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Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These include from broad biogeographic patterns, to population dynamics and adaptations to these environments. However, significant challenges remain in integrating these large-scale and fine-scale findings to develop a comprehensive understanding of mountain biodiversity. One significant challenge is the lack of genomic data, particularly in historically understudied arid regions where reptiles are a particularly diverse vertebrate group. We generatedde novogenome-wide SNP data for more than 600 specimens and integrated state-of-the-art biogeographic analyses at the community, species and population level. We, thus, provide for the first time, a holistic integration of how a whole endemic reptile community has originated, diversified and dispersed through a mountain range. Our results show that reptiles independently colonized the Hajar Mountains of eastern Arabia 11 times. After colonization, species delimitation methods suggest high levels of within-mountain diversification, supporting up to 49 putative species. This diversity is strongly structured following local topography, with the highest peaks acting as a broad barrier to gene flow among the entire community. Surprisingly, orogenic events do not seem to rise as key drivers of the biogeographic history of reptiles in this system. However, paleoclimate seems to have had a major role in this community assemblage. We observe an increase of vicariant events from Late Pliocene onwards, coinciding with an unstable climatic period of rapid shifts between hyper-arid to semiarid conditions that led to the ongoing desertification of Arabia. We conclude that paleoclimate, and particularly extreme aridification, acted as a main driver of diversification in arid mountain systems which is tangled with the generation of highly adapted endemicity. Our study provides a valuable contribution to understanding the evolution of mountain biodiversity and the role of environmental factors in shaping the distribution and diversity of reptiles in arid regions.

Adaptive genetic diversity is a key factor in conservation planning as it relates to the evolutionary potential of populations and their responses to environmental change. Developments in landscape genomics have fostered a proliferation of tests for selection that aim to identify candidate adaptive markers in natural populations. However, these tests rely on diferent assumptions and may produce contrasting results. Here we applied six tests for selection in a range-wide genomic scan of an Iberian amphibian, Pelobates cultripes, which shows spatially structured genetic variation across its range, encompassing diferent bioclimatic zones. As a cursory scan for selection, one test identifed candidate markers that describe a pattern of putatively adaptive genetic variation, highlighting coastal Atlantic localities as exhibiting putatively non-neutral patterns of genetic variation. While generalized genomic scans for selection in non-model species have limitations, exploratory searches can highlight areas to guide subsequent hypothesis-driven studies and conservation eforts., This work was developed under the project PTDC/BIA-BIC/3545/2014, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). AJDM, JOH, MCS, SBC, PT, GVA and AV were funded through national funds from Fundação para a Ciência e Tecnologia (CEECIND/01464/2017, ICETA/EEC2018/16, DL57/2016/CP1440/CT0008, CEECIND/00937/2018, and DL57/2016, respectively).

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).

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.

[Aim] Biodiversity is not uniformly distributed across the Earth’s surface, even among physiographically comparable biomes in different biogeographic regions. For lizards, the world’s large desert regions are characterized by extreme heterogeneity in species richness, spanning some of the most species-rich (arid Australia) and species-poor (central Asia) biomes overall. Regional differences in species diversity may arise as a consequence of the interplay of several factors (e.g., evolutionary time, diversification rate, environment), but their relative importance for biogeographic patterns remains poorly known. Here we use distributional and phylogenetic data to assess the evolutionary and ecological drivers of large-scale variation in desert lizard diversity. [Location] Deserts worldwide. [Major taxa studied] Lizards (non-snake squamates). [Methods] We specifically test whether diversity patterns are best explained by differences in the ages of arid-adapted lineages (evolutionary time hypothesis), by regional variation in speciation rate, by geographic area of the arid systems, and by spatial variation related to environment (climate, topography, and productivity). [Results] We found no effect of recent speciation rate and geographic area on differences in desert lizard diversity. We demonstrate that the extreme species richness of the Australian deserts cannot be explained by greater evolutionary time, because species began accumulating more recently there than in more species-poor arid regions. We found limited support for relationships between regional lizard richness and environmental variables, but these effects were inconsistent across deserts, showing a differential role of the environment in shaping the lizard diversity in different arid regions. [Main conclusions] Our results provide evidence against several classic hypotheses for interregional variation in species richness, but also highlight the complexity of processes underlying vertebrate community richness in the world’s great arid systems., This work has been funded by grants CGL2015-70390-P [Ministerio de Economía, Industria y Competitividad (MINECO) / European Regional Development Fund (FEDER), European Union (UE)] Spain, and PGC2018-098290-B-I00 [Ministerio de Ciencia, Innovación y Universidades (MCIU) / Agencia Estatal de Investigación (AEI) / FEDER, UE)]. H.T.-C. was funded by an FPI (Contratos predoctorales para la formación de doctores) grant (BES-2016-078341) from Agencia Estatal de Investigación (AEI), Ministerio de Economía, Industria y Competitividad (MINECO) and European Social Fund (ESF), Spain

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.

