An In Silico Comparison of Protocols for Dated Phylogenomics

Author(s)

Collins, Rupert A. ^{[1, 2]} ; Hrbek, Tomas ^{[1, 3]}

Affiliation

^[1] Univ Fed Amazonas, Dept Genet, Lab Evolucao & Genet Anim, Ave Rodrigo Otavio Ramos 3000, BR-69077000 Manaus, AM - Brazil

^[2] Univ Bristol, Sch Biol Sci, Life Sci Bldg, 24 Tyndall Ave, Bristol BS8 1TH, Avon - England

^[3] Brigham Young Univ, Dept Biol, 4102 LSB, Provo, UT 84602 - USA

• Document type: Journal article
• Source: Systematic Biology; v. 67, n. 4, p. 633-650, JUL 2018.
• Web of Science Citations: 2

Abstract

In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to perform in silico extractions from genomes and create directly comparable data sets for each class of marker. We then compare these data sets in terms of both phylogenetic resolution and ability to consistently and precisely estimate clade ages using fossil-calibrated molecular-clockmodels. Furthermore, we were also able to directly compare these results to previously published data sets from Sanger-sequenced nuclear exons and mitochondrial genomes under the same analytical conditions. Our results show-although with the exception of the mitochondrial genome data set and the smallest ddRADseq data set-that for uncontroversial nodes all data classes performed equally well, that is they recovered the same well supported topology. However, for one difficult-to-resolve node comprising a rapid diversification, we report well supported but conflicting topologies among themarker classes consistent with the mismodeling of gene tree heterogeneity as demonstrated by species tree analyses of single nucleotide polymorphisms. Likewise, clade age estimates showed consistent discrepancies between data sets under strict and relaxed clock models; for recent nodes, clade ages estimated by nuclear exon data sets were younger than those of the UCE, RADseq and mitochondrial data, but vice versa for the deepest nodes in the primate phylogeny. This observation is explained by temporal differences in phylogenetic informativeness (PI), with the data sets with strong PI peaks toward the present underestimating the deepest node ages. Finally, we conclude by emphasizing that while huge numbers of loci are probably not required for uncontroversial phylogenetic questions-for which practical considerations such as ease of data generation, sharing, and aggregating, therefore become increasingly important-accurately modeling heterogeneous data remains as relevant as ever for the more recalcitrant problems. (AU)

• FAPESP's process: 12/50260-6 - Structure and evolution of the Amazonian biota and its environment: an integrative approach
• Grantee: Lúcia Garcez Lohmann
• Support type: BIOTA-FAPESP Program - Thematic Grants