Cattle demographic history modelled from autosomal sequence variation

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus , with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus . Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.

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Temporal fluctuations of Y-chromosomal variation in Bos taurus

Biology Letters ◽

10.1098/rsbl.2008.0342 ◽

2008 ◽

Vol 4 (6) ◽

pp. 752-754 ◽

Cited By ~ 29

Author(s):

Emma Svensson ◽

Anders Götherström

Keyword(s):

Single Nucleotide Polymorphism ◽

Bos Taurus ◽

Demographic History ◽

Northern Europe ◽

Chromosomal Gene ◽

Chromosomal Variation ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Domestic Species ◽

History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

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Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

Genetics Selection Evolution ◽

10.1186/s12711-021-00627-0 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Fan Jiang ◽

Ruiyi Lin ◽

Changyi Xiao ◽

Tanghui Xie ◽

Yaoxin Jiang ◽

...

Keyword(s):

Gene Flow ◽

South Asia ◽

South Asian ◽

Demographic History ◽

Nervous System Development ◽

Chromosome 1 ◽

Whole Genome ◽

Chinese Populations ◽

Asian Populations ◽

History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

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An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis

PLoS ONE ◽

10.1371/journal.pone.0241038 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241038

Author(s):

Pita Sudrajad ◽

Subiharta Subiharta ◽

Yudi Adinata ◽

Af’idatul Lathifah ◽

Jun Heon Lee ◽

...

Keyword(s):

Demographic History ◽

Bos Indicus ◽

Molecular Evidence ◽

Effective Population ◽

Genome Data ◽

Bos Javanicus ◽

History Of ◽

Genome Data Analysis ◽

Almost All ◽

Insight Into

The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.

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Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

10.1101/077958 ◽

2016 ◽

Cited By ~ 3

Author(s):

Champak R. Beeravolu ◽

Michael J. Hickerson ◽

Laurent A.F. Frantz ◽

Konrad Lohse

Keyword(s):

Demographic History ◽

Composite Likelihood ◽

Model Organisms ◽

Secondary Contact ◽

Parameter Estimates ◽

Genome Sequences ◽

Frequency Spectra ◽

Genome Wide ◽

Complex Population ◽

History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

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GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data

GigaScience ◽

10.1093/gigascience/giaa005 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 1

Author(s):

Ekaterina Noskova ◽

Vladimir Ulyantsev ◽

Klaus-Peter Koepfli ◽

Stephen J O’Brien ◽

Pavel Dobrynin

Keyword(s):

Genetic Algorithm ◽

Allele Frequency ◽

Frequency Spectrum ◽

Demographic History ◽

Model Organisms ◽

Demographic Model ◽

Multiple Populations ◽

Demographic Models ◽

Allele Frequency Spectrum ◽

History Of

Abstract Background The demographic history of any population is imprinted in the genomes of the individuals that make up the population. One of the most popular and convenient representations of genetic information is the allele frequency spectrum (AFS), the distribution of allele frequencies in populations. The joint AFS is commonly used to reconstruct the demographic history of multiple populations, and several methods based on diffusion approximation (e.g., ∂a∂i) and ordinary differential equations (e.g., moments) have been developed and applied for demographic inference. These methods provide an opportunity to simulate AFS under a variety of researcher-specified demographic models and to estimate the best model and associated parameters using likelihood-based local optimizations. However, there are no known algorithms to perform global searches of demographic models with a given AFS. Results Here, we introduce a new method that implements a global search using a genetic algorithm for the automatic and unsupervised inference of demographic history from joint AFS data. Our method is implemented in the software GADMA (Genetic Algorithm for Demographic Model Analysis, https://github.com/ctlab/GADMA). Conclusions We demonstrate the performance of GADMA by applying it to sequence data from humans and non-model organisms and show that it is able to automatically infer a demographic model close to or even better than the one that was previously obtained manually. Moreover, GADMA is able to infer multiple demographic models at different local optima close to the global one, providing a larger set of possible scenarios to further explore demographic history.

