Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(11)

Published: Sept. 15, 2023

Conservation genetic analyses of many endangered species have been based on genotyping microsatellite loci and sequencing short fragments mtDNA. The increase in power resolution afforded by whole genome approaches may challenge conclusions made limited numbers maternally inherited haploid markers. Here, we provide a matched comparison versus control region (CR) for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations otter Britain, derived from regional that survived the population crash 1950s-1980s. Using resequencing data 45 samples across British stronghold populations, confirmed some aspects structure previous marker-driven studies. Importantly, showed genomic signals bottlenecks evidence surveys. Unexpectedly, two strongly divergent mitochondrial lineages were undetectable using CR fragments, east England distinct surprisingly variable. We hypothesize this previously unsuspected variability derive past releases other, non-British source around time bottleneck. Our highlights even reasonably well-studied harbor surprises, if studied modern high-throughput methods.

Language: Английский

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Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(7)

Published: June 24, 2024

Abstract Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play important ecological role. A small, protected population exists on a world heritage listed offshore island, K’gari (formerly Fraser Island). Concern regarding the persistence of has risen due their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking this population. Here, we include five new sequences dingoes. We analyze total 18 sampled mainland Australia assess genomic consequences demographic histories. Long (>1 Mb) runs homozygosity (ROHs)—indicators inbreeding—are all showed significantly higher levels very long ROH (>5 Mb), providing evidence for small size, isolation, inbreeding, strong founder effect. Our results suggest that, despite current purging strongly deleterious mutations, which, absence further reductions may facilitate populations isolation. there be little no mildly alleles, which have long-term consequences, should considered by conservation management programs.

Language: Английский

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What's on the menu? Examining native apex‐ and invasive meso‐predator diets to understand impacts on ecosystems

Ecological Solutions and Evidence, Journal Year: 2025, Volume and Issue: 6(2)

Published: April 1, 2025

Abstract Understanding how carnivores impact ecological communities is essential for guiding effective management actions and conserving biodiversity. Quantifying predators' diets, including prey selectivity, allows the assessment of relative effects native invasive predators may have on populations. In Australia, populations a native, terrestrial apex predator, dingo Canis dingo/C. familiaris , introduced subordinate mesopredators, European red fox Vulpes vulpes feral cat Felis catus co‐occur, but there limited understanding their impacts in different ecosystems. To assess possible dingoes, foxes cats prey, we examined diet selectivity across ~10,000 km 2 semi‐arid mallee ecosystem. Using macroscopic scat analysis, identified strong dietary niche separation. Larger‐bodied dingoes primarily consumed large marsupial herbivores, whereas smaller rodents birds. Foxes had broadest diet, greatest overlap with ( = 0.81), compared 0.50) or between 0.36). Livestock were 2% 7% scats. Cats more than 15 times volume small mammals threatened species such as fat‐tailed dunnarts Sminthopsis crassicaudata . also selectively to estimated availability fewer mammals. contrast, birds echidnas availability. Our results suggest intraguild competition within this ecosystem, are exerting top‐down pressure mesopredators disproportionately impacting Practical implication findings that ongoing conservation must consider variation roles these predator species, avoid indiscriminate lethal control methods. actual, rather assumed, herbivores livestock achieve integrated ecosystem management.

Language: Английский

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Ancient genomes reveal over two thousand years of dingo population structure

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(30)

Published: July 8, 2024

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes Australia—including number founding populations their routes introduction—remains uncertain. This uncertainty arises partly from complex poorly understood relationship between modern New Guinea singing dogs, suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into genomes many wild dingo populations. In this study, we analyzed genome-wide data nine ancient specimens ranging age 400 to 2,746 y old, predating introduction dogs European colonists. We uncovered evidence continent-wide population structure observed had already emerged several thousand years ago. also detected excess allele sharing coastal South Wales (NSW) compared southern Australia, irrespective any hybrid individuals. Our results consistent with demographic scenarios, including a scenario where east coast at least two waves migration source varying affinities dogs. contribute growing body derive little genomic other lineages, instead descending primarily Sahul thousands

Language: Английский

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Isolation, small population size, and management influence inbreeding and reduced genetic variation in K’gari dingoes

Conservation Genetics, Journal Year: 2024, Volume and Issue: 25(4), P. 955 - 971

Published: April 19, 2024

Abstract Small island populations are vulnerable to genetic decline via demographic and environmental stochasticity. In the absence of immigration, founder effects, inbreeding drift likely contribute local extinction risk. Management actions may also have a greater impact on small, closed populations. The social characteristics species can, however, delay threats. K’gari, ~ 1 660 km 2 off Australian east coast UNESCO World Heritage Site (Fraser Island 1842–2023), supports an isolated population approximately 70–200 dingoes that represent ideal opportunity explore small paradigm. To examine temporal spatial patterns diversity in this we analysed single nucleotide polymorphism (SNP) genotype data (72 454 SNPS) for 112 K’gari collected over 25-year period (1996 2020). Genetic was lower than mainland at earliest time point our study declined significantly following management cull 2001. We did not find any island, suggesting high levels connectivity between socially discrete packs. This connectivity, combined with structure behaviour dingoes, act concert buffer from impacts short term. Nevertheless, general variation has occurred past 20 years which suggest should be considered future planning population. Monitoring variation, together clearer understanding ecology will aid development measurable targets set ecologically meaningful timelines, help ensure continued survival culturally important

