Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins

Abstract

Establishing links between phenotypic and genotypic variation is a central goal of evolutionary biology, as they might provide important insights into evolutionary processes shaping genetic and species diversity in nature. One of the more intriguing possibilities is when no genetic divergence is found to be associated with conspicuous phenotypic divergence. In that case, speciation theory predicts that phenotypic divergence may still occur in the presence of significant gene flow-thereby resulting in little genomic divergence-when genetic loci underpinning phenotypes are under strong divergent selection. However, a finding of phenotypic distinctiveness with weak or no population genetic structure may simply result from low statistical power to detect shallow genetic divergences when small data sets are used. Here, we used a subgenomic data set of 2,386 ultraconserved elements to explore genomewide divergence between two species of Antilophia manakins, which are phenotypically distinct yet evidently lack strong genetic differentiation according to previous studies based on a limited number of loci. Our results revealed clear population structure that matches the two phenotypes, supporting the idea that smaller data sets lacked the power to detect this recent divergence event (likely <100 k ya). Indeed, we found little or no introgression between the species, as well as evidence of genomewide divergence. One implication of our study is that the Araripe plateau may be a hot spot of cryptic-diverging forest Cerrado populations. Besides their use in biogeography, subgenomic data sets may help redefine local conservation programmes by revealing cryptic population structure that may be key to population management.

A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

“…To evaluate the efficacy of harvesting target-capture data from linked-read sequencing genomes, we also mapped the Tetrapods-UCE-5kv1 probeset, which targets 5060 ultraconserved elements (UCEs; https://www.ultraconserved.org/). UCEs are genome-wide markers that are informative at both deep and shallow evolutionary timescales, and which have become widely used for phylogenomic and population genomic studies [12,13,85]. To do this, we used the phyluce pipeline for harvesting UCEs from genomes [86].…”

“…For example, collaborative endeavours to sequence thousands of bird (Bird10K project [2]) and other vertebrate genomes (Genome10K project [3]) across many countries and research groups have been launched in the past decade, and have produced promising results [4][5][6][7]. Thus, high-throughput sequencing has rapidly improved our ability to make robust inferences in various fields, including avian systematics [7][8][9], population genomics and phylogeography [10][11][12][13][14][15][16], biogeography [17,18], molecular evolution [19], and speciation [20]. There has been an especially rapid increase in the number of studies specifically using whole-genome sequencing (often combined with reduced representation approaches) to answer difficult ornithological questions [7,[20][21][22][23].…”

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

“…Understanding the factors that shape the spatial distribution of species is a long-standing challenge in comparative biology that is attributable to the complex interaction of environmental and species trait variables. Over evolutionary time scales the geographic distribution of populations might be affected by physiographic processes (Silva et al, 2019; Peter et al, 2020), climatic oscillations (Hewitt, 2000; Raposo do Amaral et al, 2018; Musher et al, 2020), biotic interactions (Araújo & Luoto, 2007; Wisz et al, 2013), and trait evolution (Alves et al, 2019), driving dispersion, extinction, and cladogenesis. Although processes such as the appearance of novel traits, interspecific competition, and colonization of new environments might lead to a single burst of range size change, in many cases species distributions are dynamic over time, oscillating between periods of range contraction followed by expansion (Davis & Shaw, 2001; Taberlet & Cheddadi, 2002; Carnaval & Moritz, 2008).…”