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

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

scholarly journals Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

2016 ◽  
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.

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

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.

scholarly journals Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago

2014 ◽  
Vol 31 (11) ◽  
pp. 2929-2940 ◽  
Author(s):  
Takehiro Sato ◽  
Shigeki Nakagome ◽  
Chiaki Watanabe ◽  
Kyoko Yamaguchi ◽  
Akira Kawaguchi ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
Snp Analysis ◽  
Japanese Archipelago ◽  
Genome Wide ◽  
History Of ◽  
The Japanese Archipelago

scholarly journals Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guilherme Debortoli ◽  
Cristina Abbatangelo ◽  
Francisco Ceballos ◽  
Cesar Fortes-Lima ◽  
Heather L. Norton ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Caste Groups

scholarly journals Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88568 ◽  
Author(s):  
Rachit K. Saxena ◽  
Eric von Wettberg ◽  
Hari D. Upadhyaya ◽  
Vanessa Sanchez ◽  
Serah Songok ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
Genome Wide ◽  
History Of

scholarly journals A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

2016 ◽  
Vol 48 (1) ◽  
Author(s):  
Arianna Manunza ◽  
Antonia Noce ◽  
Juan Manuel Serradilla ◽  
Félix Goyache ◽  
Amparo Martínez ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Wide Perspective ◽  
Spanish Goat

scholarly journals The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Humberto García-Ortiz ◽  
Francisco Barajas-Olmos ◽  
Cecilia Contreras-Cubas ◽  
Miguel Ángel Cid-Soto ◽  
Emilio J. Córdova ◽  
...  
Keyword(s):  
Demographic History ◽  
Indigenous Populations ◽  
South American ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Genomic Landscape ◽  
A Genome ◽  
Peopling Of The Americas ◽  
History Of ◽  
Genetic Makeup

AbstractThe genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15–30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4–9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.

scholarly journals Genomic Insight Into the Population Structure and Admixture History of Tai-Kadai-Speaking Sui People in Southwest China

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoyun Bin ◽  
Rui Wang ◽  
Youyi Huang ◽  
Rongyao Wei ◽  
Kongyang Zhu ◽  
...  
Keyword(s):  
Population Genetic ◽  
Southwest China ◽  
Yellow River ◽  
Southern China ◽  
Demographic History ◽  
Indigenous Populations ◽  
Guizhou Province ◽  
East Asians ◽  
Genome Wide ◽  
History Of

Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave, and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2–54.7%) and ancient coastal Southeast Asian-related ancestry (45.3–63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China.

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

2021 ◽  
Author(s):  
Emily Koot ◽  
Elise Arnst ◽  
Melissa Taane ◽  
Kelsey Goldsmith ◽  
Eleanor Dormontt ◽  
...  
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.

scholarly journals Population genomics of the maize pathogen Ustilago maydis: demographic history and role of virulence clusters in adaptation

2020 ◽  
Author(s):  
Gabriel Schweizer ◽  
Muhammad Bilal Haider ◽  
Gustavo V. Barroso ◽  
Nicole Rössel ◽  
Karin Münch ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cell Biology ◽  
Plant Pathogens ◽  
Demographic History ◽  
Ustilago Maydis ◽  
Adaptive Mutations ◽  
Effector Genes ◽  
Genome Wide ◽  
History Of ◽  
Maize Domestication

AbstractThe tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. In this species, many genes encoding secreted effector proteins reside in so-called virulence clusters in the genome, an arrangement that is so far not found in other filamentous plant pathogens. Using a combination of population genomic statistical analyses, we assessed the geographical, historical and genome-wide variation of genetic diversity in this fungal pathogen.We report evidence of two partially admixed subpopulations that are only loosely associated with geographic origin. Using the multiple sequentially Markov coalescent model, we inferred the demographic history of the two pathogen subpopulations over the last 0.5 million years. We show that both populations experienced a recent strong bottleneck starting around 10,000 years ago, coinciding with the assumed time of maize domestication. While the genome average genetic diversity is low compared to other fungal pathogens, we estimated that the rate of non-synonymous adaptive substitutions is three times higher in genes located within virulence clusters compared to non-clustered genes, including non-clustered effector genes. These results highlight the role that these singular genomic regions play in the evolution of this pathogen.Significance statementThe maize pathogen Ustilago maydis is a model species to study fungal cell biology and biotrophic host-pathogen interactions. Population genetic studies of this species, however, were so far restricted to using a few molecular markers, and genome-wide comparisons involved species that diverged more than 20 million years ago. Here, we sequenced the genomes of 22 Mexican U. maydis isolates to study the recent evolutionary history of this species. We identified two co-existing populations that went through a recent bottleneck and whose divergence date overlaps with the time of maize domestication. Contrasting the patterns of genetic diversity in different categories of genes, we further showed that effector genes in virulence clusters display a high rate of adaptive mutations, highlighting the importance of these effector arrangements for the adaptation of U. maydis to its host.

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