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

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

Cytonuclear interactions in a species of Podarcis lizard

Coevolution is the process of reciprocal evolutionary change between interacting species. This process is thought to be a major driver of biological diversification and has been linked to speciation. Coordinated evolution between nuclear and organelle genomes can occur by reciprocal changes in the functional constraints of interacting proteins, and even playing an important role in speciation. In this master's thesis, we used target-capture sequencing data from 122 individuals from two different mitochondrial lineages to test the compensatory evolution hypothesis by comparing the phylogenetic trees of three diferent types of genes: mtDNA, nuclear genes interacting with mitochondrias (oxphos genes) or random nuclear genes. Our results showed the two different mitochondrial lineages. Tajima's D test also showed mitochondria to be under strong purifying selection. However, differences were not observed between the oxphos and the nuclear genes. More studies should be carried out to confirm or not the compensatory evolution hypothesis in this lizard species with the data produced in this study.La coevolución es el proceso de cambio evolutivo recíproco entre especies que interaccionan. Se piensa que este proceso es clave en diversificaciones biológicas y ha sido relacionado con la especiación. Evolución coordenada entre genomas nucleares y de orgánulos pueden ocurrir debido a cambios recíprocos en las funciones de proteínas que interaccionan e incluso puede jugar un papel clave en la especiación. En este trabajo de fin de máster se usó datos de target-capture sequencing de 122 individuos de dos linajes mitocondriales diferentes para testar la hipótesis de evolución compensatoria mediante la comparación de árboles filogenéticos de tres tipos diferentes de genes: mtDNA, genes nucleares que interaccionan con las mitocondrias y genes nucleares aleatorios. Nuestros resultados confirmaron la presencia de los dos linajes mitocondriales. Además, Tajima's D mostró como las mitocondrias estan bajo una alta presión purificadora. Por el contrario, no se encontraron diferentes entre los genes oxphos y los genes nucleares. Más estudios deberían de realizarse para confirmar o no la hipótesis de la evolución compensatoria en estos lagartos con los datos producidos en este estudio.La coevolució és el procés de canvi evolutiu recíproc entre espècies que interaccionen. Es pensa que aquest procés és clau en diversificacions biològiques i ha estat relacionat amb l'especiació. Evolució coordenada entre genomes nuclears i d'orgànuls poden ocórrer a causa de canvis recíprocs en les funcions de proteïnes que interaccionen i fins i tot pot jugar un paper clau en l'especiació. En aquest treball de fi de màster es va usar dades de target-capturi sequencing de 122 individus de dos llinatges mitocondrials diferents per a testar la hipòtesi d'evolució compensatòria mitjançant la comparació d'arbres filogenètics de tres tipus diferents de gens: mtDNA, gens nuclears que interaccionen amb els mitocondris i gens nuclears aleatoris. Els nostres resultats van confirmar la presència dels dos llinatges mitocondrials. A més, Tajima's D va mostrar com els mitocondris estan sota una alta pressió purificadora. Per contra, no es van trobar diferents entre els gens oxphos i els gens nuclears. Més estudis haurien de realitzar-se per a confirmar o no la hipòtesi de l'evolució compensatòria en aquests llangardaixos amb les dades produïdes en aquest estudi

Colonization routes uncovered in a widely introduced Mediterranean gecko, Tarentola mauritanica

Abstract In this study, we aimed to understand the contemporary and ancient colonization routes of the Moorish gecko, Tarentola mauritanica, using simple sequence repeats. By analyzing the genetic diversity of populations in different regions, we found that Morocco is the genetic diversity hotspot for the species, followed by the Iberian Peninsula. However, historical gene flow estimates identified the Iberian Peninsula, not Morocco, as the primary contributor of colonizing individuals, along with continental Italy to a lesser extent. Currently, mainland Italy is the main source of introduced individuals, likely due to the plant nursery trade. The study suggests that human-facilitated introductions from various geographical origins, with numerous regions colonized through continental Italy during two distinct periods, are responsible for the recurrent entry of individuals belonging to the European lineage of T. mauritanica into the Mediterranean and Macaronesia. These findings can inform better monitoring surveys and conservation programs by identifying putative current colonization routes of alien species