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Inferring linguistic transmission between generations at the scale of individuals

10.1101/441246 ◽

2018 ◽

Cited By ~ 1

Author(s):

Valentin Thouzeau ◽

Antonin Affholder ◽

Philippe Mennecier ◽

Paul Verdu ◽

Frédéric Austerlitz

Keyword(s):

Linguistic Diversity ◽

Simulated Data ◽

Human Populations ◽

Linguistic Data ◽

Demographic Models ◽

History Of ◽

Best Fitting ◽

Approximate Bayesian ◽

Individual Scale ◽

The Individual

AbstractHistorical linguistics highly benefited from recent methodological advances inspired by phylogenetics. Nevertheless, no currently available method uses contemporaneous within-population linguistic diversity to reconstruct the history of human populations. Here, we develop an approach inspired from population genetics to perform historical linguistic inferences from linguistic data sampled at the individual scale, within a population. We built four demographic models of linguistic transmission at this scale, each model differing by the number of teachers involved during the language acquisition, and the relative roles of these teachers. We then compared the simulated data obtained with these models with real contemporaneous linguistic data sampled in Tajik speakers in Central Asia, an area known for its high within-population linguistic diversity, using approximate Bayesian computation methods. With these statistical methods, we were able to select the models that best explained the data, and inferred the best-fitting parameters under these selected models, demonstrating the feasibility of using contemporaneous within-population linguistic diversity to infer historical features of human cultural evolution.

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Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

10.1101/2020.04.12.037754 ◽

2020 ◽

Author(s):

Yann Bourgeois ◽

Robert Ruggiero ◽

Imtiyaz Hariyani ◽

Stéphane Boissinot

Keyword(s):

Transposable Elements ◽

Demographic History ◽

Ltr Retrotransposons ◽

Frequency Spectra ◽

Dna Transposons ◽

Genomic Landscape ◽

Demographic Processes ◽

History Of ◽

Recent Phase ◽

Positive Correlations

AbstractBackgroundThe interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons).ResultsWe observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation..ConclusionsWe demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle the effects of these processes.

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Contrasting paternal and maternal genetic histories of Thai and Lao populations

10.1101/509752 ◽

2019 ◽

Cited By ~ 1

Author(s):

Wibhu Kutanan ◽

Jatupol Kampuansai ◽

Metawee Srikummool ◽

Andrea Brunelli ◽

Silvia Ghirotto ◽

...

Keyword(s):

Iron Age ◽

Demographic History ◽

Neolithic Period ◽

Male And Female ◽

Demographic Models ◽

History Of ◽

Hill Tribes ◽

Male Specific ◽

The Hill ◽

Demic Diffusion

AbstractThe human demographic history of Mainland Southeast Asia (MSEA) has not been well-studied; in particular there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males, and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major MSEA families: Austroasiatic (AA), Tai-Kadai (TK) and Sino-Tibetan (ST). Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* (O-M95*) and O2a* (O-M324*)) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyse complete mtDNA genome sequences published previously from the same groups, and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of post-marital residence pattern on genetic diversity in patrilocal vs. matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 kya), with two later major male-specific expansions during the Neolithic period (∼4-5 kya) and the Bronze/Iron Age (∼2.0-2.5 kya). These two later expansions are characteristic of the modern AA and TK groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion and cultural diffusion) of major Thai groups and find different results from mtDNA simulations, supporting contrasting male and female genetic histories.

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Speciation despite gene flow in two owls (Aegolius ssp.): Evidence from 2,517 ultraconserved element loci

The Auk ◽

10.1093/auk/ukz012 ◽

2019 ◽

Vol 136 (2) ◽

Cited By ~ 3

Author(s):

Kevin Winker ◽

Travis C Glenn ◽

Jack Withrow ◽

Spencer G Sealy ◽

Brant C Faircloth

Keyword(s):

Gene Flow ◽

Migratory Birds ◽

Demographic History ◽

Nuclear Gene ◽

Biological Species ◽

Seasonal Migration ◽

Demographic Model ◽

Sedentary Population ◽

History Of ◽

Best Fitting

Abstract New study systems and tools are needed to understand how divergence and speciation occur between lineages with gene flow. Migratory birds often exhibit divergence despite seasonal migration, which brings populations into contact with one another. We studied divergence between 2 subspecies of Northern Saw-whet Owl (Aegolius acadicus), in which a sedentary population on the islands of Haida Gwaii, British Columbia (A. a. brooksi), exists in the presence of the other form (A. a. acadicus) during migration but not during the breeding season. Prior research showed fixed mtDNA divergence but left open the question of nuclear gene flow. We used 2,517 ultraconserved element loci to examine the demographic history of this young taxon pair. Although we did not observe fixed single nucleotide polymorphism differences between populations among our genotyped individuals, 100% of the birds were diagnosable and δaδI analyses suggested the demographic model best fitting the data was one of split-bidirectional-migration (i.e. speciation with gene flow). We dated the split between brooksi and acadicus to ~278 Kya, and our analyses suggested gene flow between groups was skewed, with ~0.7 individuals per generation coming from acadicus into brooksi and ~4.4 going the opposite direction. Coupled with an absence of evidence of phenotypic hybrids and the birds’ natural history, these data suggest brooksi may be a young biological species arising despite historic gene flow.

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