Genomic signatures of rapid adaptive divergence in a tropical montane species

Abstract

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird ( Amblyornis papuensis ). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.

Demographic history, local adaptation and vulnerability to climate change in a tropical mountain bird in New Guinea

“…Possibly the ecological conditions in this part of Central Range are unfavourable for A. macgregoriae : the annual precipitation is considerably higher here than in any region inhabited by A. macgregoriae . Interestingly, Strickland Gorge is considered an important geographic barrier also for other montane bird species (Beehler & Pratt, 2016; Ericson et al, 2021).…”

“…We used BWA mem v0.7.12 (Li & Durbin, 2009) to map the cleaned reads against the 23 largest scaffolds (including 97% of the whole genome) of the Ailuroedus stonii genome (Ericson et al, 2021). The mapping resulted in a mean coverage of 18.7X (range 4‐31X) for the 26 individuals (Tables S1–S7).…”

“…We used BWA mem v0.7.12 to map the cleaned reads against the 23 largest scaffolds (including 97% of the whole genome) of the Ailuroedus stonii genome (Ericson et al, 2021).…”

Species-specific dynamics may cause deviations from general biogeographical predictions – evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae)

“…Recent work on the New Guinean avifauna has provided empirical evidence in favour of species originating in the lowlands from which they move into the highlands over time and become relictual specialists [ 16 , 22 , 23 ], although some colonisation from mountaintop to mountaintop has also been shown to occur [ 15 ]. In addition, recent Pleistocene speciation events on New Guinea are mainly the result of changes in habitat distributions due to climate fluctuations, as this has caused species with continuous distributions to become geographically fragmented [ 24 – 26 ]. Pliocene speciation events, on the other hand, are driven mainly by geological processes such as montane uplift, which is known to have caused barriers to gene flow [ 27 – 30 ].…”

A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins

“…In this paper, we provide an overview of our workflow and discuss the challenges associated with generating genome‐scale data sets from historical avian specimens. The paper draws on our extensive experience in obtaining genetic data from avian study skins for more than 15 years (e.g., Irestedt et al, 2006; Jonsson et al, 2007; Jonsson et al, 2012), and in particular our extensive recent work with the resequencing of entire genomes from avian study skins (see, e.g., Ericson et al, 2021; Ericson et al, 2017; Ericson et al, 2019; Ernst et al, 2022; Irestedt et al, 2019; Jonsson et al, 2019; Kennedy et al, 2022). It is not our aim to review the entire field of museomics, as there are numerous laboratory and analytical methods described in the literature both for DNA extraction (e.g., Tsai et al, 2020) and for genome library preparation from museum samples (Carøe et al, 2018; Kapp et al, 2021; Meyer & Kircher, 2010); each has its own benefits and potential drawbacks.…”