期刊
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 44
卷 44, 期 -, 页码 99-+出版社
ANNUAL REVIEWS
DOI: 10.1146/annurev-ecolsys-110512-135822
关键词
high-throughput sequencing; next-generation sequencing; phylogenomics; genomic partitioning; target enrichment; hybrid enrichment; anchored phylogenomics; ultraconserved element enrichment; targeted amplicon sequencing; transcriptome sequencing; RAD sequencing; locus selection; model selection; phylogeny estimation
High-throughput genomic sequencing is rapidly changing the field of phylogenetics by decreasing the cost and increasing the quantity and rate of data collection by several orders of magnitude. This deluge of data is exerting tremendous pressure on downstream data-analysis methods providing new opportunities for method development. In this review, we present (a) recent advances in laboratory methods for collection of high-throughput phylogenetic data and(b) challenges and constraints for phylogenetic analysis of these data. We compare the merits of multiple laboratory approaches, compare methods of data analysis, and offer recommendations for the most promising protocols and data-analysis workflows currently available for phylogenetics. We also discuss several strategies for increasing accuracy, with an emphasis on locus selection and proper model choice.
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