Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types

Hui Zhen Tan,Justin J F J Jansen,Pavel S Tomkovich,Elize Ying Xin Ng,Qian Tang,Gary A Allport,Frank E Rheindt

doi:10.1038/s41598-019-54715-9

Abstract

Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.

Highlights

Extreme climatic events in the Earth’s recent past have played an important role in shaping population genetic structure of animals[1,2]
Palaearctic populations have been characterized by divisions into multiple clusters corresponding to glacial refugia during the Last Glacial Maximum (LGM)[40,41]
An exception is the steppe whimbrel, N. p. alboaxillaris, which breeds in wet grasslands in steppe valleys sympatrically with Eurasian curlew

Summary

Introduction

Extreme climatic events in the Earth’s recent past have played an important role in shaping population genetic structure of animals[1,2]. Some wide-ranging species lack or show only shallow population structure despite the vast geographical area involved[9,25,28,31,42,43,44] Explanations for these phylogeographic patterns often invoke geographical features and environmental conditions both presently and historically[44], which interact with life-history traits such as dispersal capability[9], natal homing[45], prey availability[42], non-breeding habitat preference[46], mating system[47,48,49] as well as the evolutionary history unique to each species[28]. Alboaxillaris, which breeds in wet grasslands in steppe valleys sympatrically with Eurasian curlew Both species are polytypic, ranging from the western to eastern Palaearctic and exhibiting intraspecific plumage variation. By comparing the phylogeography between two congeneric shorebird species with a similar biology but important differences in breeding habitat, we aim to shed light on habitat-specific effects of Quaternary climate oscillations on biotic differentiation across the Palaearctic

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Conclusion