This study investigates the evolution of locomotory morphology and migratory behavior in nightingale-thrushes (genus Catharus), a clade of songbirds with diverse migratory strategies. With large datasets of molecular and morphometric characters, we resolve phylogenetic relationships, identify and model migration-related morphological characters, and estimate ancestral states of those characters to infer evolutionary transitions in the migratory phenotype. While acknowledging that unknown factors (e.g., differential extinction) may confound interpretation, our results suggest that (1) migratory behavior and its functional morphology are fundamentally linked; (2) short-distance or elevational migration (not long-distance) was the ancestral state of Catharus; (3) short-distance migration was the evolutionary precursor of long-distance migration; and (4) the short-distance migrant, Hermit Thrush (C. guttatus), may be in relative phenotypic (ecological) stasis. This potentially explains the ecological incumbency of C. guttatus in temperate North America during winter, and offers a new framework for interpreting the evolutionary sequence that produced long-distance migration in this model system.

The Black-throated Gray Warbler (Setophaga nigrescens) is a migratory songbird with a widespread and continuous distribution in the North American West. Previously published morphological data support the designation of 2 putative subspecies based on subtle differences in plumage and song; however, whether these patterns are clinal or discrete has yet to be determined. Furthermore, given that patterns of morphological variation occur across multiple distinct habitats and geographical boundaries, underlying population genetic structure may be present. To investigate this question and explore the evolutionary history of S. nigrescens, we conducted the first range-wide phylogeographic analysis of this species using genetic (mitochondrial DNA [mtDNA], ND2 gene sequences), morphological (body measurements), and environmental (niche modeling) data. Overall, our results identified 2 major mtDNA clades. One clade occurs east of the Cascade-Sierra ranges throughout the southwestern, Great Basin, and Rocky Mountain regions in North America (Interior clade), while a second widespread clade is comprised of birds that span the Pacific Northwest, and also across the Great Basin and southwest into the Rocky Mountains (Coastal clade). Divergence time estimates suggest a Pleistocene epoch vicariance event. Environmental niche models predict habitat modification and fragmentation from glacial-interglacial cycles, which were frequent over the Pleistocene. Range expansion northwards following the Last Glacial Maximum was identified from neutrality tests and shifts in suitable habitat from the Mid-Holocene to present-day conditions, where both clades are likely experiencing secondary contact. We found support for nonequivalent environmental niches among both clades based on a spatial analysis of environmental variables, with the Coastal clade showing greater tolerance to both temperate and xeric climatic conditions across the North American West; however, the environmental space occupied by both clades was more similar to each other than expected by chance. High levels of geographic overlap and a lack of discrete patterns in morphology suggest few contemporary reproductive barriers to gene flow.

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. center dot Wrens are one of the most diverse songbird groups in the Americas, but we currently lack a complete understanding of their evolutionary history in relation to their relatives: the gnatcatchers, nuthatches, tree creepers, and Wallcreeper.center dot We addressed this gap in knowledge by combining existing and new sequence data to estimate a near-complete phylogenetic tree for the wrens and their allies that is largely consistent with previous studies, but not well resolved for a subgroup of the wrens.center dot This tree informed us that this group originated in Eurasia and has dispersed several times to Africa and North America in the last 20 million years.center dot By including nearly 100 phylospecies, we demonstrated that the potential underestimation of the diversity in this group may alter our understanding of this group's evolutionary history across space and time. La superfamilia de aves paseriformes Certhioidea carece de una filogenia completa, a pesar de decadas de reconocimiento como un clado y de extenso trabajo sistematico dentro de todas sus familias constituyentes. Aqui, inferimos una filogenia casi completa a nivel de especie de Certhioidea a partir de una supermatriz molecular, incluyendo el primer muestreo completo de Troglodytidae, y utilizamos esta filogenia para inferir sus historias biogeograficas y de diversificacion. Tambien inferimos una filogenia expandida que incluye cerca de 100 filoespecies putativas anteriormente documentadas en la literatura, y encontramos que incluir esta diversidad tuvo impactos notables en la historia evolutiva inferida de Certhioidea. Este arbol a nivel de filoespecies documento algunos casos de parafilia de especies, algunos previamente descritos en la literatura y otros novedosos. Encontramos que Certhioidea se origino principalmente en Eurasia y se disperso en America del Norte cinco veces en los ultimos 20 millones de anos, incluyendo en el origen a los "certhioides del Nuevo Mundo," trogloditidos y atrapamoscas, un clado llamado Orthourae en este estudio. Despues de este evento inicial de dispersion, tanto los trogloditidos como los atrapamoscas se diversificaron ampliamente en el hemisferio, con ambos linajes cruzando repetidamente entre continentes. Sin embargo, no detectamos un impacto notable de la formacion del Istmo de Panama en la frecuencia de eventos de dispersion entre America del Norte y del Sur. La inclusion de filoespecies altero esta inferencia biogeografica en algunas partes del arbol, pero en general fue en gran medida consistente. Con el muestreo a nivel de especie, encontramos que las tasas de diversificacion dentro de Certhioidea fueron en gran medida constantes a lo largo del tiempo, con una desaceleracion detectable hacia el presente. En contraste, el muestreo a nivel de filoespecie recupero una historia de diversificacion diferente, con un aumento significativo en la tasa en el nodo de la corona de Orthourae despues de dispersarse en las Americas, y tasas de especiacion aumentadas especialmente en los generos Polioptila y Henicorhina. Esta filogenia, en gran medida resuelta, para Certhioidea, ha proporcionado perspectivas importantes sobre la historia evolutiva de este grupo y brinda un marco para futuros trabajos comparativos en este fascinante clado.

