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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., This work was supported by National Funds through FCT – Foundation for Science and Technology (SALOMICS: PTDC/BIA-EVL/28475/2017); the authors also acknowledge funding from other FCT projects and FEDER funds through the Operational Programme for Competitiveness Factors – COMPETE (EVOVIV: PTDC/BIA-EVF/3036/2012; FCOMP-01-0124-FEDER-028325 and UIDB/500027/2020); and by National/FEDER funds through Ministerio de Economía y Competitividad (CGL2012-40246-C02-02). G.V.-A., A.L. and P.T. were supported by FCT (IF/01425/2014 and CEECIND/00937/2018, PD/BD/106060/2015, DL57/2016/CP1440/CT0008, respectively).

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., We compared patterns of genetic structure and diversity between microsatellites and SNPs in two amphibians from the Iberian Peninsula: Hyla molleri and Pelobates cultripes. Larger number of loci from SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset (photo: Pelobates cultripes; credits: Guillermo Velo‐Antón).

International audience; Aim: The biogeographic history of the Sahara-Sahel desert is tightly linked to its extreme and fluctuating palaeoclimate and diverse topography. For the mesic species inhabiting the region, coastal areas and the Nile Valley are perceived as the main pathways to disperse through desert habitats, but past connections may have also occurred throughout currently isolated mountain regions. Herein, we test the trans-Sahara mountain corridor hypothesis (i.e., mesic connectivity across Central Sahara highlands) and its role in the diversification of a small terrestrial vertebrate.Location: North Africa and Arabia.Taxon; Acanthodactylus boskianus (Squamata: Lacertidae).Methods: We integrated multi-locus mitochondrial and nuclear phylogenies with species’ climate-niche modelling, including palaeo-projections. Genetic analyses aimed to assess the species’ genetic structure, identify its main mitochondrial lineages and nuclear diversity, and reconstruct its ancestral biogeography. Species’ climate-niche stability was modelled independently for the Late Pleistocene-Holocene and the Plio-Pleistocene, to infer historical climatic refugia and dispersal corridors.Results: Four spatially structured mitochondrial lineages, integrating several parapatric sub-lineages, originated during the Plio-Pleistocene. Nuclear data revealed nine potential candidate species. Climatic refugia were located in mountains and desert fringes, remaining consistent for the Late Pleistocene-Holocene and the Plio-Pleistocene. Recurrent North-South climatic corridors were located along the desert periphery, while others less frequent were found across Central Sahara. Ancestral biogeography analyses recovered a recent Pleistocene colonization of the Sahel throughout eastern Sahara and either Sahara or Sahel origin for Central Sahara populations.Main conclusions: Species’ diversification was triggered by a combination of Plio-Pleistocene climatic cycles across a complex topographic region, where mountains acted as the main diversification hotspots. The historical role of Central Sahara highlands as main non-peripheral mesic refugia was corroborated. In addition, intermittent climatic connections linked Mediterranean and Sahel ecoregions with Central Sahara refugia, suggesting the existence of alternative trans-Sahara dispersal routes to the putative coastal and Nile corridors.

The recent introduction of the chytrid fungus Batrachochytrium salamandrivorans into north-eastern 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., This research was funded by the European Commission (Tender ENV.B.3/SER/2016/0028, Mitigating a new infectious disease in salamanders to counteract the loss of biodiversity), the Foundation for the Conservation of Salamanders (project “Monitoring the incidence of emerging pathogens on endemic urodeles from the Cantabrian range, Spain”). B.T. was supported by a ‘Doctorados Industriales’ grant of Comunidad de Madrid, Spain (ref. IND2020/AMB-17438). G.V.-A. was financed by the Portuguese Foundation for Science and Technology (FCT; CEECIND/00937/2018). B.C.S. was supported by an ARC DECRA (DE200100121).