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 consequences of isolation and inbreeding in an island dingo population

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

Published: Sept. 15, 2023

ABSTRACT Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia’s largest terrestrial predator, dingoes play important ecological role. A small, protected population exists on a world heritage listed offshore island, K’gari (formerly Fraser Island). Concern regarding the persistence of has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking this population. Here, we include five new sequences dingoes. We analyze total 18 whole genome sampled mainland Australia assess genomic consequences demographic histories. Long (>1 Mb) runs homozygosity (ROH) — indicators are all showed significantly higher levels very long ROH (>5 Mb), providing evidence for small size, isolation, inbreeding, strong founder effect. Our results suggest that, despite current purging strongly deleterious mutations, which, absence further reductions may facilitate populations isolation. there be little no mildly alleles, which have long-term consequences, should considered by conservation management programs. SIGNIFICANCE long-standing question genetics whether isolation always leads inevitable extinction. Here conduct first-ever analysis living island off coast (K’gari). show these animals beset diversity, likely result extensive number homozygotes. our highly allowed them persist term extremely (<200 individuals).

Language: Английский

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Genetic structure and common ancestry expose the dingo-dog hybrid myth

Evolution Letters, Journal Year: 2024, Volume and Issue: 9(1), P. 1 - 12

Published: Oct. 19, 2024

Abstract The evolutionary history of canids has been shown to be complex, with hybridization and domestication confounding our understanding speciation among various canid lineages. dingo is a recent lineage that was completely isolated from other for over 5000 years on the Australian mainland, but introduction domestic dogs in 1788 placed doubt its independence, studies highlighting between dingoes dogs. Using genomic single nucleotide polymorphism data 434 samples, we explicitly test introgression closely related groups dingoes. We found no evidence show previous work likely mischaracterized shared ancestral genetic variation as hybridization. Further, New Guinea Singing Dogs are only group significantly dingoes, which fits phylogenetic analyses. Despite more sympatric distributions dogs, have maintained their independence since arrival Australia, even areas high lethal control, indicating trajectory currently being conserved. future conservation will require policies promote coexistence pathways humans protect rangeland systems dingoes’ future.

Language: Английский

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Aboriginal flood narratives and the thunder complex in Southeast Asia

Archaeology in Oceania/Archæology & physical anthropology in Oceania, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 30, 2024

Abstract The ancestors of the dingo were brought to mainland Australia around 4000 years ago by people who arrived boat. identity these voyagers from north, however, and nature their interactions with Aboriginal population Australia, are unknown. Here, we propose that Indigenous flood narratives Kimberley contain evidence for contact between early Asian seafarers in form “thunder complex”. latter is a very specific repertoire taboos, rituals stories occurs widely among ethnographically known societies Indonesia, Philippines peninsular Malaysia, but has not previously been identified Australia. Among Southeast groups, this cultural complex revolves idea certain prohibited acts perpetrated against animals – especially “mocking” them treating as though they human precipitate punitive storm and/or flooding. We show some oral traditions region animal mockery similarly held be causative agent behind disastrous flooding events took place past creationary epoch. contend localised variant thunder reflects an episode close interaction Austronesian‐speaking introduced ancestral dingoes apparently via coast.

Language: Английский

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Genetic Monitoring of a Lethal Control Programme for Wild Canids With Complex Mating Strategies

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 22, 2024

ABSTRACT Although mammalian carnivores are ecologically important, they also drive human–wildlife conflicts. Managing using lethal control is controversial, in part because the impact of effort often uncertain due to limited abundance monitoring. We used an Australian metapopulation wild dogs as a model system investigate feasibility monitoring effective population size () detect reductions census following control. Based on microsatellite data collected over 11‐year period, we parameterised individual‐based spatial for that integrated demography, genetics, random or hierarchical mating, dispersal between subpopulations and compensatory immigration. trajectories were simulated under different proportional culling rates genetic sampling regimes. simulations without null models define 95% critical values assessing significance empirical changes time. concluded there significant (39%–62%) each subpopulation dog metapopulation, mostly likely In assuming rather than mating system, was weakened reproduction by subordinate individuals increased dominant removed, yet reduced culling. Sensitivity analyses demonstrated becomes unreliable proxy when immigration strong weak, which case can increase new genotypes. Nonetheless, our results suggest provide information about sufficiently short timescales inform management.

Language: Английский

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