Estimating genome-wide heterozygosity: effects of demographic history and marker type

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

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The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

10.1101/561399 ◽

2019 ◽

Cited By ~ 3

Author(s):

Lewis G. Spurgin ◽

Mirte Bosse ◽

Frank Adriaensen ◽

Tamer Albayrak ◽

Christos Barboutis ◽

...

Keyword(s):

Positive Selection ◽

Recombination Rate ◽

Demographic History ◽

Great Tit ◽

Genomic Variation ◽

Genomic Diversity ◽

Hapmap Project ◽

Widespread Species ◽

Continental Scale ◽

Genome Wide

AbstractA major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear “islands of differentiation” even among populations with very low levels of genome-wide differentiation. Low local recombination rate in the genome was a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.

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Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes

Communications Biology ◽

10.1038/s42003-020-1098-7 ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 2

Author(s):

Sara Lado ◽

Jean Pierre Elbers ◽

Angela Doskocil ◽

Davide Scaglione ◽

Emiliano Trucchi ◽

...

Keyword(s):

Demographic History ◽

Genomic Diversity ◽

Phylogeographic Structure ◽

Arid Environments ◽

Migration Patterns ◽

Migration Rates ◽

Global Migration ◽

Genome Wide ◽

A Genome ◽

Scale Population

AbstractDromedaries have been essential for the prosperity of civilizations in arid environments and the dispersal of humans, goods and cultures along ancient, cross-continental trading routes. With increasing desertification their importance as livestock species is rising rapidly, but little is known about their genome-wide diversity and demographic history. As previous studies using few nuclear markers found weak phylogeographic structure, here we detected fine-scale population differentiation in dromedaries across Asia and Africa by adopting a genome-wide approach. Global patterns of effective migration rates revealed pathways of dispersal after domestication, following historic caravan routes like the Silk and Incense Roads. Our results show that a Pleistocene bottleneck and Medieval expansions during the rise of the Ottoman empire have shaped genome-wide diversity in modern dromedaries. By understanding subtle population structure we recognize the value of small, locally adapted populations and appeal for securing genomic diversity for a sustainable utilization of this key desert species.

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Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is associated with behavioral differentiation

10.1101/347492 ◽

2018 ◽

Author(s):

Kaiya L. Provost ◽

William M. Mauck ◽

Brian Tilston Smith

Keyword(s):

Gene Flow ◽

Sonoran Desert ◽

Demographic History ◽

Isolation With Migration ◽

Song Recognition ◽

Behavioral Isolation ◽

The North ◽

Genome Wide ◽

Behavioral Differentiation ◽

Northern Cardinals

ABSTRACTBiogeographic barriers are thought to be important in initiating speciation through geographic isolation, but they rarely indiscriminately and completely reduce gene flow across the entire community. Understanding which species’ attributes regulate a barrier could help elucidate how speciation is initiated. Here, we investigated the association of behavioral isolation on population differentiation in Northern Cardinals (Cardinalis cardinalis) distributed across the Cochise Filter Barrier, a region of transitional habitat which separates the Sonoran and Chihuahuan deserts. Using genome-wide markers, we modeled demographic history by fitting the data to isolation and isolation-with-migration models. The best-fit model indicated that desert populations diverged in the mid-Pleistocene and there has been historically low, unidirectional gene flow into the Sonoran Desert. We then tested song recognition using reciprocal call-broadcast experiments to compare song recognition between deserts, controlling for song dialect changes within deserts. We found that male Northern Cardinals in both deserts were most aggressive to local songs and failed to recognize across-barrier songs. A correlation of genomic differentiation despite historic introgression and strong song discrimination is consistent with a model where speciation is initiated across a barrier and maintained by behavioral isolation.