Our study seeks to: (1) reduce biodiversity knowledge gaps in amphibians from desert and arid regions; (2) quantify species diversity and detect potential cryptic diversity; (3) identify environmental correlates of amphibian richness distribution, and (4) identify diversity hotspots. DNA barcoding and spatial modelling were integrated to map observed and predicted amphibian richness in Mauritania, Africa. We built two DNA barcoding libraries using one mitochondrial (COI) and one nuclear marker (RAG1). Taxon richness was calculated using species delimitation methods. A generalised linear model was employed to identify environmental correlates of amphibian richness and the distribution of diversity hotspots was predicted. We found a total of 16 anuran taxa with Afrotropic affinities, and two genera and four species were added for the amphibian list of Mauritania. Potential cryptic diversity was detected in Hoplobatrachus occipitalis. Amphibian richness was positively correlated with proximity to savannah, gravel floodplains, and with presence of seasonal wetlands, and negatively with proximity to dunes. Major diversity hotspots were predicted in southern Mauritania. Barcoding methods for both genetic markers successfully identified the taxonomic identity of specimens, also uncovering cryptic diversity in the amphibians of the Sahara-Sahel ecoregions. Amphibian richness in Mauritania increases southwards and it is mostly concentrated in areas under pressure due to habitat conversion, lacking legal protection. The combination of DNA barcoding with spatial modelling can be easily applied to any desert system to address pressing needs for research on biodiversity distribution., Funding provided by National Geographic Society (CRE-7629-04, CRE-8412-08, GEFNE-53-12), Mohammed bin Zayed Species Conservation Fund (11052709, 11052707, 13257467), Rufford Foundation (SG-15399-1, SG-17893-1), Fundação para a Ciência e Tecnologia (FCT: PTDC/BIA-BEC/099934/2008, PTDC/BIA-BIC/2903/2012), FEDER through COMPETE-Operational Programme for Competitiveness Factors (FCOMP-01-0124-FEDER-008917, -028276), and by AGRIGEN–NORTE-01-0145-FEDER-000007, supported by Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). Research conducted in the scope of the LIA “Biodiversity and Evolution”. Individual support given by FCT (contracts DL57/2016/CP1440/CT0010, IF/01425/2014, and CEECINST/00014/2018/CP1512/CT0001).

International audience

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.

The complete mitochondrial genome of Salamandra salamandra was reconstructed using bycatch sequences from an RNAseq library generated from muscle tissue. This study shows the potential of using data originally produced for transcriptome assembly to additionally generate complete mitochondrial genomes. The resulting mitogenome was circular, consisted of 16,331 bp and followed the standard vertebrate gene order. Subsequent analysis of the current mitochondrial genome sequence for the species as listed on GenBank highlighted a species misidentification.

Quaternary climatic oscillations and geographic barriers have strongly influenced the distribution and diversification of thermophilic species occurring in the Mediterranean Basin. The Western Mediterranean pond turtle, Mauremys leprosa, is widely distributed throughout the Iberian Peninsula, southern France and most of the Maghreb region, with two subspecies currently recognized. In this work, we used 566 samples, including 259 new individuals, across the species range, and sequenced two mitochondrial markers (cytochrome b gene and control region; 163 samples in a concatenated mtDNA dataset) and one nuclear intron (R35; 23 samples representing all identified sublineages) to study the evolutionary history of M. leprosa. We combined phylogenetic methods and phylogeographic continuous diffusion models with spatial analysis. Our results (1) show a high level of genetic structure in Morocco originated during the Pleistocene; (2) reveal two independent population expansion waves from Morocco to Tunisia and to southern Europe, which later expanded throughout the Iberian Peninsula, and (3) identify several secondary contact zones in Morocco. Our study also sheds new light on the role of geographical features (Moroccan mountains ranges and the Strait of Gibraltar) and Pleistocene climatic oscillations in shaping genetic diversity and structure of M. leprosa, and underlines the importance of the Maghreb as a differentiation centre harbouring distinct glacial refugia.

