Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa 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 the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate 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 >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late‐generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to 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/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.

Abstract:Divergence in migratory behavior is a potential mechanism of lineage divergence in sympatric populations and a key life history trait used in the identification of demographically independent units for conservation purposes. In the Painted Bunting (Passerina ciris), a North American songbird, populations on the Atlantic coast and interior southern United States are known to be allopatric during the breeding season, but efforts to map connectivity with wintering ranges in Mexico, Florida, and the Caribbean have been largely inconclusive. Using genomic and morphological data from natural history specimens and banded birds, we found evidence of three genetically differentiated populations with distinct wintering ranges and molt-migration phenologies. In addition to confirming that the Atlantic coast population remains allopatric throughout the annual cycle, we identified an unexpected migratory divide within the interior breeding range. Populations breeding in the Lower Mississippi River Valley winter on the Yucatán Peninsula, and are parapatric with other interior populations that winter in mainland Mexico and Central America. Across the interior breeding range, genetic ancestry is also associated with variation in wing length; suggesting that selective pressures may be promoting morphological divergence in populations with different migration strategies.

Aim: Employ phylogeographic analyses of a widespread species complex to examine the role of historical and evolutionary processes in the origin and maintenance of high species diversity in the Neotropical montane region. Location: Neotropical highlands. Taxon: Henicorhina wood-wrens (Aves, Troglodytidae). Methods: We collected mtDNA sequence data for 288 individuals thoroughly covering the range of the Henicorhina leucophrys complex from Mexico to Bolivia. Sequences were employed to characterize population structure, infer phylogenetic relationships among populations and their divergence times, examine lineage accumulation through time, and identify presumptive species using coalescent methods. We also explored the origin of elevational and latitudinal replacements involved in spatial changes in species assemblages in the Andes. Results: We found remarkable genetic structure within the complex, which consists of numerous lineages reaching >12% sequence divergence; most divergent populations occur in areas separated by topographic barriers but several of them, typically not sister to each other, co-occur with elevational segregation on mountain slopes or replace each other with latitude along the Andes. Some close relatives occur in areas separated by thousands of kilometers, with more distant relatives occupying intervening areas. The complex likely originated in the Mexican highlands and expanded extensively in South America while diverging rapidly at a constant rate into many different lineages which have persisted for millions of years. Coalescent analyses consistently revealed that the complex may comprise more than 30 species; while we do not suggest these presumptive species should be recognized by taxonomists in the absence of additional data, H. leucophrys is a distant outlier among New World birds in terms of high lineage diversity within a single recognized species. Main Conclusions: Our study captured wood-wren lineages in the act of building up diversity via divergence and persistence in allopatry, achievement of secondary sympatry, and coexistence at the landscape scale mediated by ecological and evolutionary divergence. Although dispersal by wood-wrens is restricted at present and this likely accounts for strong population structure across topographic barriers, their ranges have been dynamic, managing to disperse over much of the montane Neotropics. Phases of expansion and contraction of ranges and localized extinctions of populations likely account for phylogeographic patterns which are precursors to the origin of new species and the accumulation of diversity in tropical mountains.

In the painted bunting (Passerina ciris), a North American songbird, populations on the Atlantic coast and interior southern United States are known to be allopatric during the breeding season, but efforts to map connectivity with wintering ranges have been largely inconclusive. Using genomic and morphological data from museum specimens and banded birds, we found evidence of three genetically differentiated painted bunting populations with distinct wintering ranges and molt-migration phenologies. In addition to confirming that the Atlantic coast population remains allopatric throughout the annual cycle, we identified an unexpected migratory divide within the interior breeding range. Populations breeding in Louisiana winter on the Yucatán Peninsula and are parapatric with other interior populations that winter in mainland Mexico and Central America. Across the interior breeding range, genetic ancestry is also associated with variation in wing length, suggesting that selection may be promoting morphological divergence in populations with different migration strategies.

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.

No abstract

17Aim: Employ phylogeographic analyses of a widespread species complex to examine the role of historical and 18 evolutionary processes in the origin and maintenance of high species diversity in the Neotropical montane region. 19 20Location: Neotropical highlands. 21 22Taxon: Henicorhina wood-wrens (Aves, Troglodytidae). 23 24Methods: We collected mtDNA sequence data for 288 individuals thoroughly covering the range of the Henicorhina 25 leucophrys complex from Mexico to Bolivia. Sequences were employed to characterize population structure, infer 26 phylogenetic relationships among populations and their divergence times, examine lineage accumulation through time, 27and identify presumptive species using coalescent methods. We also explored the origin of elevational and latitudinal 28replacements involved in spatial changes in species assemblages in the Andes. 29 30Results: We found remarkable genetic structure within the complex, which consists of numerous lineages reaching 31 >12% sequence divergence; most divergent populations occur in areas separated by topographic barriers but several of 32 them, typically not sister to each other, co-occur with elevational segregation on mountain slopes or replace each other 33with latitude along the Andes. Some close relatives occur in areas separated by thousands of kilometers, with more 34 distant relatives occupying intervening areas. The complex likely originated in the Mexican highlands and expanded 35 extensively in South America while diverging rapidly at a constant rate into many different lineages which have 36 persisted for millions of years. Coalescent analyses consistently revealed that the complex may comprise more than 30 37 species; while we do not suggest these presumptive species should be recognized by taxonomists in the absence of 38 additional data, H. leucophrys is a distant outlier among New World birds in terms of high lineage diversity within a 39 single recognized species. 40 41Main Conclusions: Our study captured wood-wren lineages in the act of building up diversity via divergence and 42 persistence in allopatry, achievement of secondary sympatry, and coexistence at the landscape scale mediated by 43 ecological and evolutionary divergence. Although dispersal by wood-wrens is restricted at present and this likely 44 accounts for strong population structure across topographic barriers, their ranges have been dynamic, managing to 45 disperse over much of the montane Neotropics. Phases of expansion and contraction of ranges and localized extinctions 46 of populations likely account for phylogeographic patterns which are precursors to the origin of new species and the 47 accumulation of diversity in tropical mountains. 48 49