<scp>Genome‐wide</scp> variant analyses reveal new patterns of admixture and population structure in Australian dingoes

Cairns, Kylie M.; Crowther, Mathew S.; Parker, Heidi G.; Ostrander, Elaine A.; Letnic, Mike

doi:10.1111/mec.16998

Cited by 9 publications

(11 citation statements)

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“…Erroneous reports of hybridization from microsatellites have been found in a wide range of organisms including newts (Miralles et al., 2023), lemurs (Poelstra et al., 2022), dingoes (Cairns et al., 2023), polecats (Szatmári et al., 2021) and Cape hakes (Henriques et al., 2016). These false reports of hybridization were mainly attributed to the lack of power resulting from the use of a (very) small number of hyper‐variable loci.…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, the high risk of homoplasy (Chambers & MacAvoy, 2000; Henriques et al., 2016), the frequent occurrence of null alleles (Dakin & Avise, 2004), high mutation rate and difficulties scoring alleles (Pompanon et al., 2005; Selkoe & Toonen, 2006), are well‐documented issues inherent to the nature of microsatellites, but are often ignored, potentially leading to false reports of hybridization (e.g. Cairns et al., 2023; Poelstra et al., 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Rapid developments in sequencing technologies and protocols now ease the generation of large single nucleotide polymorphism (SNP) datasets for non‐model organisms. With their higher resolution, SNPs can estimate frequencies of hybridization more accurately (Cairns et al., 2023; Parejo et al., 2018) and solve contradictory estimates obtained from small numbers of short markers (Miralles et al., 2023).…”

Section: Introductionmentioning

confidence: 99%

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

Choquet,

Lizano,

Le Moan

et al. 2023

Molecular Ecology

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

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Choquet,

Lizano,

Le Moan

et al. 2023

Molecular Ecology

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“…Hybridization with domestic dogs was previously highlighted as a main concern for dingo conservation, since high levels of hybridization were observed in dingoes from southeastern Australia (Newsome and Corbett 1985; Jones 1990; Corbett 2001; Wilton 2001; Elledge et al 2008; Stephens et al 2015; Cairns et al 2020; Cairns 2021; Cairns et al 2021). However, a recently published study using genome-wide SNP data has shown these occurrences are less common than previously thought (Cairns et al 2023). Policy and legislation in Australia currently employs the term “wild dog” to refer to dingoes, feral domestic dogs and dingo-dog hybrids, assuming that pure dingoes are virtually extinct in the wild and that dingo-dog hybrids are common (Fleming 2001; DEPI 2013; Bird and Bowman 2016; NWDAP 2020).…”

Section: Introductionmentioning

confidence: 94%

“…Although dingoes are present across different bioregions in Australia, at least two distinct mainland dingo lineages have been identified, one in the northwest and one in the southeast, alongside one offshore lineage on K’gari (formerly known as Fraser Island) (Cairns and Wilton 2016; Cairns et al 2017; Cairns et al 2018; Greig et al 2018; Zhang et al 2020). Genome-wide SNP data suggest there may be additional biogeographic structure in the mainland dingo population (Cairns et al 2023). As the apex terrestrial predator since the extinction of the thylacine, dingoes play an important role in maintaining the ecosystems of Australia (Glen et al 2007; Johnson et al 2007; Letnic et al 2009; Wallach et al 2010; Letnic et al 2011; Letnic et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Genomic consequences of isolation and inbreeding in an island dingo population

Leon-Apodaca,

Kumar,

del Castillo

et al. 2023

Preprint

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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 an important ecological role. A small population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). While dingoes on K'gari are protected, dingoes on the mainland are only protected in certain regions, and, because of its controversial status in Australia, lethal control is commonly used for management. Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) --- indicators of inbreeding --- are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there is little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

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Aboriginal flood narratives and the thunder complex in Southeast Asia

Brumm,

Forth

2024

Archaeology in Oceania

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

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Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes

Abstract: Hybridisation between two populations or species leads to genetic admixture, which alters the genetic identity of the species or population and can result in a new hybrid species. In some cases, genetic dilution can lead to extinction of the species or populations involved

Cited by 9 publications

References 126 publications

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

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

Genomic consequences of isolation and inbreeding in an island dingo population

Aboriginal flood narratives and the thunder complex in Southeast Asia

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