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The passerine superfamily Certhioidea lacks a complete phylogeny despite decades of recognition as a clade and extensive systematic work within all its constituent families. Here, we inferred a near-complete species-level phylogeny of Certhioidea from a molecular supermatrix, including the first comprehensive sampling of the wrens (Troglodytidae), and used this phylogeny to infer its biogeographic and diversification histories. We also inferred an expanded phylogeny including nearly 100 putative phylospecies previously documented in the literature, and we found that including this diversity had notable impacts on the inferred evolutionary history of Certhioidea. This phylospecies-level tree documented a few instances of species paraphyly, some previously described in the literature and some novel. We found that Certhioidea originated largely in Eurasia and dispersed into North America five times in the last 20 million years, including at the origin of the “New World certhioids,” wrens and gnatcatchers, a clade herein named Orthourae. After this initial dispersal event, both wrens and gnatcatchers diversified extensively across the hemisphere, with both lineages repeatedly crossing between continents. However, we detected no notable impact of the formation of the Isthmus of Panama on the frequency of dispersal events between North and South America. The inclusion of phylospecies altered this biogeographic inference in some portions of the tree but overall was largely consistent. With species-level sampling, we found that diversification rates within Certhioidea were largely constant through time with a detectable deceleration toward the present. By contrast, phylospecies-level sampling recovered a different diversification history with a significant rate increase at the crown node of Orthourae after dispersing into the Americas and increased speciation rates particularly within the genera Polioptila and Henicorhina. This largely resolved phylogeny for Certhioidea has yielded important insights into the evolutionary history of this group and provides a framework for future comparative work on this fascinating clade.

 

The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We resequenced whole genomes to investigate how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpecker, species codistributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (i) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (ii) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion, and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape. 

We explored the evolutionary radiation in the House Wren complex (Troglodytes aedon and allies), the New World’s most widely distributed passerine species. The complex has been the source of ongoing taxonomic debate. To evaluate phenotypic variation in the House Wren complex, we collected 81,182 single-nucleotide polymorphisms (SNPs) from restriction site associated loci (RADseq) and mitochondrial DNA (mtDNA) from samples representing the taxonomic and geographic diversity of the complex. Both datasets reveal deep phylogeographic structuring, with several topological discrepancies. The trees highlight the evolutionary distinctiveness of eastern and western T. aedon, which were sister taxa in the SNP tree and paraphyletic on the mtDNA tree. The RADseq data reveal a distinct T. a. brunneicollis group, although STRUCTURE plots suggest admixture between western T. aedon and northern Mexican samples of T. a. brunneicollis. MtDNA data show a paraphyletic arrangement of T. a. musculus on the tree, whereas the SNP tree portrays them as monophyletic. Island taxa are distinct in both datasets, including T. a. beani (Isla Cozumel), which appears derived from T. a. musculus in eastern Mexico, and T. sissonii (Isla Socorro) and T. tanneri (Isla Clarión) although the 2 datasets disagree on their overall phylogenetic placement. Although we had only mtDNA data for T. a. martinicensis from the Lesser Antilles, we found at least 4 distinct and paraphyletic taxa from Trinidad, Granada, St. Vincent islands, and Dominica. The House Wren complex showed strong differentiation in mtDNA and RADseq datasets, with conflicting patterns likely arising from some combination of sex-biased dispersal, incomplete lineage sorting, or selection on mtDNA. The most glaring discrepancies between these 2 datasets, such as the paraphyly of eastern and western North American House Wrens in the mtDNA tree, present excellent opportunities for follow-up studies on evolutionary mechanisms that underpin phylogeographic patterns.

 

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.

 

With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of theCrotalus triseriatusgroup to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data inbpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation andbpp, whereas theSVDquartetsphylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference usingSVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within theC. triseriatusgroup, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent‐based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.