s)
Biological Evolution , Climate Change , Genetic Variation , Phylogeography
18.
Mol Ecol Resour ; 19(4): 1081-1094, 2019 Jul.
Article in English | MEDLINE | ID: mdl-30873736

ABSTRACT

Estimating geographical ranges of intra-specific evolutionary lineages is crucial to the fields of biogeography, evolution, and biodiversity conservation. Models of isolation mechanisms often consider multiple distances in order to explain genetic divergence. Yet, the available methods to estimate the geographical ranges of lineages are based on direct geographical distances, neglecting other distance metrics that can better explain the spatial genetic structure. We extended the phylogeographical interpolation method (phylin) in order to accommodate user-defined distance metrics and to incorporate the uncertainty associated with genetic distance calculation. These new features were tested with simulated and empirical data sets. Multiple distance matrices were generated including geographical, resistance, and environmental distances to derive maps of lineage occurrence. The new additions to this method improved the ability to predict lineage occurrence, even with low sample size. We used a regression framework to quantify the relationship between the genetic divergence and competing distance matrices representing potential isolation processes that are subsequently used in the interpolation process. Including uncertainty in tree topology and the different distance matrices improved the robustness of the variograms, allowing a better fit of the theoretical model of spatial dependence. The improvements to the method increase its potential application in other fields. Accurately mapping genetic divergence can help to locate potential contact zones between lineages as well as barriers to gene flow, which has a broad interest in biogeographical and evolutionary studies. Additionally, conservation efforts could benefit from the integration of genetic variation and landscape features in a spatially explicit framework.


Subject(s)
Biostatistics/methods , Computational Biology/methods , Phylogeography/methods
19.
Mol Phylogenet Evol ; 130: 81-91, 2019 01.
Article in English | MEDLINE | ID: mdl-30321698

ABSTRACT

North Africa is a climatically and topographically complex region with unique biotic assemblages resulting from the combination of multiple biogeographic realms. Here, we assess the role of climate in promoting intra-specific diversification in a Palearctic relict, the North African fire salamander, Salamandra algira, using a combination of phylogenetic and population genetic analyses, paleoclimatic modelling and niche overlap tests. We used mitochondrial DNA (Cyt-b), 9838 ddRADseq loci, and 14 microsatellite loci to characterize patterns of genetic diversity and population structure. Phylogenetic analyses recover two major clades, each including several lineages with mito-nuclear discordances suggesting introgressive patterns between lineages in the Middle Atlas, associated with a melting pot of genetic diversity. Paleoclimatic modelling identified putative climatic refugia, largely matching areas of high genetic diversity, and supports the role of aridity in promoting allopatric diversification associated with ecological niche conservatism. Overall, our results highlight the role of climatic microrefugia as drivers of populations' persistence and diversification in the face of climatic oscillations in North Africa, and stress the importance of accounting for different genomic regions when reconstructing biogeographic processes from molecular markers.


Subject(s)
Phylogeny , Salamandra/classification , Africa, Northern , Animals , DNA, Mitochondrial/genetics , Ecosystem , Genetic Variation , Genetics, Population , Microsatellite Repeats/genetics , Models, Biological , Phylogeography , Salamandra/genetics
20.
Sci Rep ; 8(1): 15925, 2018 10 29.
Article in English | MEDLINE | ID: mdl-30374044

ABSTRACT

Hybrid zones are natural laboratories allowing insights in genetic processes like lineage diversification, speciation and introgression. Using large sampling, 15 microsatellite loci and a mitochondrial marker, we examined the Pyrenean contact zone of three pond turtle taxa (Emys orbicularis orbicularis, E. o. galloitalica, E. o. occidentalis). The Pyrenees are a biogeographically important region separating many lineages endemic to the Iberian Peninsula from their Western European counterparts. We discovered limited admixture, reflecting a complex biogeographic scenario. Simulations using Approximate Bayesian Computing supported that E. o. orbicularis invaded the Iberian Peninsula in the Holocene, circumventing the Pyrenees along the Mediterranean coast, and hybridized in the northern peninsula with the local coastal subspecies galloitalica, and to a lesser extent, with occidentalis. While E. o. occidentalis, and in particular E. o. orbicularis, expanded their ranges considerably during Holocene warming, E. o. galloitalica remained largely confined to its former Iberian refuge. Admixture among the three taxa is surprisingly low, and a future taxonomic investigation that includes the unstudied subspecies of E. orbicularis from North Africa, Eastern Europe and Asia has to determine whether their current status properly reflects their evolutionary divergence or whether certain taxa should be regarded as full species.


Subject(s)
Hybridization, Genetic , Turtles/genetics , Animals , Bayes Theorem , Biological Evolution , DNA, Mitochondrial/genetics , DNA, Mitochondrial/isolation & purification , Genetic Variation , Microsatellite Repeats/genetics , Phylogeography , Principal Component Analysis
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