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

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

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/)

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

Summary: 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

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.This work was supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 864203), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M) to TMB, and 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 to SC. We acknowledge both Anders Albrechtsen and Nicolas Dussex for useful comments with introgression and mutational load analyses, respectively, and Núria Hermosilla for interesting comments about phylogenetic analysis. We further acknowledge Johanna Paijmans for helping during the downloading of some of the leopard genomes. We want to thank Prem Aguilar for his useful comments in a previous version of this manuscript as well as two anonymous reviewers. We are deeply thankful to Dr. Mohammed Qurban, chief executive officer of the National Center for Wildlife (NCW), and the former vice president of the formal Saudi Wildlife Authority Dr. Hani Tatwany for their support and encouragement since the beginning of the project. We are also grateful to all personnel involved in the Arabian Leopard programme at the Royal Commission for AlUla and their partners in the Arabian Leopard project for support, with the Approval of Saudi Wildlife Authority under permit SWA/6386. GM-R was funded by an FPI grant from the Ministerio de Ciencia, Innovación y Universidades, Spain (PRE2019-088729), AT is supported by “la Caixa”” doctoral fellowship program (LCF/BQ/DR20/11790007), BB-C was funded by FPU grant from Ministerio de Ciencia, Innovación y Universidades, Spain (FPU18/04742) and HT-C was 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

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.We must thank to an anonymous reviewer for their constructive comments provided on a previous version of the manuscript, as well as Loukia Spilani, Maria Estarellas, Juliana Tabares and Laia Pérez-Sorribes for their help and support, Albert Català for his valuable insights into palaeoclimatic registers, and Elly Margaret Tanaka and Francisco Javier Falcon Chavez for providing the axolotl custom repeat library. We also want to thank the sequencing, assembly and annotation teams of CNAG (Center Nacional d'Anàlisi Genòmica) for their help during the sequencing and sequencing data management. AT is supported by “la Caixa” doctoral fellowship programme (LCF/BQ/DR20/11790007). MP-F is supported by “la Caixa” doctoral fellowship programme (LCF/BQ/DR20/11790032). BB-C was funded by FPU grant from Ministerio de Ciencia, Innovación y Universidades, Spain (FPU18/04742). GM-R was funded by an FPI grant from the Ministerio de Ciencia, Innovación y Universidades, Spain (PRE2019-088729). 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. The work was funded by the grants PGC2018-098290-B-I00 (MCIU/AEI/FEDER, UE), Spain, and PID2021-128901NB-I00 (MCIN/AEI/10.13039/501100011033 and by ERDF, A way of making Europe), Spain to SC. We would like to thank Dan Forham and Oxford Nanopore Technologies for providing technical and fungible support for this project. Sample collection was carried out with the authorization of the governments of Catalonia, Aragon (Spain) and Andorra. License for the sacrifice of two captive-bred individuals for the genome assembly were issued by the Departament d’Acció Climàtica, Alimentació i Agenda Rural of the Catalan Government with code MBCFS-05-22. Fieldwork was authorized in Catalonia by the same institution with the permission numbers SF/298 and SF/469 for C. arnoldi and DF/90 and SF/429 for C. asper, in Aragon by Instituto Aragonés de Gestión Ambiental, Area II-Biodiversidad of the Aragonese Government with the permission numbers 24/2010/901 and 24/2012/661 and in Andorra by Departament de Medi Ambient i Sostenibilitat of the Andorran Government with the permission number EXP2200747