Fish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

Aim: The negative impacts of climate change on mammals have been largely based on assessments of total species’ assemblages or individual species at broad scales. Here, we evaluate how the predicted magnitude and velocity of climate change in the arid region of southwest Asia might affect regional functional groups of terrestrial mammals.Location: Iran.Methods: We gathered data from 186 species to map diversity hotspots of 12 functional groups, threatened species richness and total species richness. We mapped areas with high risk of exposure to extreme drying and warming events and calculated the velocity of climate change by using precipitation and temperature data from current and future periods. We then quantified the exposure of these hotspots to extreme changes in magnitude and velocity.Results: Hotspots of functional groups, threatened species and species richness were most exposed to precipitation decline in current and future scenarios (average of 17.9% and 29.9% respectively), compared to temperature rise. While most hotspots are found in mountains, hotspots located in lowlands were more exposed to extreme drying, particularly for carnivore, desert and large-bodied functional groups, as well as threatened species. These patterns remained intact when we considered only hotspots covered by existing protected areas. The impacts of velocity also varied significantly among functional groups, with highest levels for carnivore, large-bodied and specialist groups and threatened species. Main conclusions We show that climate change does not equally impact all species within a community and that vulnerability to these changes differed between functional groups. We found that the areas with the highest risk of exposure to extreme climates are located in lowlands and not in mountains. We found that extreme drying, rather than warming, is the major threat to regional mammal diversity in this arid region, particularly for large-bodied and threatened species. published

[Aim] Deserts are generally perceived as areas of low diversity, and hence receive little attention from researchers and conservationists. Squamates are the dominant group of vertebrates in arid regions, and as such represent an ideal model to study biodiversity patterns in these areas. We examine spatial patterns of diversity, evolutionary history and endemism of terrestrial squamates of the Arabian Peninsula and test hypotheses on the role of topography and history of isolation so as to identify possible environmental drivers of diversification., [Location] The Arabian Peninsula., [Taxon] Squamate reptiles (Squamata; lizards and snakes)., [Methods] We generated distribution maps for all Arabian squamate species (including yet undescribed) and reconstructed their phylogenetic relationships using existing and newly produced genetic data for nearly all the species. We assessed patterns of the distribution of species richness, phylogenetic diversity and phylogenetic endemism across the peninsula to identify areas that could be considered evolutionary or endemicity hotspots for squamates. We evaluated community turnover across the peninsula and assessed the possible environmental drivers affecting the diversity of Arabian squamates in a regression framework., [Results] The main hotspots of Arabian squamate diversity are mostly along the mountains that rim the peninsula while the most arid, central regions support a low diversity of species. The distribution of the phylogenetic diversity mirrors that of the species richness. Phylogenetic endemism is also highest in the mountains, especially when only endemic species are analysed. The deserts of northern Arabia are poor in terms of species richness and they show low connectivity to the peninsular communities. Topographic heterogeneity is the strongest predictor for Arabian squamates, followed by elevation. There is no correlation between richness and temperature., [Main conclusions] The mountains of Arabia support rich and unique squamate communities that are dominated by local radiations of closely related and narrow-ranging species. In particular, the Asir Mountains of SW Arabia, Dhofar Province of Oman and the Hajar Mountains of northern Oman and UAE show unprecedented levels of squamate endemism and phylogenetic endemism. While many generalist species range across Arabia, a low number of species is shared between the peninsula and mainland Asia, indicating an effective isolation of the Arabian fauna. Squamate richness is highest in heterogeneous, topographically complex habitats., Field work carried out for this project in Saudi Arabia was supported by Saudi Wildlife Authority (SWA). We are thankful to Taif University, Saudi Arabia, for support under Researcher Supporting project number TURSP-2020/06. The work of JŠ was supported by the Czech Science Foundation (GACR, project number 18–15286Y) and the Ministry of Culture of the Czech Republic (DKRVO 2019–2023/6.VII.c, 00023272); SC was supported by grant PGC2018-098290-B-I00 (MCIU/AEI/FEDER, UE); BB-C was funded by FPU grant FPU18/04742 (MICIU, Spain); HT-C and MS-R were funded by FPI grants (MINECO, Spain; BES-2016-078341 and BES-2013-064248, respectively), PT was supported by FCT (DL57/2016/CP1440/CT0008).

Pristurus rupestris rupestris is a gecko of the family Sphaerodactylidae adapted to the arid habitat found in the Hajar Mountains of southeastern Arabia. The complete mitochondrial genome was obtained with Illumina sequencing. The sequenced mitogenome has 13 protein-coding genes, 22 tRNAs, two rRNA genes and two non-coding regions, totalling 16,993 bp. The AT content of the obtained sequence is 52.1% (A:28.7%, T:23.4%, G:14.7%, C:33.2%). The control region has an AT content of 54.3% and a length of 1558 bp.

Effective biodiversity conservation planning starts with genetic characterization within and among focal populations, in order to understand the likely impact of threats for ensuring the long-term viability of a species. The Wonder Gecko, Teratoscincus keyserlingii, is one of nine members of the genus. This species is distributed in Iran, Afghanistan, and Pakistan, with a small isolated population in the United Arab Emirates (UAE), where it is classified nationally as Critically Endangered. Within its Arabian range, anthropogenic activity is directly linked to the species’ decline, with highly localised and severely fragmented populations. Here we describe the evolutionary history of Teratoscincus, by reconstructing its phylogenetic relationships and estimating its divergence times and ancestral biogeography. For conservation implications of T. keyserlingii we evaluate the genetic structure of the Arabian population using genomic data. This study supports the monophyly of most species and reveals considerable intraspecific variability in T. microlepis and T. keyserlingii, which necessitate broad systematic revisions. The UAE population of T. keyserlingii likely arrived from southern Iran during the Pleistocene and no internal structure was recovered within, implying a single population status. Regional conservation of T. keyserlingii requires improved land management and natural habitat restoration in the species’ present distribution, and expansion of current protected areas, or establishment of new areas with suitable habitat for the species, mostly in northern Abu Dhabi Emirate., This study was funded by the Mohamed bin Zayed Species project number 172515524 and Grant PGC2018-098290-B-I00 from the Ministerio de Economía y Competitividad, Spain (co-funded by FEDER).

The Hajar Mountains are the highest mountain range in eastern Arabia. Despite being classified as a mountain desert, it is considered one of the top biodiversity hotspots of Arabia. As a result of ...

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2–27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation., CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), Grant/Award Number: 302892/2016-8; 232916/2013-2016; Fundação para a Ciência e a Tecnologia (FCT), Grant/Award Number: PTDC/BIABEC/105083/2008, SFRH/BPD/102966/2014 and UID/BIA/50027/2013; CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior ), Grant/Award Number: 88881.132701/2016-01; Spanish Severo Ochoa Program, Grant/Award Number: SEV-2012-0262; Program Operacional Factores de Competitividade (COMPETE), Grant/Award Number: POCI-01-0145-FEDER-006821.

Oceanic islands are often inhabited by endemic species that have undergone substantial morphological evolutionary change due to processes of multiple colonizations from various source populations, dispersal, and local adaptation. Galápagos marine iguanas are an example of an island endemic exhibiting high morphological diversity, including substantial body size variation among populations and sexes, but the causes and magnitude of this variation are not well understood. We obtained morphological measurements from marine iguanas throughout their distribution range. These data were combined with genetic and local environmental data from each population to investigate the effects of evolutionary history and environmental conditions on body size and shape variation and sexual dimorphism. Our results indicate that body size and shape are highly variable among populations. Sea surface temperature and island perimeter, but not evolutionary history as depicted by phylogeographic patterns in this species, explain variation in body size among populations. Conversely, evolutionary history, but not environmental parameters or island size, was found to influence variation in body shape among populations. Finally, in all populations except one, we found strong sexual dimorphism in body size and shape in which males are larger, with higher heads than females, while females have longer heads than males. Differences among populations suggest that plasticity and/or genetic adaptation may shape body size and shape variation in marine iguanas. This study will help target future investigations to address the contribution of plasticity versus genetic adaptation on size and shape variation in marine iguanas.

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., Fundação para a Ciência e a Tecnologia. Grant Numbers: IF/01425/2014, PTDC/BIA-BIC/3545/2014, SFRH/BPD/74423/2010, SFRH/BPD/93473/2013. European Regional Development Fund (ERDF) 'Programa Operacional Factores de Competitividade – COMPETE

The importance of targeting ecological and evolutionary processes in reserve design has been widely acknowledged in the literature but rarely implemented on islands. Using Socotran reptiles as models, we aim to relate richness of widespread and restricted-range species directly with landscape variables and to compare the impact of setting conservation targets for lineages versus species. Socotra Island is a UNESCO Natural World Heritage Site, containing high levels of endemism in relation to its area, especially of reptiles, the vertebrates with the most comprehensive available genetic data. We predicted the occurrences of reptile species using distribution models and used a novel approach to interpolate maps of spatial phylogenetic patterns. Patterns of intra and interspecifc diversity and differences between spatial outputs of lineage and species richeness were related to eco-geographic variables. We evaluated differences in target achievement for each conservation unit within protected areas (PAs) under the current Zoning Plan (ZP) using gap and reserve design analyses. Although intraspecific richness was strongly correlated with interspecific richness, differences in their spatial distribution reached ~30% in some areas. Differences were more pronounced for wide-ranging than restricted-range taxa. Gap analysis indicates that most conservation units are under-represented in sanctuaries and that intra and interspecific richness were significantly higher outside PAs. This work will guide local-scale conservation planning as the ZP is due to be re-evaluated. This is one of the few studies on islands using genetic data from an entire class of vertebrates to incorporate lineage diversity in reserve design. This study provides an alternative methodological framework for supporting the use of landscape and genetic tools in reserve design, circumventing the use of phylogenetic distances and deterministic spatial interpolation of lineage diversity that can be widely applied to other systems.

Aim Identification of priority conservation areas and evaluation of coverage of the current protected areas are urgently needed to halt the biodiversity loss. Identifying regions combining similar environmental traits (climate regions) and species assemblages (biogroups) is needed for conserving the biodiversity patterns and processes. We identify climate regions and biogroups and map species diversity across the Sahara-Sahel, a large geographical area that exhibits wide environmental heterogeneity and multiple species groups with distinct biogeographical affinities, and evaluate the coverage level of current network of protected areas for biodiversity conservation. Location Sahara-Sahel, Africa. Methods We use spatially explicit climate data with the principal component analysis and model-based clustering techniques to identify climate regions. We use distributions of 1147 terrestrial vertebrates (and of 125 Sahara-Sahel endemics) and apply distance clustering methods to identify biogroups for both species groups. We apply reserve selection algorithms targeting 17% of species distribution, climate regions and biogroups to identify priority areas and gap analysis to assess their representation within the current protected areas. Results Seven climate regions were identified, mostly arranged as latitudinal belts. Concentrations of high species richness were found in the Sahel, but the central Sahara gathers most endemic and threatened species. Ten biogroups (five for endemics) were identified. A wide range of biogroups tend to overlap in specific climate regions. Identified priority areas are inadequately represented in protected areas, and six new top conservation areas are needed to achieve conservation targets. Main conclusions Biodiversity distribution in Sahara-Sahel is spatially structured and apparently related to environmental variation. Although the majority of priority conservation areas are located outside the areas of intense human activities, many cross multiple political borders and require internationally coordinated efforts for implementation and management. Optimized biodiversity conservation solutions at regional scale are needed. Our work contradicts the general idea that deserts are uniform areas and provide options for the conservation of endangered species.

The power of phylogeographic inference resides in its ability to integrate information from multiple sources in an iterative hypothesis- testing framework. In this paper, we build upon previous mtDNA-based hypotheses about the evolutionary history of the Iberian newt Lissotriton boscai using sequences of the highly variable nuclear β-fibrinogen intron 7. In addition to the nuclear sequences, we produced new mtDNA data across the species range to delineate contact zones and test the congruence between nuclear and mitochondrial datasets at the same level of spatial organization. Through a combination of phylogenetic, phylogeographic continuous diffusion, and genetic landscape modelling analyses, we infer the evolutionary history of the species. We found notable congruence between nuclear and mtDNA datasets, which confirms deep and consistent differentiation between two major lineages that originated in the Miocene. Additionally, we found a new nuclear haplogroup with no mtDNA counterpart, roughly circumscribed to the Iberian Sistema Central mountains, and extensive areas of nuclear admixture across mtDNA lineages. We describe potential historical dispersal routes from an ancestral hypothetical refugium in the western end of the Sistema Central in central Portugal and highlight how deep phylogeographic breaks do not necessarily indicate cryptic speciation events.

