DNA barcode reference library for the West Sahara-Sahel reptiles

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.National Geographic Society CRE-7629-04 CRE-8412-08 GEFNE-53-12Mohammed bin Zayed Species Conservation Fund 11052709 11052707 13257467Rufford Foundation SG-15399-1 SG-17893-1Portuguese Foundation for Science and Technology European Commission FCT: PTDC/BIA-BEC/099934/2008 PTDC/BIA-BIC/2903/2012FEDER through COMPETE-Operational Programme for Competitiveness Factors FCOMP-01-0124-FEDER-008917 FCOMP-01-0124-FEDER-028276Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) AGRIGEN-NORTE-01-0145-FEDER-000007Portuguese Foundation for Science and Technology European Commission UIDB/50027/2020 CEECINST/00014/2018/CP1512/CT0001 DL57/2016/CP1440/CT0010 CEECIND/00937/2018 IF/01425/2014 SFRH/BD/140348/2018Spanish GovernmentEuropean Commission RYC-2019-026959-I/AEI/10.13039/50110001103

Patterns of nuclear and mitochondrial DNA variation in Iberian populations of Emys orbicularis (Emydidae): conservation implications

Abstract 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, F ST 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

BioExtreme workshop, O Rosal (Galicia, España), verano 2018

La concentración de gases de efecto invernadero en la atmósfera aumenta anualmente debido, principalmente, al uso generalizado de combustibles fósiles como fuente de energía. Este incremento está detrás de una serie de cambios a nivel planetario en parámetros tan importantes como el clima (ej. cambios en el rango de temperaturas y precipitaciones globales) o los niveles de salinidad y pH de los océanos, con importantes implicaciones para la biodiversidad. Existe también un aumento en la disponibilidad de bases de datos y modelos climáticos (ej. MERRAClim, WorldClim, CHELSA, ENVIREM, CliMond, AquaMaps, Bio-ORACLE) que sirven para estimar futuros escenarios de cambio climático y escenarios del pasado reciente, como el último máximo glaciar o el Holoceno medio (ej. ecoClimate, PaleoClim, etc.). Estos modelos suelen proporcionar valores medios de temperatura (ej. temperatura media anual, temperatura media del trimestre más frío o más cálido, etc.) y valores agregados de precipitación (ej. precipitación anual, precipitación del trimestre más seco o más húmedo, etc.). Tradicionalmente, la mayoría de los estudios científicos enfocados en entender los efectos del cambio climático sobre los ecosistemas han utilizado este tipo de variables. Sin embargo, cada vez es más patente que otro tipo de parámetros del clima, como valores extremos de temperatura o precipitación, pueden afectar de manera importante a las especies y sus hábitats. El pasado verano se organizó en O Rosal (Galicia, España) (Fig.1) un workshop interdisciplinar al que acudieron especialistas en biogeografía, macroecología, herpetología, mastozoología, ecología del suelo y oceanografía con el objetivo de discutir sobre qué tipos de extremos climáticos pueden tener una mayor influencia en el funcionamiento de los ecosistemas y la distribución de los organismos. Como resultado de esta reunión se seleccionaron un conjunto de variables climáticas altamente relevantes a nivel ecológico tanto para el medio marino como para el medio terrestre, y las cuales tienen en cuenta la intensidad y duración de los eventos climáticos extremos

Allopatric diversification and evolutionary melting pot in a North African Palearctic relict: the biogeographic history of Salamandra algira

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

Where are you from, stranger? The enigmatic biogeography of North African pond turtles (Emys orbicularis) .