First record of dermal fluorescence in the desert-adapted Stenodactylus and Trigonodactylus geckos

© 2024 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).Even though steadily increasing, biofluorescence is a rarely documented phenomenon in vertebrates. Within geckos, only six species have been shown to produce fluorescence and only one case of dermal fluorescence has been reported. Here, we report on the discovery of dermal fluorescence in the Dune Sand Gecko (Stenodactylus doriae), the Eastern Sand Gecko (S. leptocosymbotes), and the Arabian Web-footed Sand Gecko (Trigonodactylus arabicus), three closely-related, nocturnal, desert-adapted Arabian geckos. We show that there are interspecific differences in fluorescent regions which might be linked to the habitat preference and behaviour of each species. Our results are in agreement with prior hypotheses suggesting that desert-adapted geckos might use dermal biofluorescence for conspecific signalling. With the present work, we expand the current knowledge on skin fluorescence in reptiles and provide new insights on fluorescence of desert-adapted geckos.BB-C is funded by FPU grant from Ministerio de Ciencia, Innovación y Universidades, Spain (FPU18/04742), AT is funded by “la Caixa” doctoral fellowship programme (LCF/BQ/DR20/11790007), and GM-R is funded by an FPI grant from the Ministerio de Ciencia, Innovación y Universidades, Spain (PRE2019-088729). SC is supported by PID2021-128901NB-I00 funded by MCIN/AEI/10.13039/501100011033 and by ERDF, a way of making Europe. No in vivo experiments were performed.Peer reviewe

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 taxa.This article is published as Talavera A, Valbuena-Ureña E, Burriel-Carranza B, Mochales-Riaño G, Adams DC, Amat F, Carbonell F, Carranza S. 2024. Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies. PeerJ 12:e17550 https://doi.org/10.7717/peerj.17550. Copyright 2024 Talavera et al. Distributed under Creative Commons CC-BY 4.0

Evolution along allometric lines of least resistance: Morphological differentiation in Pristurus geckos [Dataset]

In this folder you can find the morphological dataset and the phylogenetic data necessary for the analyses described in the 'software' folder. # Morphological data These are the linear measurements in millimeters of Pristurus specimens (morpho_pristurus.csv) and the average for each species (morpho_sp_final.csv). The linear measurements are as follows: - SVL: Snout-Vent Length (Body size). - TrL: Trunk Length. - HL: Head Length. - HW: Head Width. - HH: Head Height. - Lhu: Length of the humerus. - Lun: Length of the ulna. - Lfe: Length of the femur. - Ltb: Length of the tibia. # Phylogenetic data Consensus tree in Nexus format (pristurus_tree_final.nex) and posterior phylogenetic trees in RDS format (posterior_pristurus_final.rds) of Pristurus, extracted from a published phylogeny of Afro-Arabian squamates (Tejero-Cicuéndez et al. 2021 Systematic Biology).Species living in distinct habitats often experience unique ecological selective pressures, which can drive phenotypic divergence. However, how ecophenotypic patterns are affected by allometric trends and trait integration levels is less well understood. Here we evaluate the role of allometry in shaping body size and body form diversity in Pristurus geckos utilizing differing habitats. We found that patterns of allometry and integration in body form were distinct in species with different habitat preferences, with ground-dwelling Pristurus displaying the most divergent allometric trend and high levels of integration. There was also strong concordance between intraspecific allometry across individuals and evolutionary allometry among species, revealing that differences in body form among individuals were predictive of evolutionary changes across the phylogeny at macroevolutionary scales. This suggested that phenotypic evolution occurred along allometric lines of least resistance, with allometric trajectories imposing a strong influence on the magnitude and direction of size and shape changes across the phylogeny. When viewed in phylomorphospace, the largest rock-dwelling species were most similar to the smallest ground-dwelling species, and vice versa. Thus, in Pristurus, phenotypic evolution along the differing habitat-based allometric trajectories resulted in similar body forms at differing body sizes in distinct ecological habitats.MCIU/AEI/FEDER, UE, Award: PGC2018-098290-B-I00European Commission, Award: PID2021-128901NB-I00Agencia Estatal de Investigación, Award: FJC2021-046832-IAlexander von Humboldt FoundationThe Neurosciences Foundation, Award: DBI-1902511Peer reviewe

