Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)

In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies

Pristurus guweirensis Haas, 1943 (Gekkota: Sphaerodactylidae): the most abundant and widely distributed species of Pristurus previously referred to as Pristurus sp. 1

Peer reviewe

Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes

The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.This work was supported by grants PGC2018-098290-B-I00 (MCIU/AEI/FEDER, UE), Spain, PID2021-128901NB-I00 (MCIN/AEI/10.13039/501100011033 and by ERDF, A way of making Europe), Spain, and grant 2021-SGR-00751 from the Departament de Recerca i Universitats from the Generalitat de Catalunya, Spain to SC. GM-R is supported by an FPI grant from the Ministerio de Ciencia, Innovación y Universidades, Spain (PRE2019-088729), BB-C is supported by FPU grant from Ministerio de Ciencia, Innovación y Universidades, Spain (FPU18/04742), AT is supported by “la Caixa” doctoral fellowship program (LCF/BQ/DR20/11790007), HT-C is supported by a “Juan de la Cierva - Formación” postdoctoral fellowship (FJC2021-046832-I) funded by MCIN/AEI/10.13039/501100011033 and by the European Union NextGenerationEU/PRTR, GV-A was supported by the FCT (CEECIND/00937/2018) and recently by a Ramón y Cajal research grant (Ref. RYC-2019-026959-I/AEI/10.13039/501100011033), JŠ was supported by the Czech Science Foundation (GAČR) under grant number 22-12757S and by the Charles University Research Centre under grant number 204069 and FM-F and JCB are supported by FCT - Fundação para a Ciencia e Tecnologia de Portugal (DL57/2016/CP1440/CT0010, CEECINST/00014/2018/CP1512/CT0001, respectively).Peer reviewe

The Hajar Mountains of Southeastern Arabia: a laboratory to understand how reptile diversity is generated, distributed and maintained in arid environments

This thesis provides new insights into the evolution of biodiversity in arid regions by exploring the patterns and drivers of reptile diversity in the Hajar Mountains of Southeastern Arabia. We first assemble a genomic dataset including the entire endemic reptile community to unravel the diversity, distribution and structure of reptiles at multiple biological scales. Then, we focus on four particular groups to assess the systematics of some selected taxa, to investigate the effects of gene flow on species delimitation, and to evaluate the conservation status of one of its most imperiled species. Results show that reptile diversity is greatly structured, with paleoclimate emerging as a determinant driver in the evolution of this montane arid community. We reveal high levels of cryptic diversity leading to the description of four new species of geckos, and show that coastal development is having a negative impact on the survival of a Critically Endangered species. Additionally, we evaluate the performance of the genomic techniques used in this thesis and discuss their strengths and limitations for species delimitation and description.Aquesta tesi ofereix nous punts de vista en l’evolució de la biodiversitat en regions àrides, explorant els patrons i processos que afecten la diversitat de rèptils a les muntanyes dels Hajars del sud-est de la Península Aràbiga. Primer, generem un “dataset” genòmic incloent tota la comunitat endèmica de rèptils per descobrir la diversitat, la distribució i l’estructura dels rèptils a diverses escales biològiques. Després, ens centrem en quatre casos d’estudi amb la finalitat de determinar la sistemàtica d’alguns taxons concrets, investigar els efectes del flux genètic en la delimitació d’espècies i avaluar l’estat de conservació d’una de les espècies més amenaçades de les muntanyes. Els resultats mostren que la diversitat de rèptils està molt estructurada, amb el paleoclima emergint com a un procés determinant en la formació i evolució d’aquesta comunitat. També, desvelem alts nivells de diversitat críptica descrivint quatre noves espècies de dragons, i demostrem que el desenvolupament costaner està tenint un impacte negatiu en la supervivència d’una espècie que es troba en Perill Crític d’extinció. Finalment, avaluem les diferents tècniques genòmiques utilitzades en aquesta tesi i discutim les seves avantatges i limitacions per a la delimitació i descripció d’espècies.Programa de Doctorat en Biomedicin

Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies

The Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxaThe Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxaThe Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described tax

