Using computational simulations to quantify genetic load and predict extinction risk

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Авг. 15, 2022

Abstract Small and isolated wildlife populations face numerous threats to extinction, among which is the deterioration of fitness due an accumulation deleterious genetic variation. Genomic tools are increasingly used quantify impacts variation in small populations; however, these approaches remain limited by inability accurately predict selective dominance effects individual mutations. Computational simulations offer alternative complementary tool that can help overcome limitations, though such have yet be widely employed. In this Perspective, we aim encourage conservation genomics researchers adopt greater use computational aid quantifying predicting threat poses extinction. We first provide overview components a simulation variation, describing key parameters involved models. Next, clarify several misconceptions about essential parameter, distribution (DFE) new mutations, review recent debates over what most appropriate DFE are. conclude comparing modern those long been employed population viability analysis, weighing pros cons ‘genomics-informed’ approach, discussing areas for future research. Our Perspective will facilitate broader genomics, enabling deeper understanding biodiversity.

Язык: Английский

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Museomics

Current Biology, Год журнала: 2022, Номер 32(21), С. R1214 - R1215

Опубликована: Ноя. 1, 2022

Язык: Английский

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Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul

NAR Genomics and Bioinformatics, Год журнала: 2023, Номер 5(2)

Опубликована: Март 29, 2023

Abstract Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to grasslands and steppes of central Asia. Population strongholds in Mongolia China face growing challenges from climate change, habitat fragmentation, poaching, other sources. These threats, combined with O. manul’s zoo collection popularity value evolutionary biology, necessitate improvement species genomic resources. We used standalone nanopore sequencing assemble 2.5 Gb, 61-contig nuclear assembly 17097 bp mitogenome for manul. The primary had 56× coverage, contig N50 118 Mb, 94.7% BUSCO completeness score Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto fishing (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 chromosomes an inferred total gap length less than 400 kilobases. Modified basecalling variant phasing produced alternate pseudohaplotype allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, putative novel loci. assembled successfully resolved existing discordance Felinae mtDNA phylogenies. All drafts generated 158 Gb sequence using seven minION flow cells.

Язык: Английский

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The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards

Communications Biology, Год журнала: 2023, Номер 6(1)

Опубликована: Авг. 5, 2023

The translocation of individuals around the world is leading to rising incidences anthropogenic hybridization, particularly between domestic and wild congeners. We apply a landscape genomics approach for thousands mallard (Anas platyrhynchos) samples across continental island populations determine result over century supplementation practices. establish that single game-farm breed source contemporary release programs in Eurasia North America, as well established feral New Zealand Hawaii. In particular, we identify central Europe eastern America epicenters ongoing conclude mallards continues affect genetic integrity mallards. Conversely, self-sustaining Hawaii not only show strong differentiation from their original stock, but also signatures local adaptation occurring less than half-century since releases have ceased. 'wild' singular, even are capable responding natural processes. Although considered paradoxical biological conservation, understanding capacity wildness among admixed human landscapes critical such interactions increase Anthropocene.

Язык: Английский

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On the road to losing connectivity: Faecal samples provide genome‐wide insights into anthropogenic impacts on two large herbivore species in central India

Molecular Ecology, Год журнала: 2024, Номер 33(16)

Опубликована: Июль 3, 2024

Abstract Humans have impacted most of the planet, and ensuing fragmentation results in small, isolated habitat patches posing a risk genetic diversity loss, inbreeding, load. Understanding how natural anthropogenic landscape features affect gene flow among is critical for maintaining connectivity. Genome‐wide data are required to comprehend impacts recent fragmentation, which can be challenging when only non‐invasive samples available. Here, we build upon advancements conservation genomics address connectivity two large herbivores, gaur ( Bos gaurus ) sambar Rusa unicolor central India. Given their associations, expected these species respond similarly fragmentation. We used faecal‐DNA methylation‐based host‐DNA enrichment with modified ddRAD protocol generate genome‐wide single‐nucleotide polymorphism (SNP) 124 99 individuals. Our findings reveal that populations India fragmented, displaying high differentiation, drift significantly affecting small like Umred Karhandla Wildlife Sanctuary. Although shows low structure, another population, Bor Tiger Reserve genetically differentiated. suggest although land cover change roads restrict animal movement, extent this impact varies across species. show different differently features, even similar associations. highlight requiring urgent intervention. Such multi‐species approaches enhance our understanding cross‐species patterns. shifting from single‐species holistic approach rapidly developing landscapes better manage co‐occurring endangered

Язык: Английский

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A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies

Molecular Ecology Resources, Год журнала: 2025, Номер unknown

Опубликована: Апрель 17, 2025

ABSTRACT Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and plethora of bioinformatic approaches are eDNA‐based community composition analysis. Simulation studies careful evaluation taxonomic classifiers essential to establish reliable benchmarks improve the accuracy reproducibility findings. Here we present comprehensive nine exploring three mitochondrial markers (12S rDNA, 16S rDNA COI) in Australian vertebrates. Curated reference databases exclusion database tests were simulate diverse species compositions, including positive control two negative datasets. Using these simulated datasets ranging from 36 302 marker genes, able identify between 19% 89% using markers. We show that MMSeqs2 Metabuli generally outperform BLAST with 10% 11% higher F1 scores 12S markers, respectively, Naive Bayes Classifiers such as Mothur sequence‐based except COI by 11%. Database reveal less susceptible false positives compared Kraken2 default parameters. Based on findings, recommend classification vertebrates given its ability species‐level assignments while reducing number positives. Our work contributes establishment best practices biodiversity analysis ultimately increase reliability monitoring context conservation.

