Comparative phylogeographic inference with genome-wide data from aggregated population pairs

Author(s)

Xue, Alexander T. ^{[1, 2, 3, 4, 5]} ; Hickerson, Michael J. ^{[6, 3, 4]}

Affiliation

^[1] Rutgers State Univ, Human Genet Inst New Jersey, Piscataway, NJ 08854 - USA

^[2] Rutgers State Univ, Dept Genet, Piscataway, NJ 08854 - USA

^[3] CUNY, Grad Ctr, Subprogram Ecol Evolutionary Biol & Behav, Dept Biol, New York, NY 10016 - USA

^[4] CUNY City Coll, Subprogram Ecol Evolutionary Biol & Behav, Dept Biol, New York, NY 10031 - USA

^[5] Cold Spring Harbor Lab, Simons Ctr Quantitat Biol, Cold Spring Harbor, NY 11724 - USA

^[6] Amer Museum Nat Hist, Div Invertebrate Zool, New York, NY 10024 - USA

• Document type: Journal article
• Source: Evolution; v. 74, n. 5, p. 808-830, MAY 2020.
• Web of Science Citations: 0

Abstract

Comparing divergences across multiple sister population pairs has been a focus in phylogeography since its inception. Initial approaches used organelle genetic data and involved qualitative comparisons of phylogenetic patterns to evaluate hypotheses of shared and variable evolutionary responses. This endeavor has progressed with coalescent model-based statistical techniques and advances in next-generation sequencing, yet there remains a need for methods that can exploit aggregated genomic-scale data within a unified analytical framework. To this end, we introduce the aggregate joint site frequency spectrum (ajSFS) by validating its use within a hierarchical Bayesian framework through several in silico experiments. Subsequently, we applied our method against two published restriction site-associated DNA marker datasets consisting of eight local replicates of a lamprey species pair and six co-distributed passerine taxon pairs, respectively, with the aim of inferring variability in co-divergence and co-migration histories. We found that the lamprey population pairs exhibited temporal synchrony in both co-divergence and collective secondary contact times, yet an idiosyncratic pattern in secondary migration intensities. In contrast, the bird population pairs displayed thoroughly asynchronous co-divergence histories. Our results demonstrate that the ajSFS can be exploited for complex and flexible co-demographic inference, opening up new possibilities for comparative phylogeography and population genomic studies. (AU)

• FAPESP's process: 13/50297-0 - Dimensions US-BIOTA São Paulo: a multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic forest hotspot
• Grantee: Cristina Yumi Miyaki
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants