Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important ...for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90–0.99) vs. 0.58 (CI = 0.50–0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.
We determined the effects of past and future climate changes on the distribution of the Montivipera raddei species complex (MRC) that contains rare and endangered viper species limited to Iran, ...Turkey and Armenia. We also investigated the current distribution of MRC to locate unidentified isolated populations as well as to evaluate the effectiveness of the current network of protected areas for their conservation. Present distribution of MRC was modeled based on ecological variables and model performance was evaluated by field visits. Some individuals at the newly identified populations showed uncommon morphological characteristics. The distribution map of MRC derived through modeling was then compared with the distribution of protected areas in the region. We estimated the effectiveness of the current protected area network to be 10%, which would be sufficient for conserving this group of species, provided adequate management policies and practices are employed. We further modeled the distribution of MRC in the past (21,000 years ago) and under two scenarios in the future (to 2070). These models indicated that climatic changes probably have been responsible for an upward shift in suitable habitats of MRC since the Last Glacial Maximum, leading to isolation of allopatric populations. Distribution will probably become much more restricted in the future as a result of the current rate of global warming. We conclude that climate change most likely played a major role in determining the distribution pattern of MRC, restricting allopatric populations to mountaintops due to habitat alterations. This long-term isolation has facilitated unique local adaptations among MRC populations, which requires further investigation. The suitable habitat patches identified through modeling constitute optimized solutions for inclusion in the network of protected areas in the region.
In the south of France, the so-called climate hiatus from 1998 to 2013 was associated with a late winter cooling which has affected the phenology of several reptiles and amphibian species, delaying ...their dates of first appearances in spring. This episode has been related to a period of frequently negative values of the North Atlantic Oscillation index (NAO
i
). The recent increase of this index after this episode marks the end of the “hiatus” and provides an opportunity to verify the impact of the North Atlantic Oscillation (NAO) on the fauna of the North Mediterranean region. Most of the emergence dates of amphibians and reptiles in spring have rapidly advanced from 1983 to 1997 and then receded or stabilized from 1998 to 2010. They began to advance again since 2010. These phenological changes covary with the temperature of February–March in the study area, which is itself related to the variations of the NAO index. These changes confirm the influence of the NAO on the phenology of terrestrial organisms in northern Mediterranean where its influence is sometimes assumed to be attenuated.
A series of phylogeographic studies in the Maghreb identified a repeated pattern of deep genetic divergence between an eastern (Tunisia) and western (Morocco) lineage for several taxa but lack of ...sampling in Algeria made it difficult to know if the range limits between the eastern and western lineages were shared among taxa or not. To address this question, we designed a comparative phylogeographic study using 8 reptile and 3 amphibian species with wide distribution in the Maghreb as models. We selected species where previous studies had identified an East-West phylogeographic divide and collected sampled in Algeria to 1) examine whether the simple East-West divergence pattern still holds after filling the sampling gap in Algeria or if more complex diversity patterns emerge; 2) if the E-W pattern still holds, test whether the limits between the E and W clades are shared between species, suggesting that common historical process caused the E-W divergences; 3) if E-W limits are shared between species, use information on the age of the divergence to identify possible geological or climatic events that could have triggered these E-W differentiations. We found that the E-W pattern was generally maintained after additional sampling in Algeria and identified two common disjunction areas, one around the Algeria-Morocco border, the other one in Kabylia (central Algeria), suggesting that common historical mechanisms caused the E-W divergences in the Maghreb. Our estimates for the times to most common recent ancestors to the E and W clades span a wide range between the Messinian salinity crisis and the Plio-Pleistocene limit (except for one older split), suggesting different origins for the initial divergences and subsequent preservation of the E and W lineages in common climatic refugia in the west and the east of the Maghreb.