Lay Summary center dot The House Wren (Troglodytes) complex consists of at least 5 distinct evolutionary groups distributed from Canada to southern South America. center dot Morphological variation led taxonomists to name over 25 subspecies. center dot We used mitochondrial DNA (mtDNA; 349 individuals) and a genome-wide survey of single nucleotide polymorphisms (RADseq; 184 individuals) to evaluate evolutionary patterns and determine their relationship to current taxonomy. center dot The mtDNA data showed considerable differentiation, especially in island forms T. sissonii (Isla Socorro), T. a. beani (Isla Cozumel), and T. tanneri (Isla Clarion), and T. martinicensis, the latter of which includes several clades that were not monophyletic. center dot MtDNA suggested that eastern and western samples of T. aedon were not monophyletic, whereas they were in the RADseq analyses; the cause of the discordance is unclear. center dot We suggest that the RADseq data provide the most appropriate basis for classification and understanding House Wren evolution, and they show a high degree of phylogeographic differentiation and support for these taxonomic groups: eastern and western T. aedon, T. sissonii, T. tanneri, T. beani, and T. a. musculus. 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 Clarion) 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.

We assembled datasets of genetic (genomic ultraconserved elements [UCEs], mtDNA) and phenotypic (morphology, voice) characters to address species limits and taxonomy in the slaty-backed nightingale-thrush Catharus fuscater (Passeriformes: Turdidae), a polytypic complex of songbirds with a broad montane distribution in Central and South America. We identified 10 allopatric populations that have been evolving independently for multiple glacial cycles. Genetic structure is broadly correlated with divergence in phenotypic characters, including plumage colour, iris colour, maxilla (bill) colour, and the acoustic structure of vocalizations (calls and songs). We propose an integrative taxonomic revision that recognizes seven species in the complex, including a newly described species from eastern Panama, and four subspecies, of which two are newly described.

TheAmaurospiza‘seedeaters’ are bamboo‐specialized mixed strategists, most often found in bamboos in vegetative state, feeding on buds, shoots, petioles and insects. As bamboos die after flowering, birds may wander in search of live vegetative bamboo. The three currently recognized species ofAmaurospizaare allopatrically distributed: the Blackish‐blue SeedeaterAmaurospiza moestain the Atlantic Forest of Argentina, Brazil and Paraguay, and in forest enclaves in the Cerrado; the recently described Carrizal SeedeaterAmaurospiza carrizalensisknown from a few localities in southeastern Venezuela; and the Blue SeedeaterAmaurospiza concolordistributed patchily from Mexico to Peru. Three subspecies are recognized withinA. concolor:relictain southwest Mexico,concolorfrom southern Mexico to Panama andaequatorialisfrom southwest Colombia to northwest Peru. Full species status has been advocated forrelictaandaequatorialisbut evidence supporting their recognition is weak, whilerelictawas described in the monospecific genusAmaurospizopsis. Here we (1) test the monophyly ofAmaurospiza, (2) reconstruct the phylogenetic relationships of all its constituent taxa using mitochondrial and nuclear markers, (3) re‐assess species limits inAmaurospizawith the aid of vocalizations and genetic and plumage data, and (4) discuss the link between bamboo life history, biogeographical patterns and extent of genetic differentiation.Amaurospizawas found to be monophyletic in both theND2and multilocus analyses. In theND2treeA. moestaandA. carrizalensiswere sister to each other,A. concolorwas found to be paraphyletic becauseaequatorialiswas placed as sister tomoesta–carrizalensis, and a clade including nominateconcolorandrelictawas sister to all the other taxa. The multilocus tree showed the same relationships, but lacked nuclear samples ofrelicta. MeanND2pairwise distance betweenconcolorandaequatorialis(8.3%) was greater than that betweenmoestaandcarrizalensis(5.7%), whilerelictadiverged on average 1.0% from nominateconcolor. The South American clade has more slender bills and white underwing coverts, while the Central American clade has thicker bills and bluish underwing coverts. All taxa exhibited typicalAmaurospizasongs with quickly delivered, warbled, pure and fairly high‐pitched musical notes. Number of inflections/second exhibited a stepped pattern, withconcolorandrelictaon the lower end andcarrizalensis,aequatorialisandmoestaon the upper end. Similarly,moesta,carrizalensisandaequatorialishad overall more inflections per note thanconcolorandrelicta. Linear discriminant analysis using nine acoustic variables correctly assigned all 62 songs to the correct taxon. Morphology, plumage, vocalizations and phylogenetic data indicate thataequatorialisshould be afforded full species status as the Ecuadorian Seedeater (A. aequatorialis), suggest keepingrelictaas a subspecies ofA. concolorand support continued recognition ofA. carrizalensis. Our data support mergingAmaurospizopsisintoAmaurospiza.

