Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

Grant, W. Stewart; Ming, Liu; Gao, Tianxiang; Yanagimoto, Takashi

doi:10.1016/j.ympev.2012.06.006

Cited by 88 publications

(78 citation statements)

References 80 publications

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“…Recent population growth (which is not observed here) can mask earlier demographic history (Grant et al 2012). Similarly, population structure can alter the distribution of coalescence points (Pannell 2003).…”

Section: Bspsmentioning

confidence: 72%

Climate Change Influenced Female Population Sizes Through Time Across the Indonesian Archipelago

et al. 2013

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Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world's richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia's complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15-20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum. Keywords Indonesia, Mitochondrial Dna, Bayesian Skyline PlotThis open access article is available in Human Biology: http://digitalcommons.wayne.edu/humbiol/vol85/iss1/6 Abstract Lying at the crossroads of Asia and the Pacific world, the Indonesian archipelago hosts one of the world's richest accumulations of cultural, linguistic, and genetic variation. While the role of human migration into and around the archipelago is now known in some detail, other aspects of Indonesia's complex history are less understood. Here, we focus on population size changes from the first settlement of Indonesia nearly 50 kya up to the historic era. We reconstructed the past effective population sizes of Indonesian women using mitochondrial DNA sequences from 2,104 individuals in 55 village communities on four islands spanning the Indonesian archipelago (Bali, Flores, Sumba, and Timor). We found little evidence for large fluctuations in effective population size. Most communities grew slowly during the late Pleistocene, peaked 15-20 kya, and subsequently declined slowly into the Holocene. This unexpected pattern may reflect population declines caused by the flooding of lowland hunter/gatherer habitat during sea-level rises following the last glacial maximum.The prehistory of Island Southeast Asia is made especially complex by its position as a waypoint between mainland Asia, Australia, and the Pacific world. The region's prehistory is dominated by population movements, beginning with its first settlement by modern humans approximately 50 kya and continuing to the Islamization of Indonesia during the historic period. Reflecting the rich cultural and linguistic diversity of Indonesia's inhabitants, these eras have also left their mark on the genetic diversity of the individuals who inhabit Indonesia today (Cox et al.

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Section: Bspsmentioning

confidence: 72%

Climate Change Influenced Female Population Sizes Through Time Across the Indonesian Archipelago

et al. 2013

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“…These involve the deep genealogy that supports reciprocal monophyly ( Fig. 4a; see "Materials and methods" section), and the fact that the observations of incongruence are exclusively from a post-glacially colonized secondary contact zone, isolated from the main Pacific range of C. pallasii, whereas extensive data from the native basin have not demonstrated any alien mitochondria (Liu et al 2011;Gorbachev et al 2012;Grant et al 2012, Laakkonen et al 2013. Also, as all the deviating mitochondria in NE European Pacific herring are clearly part of the contemporary diversity of the Atlantic herring and sometimes even have identical cyt-b sequence (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Considering the pre-Pleistocene divergence of the Pacific and Atlantic herring taxa in their native basins, the mitochondrial lineages are judged to be reciprocally monophyletic and deeply enough diverged to rule out any hypothesis of ancestral polymorphism as alternative cause of character incongruence. Their genealogy involves minimum 4 % observed inter-species cyt-b divergence contrasted by <1.5 % within the main lineages (or π = 1 %; Laakkonen et al 2013); and there are extensive data on segregation of the lineages between the two oceans and the two taxa in samples from elsewhere but the post-glacial secondary contact zone dealt with in this study (Liu et al 2011;Gorbachev et al 2012;Grant et al 2012;Teacher et al 2012;Laakkonen et al 2013;but cf. McCusker et al 2013).…”

Section: Rationalementioning

confidence: 94%

Introgressive hybridization between the Atlantic and Pacific herrings (Clupea harengus and C. pallasii) in the north of Europe

et al. 2014

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“…Our BSP plot shows a long period of stasis from approximately 64-20 kya. This is an artifact of the analysis, where signals prior to the last major effective population size change are lost (Grant et al 2012;Grant 2015). This period of stasis was trimmed in the final figure to show just the plot from 32 kya.…”

Section: Historical Demographymentioning

confidence: 99%

Biogeography and demography of an Australian native bee Ceratina australensis (Hymenoptera, Apidae) since the last glacial maximum

Dew¹,

Rehan²,

Schwarz³

2016

JHR

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The small carpenter bees, genus Ceratina, are highly diverse, globally distributed, and comprise the sole genus in the tribe Ceratinini. Despite the diversity of the subgenus Neoceratina in the Oriental and IndoMalayan region, Ceratina (Neoceratina) australensis is the only ceratinine species in Australia. We examine the biogeography and demography of C. australensis using haplotype variation at 677 bp of the barcoding region of COI for specimens sampled from four populations within Australia, across Queensland, New South Wales, Victoria and South Australia. There is geographic population structure in haplotypes, suggesting an origin in the northeastern populations, spreading to southern Australia. Bayesian Skyline Plot analyses indicate that population size began to increase approximately 18,000 years ago, roughly corresponding to the end of the last glacial maximum. Population expansion then began to plateau approximately 6,000 years ago, which may correspond to a slowing or plateauing in global temperatures for the current interglacial period. The distribution of C. australensis covers a surprisingly wide range of habitats, ranging from wet subtropical forests though semi-arid scrub to southern temperate coastal dunes. The ability of small carpenter bees to occupy diverse habitats in ever changing climates makes them a key species for understanding native bee diversity and response to climate change.

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Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

Cited by 88 publications

References 80 publications

Climate Change Influenced Female Population Sizes Through Time Across the Indonesian Archipelago

Climate Change Influenced Female Population Sizes Through Time Across the Indonesian Archipelago

Introgressive hybridization between the Atlantic and Pacific herrings (Clupea harengus and C. pallasii) in the north of Europe

Biogeography and demography of an Australian native bee Ceratina australensis (Hymenoptera, Apidae) since the last glacial maximum

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