Although classified among the greatest threats to the world's biodiversity, the effects of land use and their scale dependency are left unexplored in many taxonomic groups. Reptiles are among the ...most data‐deficient vertebrates in this respect, although their ecological traits make them highly sensitive to habitat modifications. We tested whether land use gradients shape the distributions of Mediterranean reptiles at regional and local scales, and whether species’ ecological traits and phylogeny explain these patterns. Reptiles are generally rare and hard to survey through standardized protocols. We overcame these obstacles by modeling an original data set of 18164 opportunistic occurrence records for 14 reptile species with spatially‐explicit point process models incorporating known sources of sampling heterogeneity and spatially autocorrelated error. At a regional scale, reptiles favored open habitats and tended to avoid urban areas. At a local scale, the persistence of open habitats did better than forest resulting from land abandonment in maintaining reptiles within a heavily anthropogenic matrix. Contrary to our expectations, the absence of any clear trait or phylogenetic signals suggests that these responses are mediated by a complex interplay between species’ ecology and regional biogeographic history. These results demonstrate that reptile responses to land use are scale‐dependent and locally exacerbated when anthropogenic pressure is high. We further show that land abandonment is insufficient to preserve reptiles in the face of anthropogenic pressures unless patches of suitable habitat are effectively maintained. Eventually, our study further illustrates the effectiveness of volunteer‐based opportunistic sampling in testing hypotheses on the determinants of rare species’ distributions.
The evolutionary history of the biota of North Africa and Arabia is inextricably tied to the complex geological and climatic evolution that gave rise to the prevalent deserts of these areas. Reptiles ...constitute an exemplary group in the study of the arid environments with numerous well-adapted members, while recent studies using reptiles as models have unveiled interesting biogeographical and diversification patterns. In this study, we include 207 specimens belonging to all 12 recognized species of the genus Stenodactylus. Molecular phylogenies inferred using two mitochondrial (12S rRNA and 16S rRNA) and two nuclear (c-mos and RAG-2) markers are employed to obtain a robust time-calibrated phylogeny, as the base to investigate the inter- and intraspecific relationships and to elucidate the biogeographical history of Stenodactylus, a genus with a large distribution range including the arid and hyper-arid areas of North Africa and Arabia.
The phylogenetic analyses of molecular data reveal the existence of three major clades within the genus Stenodactylus, which is supported by previous studies based on morphology. Estimated divergence times between clades and sub-clades are shown to correlate with major geological events of the region, the most important of which is the opening of the Red Sea, while climatic instability in the Miocene is hypothesized to have triggered diversification. High genetic variability is observed in some species, suggesting the existence of some undescribed species. The S. petrii - S. stenurus species complex is in need of a thorough taxonomic revision. New data is presented on the distribution of the sister species S. sthenodactylus and S. mauritanicus.
The phylogenetic hypothesis for the genus Stenodactylus presented in this work permits the reconstruction of the biogeographical history of these common desert dwellers and confirms the importance of the opening of the Red Sea and the climatic oscillations of the Miocene as major factors in the diversification of the biota of North Africa and Arabia. Moreover, this study traces the evolution of this widely distributed and highly specialized group, investigates the patterns of its high intraspecific diversity and elucidates its systematics.
The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are ...among the paramount examples of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological diversification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients.
Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation.
Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of diversification and endemism in this biodiversity hotspot. High rates of niche conservatism, low genetic diversity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems.
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.
is a North African amphibian that was introduced in southern France early the 20th century and has spread south and north along the Mediterranean coastal plains up to 170 km. In order to disentangle ...the conservation implications of the spread of
for sensitive native species, we examined the impact of long-term climate warming on the basis of niche overlap analysis, taking into account abiotic factors. The study area covered the distribution ranges of all genus
species in northwestern Africa (659,784 km
), Sicily (27,711 km
), the Iberian Peninsula, and southern France (699,546 km
). Niche overlap was measured from species environmental spaces extracted via PCA, including climate and relief environmental variables. Current and future climatic suitability for each species was assessed in an ensemble-forecasting framework of species distribution models, built using contemporary species data and climate predictors and projected to 2070's climatic conditions. Our results show a strong climatic niche overlap between
and native and endemic species in the Iberian Peninsula. In this context, all species will experience an increase in climatic suitability over the next decades, with the only exception being
, which could be negatively affected by synergies between global warming and cohabitation with
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.
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