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 sequenced the mitochondrial ND2 gene for 290 Bushtits (Psaltriparus minimus) sampled from northern Washington to Guatemala. Phylogenetic analysis sorted specimens into 2 main lineages residing either west (coastal) or east (inland) of the Sierra Nevada and Cascades. These lineages are separated by 3.5% sequence divergence and correspond with the distributions of 2 long-recognized phenotype groupings (brown-capped and plumbeous, respectively). Three additional monophyletic geographically structured lineages were identified. Birds from southmost Baja California (Sierra de la Laguna) segregate from other coastal samples whereas the inland lineage includes additional lineages occurring in southeastern Mexico (Morelos, Puebla, Guerrero, and Oaxaca) plus Guatemala, and southwestern Mexico (Michoaca ' n). Examination of museum specimens revealed that a black-eared phenotype occurs sporadically in the interior lineage in southern U.S. and northern Mexico, increasing in frequency to the south, corresponding roughly with these southern Mexican mtDNA lineages. Degree of sequence divergence between the 2 main lineages suggests a relatively early divergence, and ample time for 2-way introgression to occur. However, only 1 of our sampling localities (Lake Co., Oregon; n 1/4 4) was mixed for coastal (n 1/4 1) and interior (n 1/4 3) lineages suggesting the possibility of reproductive isolation between the 2 main lineages. Received 31 January 2022. Accepted 8 December 2022.

Cryptic species are closely related taxa that are difficult to separate morphologically, but are reproductively isolated. Here we examine the warbling vireo complex (Vireo gilvus), a widespread songbird speculated to be comprised of more than one cryptic species. We included three taxa within the complex: two of the western (Vireo gilvus swainsonii and Vireo gilvus brewsteri) subspecies and the single eastern (Vireo gilvus gilvus) subspecies. We used mtDNA and microsatellite loci to assess the congruence of genetic data to the current subspecies boundaries. We then incorporated bioacoustic, morphometric and ecological niche modelling analyses to further examine differences. We found two genetic groups with mtDNA analysis, splitting eastern and western warbling vireos. Microsatellite analyses revealed four genetic groups: an eastern group, a Black Hills group and two western groups that do not agree with current western subspecies boundaries based on phenotypic data. Our results suggest that eastern and western warbling vireos have been reproductively isolated for a long period of time and therefore may be best treated as separate species. However, more research into areas of contact to examine the presence of hybridization is advised before making a taxonomic revision. Differences between the two western genetic groups appear less clear, requiring additional research.

Sceloporus subniger Poglaygen & Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting S. subniger may be a composite of several distinct species, we examined in more detail the genetic structure of S. subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing thousands of genomic regions from 12 specimens to specifically evaluate the genetic distinctiveness of populations from western Michoacán and adjacent Jalisco along with the newly discovered population in the Sierra de Mascota in western Jalisco. We also recorded morphological data from 47 museum specimens to compare to our genetic data. Results from our analyses of the genetic data, augmented by specimen measurements and scale counts, support the notion that S. subniger is indeed a composite of distinct species. Montane bunchgrass lizards from western Michoacán and adjacent Jalisco, and from the Sierra de Mascota in western Jalisco, each represent distinct new species, which we describe and name here.

