Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

Abstract Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.]

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Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data

Antonie van Leeuwenhoek ◽

10.1007/s10482-015-0556-6 ◽

2015 ◽

Vol 108 (5) ◽

pp. 1037-1046 ◽

Cited By ~ 24

Author(s):

Yucheng Zhang ◽

Sai Qiu

Keyword(s):

Genome Sequence ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data

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An Approximate Bayesian Computation Approach to Examining the Phylogenetic Relationships among the Four Gibbon Genera using Whole Genome Sequence Data

10.1101/009498 ◽

2014 ◽

Author(s):

Krishna Veeramah ◽

August E Woerner ◽

Laurel Johnstone ◽

Ivo Gut ◽

Marta Gut ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phylogenetic Relationships ◽

Approximate Bayesian Computation ◽

Whole Genome Sequence ◽

Sequencing Error ◽

Computation Method ◽

Bayesian Computation ◽

Whole Genome ◽

Approximate Bayesian

Gibbons are believed to have diverged from the larger great apes ~16.8 Mya and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the familyHylobatidaeis divided into four genera,Nomascus,Symphalangus,HoolockandHylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mtDNA, the Y chromosome, and short autosomal sequences have been inconclusive. To examine the relationships among gibbon genera in more depth, we performed 2nd generation whole genome sequencing to a mean of ~15X coverage in two individuals from each genus. We developed a coalescent-based Approximate Bayesian Computation method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. AlthoughHoolockandSymphalangusare likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Our combined results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1x10-9/site/year this speciation process occurred ~5 Mya during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.

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Faculty Opinions recommendation of Optimal algorithms for haplotype assembly from whole-genome sequence data.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13339986.14707085 ◽

2011 ◽

Author(s):

Alejandro Schaffer

Keyword(s):

Genome Sequence ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Optimal Algorithms ◽

Genome Sequence Data ◽

Haplotype Assembly

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TIGER: inferring DNA replication timing from whole-genome sequence data

Bioinformatics ◽

10.1093/bioinformatics/btab166 ◽

2021 ◽

Cited By ~ 1

Author(s):

Amnon Koren ◽

Dashiell J Massey ◽

Alexa N Bracci

Keyword(s):

Dna Replication ◽

Genome Sequence ◽

Genomic Dna ◽

Sequence Data ◽

Replication Timing ◽

Whole Genome Sequence ◽

Supplementary Information ◽

Whole Genome ◽

Genome Sequence Data ◽

Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

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Whole genome sequence data of Bacillus australimaris strain B28A, isolated from Marine Water in India

Data in Brief ◽

10.1016/j.dib.2021.107240 ◽

2021 ◽

pp. 107240

Author(s):

Wael Ali Mohammed Hadi ◽

Boby T Edwin ◽

A Jayakumaran Nair

Keyword(s):

Genome Sequence ◽

Sequence Data ◽

Marine Water ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data

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Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan

Data in Brief ◽

10.1016/j.dib.2020.106416 ◽

2020 ◽

Vol 33 ◽

pp. 106416

Author(s):

Asset Daniyarov ◽

Askhat Molkenov ◽

Saule Rakhimova ◽

Ainur Akhmetova ◽

Zhannur Nurkina ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Genome Sequence ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data

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Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

Scientific Reports ◽

10.1038/srep39719 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 10

Author(s):

Lynsey K. Whitacre ◽

Jesse L. Hoff ◽

Robert D. Schnabel ◽

Sara Albarella ◽

Francesca Ciotola ◽

...

Keyword(s):

Genome Sequence ◽

Birth Defect ◽

Genetic Basis ◽

Sequence Data ◽

Model Organism ◽

Bubalus Bubalis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data

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46 Footprints of Selection in Angus and Hanwoo Beef Cattle Using Imputed Whole Genome Sequence Data

Journal of Animal Science ◽

10.1093/jas/skab235.042 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 25-25

Author(s):

Muhammad Yasir Nawaz ◽

Rodrigo Pelicioni Savegnago ◽

Cedric Gondro

Keyword(s):

Beef Cattle ◽

Genome Sequence ◽

Sequence Data ◽

Whole Genome Sequence ◽

Fixation Index ◽

Whole Genome ◽

Extended Haplotype Homozygosity ◽

Extended Haplotype ◽

Genome Sequence Data ◽

Genomic Regions

Abstract In this study, we detected genome wide footprints of selection in Hanwoo and Angus beef cattle using different allele frequency and haplotype-based methods based on imputed whole genome sequence data. Our dataset included 13,202 Angus and 10,437 Hanwoo animals with 10,057,633 and 13,241,550 imputed SNPs, respectively. A subset of data with 6,873,624 common SNPs between the two populations was used to estimate signatures of selection parameters, both within (runs of homozygosity and extended haplotype homozygosity) and between (allele fixation index, extended haplotype homozygosity) the breeds in order to infer evidence of selection. We observed that correlations between various measures of selection ranged between 0.01 to 0.42. Assuming these parameters were complementary to each other, we combined them into a composite selection signal to identify regions under selection in both beef breeds. The composite signal was based on the average of fractional ranks of individual selection measures for every SNP. We identified some selection signatures that were common between the breeds while others were independent. We also observed that more genomic regions were selected in Angus as compared to Hanwoo. Candidate genes within significant genomic regions may help explain mechanisms of adaptation, domestication history and loci for important traits in Angus and Hanwoo cattle. In the future, we will use the top SNPs under selection for genomic prediction of carcass traits in both breeds.

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