Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills

Abstract

While many conifers produce annually variable seed crops, serotinous species (which hold seeds in cones for multiple years) represent unusually stable food resources for seed predators. Such stability is conducive to residency and potentially population divergence of consumers as exemplified by the Cassia crossbill (Loxia sinesciuris) in North America. We used genotyping by sequencing (GBS) to test whether three Mediterranean subspecies of common crossbills (L. curvirostra) associated with the serotinous Aleppo pine (Pinus halepensis) were more genetically distinct than European crossbills associated with nonserotinous conifers. We assembled a Cassia crossbill draft genome as a reference for mapping GBS reads and as a first step towards a more contiguous genome assembly. We found clear patterns of genetic divergence for each of the P. halepensis-associated subspecies. Geographic isolation, as promoted by resource stability and residency, is associated with genetic divergence of two of these subspecies. However, geographic isolation cannot account for divergence of L. c. hispana. Instead, resource stability likely contributed to divergence by reducing dispersal and increasing resource competition that may limit breeding by immigrants. In contrast, we found no differentiation among common crossbills associated with less stable resources, and only slight differentiation between common crossbills and parrot crossbills (L. pytyopsittacus). The substantial morphological divergence between common and parrot crossbills has likely originated or been maintained by selection despite gene flow generated by spatiotemporal resource fluctuation. Our results indicate that phenological as well as morphological characteristics of conifers have influenced crossbill diversification, and suggest a possible link between resource stability and population divergence.

On the relative importance of ecology and geographic isolation as drivers for differentiation of call types of red crossbill Loxia curvirostra in the Palearctic

“…These results suggest that the same drivers of differentiation are acting in the western Palearctic north of 44°N as in the south, yet under different circumstances. This result is confirmed by Parchman et al (), who found that red crossbills living in geographically isolated areas with a stable food resource (here Pinus halepensis ) were genetically distinct from other red crossbills.…”

Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations

“…[135,136], Fringilla coelebs [137,138], and Loxia spp. [139]. Similarly deep splits between Iberian and Maghrebian populations of the same species were PLOS ONE found in other terrestrial vertebrates, such as in amphibians, reptiles [25,140], and in mammals [141][142][143][144].…”

Morphological divergence among Spanish Common Crossbill populations and adaptations to different pine species

“…Genomic research is underway to determine to what extent this ecological specialization and morphological divergence is linked to genetics. Preliminary results already have shown that genetic differences between presumably conspecific Crossbill populations within Spain are far greater than between heterospecific Common and Parrot Crossbills (Parchman et al 2018). In view of the potential for movement and habitat selection by Crossbills, it is important to improve our understanding of dispersal of these birds (e.g.…”

“…While Mezquida and Benkman (2005) noted that these cones appeared to have evolved levels of defence that have excluded Crossbills foraging on this pine, Crossbills are indeed not common, but are nonetheless rather widespread in Aleppo Pine forests. Genetic data indicate they are apparently resident, at least in southern Iberia, and presumably only forage on Aleppo Pine cones just as on the Balearics and in northern Africa (Parchman et al 2018). We have confirmed here that they have a distinct biometry, suggesting they are well adapted to this mainland Aleppo Pine variety.…”

“…Although current classifications reflect resource use, they are based on geographical criteria, and it is assumed that subspecies do not geographically overlap. In strong contrast to this approach, more recent research has revealed morphometric and genetic segregation according to conifer species among (partially) sympatric crossbill populations (Groth 1993, Benkman 2003, Parchman et al 2016) that may also be applicable to Iberian Crossbills (Alonso et al 2006, Borrás et al 2008, Edelaar et al 2012, Parchman et al 2018).…”