Evolution along allometric lines of least resistance: morphological differentiation in Pristurus geckos

Species living in distinct habitats often experience unique ecological selective pressures, which can drive phenotypic divergence. However, how ecophenotypic patterns are affected by allometric trends and trait integration levels is less well understood. Here we evaluate the role of allometry in shaping body size and body form diversity in Pristurus geckos utilizing differing habitats. We found that patterns of allometry and integration in body form were distinct in species with different habitat preferences, with ground-dwelling Pristurus displaying the most divergent allometric trend and high levels of integration. There was also strong concordance between intraspecific allometry across individuals and evolutionary allometry among species, revealing that differences in body form among individuals were predictive of evolutionary changes across the phylogeny at macroevolutionary scales. This suggested that phenotypic evolution occurred along allometric lines of least resistance, with allometric trajectories imposing a strong influence on the magnitude and direction of size and shape changes across the phylogeny. When viewed in phylomorphospace, the largest rock-dwelling species were most similar to the smallest ground-dwelling species, and vice versa. Thus, in Pristurus, phenotypic evolution along the differing habitat-based allometric trajectories resulted in similar body forms at differing body sizes in distinct ecological habitats.This work was funded in part by PGC2018-098290-B-I00 (Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación/FEDER, UE) and PID2021-128901NB-I00 (MCIN/AEI/10.13039/501100011033 and by European Regional Development Fund, a way of making Europe), Spain to S.C. H.T.C. is supported by a “Juan de la Cierva—Formación” postdoctoral fellowship (FJC2021-046832-I). I.M. was funded by the Alexander von Humboldt Foundation through a Humboldt Research Fellowship, and partially funded by the project PID2022-138275NB-I00 granted by FEDER/Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación. A.T. is supported by the “la Caixa” doctoral fellowship program (LCF/BQ/DR20/11790007). G.R. was funded by an FPI grant from the Ministerio de Ciencia, Innovación y Universidades, Spain (PRE2019-088729). B.B.C. was funded by an FPU grant from Ministerio de Ciencia, Innovación y Universidades, Spain (FPU18/04742). D.C.A. was funded in part by the National Science Foundation Grant (DBI-1902511).Peer reviewe

Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict

The Montseny brook newt (Calotriton arnoldi), considered the most endangered amphibian in Europe, is a relict salamandrid species endemic to a small massif located in northeastern Spain. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here, we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (Calotriton asper), combining whole-genome and ddRADseq data. Our results reveal significant demographic oscillations which accurately mirrored Europe's climatic history. Although severe bottlenecks have led to depauperate genomic diversity and long runs of homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of population fragmentation

Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict

The Montseny brook newt (Calotriton arnoldi), considered the most endangered amphibian in Europe, is a relict salamandrid species endemic to a small massif located in northeastern Spain. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here, we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (Calotriton asper), combining whole-genome and ddRADseq data. Our results reveal significant demographic oscillations which accurately mirrored Europe’s climatic history. Although severe bottlenecks have led to depauperate genomic diversity and long runs of homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of population fragmentation.This article is published as Talavera, Adrián, Marc Palmada-Flores, Bernat Burriel-Carranza, Emilio Valbuena-Ureña, Gabriel Mochales-Riaño, Dean C. Adams, Héctor Tejero-Cicuéndez et al. "Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict." iScience 27 (2024): 108665. © 2023 The Authors.This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)