Climate change from an ectotherm perspective: evolutionary consequences and demographic change in amphibian and reptilian populations

Biodiversity and Conservation, Journal Year: 2024, Volume and Issue: 33(3), P. 905 - 927

Published: Feb. 14, 2024

Abstract Understanding how natural populations will respond to contemporary changes in climate is becoming increasingly urgent and of fundamental importance for the preservation future biodiversity. Among vertebrates, amphibians reptiles are more sensitive environmental perturbations than endotherms ectotherm diversity likely be disproportionally impacted by change. Notwithstanding concerns surrounding change resilience populations, accurately predicting population trajectories based on ecological physiological data alone remains challenging much can learnt studying have responded past. Genomic approaches now assay genetic at an unprecedented scale but date been relatively underutilised when demographic history reptiles. In this review, we first summarise changing climatic conditions may influence phenotype translate fitness dynamics. We then discuss relative role past shaping has traditionally approached a phylogeographic context expanding genomic resources species leveraged improve study demography many amphibian reptilian groups. An integrative approach that links known proximate effects due change, with ultimately enable us generate accurate models our ability assess

Language: Английский

---

A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

Journal of Heredity, Journal Year: 2023, Volume and Issue: 114(5), P. 445 - 458

Published: April 5, 2023

In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for green anole. Dozens assemblies were subsequently over next decade, yet these largely inadequate answering fundamental questions regarding evolution in squamates due to their lack contiguity annotation. As "genomics age" beginning hit its stride many organismal study systems, progress stagnant following publication anole genome. fact, zero (chromosome-level) genomes between years 2012 and 2017. However, since 2018, an exponential increase has materialized with 24 additional species across tree life. field genomics is rapidly evolving, we provide systematic review from evolutionary perspective. We collated near-complete list publicly available more than half-a-dozen international third-party repositories systematically evaluated them regard overall quality, phylogenetic breadth, usefulness continuing accurate efficient insights into reptiles. This both highlights catalogs currently genomic resources ability address broader vertebrates, specifically sex chromosome microchromosome evolution, while addressing why may have received less historical focus caused lag behind peer taxa.

Language: Английский

---

Phylogenomics reveals the timescale of diversification in Amblycera

Systematic Entomology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Abstract Recently, genomic approaches have helped to resolve phylogenetic questions in many groups of parasitic organisms, including lice (Phthiraptera). However, these still not been applied one the most diverse lice, Amblycera. To fill this gap, we phylogenomic methods based on genome‐level exon sequence data relationships within and among families Our trees support monophyly Ricinidae Laemobothriidae. Trimenoponidae Gyropidae are monophyletic, indicating that they should be merged into a single family. The placement Trinoton is unstable with respect Boopiidae Menoponidae, suggest recognizing Trinotonidae as separate At genus level, genera Colpocephalum , Hohorstiella Menacanthus Ricinus were recovered paraphyletic. Regarding generic complexes, tree revealed complex but paraphyletic, traditionally placed group. Dating analysis suggests divergence Amblycera occurred shortly after Cretaceous–Paleogene boundary 66 Mya. Cophylogenetic analyses host‐switching events during diversification Amblycera, evolutionary history does tightly mirror its hosts. Ancestral host reconstructions ancestral was likely bird, two switching mammals. By combining phylogenomics, molecular dating cophylogenetic analyses, provide first large‐scale picture amblyceran evolution, which will serve basis for future studies

Language: Английский

---

A Literature Review of Stochastic Modeling for Phylogenetic Comparative Analysis in Trait Evolution

Mathematics, Journal Year: 2025, Volume and Issue: 13(3), P. 361 - 361

Published: Jan. 23, 2025

Evolutionary inferences from phylogenetic trees can be modeled stochastically using a range of mathematical frameworks. Among these, stochastic differential equations (SDEs) provide particularly flexible and powerful approach to capturing the continuous-time dynamics evolutionary processes. This review summarizes advances in modeling for trait evolution along tree, with focus on (SDEs), Gaussian non-Gaussian processes, time series models that expressed as special cases general frameworks, depending questions being addressed or types data analyzed. We explore current developments future research directions comparative analysis evolution.

