Genomic Introgression Between Critically Endangered and Stable Species of Darwin's Tree Finches on the Galapagos Islands

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 1, 2025

Natural hybridisation among rare or endangered species and stable congenerics is increasingly topical for the conservation of species-level diversity under anthropogenic impacts. Evidence beneficial genes being introgressed into selected in hybrids raises concurrent questions about its evolutionary significance. In Darwin's tree finches on island Floreana (Galapagos Islands, Ecuador), Critically Endangered medium finch (Camarhynchus pauper) undergoes introgression with small parvulus), regularly backcross C. parvulus. Earlier studies 2005-2013 documented an increase frequency Camarhynchus using field-based microsatellite data. With single nucleotide polymorphism (SNP) data from same sampled 2005 2013 (n = 95), we examine genome-wide divergence across parental hybrid birds evidence selection hybrids. We found that just 18% previously assigned based microsatellites could be to SNPs. Over half (63%) were reassigned parvulus, though showed concordance prior assignments. Of 4869 private alleles birds, 348 at a high (≥ 0.30) exceeded their origin 89%-96% time. For detected both years (N 536) between 11%-76% underwent 13%-61% decrease 2013, which was sensitive sampling effort. identified 28 candidates via local PCA outlier tests. Alleles annotated associated inflammation, immunity, brain function development. provide critically may aid retention adaptive genetic threatened extinction.

Language: Английский

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Hybridization and Introgression in Black Hakes (Merluccius polli and M. senegalensis): Evolutionary Dynamics and Conservation Implications in the Contact Zone Exploited by Multi‐Species Fisheries

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

ABSTRACT Hybridization is relatively common between closely related species that share part of their distribution. Understanding its dynamics important both for conservation purposes and to determine role as an evolutionary mechanism. Here we have studied the case black hakes ( Merluccius polli senegalensis ) in contact zone. The area study located FAO fishing 34, Mauritania Senegal waters, where are exploited jointly multi‐species fisheries involving national foreign fleets. Using a ddRADSeq approach based on set 5820 SNPs total 240 individuals, identified one F 1 hybrid several backcrossed individuals among 90 M. samples none obtained 2020, suggesting unidirectional introgression towards . signals were not found any 60 historical from 2000. Excluding hybrids developing two separate sets (5093 2794 ), our results detected distinct genetic clusters within show different diversity estimates, with showing higher potential vulnerability exploitation. This pattern was observed contemporary samples, groups presented subtle depth segregation. Moreover, 109 outlier loci groups, could be developed into molecular markers further differentiation contribute improved stock assessment management these demersal resources.

Language: Английский

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Genome-wide patterns of diversity in the European midwife toad complex: phylogeographic and conservation prospects

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

Language: Английский

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Unraveling the genomic diversity and admixture history of captive tigers in the United States

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(39)

Published: Sept. 19, 2024

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal informing conservation efforts. However, few investigated genomic housed in captive populations. For tigers ( Panthera tigris ), individuals vastly outnumber those wild, but their remains largely unexplored. Privately owned tiger populations remained an enigma community, some believing that these are severely inbred, while others believe they may be a source now-extinct diversity. Here, we present large-scale genetic study private (non-zoo) population United States, also known as “Generic” tigers. We find Generic has admixture fingerprint comprising all six extant wild subspecies. Of 138 sequenced for purpose this study, no individual had ancestry from only one show comparable amount relative to most subspecies, variants, fewer deleterious mutations. observe inbreeding coefficients similar populations, although there within both substantially inbred. Additionally, develop reference panel can used imputation accurately distinguish assign ultralow coverage (0.25×) data. By providing cost-effective alternative whole-genome sequencing (WGS), provides resource assist efforts ex- situ

Language: Английский

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Does hybridisation with an invasive species threaten Europe’s most endangered reptile? Genomic assessment of Aeolian lizards on Vulcano Island

iScience, Journal Year: 2024, Volume and Issue: 27(11), P. 111097 - 111097

Published: Oct. 5, 2024

Interspecific hybridization can be consequential for insular species. The Critically Endangered Aeolian wall lizard, Podarcis raffonei, severely declined due to interactions with the invasive Italian siculus. largest population of P. raffonei survives on a narrow peninsula (Capo Grosso) that is mildly connected island Vulcano, which has been entirely invaded by Recent observation individuals an intermediate phenotype raised concern over risk might swamp this last stronghold. We genetically characterized lizards from considering showing multiple phenotypes (native, invasive, and "intermediate"). Hybridization rate was low (∼3%), just two F1 hybrids backcrosses, suggesting does not currently represent major threat. However, we identified genetic diversity, small effective size, Ne/Nc ratio. Management strategies are urgently needed control species maintain diversity raffonei.