Reptiles & amphibians of the Hajar Mountains

The Hajar Mountain range is the highest in eastern Arabia, forming a spectacular isolated wall of rock that rises dramatically from the sea below. It runs northwest to southeast in a 650 km continuous arc parallel to the Oman and UAE coastline along the Gulf of Oman, from the Musandam Peninsula to Ras Al Hadd. This impressive massif is flanked by the sea to the East and by very large gravel and sand deserts to the West and South. Cut by deep wadis, these arid mountains have a complex topography and can be divided into three distinct blocks; Western Hajars, Jebel Akhdar and Eastern Hajars; separated by some topographical discontinuities. With a maximum elevation of 3,009 m, Jebel Shams in the Jebel Akhdar massif is the highest peak, although several peaks above 2,000 m also occur in the Eastern and Western Hajars. The Hajar Mountains originated about 30 Mya due to the tectonic motions that resulted in the opening of the Red Sea and the Gulf of Aden but final uplift occurred approximately 4–6 Mya. The Hajar Mountains are usually referred to as a mountain desert for its arid conditions but it is actually one of the most climatically variable areas in southeastern Arabia. Owing to its geological origin, high elevations, very deep canyons and geographic isolation from other mountains, high levels of species richness and endemicity are recorded in several animal and plant groups, making the Hajar Mountains a focal point of conservation in Arabia. To date, 28 species of reptiles and two amphibians inhabit the Hajar Mountains and this number is likely to increase in the next few years as a result of ongoing research. Of these species, 19 are endemic to the massif, which means that they do not live anywhere else in the world, highlighting the importance of the Hajar Mountains as a hotspot of reptile diversity and endemicity.Scientific research has been funded by grants CGL2015-70390-P and PGC2018-098290-B-I00 funded by MCIN/AEI /10.13039/501100011033/ and by FEDER, a way to make Europe, and by project 22412027 from the Ministry of Environment and Climate Affairs, Oman to S. Carranza. B. Burriel-Carranza is supported by an FPU grant (FPU18/04742) (MCIU, Spain).Peer reviewe

A field guide to the reptiles of Oman

Los reptiles son un grupo muy interesante de vertebrados terrestres. Han habitado nuestro planeta durante más de 250 millones de años y están adaptados a vivir en una amplia variedad de entornos. Hay más de 11.500 especies diferentes de reptiles en todo el mundo, divididas en tortugas, serpientes, lagartos y cocodrilos, que se caracterizan por su cubierta exterior escamosa. A pesar de su glorioso pasado, no siempre son bien apreciados por los humanos, especialmente en comparación con los mamíferos y las aves, ya que causan muchas muertes anualmente en todo el mundo. El Sultanato de Omán se considera el tercer país más grande de la Península Arábiga. Con sus vastos paisajes terrestres y marinos, alberga una de las biodiversidades más ricas de Arabia. Su fauna y vegetación únicas en las partes Norte y Central del país comparten especies con Irán y Pakistán, mientras que las del Sur presentan afinidades africanas. El Sultanato de Omán tiene aproximadamente el 50% del número total de especies de reptiles de la Península Arábiga, lo que lo convierte en uno de los países con mayor diversidad de reptiles de Arabia. A pesar de esta gran diversidad, todavía existen muchas lagunas en el conocimiento de la historia de vida, el tamaño de la población y la distribución real de los reptiles de Omán. Además de eso, se espera que el cambio climático cause más estrés por el incremento del calor, cambiando los hábitats naturales de muchas especies de reptiles y haciendo muy difícil predecir cómo estos se verán afectados.Scientific research in Oman has been funded by grants CGL2015-70390-P (MINECO/FEDER, UE) Spain, PGC2018-098290-B-I00 (MCIU/AEI/FEDER, UE) Spain, and by project 22412027 from the Ministry of Environment and Climate Affairs, Oman to S. Carranza. B. Burriel-Carranza is supported by an FPU grant (FPU18/04742) (MCIU, Spain)

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes

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

Sclerophrys arabica (Arabian Toad). Predation.

This video demonstrates behavior. Most videos in this collection have no audible language and for those that do, the language isn't necessary to understand the behavior. For that reason, transcripts are not provided.Integrative Biolog