Язык: Английский

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Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity

Ecology and Evolution, Год журнала: 2025, Номер 15(4)

Опубликована: Апрель 1, 2025

ABSTRACT The utility and importance of whole‐genome sequences are recognized across various fields, including evolution conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high‐quality DNA is impossible. In such cases, an alternative may be employ synteny‐based a genome from closely related taxon more complete genomes. Here we update the reference Pinta Island Galapagos giant tortoise ( Chelonoidis abingdonii ) without conducting additional sequencing through rescaffolding against most chromosome‐level assembly, Aldabra Aldabrachelys gigantea ). This effort resulted in much genome, CheloAbing_2.0, with N50 two orders magnitude longer large reductions L50 number gaps. We then examined impact CheloAbing_2.0 estimates runs homozygosity (ROH) resequencing data 37 individual tortoises 13 extant lineages test mechanisms by which fragmented assembly over‐ or underestimate extent ROH. use inbreeding, ROH proportion (F ), (N cumulative length (S were statistically different those derived earlier assembly. improved will serve as resource future efforts focusing ecology, evolution, conservation this species group. More broadly, our results highlight scaffolding promising generating needing types.

Язык: Английский

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Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Фев. 4, 2025

The taxonomic classification of a falcon population found in the Mongolian Altai region Asia has been heavily debated for two centuries and previous studies have inconclusive, hindering more informed conservation approach. Here, we generated chromosome-level gyrfalcon reference genome using Vertebrate Genomes Project (VGP) assembly pipeline. Using whole sequences 49 falcons from different species populations, including "Altai" falcons, analyzed their structure, admixture patterns, demographic history. We find that are genomic mosaics saker ancestries, carry distinct W mitochondrial haplotypes cluster with lanner falcon. maternally-inherited diverged 422,000 years before present (290,000–550,000 YBP) ancestor sakers gyrfalcons, both which, turn, split 109,000 YBP (70,000–150,000 YBP). chromosome 31 coding variants 29 genes may possibly influence important structural, behavioral, reproductive traits. These findings provide insights into question as candidate species.

Язык: Английский

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PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793

Scientific Data, Год журнала: 2023, Номер 10(1)

Опубликована: Июнь 1, 2023

Abstract Mussels of order Unionida are a group strictly freshwater bivalves with nearly 1,000 described species widely dispersed across world ecosystems. They highly threatened showing the highest record extinction events within faunal taxa. Conservation is particularly concerning in occurring Mediterranean biodiversity hotspot that exposed to multiple anthropogenic threats, possibly acting synergy. That case dolphin mussel Unio delphinus Spengler, 1793, endemic western Iberian Peninsula recently strong population declines. To date, only four genome assemblies available for and one European species. We present first assembly . used PacBio HiFi generate contiguous assembly. The 2.5 Gb long, possessing 1254 contigs contig N50 length 10 Mbp. This most date an essential resource investigating species’ biology evolutionary history ultimately will help support conservation strategies.

Язык: Английский

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Genomes of two Extinct‐in‐the‐Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights

Molecular Ecology Resources, Год журнала: 2023, Номер unknown

Опубликована: Март 6, 2023

Genomics can play important roles in biodiversity conservation, especially for Extinct-in-the-Wild species where genetic factors greatly influence risk of total extinction and probability successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) Lister's gecko (Lepidodactylus listeri) are two endemic reptile that went extinct the wild shortly after introduction a predatory snake. After decade management, captive populations have expanded from 66 skinks 43 geckos to several thousand individuals; however, little is known about patterns variation these species. Here, we use PacBio HiFi long-read Hi-C sequencing generate highly contiguous reference genomes both reptiles, including XY chromosome pair skink. We then analyse diversity infer ancient demography more recent histories inbreeding. observe high genome-wide heterozygosity (0.007 heterozygous sites per base-pair) (0.005), consistent with large historical population sizes. However, nearly 10% genome falls within long (>1 Mb) runs homozygosity (ROH), resulting at all major histocompatibility complex (MHC) loci. In contrast, detect single ROH gecko. lengths related may established populations. Despite shared wild, our results suggest differences species' implications management. show how contribute evolutionary conservation insights, provide resources future population-level comparative genomic studies reptiles.

Язык: Английский

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