Amphibian reproductive modes are diverse and are characterised by complex adaptations, including vast variability in life history traits and different parental investment strategies. For instance, viviparity is rare in urodeles despite the potential ecological advantages gained in such populations by having semi-independency from water. The fire salamander, Salamandra salamandra, shows remarkable intraspecific variation in reproductive modes, with two strategies co-occurring: a common reproductive mode, larviparity (parturition of aquatic larvae), and a phylogenetically derived reproductive mode, pueriparity (parturition of terrestrial juveniles). Pueriparous populations of S. salamandra have at least two independent origins, the first originating from its northern distribution in the Iberian Peninsula, and the second at two insular populations on the northwestern Iberian coast. Here, we analyse the patterns of variability of some life-history traits in larviparous and pueriparous populations of S. salamandra, including pueriparous populations from the two independent origins, to understand how these traits relate to the evolutionary transitions in reproductive modes in S. salamandra. Our study shows differences in female body size and clutch and brood size between larviparous and pueriparous fire salamanders. We did not find differences in female investment between reproductive modes, and thus, the evolution to pueriparity in S. salamandra is likely characterised by the re-allocation of eggs to matrotrophy. Our study also confirms pueriparity and larviparity as the characteristic reproductive modes for insular and coastal/mainland S. s. gallaica populations, respectively, revealing the potential presence of pueriparity in one coastal population. This comparative analysis sheds light on the maternal factors that might have driven, or are related to, the evolution of pueriparity in this unique biological system and sets up the basis for testing different hypotheses that include climatic, ecological, physiological, and genetic factors as drivers of this evolutionary transition., This research also received support from the SYNTHESYS Project http://www.synthesys.info/ which is financed by European Community Research Infrastructure Action under the FP7 ‘‘Capacities’’ Programme at the Museo Museo Nacional de Ciencias Naturales (CSIC) (Ref: ES-TAF-1987).

The distribution and conservation status of Emys orbicularis occidentalis is reviewed for Morocco. Populations are highly fragmented and vulnerable. The species is largely restricted to mountainous areas in the western Rif and Middle Atlas, with scattered observations of isolated individuals in the Gharb plain and the eastern Rif. Our literature survey and fieldwork indicate an accelerated regression of Emys populations along the Moroccan Atlantic coast due to habitat loss. At the same time, we found European pond turtles having a wider distribution in the Rif Mountains than previously known. However, in the central and western Rif, the species is increasingly threatened by expanding cannabis plantations. Other country-wide menaces include water pollution, catching of turtles for pets, desertification, and possibly competition with another terrapin species (Mauremys leprosa).

Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (F(ST) range: 0.06-0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts.

12 páginas, 5 figuras, 2 tables.., The European pond turtle (Emys orbicularis) is threatened and in decline in several regions of its natural range, due to habitat loss combined with population fragmentation. In this work, we have focused our efforts on studying the genetic diversity and structure of Iberian populations with a fine-scale sampling (254 turtles in 10 populations) and a representation from North Africa and Balearic island populations. Using both nuclear and mitochondrial markers (seven microsatellites, *1048 bp nDNA and *1500 bp mtDNA) we have carried out phylogenetic and demographic analyses. Our results show low values of genetic diversity at the mitochondrial level although our microsatellite dataset revealed relatively high levels of genetic variability with a latitudinal genetic trend decreasing from southern to northern populations. A moderate degree of genetic differentiation was estimated for Iberian populations (genetic distances, FST values and clusters in the Bayesian analysis). The results in this study combining mtDNA and nDNA, provide the most comprehensive population genetic data for E. orbicularis in the Iberian Peninsula. Our results suggest that Iberian populations within the Iberian–Moroccan lineage should be considered as a single subspecies with five management units, and emphasize the importance of habitat management rather than population reinforcement (i.e. captive breeding and reintroduction) in this long-lived species., GV-A is supported by a grant from Galician Government (Conselleria de Innovacion Industria e Comercio, Xunta de Galicia). Funding was provided by Research grants from Xunta de Galicia PGIDT01MAM37101PR, PGIDIT05RFO37101PR) and Catedra Filgueira Valverde-Universidade de Vigo to ACR.

Abstract Based on more than 1100 samples of Emys orbicularis and E. trinacris, data on mtDNA diversity and distribution of haplotypes are provided, including for the first time data for Armenia, Georgia, Iran, and the Volga, Ural and Turgay River Basins of Russia and Kazakhstan. Eight mitochondrial lineages comprising 51 individual haplotypes occur in E. orbicularis, a ninth lineage with five haplotypes corresponds to E. trinacris. A high diversity of distinct mtDNA lineages and haplotypes occurs in the south, in the regions where putative glacial refuges were located. More northerly parts of Europe and adjacent Asia, which were recolonized by E. orbicularis in the Holocene, display distinctly less variation; most refuges did not contribute to northern recolonizations. Also in certain southern European lineages a decrease of haplotype diversity is observed with increasing latitude, suggestive of Holocene range expansions on a smaller scale.