The genomic signature of speciation with gene flow is often attributed to the strength of divergent selection and recombination rate in regions harboring targets for selection. In contrast, allopatric speciation provides a different geographic context and evolutionary scenario, whereby introgression is limited by isolation rather than selection against gene flow. Lacking shared divergent selection or selection against hybridization, we would predict the genomic signature of allopatric speciation would largely be shaped by genomic architecture—the nonrandom distribution of functional elements and chromosomal characteristics—through its role in affecting the processes of selection and drift. Here, we built and annotated a chromosome-scale genome assembly for a songbird (Passeriformes: Certhia americana). We show that the genomic signature of allopatric speciation between its two primary lineages is largely shaped by genomic architecture. Regionally, gene density and recombination rate variation explain a large proportion of variance in genomic diversity, differentiation, and divergence. We identified a heterogeneous landscape of selection and neutrality, with a large portion of the genome under the effects of indirect selection. We found higher proportions of small chromosomes under the effects of indirect selection, likely because they have relatively higher gene density. At the chromosome scale, differential genomic architecture of macro- and microchromosomes shapes the genomic signatures of speciation: chromosome size has: 1) a positive relationship with genetic differentiation, genetic divergence, rate of lineage sorting in the contact zone, and proportion neutral evolution and 2) a negative relationship with genetic diversity and recombination rate.

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.

The Common Black Hawk (Buteogallus anthracinus), a widespread neotropical raptor, has been known since the 1970s to nest as far north as western Texas, but few breeding records exist for the adjacent area of northcentral Mexico. In 2015 we located two active nest sites within the Maderas del Carmen Flora and Fauna Protection Area at northwestern Coahuila. The nest sites were in Pecan (Cala illinoiensis) and Arizona Pine (Pinus arizonica) trees, both near natural pennanent water sources. Our recent nest site records along with others in eastern Coahuila suggest the existence of a corridor connecting Texas and Nuevo Leon populations, highlighting the importance of u-ansboundary natural protected areas for species conservation.

The Pleistocene glacial cycles had a strong influence on the demography and genetic structure of many species, particularly on northern-latitude taxa. Here we studied the phylogeography of the white-eared hummingbird (Hylocharis leucotis), a widely distributed species of the highlands of Mexico and Central America. Analysis of mitochondrial DNA (mtDNA) sequences was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. Analyses of 108 samples from 11 geographic locations revealed population structure and genetic differentiation among populations separated by the Isthmus of Tehuantepec (IT) and the Motagua-Polochic-Jocotán (MPJ) fault barriers. ENM predicted a widespread distribution of suitable habitat for H. leucotis since the Last Inter Glacial (LIG), but this habitat noticeably contracted and fragmented at the IT. Models for historical dispersal corridors based on population genetics data and ENM revealed the existence of corridors among populations west of the IT; however, the connectivity of populations across the IT has changed little since the LIG. The shallow geographic structure on either side of the isthmus and a star-like haplotype network, combined with the long-term persistence of populations across time based on genetic data and potential dispersal routes, support a scenario of divergence with migration and subsequent isolation and differentiation in Chiapas and south of the MPJ fault. Our findings corroborate the profound effects of Pleistocene climatic fluctuations on the evolutionary history of montane taxa but challenge the generality of expanded suitable habitat (pine-oak forests) during glacial cycles.

Most species and therefore most hybrid zones have historically been described using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. The Northwestern Crow ( Corvus caurinus ) and American Crow ( Corvus brachyrhynchos ) are sister taxonomic species with a continuous distribution that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate whether these crows are genetically differentiated and the extent to which they may hybridize. We found that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >1,400 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines were both centered in southwestern British Columbia, farther north than previously postulated. The mtDNA cline was narrower than the nuDNA cline, consistent with Haldane’s rule but not sex-biased dispersal. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, consistent with potentially recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.

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 / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of a 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 U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, 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.

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 the Crotalus triseriatus group 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 in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, 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.

The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates , Ramphocaenus , a Polioptila guianensis complex, and the remaining members of Polioptila . Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris , which formed a clade sister to all species within Polioptila . Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4–6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.

Mountain formation in Mexico has played an important role in the diversification of many Mexican taxa. The Trans-Mexican Volcanic Belt in particular has served as both a cradle of diversification and conduit for dispersal. We investigated the evolutionary history of the Isthmura bellii group of salamanders, a widespread amphibian across the Mexican highlands, using sequence capture of ultraconserved elements. Results suggest that the I. bellii group probably originated in southeastern Mexico in the late Miocene and later dispersed across the Trans-Mexican Volcanic Belt and into the Sierra Madre Occidental. Pre-Pleistocene uplift of the Trans-Volcanic Belt likely promoted early diversification by serving as a mesic land-bridge across central Mexico. These findings highlight the importance of the Trans-Volcanic Belt in generating Mexico's rich biodiversity.