The effects of Pleistocene climate change on biotic differentiation in a montane songbird clade from Wallacea

Ng, Nathaniel S. R.; Wilton, Peter R.; Prawiradilaga, Dewi M.; Tay, Y. C.; Indrawan, Mochamad; Garg, Kritika M.; Rheindt, Frank E.

doi:10.1016/j.ympev.2017.05.007

Cited by 21 publications

(20 citation statements)

References 73 publications

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“…LIPI also maintain official national records and documentation of their samples. To obtain genome-wide markers (SNPs) with next-generation sequencing, we modified a protocol for ddRADseq (Peterson et al 2012) following Tay et al (2016) and used the restriction enzymes EcoRI-HF and MspI because they worked well for other taxa (Garg et al 2016;Ng et al 2017). During optimisation of the RADseq protocol, we selected a Sera-Mag® bead ratio that produced DNA fragments within a range of 250-650 base pairs (bp) (Appendix A).…”

Section: Sample Collectionmentioning

confidence: 99%

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

et al. 2018

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The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but Critically Endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used > 12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using > 2,000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit.

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Section: Sample Collectionmentioning

confidence: 99%

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

et al. 2018

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“…www.nature.com/scientificreports/ evolution by appropriating novel traits through horizontal gene transfer and genetic introgression [10][11][12][13] . This transfer of traits is now well-documented across a wide variety of model and non-model organisms [14][15][16][17][18][19][20] . Such phenotypic appropriation has occurred even in some populations of modern humans (Homo sapiens) which are known to carry traits conferred to them through genetic introgression from ancient, now-extinct hominine lineages 21,22 .…”

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confidence: 92%

The conservation value of admixed phenotypes in a critically endangered species complex

Sadanandan

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Sridharan

et al. 2020

Sci Rep

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In today’s environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.

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“…For example, in the northern hemisphere, glacial ice sheets have covered substantial areas of suitable habitat, forcing many species into small refugial pockets [ 2 , 4 , 5 ]. In contrast, in many shallow coastal parts of the world, especially across Australasia, genetic connectivity among isolated populations may increase during periods of global cooling, as the global sea level drops by up to 120 m, allowing for the formation of land bridges and connectivity [ 1 , 6 – 8 ]. However, research on the evolutionary impact of Quaternary glaciations on species-rich tropical mountains is still in its infancy.…”

Section: Introductionmentioning

confidence: 99%

Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea

et al. 2020

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Background Quaternary climate fluctuations are an engine of biotic diversification. Global cooling cycles, such as the Last Glacial Maximum (LGM), are known to have fragmented the ranges of higher-latitude fauna and flora into smaller refugia, dramatically reducing species ranges. However, relatively less is known about the effects of cooling cycles on tropical biota. Results We analyzed thousands of genome-wide DNA markers across an assemblage of three closely related understorey-inhabiting scrubwrens ( Sericornis and Aethomyias ; Aves) from montane forest along an elevational gradient on Mt. Wilhelm, the highest mountain of Papua New Guinea. Despite species-specific differences in elevational preference, we found limited differentiation within each scrubwren species, but detected a strong genomic signature of simultaneous population expansions at 27-29 ka, coinciding with the onset of the LGM. Conclusion The remarkable synchronous timing of population expansions of all three species demonstrates the importance of global cooling cycles in expanding highland habitat. Global cooling cycles have likely had strongly different impacts on tropical montane areas versus boreal and temperate latitudes, leading to population expansions in the former and serious fragmentation in the latter.

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The effects of Pleistocene climate change on biotic differentiation in a montane songbird clade from Wallacea

Cited by 21 publications

References 73 publications

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

The conservation value of admixed phenotypes in a critically endangered species complex

Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea

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