Examining historical and contemporary processes underlying current patterns of genetic variation is key to reconstruct the evolutionary history of species and implement conservation measures promoting their long-term persistence. Combining phylogeographic and landscape genetic approaches can provide valuable insights, especially in regions harboring high levels of biodiversity that are currently threatened by climate and land cover changes, like southern Iberia. We used genetic (mtDNA and microsatellites) and spatial data (climate and land cover) to infer the evolutionary history and contemporary genetic connectivity in a short-range endemic salamander subspecies, Salamandra salamandra longirostris, using a combination of ecological niche modelling, phylogeographic, and landscape genetic analyses. Ecological-based analyses support a role of the Guadalquivir River Basin as a major vicariant agent in this taxon. The lower genetic diversity and greater differentiation of peripheral populations, together with analyses of climatically stable areas throughout time, suggest the persistence of a population in the central part of the current range since the Last Inter Glacial [LIG; ~ 120,000–140,000 years BP], and a micro refugium in the eastern end of the range. Habitat heterogeneity plays a major role in shaping patterns of genetic differentiation in S. s. longirostris, with forests representing key areas for its long-term persistence under scenarios of environmental change. Our study stresses the importance of maintaining population genetic connectivity in low-dispersal organisms under rapidly changing environments, and will inform management plans for the long-term survival of this evolutionarily distinct Mediterranean endemic., This work was funded by FEDER funds through the Operational Programme for Competitiveness Factors—COMPETE—and by National Funds through FCT—Foundation for Science and Technology—under the PTDC/BIA-EVF/3036/2012, PTDC/BIA-BEC/099915/2008, POCI-01-0145-FEDER-006821 and FCOMP- 01-0124-FEDER-028325. GVA, HG, GCD, AL and PT are supported by FCT (IF/01425/2014, SFRH/BPD/102966/2014, SFRH/BD/89750/2012, PD/BD/106060/2015, SFRH/BPD/93473/2013), respectively.

phylin is a package for the r programming environment which offers different methods to spatially interpolate genetic information from phylogeographic data. These interpolations can be used to predict the spatial occurrence of different lineages within a phylogeny using a modified method of kriging, which allows the usage of a genetic distance matrix to derive a model of spatial dependence. phylin improves the available methods to generate interpolated surfaces from a phylogenetic trees by assessing the autocorrelation structure of the genetic information, interpolating the genetic data based on a statistical model, estimating the uncertainty of the predictions and identifying lineage occurrence and contact zones probability without projection of pairwise genetic distances into mid-points between sample locations. The package also includes methods to plot interpolation surfaces and provide summary tables from the generated data and models. We provide an example of the usefulness of this tool by inferring the spatial occurrence of distinct historical evolutionary lineages of the Lataste's viper (Vipera latastei Boscá, 1878) in the Iberian Peninsula and identifying potential contact areas. The maps of phylogenetic patterns obtained with these methods provide a spatial context to test hypotheses related to processes underlying the geographic distribution of genetic diversity and to inform conservation planning.

The evolution of the mitochondrial genome and its potential adaptive impact still generates vital debates. Even if mitochondria have a crucial functional role, as they are the main cellular energy suppliers, mitochondrial DNA (mtDNA) introgression is common in nature, introducing variation in populations upon which selection may act. Here we evaluated whether the evolution of mtDNA in a rodent species affected by mtDNA introgression is explained by neutral expectations alone. Variation in one mitochondrial and six nuclear markers in Myodes glareolus voles was examined, including populations that show mtDNA introgression from its close relative, Myodes rutilus. In addition, we modelled protein structures of the mtDNA marker (cytochrome b) and estimated the environmental envelopes of mitotypes. We found that massive mtDNA introgression occurred without any trace of introgression in the analysed nuclear genes. The results show that the native glareolus mtDNA evolved under past positive selection, suggesting that mtDNA in this system has selective relevance. The environmental models indicate that the rutilus mitotype inhabits colder and drier habitats than the glareolus one that can result from local adaptation or from the geographic context of introgression. Finally, homology models of the cytochrome b protein revealed a substitution in rutilus mtDNA in the vicinity of the catalytic fraction, suggesting that differences between mitotypes may result in functional changes. These results suggest that the evolution of mtDNA in Myodes may have functional, ecological and adaptive significance. This work opens perspective onto future experimental tests of the role of natural selection in mtDNA introgression in this system.

