Consequences of divergence and introgression for speciation in Andean cloud forest birds

Abstract

Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet, it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence and introgression on plumage differentiation between ecologically similar allopatric replacements of Andean cloud forest birds. Through analyses of short-read genome-wide sequences from over 160 individuals in 16 codistributed lineages, I found that plumage divergence is associated with deep genetic divergence, implicating a prominent role of geographic isolation in speciation. By contrast, lineages that lack plumage divergence across the same geographic barrier are more recently isolated or exhibit a signature of secondary genetic introgression, indicating a negative relationship between gene flow and divergence in phenotypic traits important to speciation. My results suggest that the evolutionary outcomes of cycles of isolation and divergence in this important theatre of biotic diversification are sensitive to time spent in the absence of gene flow.

Assessing biological factors affecting postspeciation introgression

“…For example, some previous analyses have assessed factors influencing general introgression patterns with different approaches. For example, Winger () evaluated the relationship between introgression and plumage differentiation for 16 lineages of Andean cloud forest birds within a geographically and ecologically structured study. He found evidence for introgression across a geographic barrier between lineage pairs with uniform plumage patterns, but not between pairs with divergent plumage.…”

Why is Amazonia a ‘source’ of biodiversity? Climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae)

“…the acquisition of novel distributions) in the Neotropics, specifically with regard to Amazonian lineage emigration? In general, Neotropical diversification is widely attributed to allopatric isolation across biogeographic barriers [5 -9], even though these barriers are often species-specific [1] and spatio-temporally semi-permeable [6,10,11]. Dispersal across biogeographic barriers is often considered to be a stochastic process [12].…”

Minor allele frequency thresholds strongly affect population structure inference with genomic data sets

“…In particular, minor allele frequency (MAF) thresholds directly influence the SFS by imposing a cutoff on the minimum allele frequency allowed to incorporate a specific genetic variant. However, despite its potential importance, the two most popular comprehensive bioinformatic pipelines for RADseq data alternatively include (Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013) or exclude (Eaton, 2014) the option to set MAF thresholds during variant calling, with the result that among empirical studies MAF thresholds are only sometimes reported (e.g., Winger, 2017, Blanco-Bercial & Bucklin, 2016.…”