Abstract The European pond turtle (Emys orbicularis) is a Nearctic element in the African fauna and thought to have invaded North Africa from the Iberian Peninsula. All North African populations are currently identified with the subspecies E. o. occidentalis. However, a nearly range-wide sampling in North Africa used for analyses of mitochondrial and microsatellite DNA provides evidence that only Moroccan populations belong to this taxon, while eastern Algerian and Tunisian pond turtles represent an undescribed distinct subspecies. These two taxa are most closely related to E. o. galloitalica with a native distribution along the Mediterranean coast of northern Spain through southern France to western and southern Italy. This group is sister to a clade comprising several mitochondrial lineages and subspecies of E. orbicularis from Central and Eastern Europe plus Asia, and the successive sisters are E. o. hellenica and E. trinacris. Our results suggest that E. orbicularis has been present in North Africa longer than on the Iberian Peninsula and that after an initial invasion of North Africa by pond turtles from an unknown European source region, there was a phase of diversification in North Africa, followed by a later re-invasion of Europe by one of the African lineages. The differentiation of pond turtles in North Africa parallels a general phylogeographic paradigm in amphibians and reptiles, with deeply divergent lineages in the western and eastern Maghreb. Acknowledging their genetic similarity, we propose to synonymize the previously recognized Iberian subspecies E. o. fritzjuergenobsti with E. o. occidentalis sensu stricto. The seriously imperiled Moroccan populations of E. o. occidentalis represent two Management Units different in mitochondrial haplotypes and microsatellite markers. The conservation status of eastern Algerian pond turtles is unclear, while Tunisian populations are endangered. Considering that Algerian and Tunisian pond turtles represent an endemic taxon, their situation throughout the historical range should be surveyed to establish a basis for conservation measures

Evaluating taxonomic inflation: towards evidence-based species delimitation in Eurasian vipers (Serpentes: Viperinae)

International audienceThe designation of taxonomic units has important implications for the understanding and conservation ofbiodiversity. Eurasian vipers are a monophyletic group of viperid snakes (Serpentes, Viperinae), currently comprising fourgenera (Daboia, Macrovipera, Montivipera and Vipera) and up to 40 species. Taxonomic units have been described usinga wide variety of methods and criteria, and consequently, considerable controversy still surrounds the validity of somecurrently listed species. In order to promote a consensus- and evidence-based taxonomy of Eurasian vipers, we analysedpublished mitochondrial and nuclear DNA sequences for this group to reconstruct phylogenetic relationships among currentlyrecognized viper species.We also compiled information on external morphology to assess their morphological distinctiveness.Phylogenetic inference based on mtDNA sequences shows contrasting levels of divergence across genera and species andidentifies several instances of non-monophyly in described species. Nuclear DNA sequences show extremely low levels ofgenetic variation, with a widespread pattern of allele sharing among distant species, and even among genera. Revision ofmorphological data shows that most species designations rely on scalation traits that overlap extensively among species ofthe same genus. Based on our combined assessment, we recognize 15 taxa as valid species, three taxa which likely representspecies complexes, 17 taxa of doubtful validity as species, and five taxa for which species status is maintained but furtherresearch is highly recommended to assess taxonomic arrangements. We stress the need to implement integrative taxonomicapproaches for the recognition of evidence-based taxonomic units in Eurasian viper

Conservation Biogeography of the Sahara‐Sahel: additional protected areas are needed to secure unique biodiversity

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.info:eu-repo/semantics/publishedVersio

Turtle Carapace Anomalies: The Roles of Genetic Diversity and Environment

Background: Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales. Methodology/Principal Findings: In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3 % to 69 % in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium. Conclusions/Significance: Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants an

Conclusiones y propuestas de manejo de las poblaciones y especies de anfibios y reptiles alóctonos en España

El criterio fundamental para considerar que una especie es alóctona en el territorio español se basa en la constatación de que la colonización no ha sido natural, sino de origen antrópico.Peer Reviewe

Salamandra común – Salamandra salamandra (Linnaeus, 1758)

Anfibios - Orden Caudata - Familia Salamandridae en la Enciclopedia Virtual de Vertebrados Españoles, http://www.vertebradosibericos.org/.A comprehensive review of the natural history of the Fire Salamander in Spain.Peer reviewe