Aim Compare the performance of continental and regional models in predicting species distributions at range margins. Selection of study area extent, resolution and threshold affects ecological model predictions. At range margins of species distribution, local populations may be restricted to suboptimal environments distinct from the species' global range, which may be missed by continental models. Location Africa and West Africa. Methods We analysed differences in predicted distributions at range margins of three widespread African species that in West Africa occur in peripheral populations restricted to particular habitats. We made comparisons between models built with data from the complete and restricted range of species' distributions (Africa and West Africa, respectively), with coarse and fine resolutions (10 × 10 km and 1 × 1 km, respectively), and classified with three thresholds of species presence (minimum training presence, 10th percentile training presence and maximum training sensitivity plus specificity thresholds). We predicted the species' distributions and quantified environmental variable importance and profile using maximum entropy and estimated niche breadth parameters with ecological niche factor analysis. Results We found differences between model types in niche breadth estimates and also in response curves of the most important variables, suggesting that fine resolution models are more accurate at selecting marginal habitats in West Africa than in Africa. The predictions of species distributions differed with model extent, resolution and threshold analysed. Models built with the complete species environmental range and with coarse resolution tended to overestimate species distributions at the edge, but accuracy increased when more restrictive thresholds were used. In West Africa, independently of the resolution, the threshold value was less important for maximizing agreement between predicted probabilities and observed distribution. Main conclusions At range margins of species distributions, regional models with precise data and conservative thresholds should be preferred over continental models with coarser resolution to identify suitable areas for peripheral populations.

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.

Accounting for evolutionary relationships between and within species is important for biodiversity conservation planning, but is rarely considered in practice. Here we introduce a novel framework to identify priority conservation areas accounting for phylogenetic and intraspecific diversity, integrating concepts from phylogeny, phylogeography, spatial statistics and spatial conservation prioritization. The framework allows planners to incorporate and combine different levels of evolutionary diversity and can be applied to any taxonomic group and to any region in the world. We illustrate our approach using amphibian and reptile species occurring in a biodiversity hotspot region, the Iberian Peninsula. We found that explicitly incorporating phylogenetic and intraspecific diversity in systematic conservation planning provides advantages in terms of maximizing overall biodiversity representation while enhancing its persistence and evolutionary potential. Our results emphasize the need to account for the evolutionary continuum in order to efficiently implement biodiversity conservation planning decisions.

Summary1. Artificialneuralnetworks(ANNs)areknownfortheirpowerfulpredictivepowerintheanalysisof both linear and nonlinear relationships. They have been successfully applied to several fieldsincludingecologicalmodellingandpredictivespecies’distributions.2. Here we present Simapse – Simulation Maps for Ecological Niche Modelling, a free and open-source application written in Python and available to the most common platforms. It uses ANNswith back-propagation to build spatially explicit distribution models from species data (pres-ence⁄absence,presence-onlyandabundance).3. The main features include the automatic production of replicates with different sub-samplingmethodsandtotalcontrolofANNstructureandlearningparameters.4. Simapse uses common text formats as main input and output and provides assessment of vari-ableimportanceandbehaviourandmeasurementofmodelfitness.Key-words: artificial neural networks, ecological niche modelling, Python, species distributionIntroduction Artificial neural networks (ANNs) have been used in scientificfieldswherepatternrecognitionisaprimaryneedanditsappli-cation to biological systems had a considerable growth duringthepastdecades(Lek et al. 1996;LekGO¨zesmi,Tan & O¨zesmi 2006a). As a machine learning algorithm, it iswith no surprise that ANNs are increasingly being used inecological studies. These algorithms are usually seen as morepowerful to deal with complex ecological datasets than othermethods (Brosse & Lek 2000; Olden, Lawler & Poff 2008;O¨zesmi et al.2006b;Pearson et al. 2002).AcommontypeofANNisthefeed-forwardneuralnetworkwith back-propagation learning (BPN; Lek & Gue´gan 1999).Thisnetworkhasalayeredstructureofneuronsconnectingtheinputs to an output through one or several hidden layers (seesupplementary material Fig. S1 for more details). The BPNhasbeenusedtomodelecologicalsystemsowingtoitsefficientlearning ability and to its simple nature that makes it easy tounderstand (Lek & Gue´gan 1999; O¨zesmi, Tan & O¨zesmi2006a).TheunitoftheBPNisanartificialneuronwithanacti-vation function, usually linear or sigmoid. Itsquashes the sumof the products of all connecting weights and the respectiveneuron output in the previous layer to a value to be passed tothenextlayerofneuronsbytheconnectingweights.

