Genomic population structure aligns with vocal dialects in Palm Cockatoos (<i>Probosciger aterrimus</i>); evidence for refugial late-Quaternary distribution?

Keighley, Miles V.; Heinsohn, Robert; Langmore, Naomi E.; Murphy, Stephen; Peñalba, Joshua V.

doi:10.1080/01584197.2018.1483731

Cited by 15 publications

(9 citation statements)

References 61 publications

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“…The lack of actual genetic intermixing thus arises despite possible intermixing of flocks from different genetic clusters in non-breeding areas used temporarily, which indicates very limited effective dispersal leading to recruitment into non-natal genetic clusters. This can arise by individual recognition within social groups strongly attached to natal and breeding colonies in this species, which may be achieved through complex organisation and behaviour facilitated by informative vocalisations 78 and dialects common among parrots 16 , 17 , 79 .…”

Section: Discussionmentioning

confidence: 99%

Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers

Blanco

Morinha

Roques

et al. 2021

Sci Rep

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Behavioural and socio-cultural traits are recognized in the restriction of gene flow in species with high cognitive capacity and complex societies. This isolation by social barriers has been generally overlooked in threatened species by assuming disrupted gene flow due to population fragmentation and decline. We examine the genetic structure and ecology of the global population of the Critically Endangered red-fronted macaw (Ara rubrogenys), an endemic species to the inter-Andean valleys of Bolivia. We found a fine-scale genetic structuring in four genetic clusters. Genetic diversity was higher in wild compared to captive-bred macaws, but similar to that of captive wild-caught macaws. We found no clear evidence of severe genetic erosion in the population in recent decades, but it was patent in historic times, overlapping with drastic human habitat transformation and macaw persecution over millennia. We found no evidence of geographical and ecological barriers, owing to the high dispersal ability, nesting and foraging habits between genetic clusters. The lack of genetic intermixing despite long-distance foraging and seasonal movements suggests recruitment in natal colonies and other social factors reinforcing philopatry-related genetic structure. Conservation efforts should be specifically focussed on major threats in each genetic cluster as independent conservation units, and also considered in ex-situ management.

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Section: Discussionmentioning

confidence: 99%

Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers

Blanco

Morinha

Roques

et al. 2021

Sci Rep

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“…We have benefited from the HyRAD genome–complexity–reduction method to obtain genetic data from these valuable samples. HyRAD has been increasingly used in different laboratories, not only to identify genetic variation in historical material (Crates et al., 2019; Keighley, Heinsohn, Langmore, Murphy, & Peñalba, 2019; Linck et al., 2017; Linck, Freeman, & Dumbacher, 2019; Schmid et al., 2017), but also in ancient DNA (Schmid et al., 2017). Indeed, these methods based on hybridization capture allow us to retrieve even very small quantities of degraded DNA, which often remain unquantifiable before capture (Table S1).…”

Section: Discussionmentioning

confidence: 99%

Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland

Gauthier

Pajkovic

Neuenschwander

et al. 2020

Molecular Ecology Resources

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Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization‐capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within‐species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.

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“…This accords with their current classification as C. h. superciliosa and suggests they maintained male-mediated gene flow during the LGM across then-exposed savannah woodlands and grasslands (Nix and Kalma 1972;Williams et al 2009). Grey shrike-thrush currently inhabit savannah areas within PNG and relatively shallow divergence across Torres Strait has been repeatedly observed in savannahadapted species (Keighley et al 2019;Murphy et al 2007;Toon et al 2017;Williams et al 2008;Wüster et al 2005) compared with deeper divergence observed in mesic closed forest-adapted species (Joseph et al 2001;Kearns et al 2011;Krajewski et al 2004;Macqueen et al 2011Macqueen et al , 2010Norman et al 2007;Rawlings and Donnellan 2003;Zwiers et al 2008). A mitochondrial lineage unique to the Trans-Fly was estimated to have diverged from mainland Australian and east PNG lineages 0.38-0.76 Ma.…”

Section: Evidence Of Biogeographical Barriers Driving Divergence Durimentioning

confidence: 96%

Pleistocene-dated biogeographic barriers drove divergence within the Australo-Papuan region in a sex-specific manner: an example in a widespread Australian songbird

et al. 2019

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Understanding how environmental change has shaped species evolution can inform predictions of how future climate change might continue to do so. Research of widespread biological systems spanning multiple climates that have been subject to environmental change can yield generalizable inferences about the neutral and adaptive processes driving lineage divergence during periods of environmental change. We contribute to the growing body of multi-locus phylogeographic studies investigating the effect of Pleistocene climate change on species evolution by focusing on a widespread Australo-Papuan songbird with several mitochondrial lineages that diverged during the Pleistocene, the grey shrike-thrush (Colluricincla harmonica). We employed multi-locus phylogenetic, population genetic and coalescent analyses to (1) assess whether nuclear genetic diversity suggests a history congruent with that based on phenotypically defined subspecies ranges, mitochondrial clade boundaries and putative biogeographical barriers, (2) estimate genetic diversity within and genetic differentiation and gene flow among regional populations and (3) estimate population divergence times. The five currently recognized subspecies of grey shrike-thrush are genetically differentiated in nuclear and mitochondrial genomes, but connected by low levels of gene flow. Divergences among these populations are concordant with recognized historical biogeographical barriers and date to the Pleistocene. Discordance in the order of population divergence events based on mitochondrial and nuclear genomes suggests a history of sex-biased gene flow and/or mitochondrial introgression at secondary contacts. This study demonstrates that climate change can impact sexes with different dispersal biology in different ways. Incongruence between population and mitochondrial trees calls for a genome-wide investigation into dispersal, mitochondrial introgression and mitonuclear evolution.

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Genomic population structure aligns with vocal dialects in Palm Cockatoos (Probosciger aterrimus); evidence for refugial late-Quaternary distribution?

Cited by 15 publications

References 61 publications

Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers

Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers

Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland

Pleistocene-dated biogeographic barriers drove divergence within the Australo-Papuan region in a sex-specific manner: an example in a widespread Australian songbird

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