Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex

Abstract

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or “sibling”) lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group’s range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E.difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

Cryptic and extensive hybridization between ancient lineages of American crows

“…For each individual crow, we calculated a maximum likelihood estimate of the genomic hybrid index and the average intertaxon heterozygosity across ancestry-informative loci using r package Introgress (Gompert & Buerkle, 2010 and hzar.makeCline1DNormal (Leaché et al, 2017;Linck et al, 2019;Scordato et al, 2017). For both mtDNA and overall nuDNA, we fit models without exponential tails, restricted parameter search space to a liberal yet reasonable range of values (cline centre > 500 km and < 3,500 km, cline width < 3,500 km; Derryberry et al, 2014) and fixed means, variances, and allele frequencies at cline ends to the observed values of the terminal populations (Linck et al, 2019;Lipshutz et al, 2019). We ran the Markov chain Monte Carlo (MCMC) optimizer for three iterative cycles using hzar.chain.doSeq, retaining the third run for subsequent analysis (Derryberry et al, 2014).…”

Within-island diversification in a passerine bird

“…However, decisions based solely on phylogenetic support need to be interpreted with caution, as phylogenetic topologies are sometimes unable to discriminate among alternative biogeographic hypotheses and are sensitive to incomplete sampling [18][19][20][21][22]. For example, monophyly can be recovered even in the case of multiple colonizations if sister lineages from the source areas went extinct or were not sampled due to insufficient geographical sampling.…”

Molecular phylogenetics of Doraditos (Aves, Pseudocolopteryx): Evolution of cryptic species, vocal and mechanical sounds

“…This suggests that auditory modalities of communication may frequently be more important than visual ones in species recognition systems in the family. This is further supported by the lack of (Seutin & Simon, 1988; Winker, 1994), or extremely reduced (Manthey & Robbins, 2016) hybridization between vocally differentiated sibling species‐pairs in sympatry, and the extensive hybridization among lineages with morphological and vocal similarities (Linck et al, 2019; Rush et al., 2009). The structural differences in vocalizations between P. flaviventris and P. citreola exceed those of recently diverged sibling species‐pairs including Empidonax alnorum and E. trailli, and Contopus virens and C. sordidulus .…”