Language: Английский

---

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: Dec. 8, 2023

Abstract Background Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain conspicuous gap in molecular studies of marine adaptation vertebrates. Results Here, we generate four new annotated snake genomes, three these at chromosome-scale ( Hydrophis major , H . ornatus and H. curtus ), perform detailed comparative genomic analyses their closest terrestrial relatives. Phylogenomic highlight possibility near-simultaneous speciation root synteny maps show intra-chromosomal variations that will be important targets for future this system. We then used strict screen positive selection (against background seven genomes) identify genes over-represented hypoxia adaptation, sensory perception, immune response morphological development. Conclusions provide best reference genomes currently available prolific medically elapid radiation. Our phylogenetic complexity conserved genome structure Positively selected marine-associated promising candidates future, functional linking genetic signatures phenotypes other

Language: Английский

---

A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei

Journal of Heredity, Journal Year: 2023, Volume and Issue: 114(3), P. 279 - 285

Published: March 2, 2023

Abstract The Aeolian wall lizard, Podarcis raffonei, is an endangered species endemic to the archipelago, Italy, where it present only in 3 tiny islets and a narrow promontory of larger island. Because extremely limited area occupancy, severe population fragmentation observed decline, has been classified as Critically Endangered by International Union for Conservation Nature (IUCN). Using Pacific Biosciences (PacBio) High Fidelity (HiFi) long-read sequencing, Bionano optical mapping Arima chromatin conformation capture sequencing (Hi-C), we produced high-quality, chromosome-scale reference genome including Z W sexual chromosomes. final assembly spans 1.51 Gb across 28 scaffolds with contig N50 61.4 Mb, scaffold 93.6 BUSCO completeness score 97.3%. This constitutes valuable resource guide potential conservation efforts more generally squamate reptiles that are underrepresented terms available high-quality genomic resources.

Language: Английский

---

Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics

Journal of Heredity, Journal Year: 2024, Volume and Issue: 115(5), P. 487 - 497

Published: May 9, 2024

We present genome assemblies for 18 snake species representing families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new assemblies, we extracted thousands of loci commonly used in systematic phylogenomic studies on snakes, including target-capture datasets composed ultraconserved elements (UCEs) anchored hybrid enriched (AHEs), as well traditional Sanger loci. Phylogenies inferred from the two were identical with each other strongly congruent previously published phylogenies. To show additional utility non-model genomes investigative evolutionary research, mined New Guinea island endemics our dataset (S. admiraltiensis T. doriae) ATP1a3 gene, a thoroughly researched indicator resistance to toad toxin ingestion by squamates. find that both snakes possess genotype despite their endemism Guinea, region absent any toads until human-mediated introduction Cane Toads 1930s. These substitutions suggest same bufotoxin Australian congenerics (Stegonotus australis mairii) which forage invasive Toads. Herein, short-read high-coverage genomes, improving deficit available squamate associated voucher specimens.

Language: Английский

---

Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia

Systematic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: July 1, 2024

Abstract Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive formation biotas. These span from broad biogeographic patterns to population dynamics adaptations these environments. However, significant challenges remain integrating large-scale fine-scale findings develop a comprehensive biodiversity. One challenge is lack genomic data, especially historically understudied arid regions where reptiles are particularly diverse vertebrate group. In present study, we assembled de novo genome-wide SNP dataset for complete endemic reptile fauna range (19 described species with more than 600 specimens sequenced), integrated state-of-the-art analyses at population, species, community level. Thus, provide holistic integration how whole has originated, diversified dispersed through system. Our results show independently colonized Hajar Mountains southeastern Arabia 11 times. After colonization, delimitation methods suggest high levels within-mountain diversification, supporting up 49 deep lineages. This diversity strongly structured following local topography, highest peaks acting as barrier gene flow among entire community. Interestingly, orogenic events do not seem key drivers history this Instead, past climatic had major role assemblage. We observe an increase vicariant Late Pliocene onwards, coinciding unstable period rapid shifts between hyper-arid semiarid conditions led ongoing desertification Arabia. conclude paleoclimate, extreme aridification, acted main driver diversification systems which tangled generation highly adapted endemicity. Overall, study does only valuable contribution evolution but also offers flexible scalable approach can be reproduced any taxonomic group discrete environment.

Language: Английский

---

Understanding vertebrate immunity through comparative immunology

Nature reviews. Immunology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 24, 2024

Language: Английский

---

Reptile Evolution and Genetics: An Overview

Animals, Journal Year: 2023, Volume and Issue: 13(12), P. 1924 - 1924

Published: June 8, 2023

The study of evolution has been indissolubly linked to the heredity since its inception [1]. [...]

Language: Английский

---