Language: Английский

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Unraveling the Genomic Diversity and Admixture History of Captive Tigers in the United States

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 22, 2023

Abstract Genomic studies of rare and endangered species have focused broadly on describing diversity patterns resolving phylogenetic relationships, with the overarching goal informing conservation efforts. However, few investigated genomic potentially housed in captive populations. For tigers ( Panthera tigris ) particular, individuals vastly outnumber those wild, yet population remains largely unexplored. Here, we present first large-scale genetic study private (non-zoo) tiger United States (U.S.), also known as ‘Generic’ tigers. We find that U.S. Generic has an admixture fingerprint comprising all six extant wild subspecies P. t. altaica , Amur; Bengal; corbetti Indochinese; jacksoni Malayan; amoyensis South China; sumatrae Sumatran). show a comparable amount to most subspecies, relatively variants, fewer deleterious mutations. observe inbreeding coefficients are similar populations, suggesting populations is not pervasive, although there some within substantially inbred. Our results elucidate history Additionally, develop reference panel for it can be used imputation accurately distinguish assign ancestry even ultra-low coverage (0.25×) data. The will provide resource assist

Language: Английский

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Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(24), P. 6854 - 6873

Published: Oct. 30, 2023

Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been molecular markers of choice identify admixed individuals. However, with advent high-throughput sequencing easing generation genome-wide datasets, incorrect reports resulting from microsatellite technical artefacts uncovered a growing number taxa. In marine zooplankton genus Calanus (Copepoda), whose used as indicators, suggested between C. finmarchicus and glacialis, while other nuclear (InDels) never detected any individuals, leaving scientific community divided. Here, for first time, we investigated potential among finmarchicus, helgolandicus hyperboreus using two large independent SNP datasets. These were derived firstly protocol target-capture applied 179 individuals collected 17 sites across North Atlantic Arctic Oceans, including sympatric areas, second published RNA sequences. All SNP-based analyses congruent showing that distinct do not appear hybridize. We then thoroughly re-assessed hybrids, support transcriptomes, identified issues plaguing eight out 10 microsatellites, size homoplasy, paralogy, null alleles even primer pairs targeting same locus. Our study illustrates how deceptive can be when investigation hybridization.

Language: Английский

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Genomic introgression between critically endangered and stable species of Darwin's tree finches on the Galapagos Islands

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

Published: June 3, 2024

Abstract Natural hybridisation among rare or endangered species and stable congenerics is increasingly topical for the conservation of species-level diversity under anthropogenic impacts. Evidence beneficial genes being introgressed into selected in hybrids raises concurrent questions about its evolutionary significance. In Darwin’s tree finches on island Floreana (Galapagos Islands, Ecuador), Critically Endangered medium finch (C amarhynchus pauper ) undergoes introgression with small ( Camarhynchus parvulus ), regularly backcross C. parvulus. Earlier studies 2005-2013 documented an increase frequency using field-based microsatellite data. With single nucleotide polymorphism (SNP) data from same sampled 2005 2013 (n = 95), we examine genome-wide divergence across parental hybrid birds evidence selection hybrids. assessing previous estimates found that just 18% previously assigned based microsatellites were to SNPs. Over half (63%) reassigned parvulus, though showed concordance prior assignments. Of 4869 private alleles birds, 348 at a high (≥0.30) exceeded their origin 89-96% time. Across two years, 3436 (70.6%) underwent substantial allele decrease. these, 28 identified as candidate loci via local PCA genome scans outlier tests. Alleles annotated associated inflammation, immunity, brain function development. We provide critically Darwins’ retained by years may aid retention genetic threatened extinction.

Language: Английский

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Measuring interspecific admixture in endangered Houston toads (Bufo [= Anaxyrus] houstonensis) at a main recovery site in the Lost Pines ecosystem of Texas, USA

Conservation Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 30, 2024

Language: Английский

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Contrast and Genomic Characterisation of Ancient and Recent Interspecific Introgression Between Deeply Diverged Moustache Toads (Leptobrachium)

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(23)

Published: Oct. 28, 2024

Recent genomic analyses have provided new insights into the process of interspecific introgression and its consequences on species evolution. Most recent studies, however, focused hybridization between recently radiated species, with few examining outcomes ancient across deeply diverged species. Using whole genome data moustache toads (Leptobrachium), we identified signals three events among nine that at Eocene. An from L. leishanense to ancestral branch (C1) liui introduced adaptive variants. The highly introgressed regions include genes important functions in odorant detection immune responses. These are preserved all descendent populations liui_C1, these likely been positively selected over a long filtering process. A occurred huashen tengchongense, being mostly neutral. Furthermore, one F1 hybrid individual was detected sympatric ailaonicum promustache. largely disappeared after removing individual, indicating an occasional but minimal introgression. Further examination divergent low revealed both pre-mating isolation genetic incompatibility as potential mechanisms resisting maintaining boundaries. Additionally, no large X-effect found events. Hybridization amphibian may be common, detectable introgressions less so, neutral rare potentially adaptive. Our findings complement work, together they provide better understanding characteristics significance adaptation

Language: Английский

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