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

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Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization

Genome Research, Journal Year: 2023, Volume and Issue: 33(9), P. 1527 - 1540

Published: Aug. 17, 2023

Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity chromosome-scale DNA sequences some key taxa. One those limiting taxa has elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes enlarged genomes. Here, we report genome assembly for zebra shark Stegostoma tigrinum, an endangered that a relatively small among sharks (3.71 Gb), as well whale Rhincodon typus Our analysis using male-female comparison identified X Chromosome, first genomically characterized sex chromosome. The Chromosome harbors Hox C cluster whose intact linkage not shown elasmobranch fish. sequenced genomes show gradualism length remarkable length-dependent characteristics-shorter tend to higher GC content, gene density, synonymous substitution rate, simple tandem repeat content smaller lower interspersed content. We challenge traditional binary classification karyotypes without so-called microchromosomes. Even microchromosomes, characteristics persist widely in nonmammalian vertebrates. investigation underpins their unique provides clues understanding how accommodate intragenomic heterogeneity realize complex readout. It also paves way dissecting more variable sizes be at high quality.

Language: Английский

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A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Background The increasing number of chromosome-level genome assemblies has advanced our knowledge and understanding macroevolutionary processes. Here, we introduce the desert horned lizard, Phrynosoma platyrhinos, an iguanid lizard occupying extreme conditions American southwest. We conduct analysis chromosomal structure composition this species compare these features across genomes 12 other reptiles (5 lizards, 3 snakes, turtles, 1 bird). Findings was sequenced using Illumina paired-end reads assembled scaffolded Dovetail Genomics Hi-C Chicago long-range contact data. resulting assembly a total length 1,901.85 Mb, scaffold N50 273.213 includes 5,294 scaffolds. is composed 6 macrochromosomes 11 microchromosomes. A 20,764 genes were annotated in assembly. GC content gene density are higher for microchromosomes than macrochromosomes, while repeat element distributions show opposite trend. Pathway analyses provide preliminary evidence that microchromosome macrochromosome functionally distinct. Synteny indicates large blocks conserved among closely related species, whereas frequent fusion fission events reptiles, even between species. Conclusions Our results demonstrate dynamic karyotypic evolution Reptilia, with inferred splits, fusions, rearrangements have resulted shuffling also new distinct within reptiles.

Language: Английский

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Rethinking asexuality: the enigmatic case of functional sexual genes inLepraria(Stereocaulaceae)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 13, 2024

Abstract Background The ubiquity of sex across eukaryotes, given its high costs, strongly suggests it is evolutionarily advantageous. Asexual lineages can avoid, for example, the risks and energetic costs recombination, but suffer short-term reductions in adaptive potential long-term damage to genome integrity. Despite these lichenized fungi have frequently evolved asexual reproduction, likely because allows retention symbiotic algae generations. relatively speciose fungal genus Lepraria thought be exclusively asexual, while sister Stereocaulon completes a sexual reproductive cycle. A comparison clades should shed light on evolution asexuality lichens general, as well apparent maintenance , specifically. Results In this study, we assembled annotated representative long-read genomes from putatively added short-read assemblies an additional 22 individuals both genera. Comparative genomic analyses revealed that genera were heterothallic, with intact mating-type loci idiomorphs present each genus. Additionally, identified assessed 29 genes involved meiosis mitosis 45 contribute formation structures (ascomata). All appeared functional nearly all failed identify general pattern relaxation selection lineage. Together, results suggest may capable including mate recognition, meiosis, production ascomata. Conclusions machinery essential sex, over 200 years careful observations by lichenologists produced no evidence canonical reproduction . We instead form parasexual perhaps repurposing MAT meiosis-specific genes. This may, turn, allow avoid consequences asexuality, maintaining benefit unbroken bond their algal symbionts.

Language: Английский

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Fixed Allele Differences Associated With the Centromere Reveal Chromosome Morphology and Rearrangements in a Reptile (Varanus acanthurus BOULENGER)

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(6)

Published: June 1, 2023

Abstract Chromosome rearrangements are often implicated with genomic divergence and proposed to be associated species evolution. Rearrangements alter the structure interfere homologous recombination by isolating a portion of genome. Integration multiplatform next-generation DNA sequencing technologies has enabled putative identification chromosome in many taxa; however, integrating these data sets cytogenetics is still uncommon beyond model genetic organisms. Therefore, achieve ultimate goal for classification eukaryotic organisms, physical mapping remains critical. The ridge-tailed goannas (Varanus acanthurus BOULENGER) group dwarf monitor lizards comprised several found throughout northern Australia. These exhibit extreme at both genic chromosomal levels. polymorphisms widespread extending across much their distribution, raising question if within V. complex. We used combined cytogenetic approach test homology divergent populations morphologically similar rearrangements. showed that more than one pair was involved This finding provides evidence support de novo have occurred populations. characterized fixed allele differences originating vicinity centromeric region. then compared this region other assembled genomes reptiles, chicken, platypus. demonstrated synteny genes Reptilia conserved despite centromere repositioning taxa.