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The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula

BMC Genomics ◽

10.1186/s12864-021-08203-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

André Flores-Bello ◽

Neus Font-Porterias ◽

Julen Aizpurua-Iraola ◽

Sara Duarri-Redondo ◽

David Comas

Keyword(s):

Iberian Peninsula ◽

Demographic History ◽

Ethnically Diverse ◽

Human Populations ◽

Minority Ethnic Group ◽

Fine Scale ◽

Genome Wide ◽

Wide Range ◽

Y Chromosome Str ◽

Western Eurasia

Abstract Background The general picture of human genetic variation has been vastly depicted in the last years, yet many populations remain broadly understudied. In this work, we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. Mercheros have been roughly characterised by an itinerant history, common traditional occupations, and the usage of their own language. Results Here, we examine the demographic history and genetic scenario of Mercheros, by using genome-wide array data, whole mitochondrial sequences, and Y chromosome STR markers from 25 individuals. These samples have been complemented with a wide-range of present-day populations from Western Eurasia and North Africa. Our results show that the genetic diversity of Mercheros is explained within the context of the Iberian Peninsula, evidencing a modest signal of Roma admixture. In addition, Mercheros present low genetic isolation and intrapopulation heterogeneity. Conclusions This study represents the first genetic characterisation of the Merchero population, depicting their fine-scale ancestry components and genetic scenario within the Iberian Peninsula. Since ethnicity is not only influenced by genetic ancestry but also cultural factors, other studies from multiple disciplines are needed to further explore the Merchero population. As with Mercheros, there is a considerable gap of underrepresented populations and ethnic groups in publicly available genetic data. Thus, we encourage the consideration of more ethnically diverse population panels in human genetic studies, as an attempt to improve the representation of human populations and better reconstruct their fine-scale history.

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Genome - wide variation and demographic history of small cats with a focus on Felis species

Canadian Journal of Biotechnology ◽

10.24870/cjb.2017-a3 ◽

2017 ◽

Vol 1 (Special Issue) ◽

pp. 15-15

Author(s):

Anubhab Khan ◽

Rithvik Vinekar ◽

Prachi Thatte ◽

Uma Ramakrishnan

Keyword(s):

Demographic History ◽

Genome Wide ◽

History Of

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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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Coupling Wright-Fisher and coalescent dynamics for realistic simulation of population-scale datasets

10.1101/674440 ◽

2019 ◽

Author(s):

Dominic Nelson ◽

Jerome Kelleher ◽

Aaron P. Ragsdale ◽

Gil McVean ◽

Simon Gravel

Keyword(s):

State Of The Art ◽

Demographic History ◽

Recent Past ◽

Computationally Efficient ◽

Effective Population ◽

Genome Data ◽

Coalescent Simulations ◽

Genome Wide ◽

Fisher Model ◽

Ancestry Proportions

1AbstractCoalescent simulations are widely used to examine the effects of evolution and demographic history on the genetic makeup of populations. Thanks to recent progress in algorithms and data structures, simulators such as the widely-used msprime [1] now provide genome-wide simulations for millions of individuals. However, this software relies on classic coalescent theory and the corresponding assumptions that sample sizes are small relative to effective population size and that the region being simulated is short. Here we show that coalescent simulations of long regions of the genome exhibit large biases in identity-by-descent (IBD), long-range linkage disequilibrium (LD), and ancestry patterns, particularly when sample size is large. We present a Wright-Fisher extension to msprime, and show that it produces more realistic distributions of IBD, LD, and ancestry proportions, while also addressing more subtle biases of the coalescent. Further, these extensions are more computationally efficient than state-of-the-art coalescent simulations when simulating long regions, including whole-genome data. For shorter regions, efficiency and accuracy can be maintained via a flexible hybrid model which simulates the recent past under the Wright-Fisher model and uses coalescent simulations in the distant past.

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The genomic impact of European colonization of the Americas

10.1101/676437 ◽

2019 ◽

Cited By ~ 1

Author(s):

Linda Ongaro ◽

Marilia O. Scliar ◽

Rodrigo Flores ◽

Alessandro Raveane ◽

Davide Marnetto ◽

...

Keyword(s):

Gene Flow ◽

Demographic History ◽

Colonial Era ◽

Genome Wide ◽

A Genome ◽

European Colonization ◽

High Degree ◽

The Impact ◽

North And South America ◽

North And South

AbstractThe human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas.We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

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Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) grown on indigenous Māori land

10.22541/au.161912114.47713005/v1 ◽

2021 ◽

Author(s):

Emily Koot ◽

Elise Arnst ◽

Melissa Taane ◽

Kelsey Goldsmith ◽

Peri Tobias ◽

...

Keyword(s):

New Zealand ◽

Demographic History ◽

Gene Pools ◽

Phylogenetic Studies ◽

Aotearoa New Zealand ◽

Genome Wide ◽

History Of ◽

Demographic Modelling ◽

Management And Conservation ◽

Leptospermum Scoparium

Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9 –12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.

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