8 páginas, 3 figuras, 2 tables et al.., [EN]Species that contain populations with different reproductive modes offer excellent opportunities to study the transition between such strategies. Salamandra salamandra (Linnaeus, 1758) is one of two species within the Salamandra–Lyciasalamandra clade which displays two reproductive modes simultaneously. Along the S. salamandra distribution, the common reproductive mode is ovoviviparity although the species also has viviparous populations in the northern Iberian Peninsula. The occurrence of viviparity has recently been reported in two small offshore island populations on the Atlantic coast (NW Iberia), which originated after the last glacial period (8000–9000 years ago). In this paper, we analysed ovoviviparous, hybrid and viviparous populations (inland and mainland) from 17 localities across the northern Iberian Peninsula using two mitochondrial markers (Cyt b and COI, c. 1100 bp). Phylogenetic and phylogeographic analyses highly support that viviparity arose as an evolutionary novelty in the S. salamandra island populations and that viviparous populations are therefore not monophyletic. The recent insularity of Atlantic island populations leads us to conclude that the transition from ovoviviparity to viviparity can happen in a very short-time span. Additionally, to determine the likely source of this evolutionary transition, we discuss how ecological pressures could have an effect on the maintenance of the ovoviviparous reproductive mode. Hence, taking into account the results of this study, we propose the consideration of the island populations as an evolutionary unit for conservation purposes., [ES]Las especies que contienen poblaciones con diferentes modos de reproduccion ofrecen las mejores oportunidades para estudiar la transicion entre ambas estrategias. Salamandra salamandra es una de las dos especies dentro del clado Salamandra-Lyciasalamandra, la cual muestra simultaneamente los dos modos de reproduccion . A lo largo de la distribucion de S. salamandra, el ovoviviparismo es el modo comu´ n de reproduccion, aunque tambien presenta poblaciones vivıparas en el norte de la Penınsula Iberica. Sin embargo, la aparicion del viviparismo ha sido citada recientemente en poblaciones de dos pequeñas islas continentales situadas cercanas a la costa atlantica (Noroeste de la Penınsula Iberica), originadas despues del ultimo periodo glacial (hace 8000–9000 años). En este artıculo, analizamos mediante marcadores mitocondriales (Cyt b y COI, 1100 pb) poblaciones ovovivıparas, hıbridas y vivıparas (costeras y del interior) procedentes de 17 localidades a lo largo del norte de la Penınsula Iberica. Los analisis filogeneticos y filogeograficos corroboran un origen del viviparismo como novedad evolutiva en las poblaciones insulares de S. salamandra, descartando por lo tanto, la monofilia de las poblaciones vivıparas. A su vez, la reciente insularidad de las islas Atlanticas, nos permiten estimar que la transicion del ovoviviparismo al viviparismo puede ocurrir en un breve periodo de tiempo. Igualmente, para determinar la posible causa de esta transicion evolutiva, discutimos la posibilidad de como determinadas presiones ecologicas pudieron haber afectado al mantenimiento del ovoviviparismo como estrategia reproductora. Por lo tanto, y teniendo en cuenta los resultados de este estudio, proponemos considerar a las poblaciones isleñas como una unidad evolutiva para propuestas de conservacion., Guillermo Velo-Anton is supported by a grant from Galician Government (Conselleria de Innovacion, Industria e Comercio, Xunta de Galicia). This research was funded by a grant from the Organismo Autonomo de Parques Nacionales (072B/2002). Animals were captured with permission from Xunta de Galicia. Samplings in the National Park were greatly facilitated by all the staff from the different islands.

Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long-term political instability of the Sahara-Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara-Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro-hotspots of biodiversity. Molecular-based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara-Sahel and supports recently hypothesised dispersal corridors and refugia. Micro-scale water-features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara-Sahel. Current research is providing insights into key evolutionary and ecological processes, including causes and timing of radiation and divergence for multiple taxa, and associating the onset of the Sahara with diversification processes for low-mobility vertebrates. Examples of phylogeographic patterns are showing the importance of allopatric speciation in the Sahara-Sahel, and this review presents a synthetic overview of the most commonly hypothesised diversification mechanisms. Studies are also stressing that biodiversity is threatened by increasing human activities in the region, including overhunting and natural resources prospection, and in the future by predicted global warming. A representation of areas of conflict, landmines, and natural resources extraction illustrates how human activities and regional insecurity are hampering biodiversity research and conservation. Although there are still numerous knowledge gaps for the optimised conservation of biodiversity in the region, a set of research priorities is provided to identify the framework data needed to support regional conservation planning.