Agama boulengeri is a West African endemic lizard. It occurs in arid rocky areas in the Mauritanian mountains and Kayes region of Mali. Data on the distribution of Agama boulengeri is however very coarse, and the contribution of climatic and habitat factors for population isolation are unknown. Using Maxent, GLM, and high-resolution data, we generated environmental niche models, and quantified suitable areas for species occurrence. Field observations and predicted suitable areas were used to evaluate the conservation status of Agama boulengeri. Results revealed the species occurs preferentially close to gueltas, bare areas, and rocky deserts and in areas of increasing rainfall. Suitable cells were mostly located in Mauritania, and four potentially fragmented subpopulations were identified. The conservation status of Agama boulengeri was determined to be of Least Concern.

Jose C. Brito*, Francisco Alvares, Fernando Martinez-Freiria, Pablo Sierra, Neftali Sillero and Pedro Tarroso 1 CIBIO – Centro de Investigacao em Biodiversidade e Recursos Geneticos da Universidade do Porto. Instituto de Ciencias Agrarias de Vairao, R. Padre Armando Quintas, 4485-661 Vairao, Portugal, e-mail: jcbrito@mail.icav.up.pt 2 Dpto. de Biologia Animal, Parasitologia, Ecologia, Edafologia y Quimica Agricola, Universidad de Salamanca. Campus Miguel de Unamuno, edificio de Farmacia 5 pl., 37007 Salamanca, Spain 3 A Cancela, Chain 77, 36826 Ponte Caldelas, Pontevedra, Spain 4 Centro de Investigacao em Ciencias Geo-Espaciais (CICGE) da Universidade do Porto. R. Campo Alegre 687, 4169-007 Porto, Portugal

There has been considerable recent interest concerning the impact of climate change on a wide range of taxa. However, little is known about how the biogeographic affinities of taxa may affect their responses to these impacts. Our main aim was to study how predicted climate change will affect the distribution of 28 European bat species grouped by their biogeographic patterns as determined by a spatial Principal Component Analysis. Using presence-only modelling techniques and climatic data (minimum temperature, average temperature, precipitation, humidity and daily temperature range) for four different climate change scenarios (IPCC scenarios ranging from the most extreme A1FI, A2, B2 to the least severe, B1), we predict the potential geographic distribution of bat species in Europe grouped according to their biogeographic patterns for the years 2020-2030, 2050-2060 and 2090-2100. Biogeographic patterns exert a great influence on a species' response to climate change. Bat species more associated with colder climates, hence northern latitudes, could be more severely affected with some extinctions predicted by the end of the century. The Mediterranean and Temperate groups seem to be more tolerant of temperature increases, however, their projections varied considerably under different climate change scenarios. Scenario A1FI was clearly the most detrimental for European bat diversity, with several extinctions and declines in occupied area predicted for several species. The B scenarios were less damaging and even predicted that some species could increase their geographical ranges. However, all models only took into account climatic envelopes whereas available habitat and species interactions will also probably play an important role in delimiting future distribution patterns. The models may therefore generate 'best case' predictions about future changes in the distribution of European bats.

There are an increasing number of studies that are now focussing on the influence of climate change on species’ distributions. However, access to predictive climatic datasets for future scenarios is difficult due to their specific formats and/or the need to be geographically downscaled. The TYN dataset is freely available to users and provides a synthetic format with several climatic models and IPCC future climate scenarios. Moreover, the CRU historical dataset (1901–2000) is also available which allows users to create baseline models for current climatic variables. E-clic is a free, user-friendly software package that offers three different ways to convert these two datasets into a spatially explicit raster format which is compatible with the most common geographic information systems and usable on different platforms.