Language: Английский

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Population genomics of flat‐tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(7)

Published: March 6, 2024

Abstract Phrynosoma mcallii (flat‐tailed horned lizards) is a species of conservation concern in the Colorado Desert United States and Mexico. We analysed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, model demography. identified River as main geographic feature contributing with populations west this barrier further subdivided by Salton Sea. Phylogenetic analysis confirms that northwestern are nested within southeastern populations. The best‐fit demographic indicates Pleistocene divergence across River, significant bidirectional gene flow, severe Holocene bottleneck. These patterns suggest management strategies should focus on maintaining both sides recommend additional lands Mexico be considered for similar goals those Rangewide Management Strategy. also periodic rangewide genomic sampling monitor ongoing attrition diversity, hybridization, changing structure due habitat fragmentation, climate change, other long‐term impacts.

Language: Английский

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Squamates as a model to understand key dental features of vertebrates

Developmental Biology, Journal Year: 2024, Volume and Issue: 516, P. 1 - 19

Published: July 26, 2024

Thanks to their exceptional diversity, teeth are among the most distinctive features of vertebrates. Parameters such as tooth size, shape, number, identity, and implantation can have substantial implications for ecology certain social behaviors toothed species. Despite decades research primarily focused on mammalian dentition, particularly using laboratory mouse model, squamate reptiles ("lizards" snakes) offer a wide array types dentition variations. This which includes differences in function, replacement capacity, provides invaluable opportunities investigating these fundamental properties. The central bearded dragon (Pogona vitticeps), popular pet species with well-established husbandry practices, is particular interest. It broad spectrum morphs spontaneous mutants exhibits range heterodont phenotypes, including variation implantation, renewal at both posterior anterior positions. These characteristics position crucial model organism developmental studies gaining deeper insights into evolutionary patterns vertebrate dentitions. In this article, we provide an overview current understanding its development, replacement. Furthermore, discuss significant advantages offered by organisms aspects dentition.

Language: Английский

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Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae)

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Oct. 26, 2024

The ubiquity of sex across eukaryotes, given its high costs, strongly suggests it is evolutionarily advantageous. Asexual lineages can avoid, for example, the risks and energetic costs recombination, but suffer short-term reductions in adaptive potential long-term damage to genome integrity. Despite these lichenized fungi have frequently evolved asexual reproduction, likely because allows retention symbiotic algae generations. fungal genus Lepraria thought be exclusively asexual, while sister Stereocaulon completes a sexual reproductive cycle. A comparison clades should shed light on evolution asexuality lichens general, as well apparent maintenance Lepraria, specifically. In this study, we assembled annotated representative long-read genomes from putatively Stereocaulon, added short-read assemblies an additional 22 individuals both genera. Comparative genomic analyses revealed that genera were heterothallic, with intact mating-type loci idiomorphs present each genus. Additionally, identified assessed 29 genes involved meiosis mitosis 45 contribute formation structures (ascomata). All appeared functional nearly all failed identify general pattern relaxation selection lineage. Together, results suggest may capable including mate recognition, meiosis, production ascomata. machinery essential sex, over 200 years careful observations by lichenologists produced no evidence canonical reproduction Lepraria. We instead form parasexual perhaps repurposing MAT meiosis-specific genes. This may, turn, allow avoid consequences asexuality, maintaining benefit unbroken bond their algal symbionts.

Language: Английский

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Chromosome-Level Genome Assembly of the Cape Cliff Lizard (Hemicordylus capensis)

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(2)

Published: Jan. 9, 2023

Squamates represent a highly diverse and species-rich vertebrate group that is remarkably understudied from genomic perspective. A scarcity of data particularly evident for scincomorph lizards, which encompass over 10% all living squamates, high-quality resources are currently lacking. To address this knowledge gap, we present the first chromosome-level reference genome group, generated male Cape cliff lizard (Hemicordylus capensis), using accurate PacBio HiFi long-read sequencing data, long-range Omni-C chromosomal conformation capture transcriptomic annotation. The rHemCap1.1 assembly spans 2.29 Gb, with scaffold N50 359.65 Mb, includes 25,300 protein-coding genes, BUSCO completeness score 95.5% (sauropsida_odb10). We have most contiguous complete squamate publicly available to date. Furthermore, used short-read resequencing 35 males females applied differential coverage approach infer sex-determination system species, was previously unknown. Our results suggest species has XX/XY sex chromosomes, representing evidence determination in family Cordylidae. This will help establish as an evolutionary model studying variation body armor, key trait cordylids other groups. Lastly, continental African and, such, represents valuable resource not only further research but also closely related

Language: Английский

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Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii

Journal of Heredity, Journal Year: 2023, Volume and Issue: 114(4), P. 410 - 417

Published: May 17, 2023

Abstract Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant species like Blainville’s horned lizard, Phrynosoma blainvillii, due its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from orbital sinuses), status as Species Special Concern in California. Rangewide decline since early 20th century, basis conservation status, has been driven mainly by habitat conversion, over-collecting, invasion a non-native ant displaces native prey base. Here, we report scaffold-level genome assembly P. blainvillii part California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads Hi-C chromatin-proximity sequencing technology. The de novo 78 scaffolds, total length ~2.21 Gb, scaffold N50 ~352 Mb, BUSCO score 97.4%. is second which reference assembled represents considerable improvement terms contiguity completeness. Combined with landscape genomics data compiled CCGP, this will strategize efforts maintain and/or restore local diversity, where interventions rescue, translocation, strategic land preservation only means other low-vagility survive fragmented habitats

Language: Английский

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