Genomewide ancestry and divergence patterns from low‐coverage sequencing data reveal a complex history of admixture in wild baboons

Wall, Jeffrey D.; Schlebusch, Stephen A; Alberts, Susan C.; Cox, Laura A.; Snyder‐Mackler, Noah; Nevonen, Kimberly A.; Carbone, Lucia; Tung, Jenny

doi:10.1111/mec.13684

Cited by 73 publications

(110 citation statements)

References 72 publications

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“…Blischak, Wenzel, and Wolfe () used ultra‐low‐coverage genome data (~0.005×–0.007×) for annotation and gene prediction of more than 10,000 contigs for primer design of phylogenetic markers in the plant genus Penstemon . Wall et al, () analysed lcWGR data of yellow baboons ( Papio cynocephalus ), Anubis baboons ( P. anubis ) and their hybrids in the Amboseli ecosystem of Kenya. They found genetic differentiation between parent taxa and enough evidence to infer a complex admixture history involving intermittent but multiple hybridization events that did not indicate fitness reduction in hybrids.…”

Section: Applications Of Wgr In Conservation and Managementmentioning

confidence: 99%

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

2017

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Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.

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Section: Applications Of Wgr In Conservation and Managementmentioning

confidence: 99%

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

2017

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“…The necessary depth of coverage will depend on the research question and desired analytical framework of a particular study. For example, although single nucleotide variant calling is usually only recommended for samples with depths of coverage greater than 15-20× (Meynert, Ansari, FitzPatrick, & Taylor, 2014;Sims, Sudbery, Ilott, Heger, & Ponting, 2014), an increasing number of population genetic software can accommodate low to medium coverage (4-15×) data by using, for example, genotype likelihoods or haploid calling methods (Korneliussen & Moltke, 2015;Therkildsen & Palumbi, 2017;Vieira, Albrechtsen, & Nielsen, 2016;Wall et al, 2016).…”

Section: Roadmap For Hybridization Capture Of Noninvasive Samplesmentioning

confidence: 99%

A roadmap for high‐throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

White

Fontsere

Lizano

et al. 2019

Molecular Ecology Resources

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Large‐scale genomic studies of wild animal populations are often limited by access to high‐quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high‐throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality‐assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%–3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.

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“…Recent target enrichment methodologies have provided methodological advances in acquiring more information from NI samples (Perry et al., ; Snyder‐Mackler et al., ; Wall et al., ). These enrichment methods are performed with the use of biotinylated RNA baits that hybridize with the DNA from species of interest, which are subsequently isolated and sequenced.…”

Section: Introductionmentioning

confidence: 99%

“…Recent target enrichment methodologies have provided methodological advances in acquiring more information from NI samples (Perry et al, 2010;Snyder-Mackler et al, 2016;Wall et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

The impact of endogenous content, replicates and pooling on genome capture from faecal samples

Hernández-Rodríguez

Arandjelovic

Lester

et al. 2017

Molecular Ecology Resources

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Target‐capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off‐target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.

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Genomewide ancestry and divergence patterns from low‐coverage sequencing data reveal a complex history of admixture in wild baboons

Cited by 73 publications

References 72 publications

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

A roadmap for high‐throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

The impact of endogenous content, replicates and pooling on genome capture from faecal samples

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