Animal domestication was a major step forward in human prehistory, contributing to the emergence of more complex societies. At the time of the Neolithic transition, zebu cattle (Bos indicus) were probably the most abundant and important domestic livestock species in Southern Asia. Although archaeological evidence points toward the domestication of zebu cattle within the Indian subcontinent, the exact geographic origins and phylogenetic history of zebu cattle remains uncertain. Here, we report evidence from 844 zebu mitochondrial DNA (mtDNA) sequences surveyed from 19 Asiatic countries comprising 8 regional groups, which identify 2 distinct mitochondrial haplogroups, termed I1 and I2. The marked increase in nucleotide diversity (P < 0.001) for both the I1 and I2 haplogroups within the northern part of the Indian subcontinent is consistent with an origin for all domestic zebu in this area. For haplogroup I1, genetic diversity was highest within the Indus Valley among the three hypothesized domestication centers (Indus Valley, Ganges, and South India). These data support the Indus Valley as the most likely center of origin for the I1 haplogroup and a primary center of zebu domestication. However, for the I2 haplogroup, a complex pattern of diversity is detected, preventing the unambiguous pinpointing of the exact place of origin for this zebu maternal lineage. Our findings are discussed with respect to the archaeological record for zebu domestication within the Indian subcontinent.

A survey of the Iberian lynx was conducted in Portugal between January 2002 and November 2003 in order to define lynx status and distribution baselines. Intensive search for lynx scats, scat DNA analysis, and camera trapping were used in areas of potential lynx presence. Over 4,200 km were investigated during a global searching effort of 1,975 man-hours. DNA obtained from 168 scats was analyzed, producing no positive lynx amplifications. Camera trapping represented a total effort of 5,647 camera-days in three potential lynx areas, producing no positive detections. Although results cannot confirm the species’ extinction, the scenario is rather pessimistic and the Iberian lynx is probably no longer present in Portugal. Presently, considering the Portuguese lynx’s historical range, the only significantly suitable areas for the species are located in the southeastern part of the country bordering Andalusia where no recent evidence of lynx presence was recorded.

A climate envelope approach was used to model the distributions of the intertidal gastropod Patella rustica, to test the robustness of forecast responses to climate change. The model incorporated variables that were likely to determine the abundance and the northern range limit of this species in the NE Atlantic. The model was built using classification and regression tree analysis (CART) trained with historical distribution data from the mid 1950s and a set of corresponding climatic and oceanographic variables. Results indicated air and sea temperature, in particular during the reproductive and settlement periods, as the main determinants of the Atlantic distribution of P. rustica. The model was subsequently fed with contemporary climatic data and its output was compared with the current distribution and abundance of P. rustica, assessed during a 2002–2003 survey. The model correctly hindcasted the recent collapse of a distributional gap in northern Portugal, as well as an increase in abundance at locations within its range. The predicted northward expansion of the northern range limit did not occur because the absence of the species was confirmed in a survey encompassing the whole Atlantic French coast up to Brest. Stretches of unsuitable habitat too long to be overcome by dispersal are the likely mechanism controlling the northern limit of the distribution of this intertidal species.

International audience; At northern temperate latitudes trees haveadjusted their ranges substantially in response to changingclimates during the Holocene. Results from dispersalmodel simulations suggest that postglacial migration ratesmay have been over-estimated from fossil pollen data. As acontribution to this debate, we infer the migration rates ofAbies alba(Mill.), silver fir, as a case-study species, byusing a spatially explicit approach based on fossil pollenbut taking into account its modern genetic diversity pattern. Maximum estimates of migration rates from fossil pollendata alone are higher than 700 m yr-1during the Holocene.Considering the potential refugia as suggested from all thefossil data but restricting the area over which silver firexpanded from each glacial refugium using data on thecurrent haplotype distribution, the estimated maximummigration rates of silver fir are less than 250 m yr-1.Genetic information may allow for (1) the exclusion of thoserefugial areas where the species may have survived duringthe last glacial period but from which it did not spread orspread only very locally and (2) the delineation of the areas. over which the species spread from each glacial refugium.The estimated rates in the present study are generally con-sistent with rates suggested from modelling approaches.This study shows that integrating fossil pollen records canimprove simulations of dispersal processes and, thus, allowfor better predictions of future changes in tree species’ranges.