NAOC - Washington, DC (1 Viewer)

[Peter Kovalik]

6th North American Ornithological Conference (NAOC) in Washington, DC, August 16–20, 2016.

[Program]

e.g.

FitzGerald, Alyssa Phylogeography of the Gray-cheeked Thrush (Catharus minimus)/ Bicknell’s Thrush (C. bicknelli) species complex

Chesser, Robert A UCE-based genus-level phylogeny of suboscine birds

Moyle, Robert Genomic insights into speciation in a widespread Pacific island bird lineage

Braun, Edward The genome of Bambusicola thoracicus and insights on molecular evolution in Phasianidae

Hosner, Peter Avian diversification in the Philippine archipelago

Oswald, Jessica Willet be one species or two?: A genomic view of the evolutionary history of Tringa semipalmata

Taylor, Rebecca Allochrony and speciation in the bandrumped storm-petrel (Hydrobates spp.) species complex

Selvatti, Alexandre Out of Africa: An African origin of the Old World Suboscines (Passeriformes: Eurylaimides) and the successful diversification of the ground-foraging pittas (Pittidae)

Wang, Ning Phylogenomics and mitogenomics place enigmatic phasianids (Aves: Galliformes)

Reddy, Sushma The impact of taxon sampling and data type on difficult problems in phylogenomics: Birds in a bush revisited?

Rodríguez-Gómez, Flor Using phylogenomic markers to test the taxonomy and evolution of Atthis hummingbirds spanning the Isthmus of Tehuantepec in Mexico

Younger, Jane Cryptic diversification within the Newtonia of Madagascar: evidence from ultra-conserved elements, nuclear introns and mitochondrial sequences

Benz, Brett Phylogenetic relationships of myzomelid honeyeaters reveal contrasting patterns of diversification in Australasia

Mason, Nicholas Endemism in the Pacific lowlands of Mexico: Phylogeography of the White-collared Seedeater (Sporophila torqueola)

Perktas, Utku Integrating morphology, phylogeography, and ecological niche modeling to explore population differentiation in North African Common Chaffinches

Mauck, William Phylogenomics of Lories and Lorikeets (Order: Psittaciformes)

Rocha-Méndez, Alberto When molecules do not follow morphology: Phylogeography of the Atlapetes albinucha complex (Aves, Emberizidae).

Cheek, Rebecca Mitochondrial DNA suggests recent origins in two coastal avian subspecies in northwestern North America.

Beehler, Bruce Molecular Systematics and the Realignment of the Avifauna of the New Guinea Region

Barrera De la Garza, Tania Phylogeographic Analysis of the Green Violetear (Colibri thalassinus)

Miyaki, Cristina Multilocus phylogeographical analysis of the species complex Amazona aestiva/A. ochrocephala (Aves, Psittacidae)

Keith, Katrina A reassessment of the systematics and biogeographic history of Troglodytes wrens.

Antalffy, Janine Evolutionary biogeography of the white-browed laughingthrush in china’s sichuan basin

Miranda, Hector Mitogenomic Phylogeography of the Peacock-Pheasants Polyplectron of Southeast Asia

Huntley, Jerry A tale of the nearly tail-less: the biogeography of the Crombecs (genus: Sylvietta)

Guimaraes Capurucho, Joao Marcos Phylogeography of the Neopelma genus (Tyrant-manakins), connecting the Amazon, Cerrado, and Atlantic Forest histories

Andersen, Michael Molecular phylogeny and biogeography of kingfishers (Alcedinidae)

Cracraft, Joel Global avian biogeography: a test of two worldviews

Tsai, Whitney Next-generation sequencing of museum skins uncovers Mexican endemic bird lineages

Musher, Lukas Phylogenomic analysis using ultraconserved elements reveals cryptic diversity in the complex Neotropical genus Pachyramphus

White, Emma Species Limits in Red Warblers

Barrowclough, George Phylogeography and geographic variation in the Red-bellied Woodpecker (Melanerpes carolinus)

Peters, Jeffrey Speciation with gene flow in Anas ducks

 

[Peter Kovalik]

Abstract Book

Abstract Book

 

[Jim LeNomenclatoriste]

"Phylogenomics of Lories and Lorikeets " and "Reassessment of the systematic and biogeographic history of Troglodytes wrens " seem to be interesting.

 

[Kratter]

Here's the program, which includes titles, first author and rooms and times of the talks and posters.
http://naoc2016.com/NAOC-Media-Kit/NAOC-Program_session-schedule.pdf

Andy

 

[Jim LeNomenclatoriste]

"Phylogenomics of Lories and Lorikeets "

Is there an abstract of this publication ?

 

[Peter Kovalik]

Lories and Lorikeets

Is there an abstract of this publication ?

W. Mauck, M. Andersen, B. Benz & B. Smith. Phylogenomics of Lories and Lorikeets (Order: Psittaciformes)

Lories and Lorikeets (Loriini) are nectarivorous parrots that occur from Indonesia throughout New Guinea, Australia, and Polynesia. The clade exhibits a wide variation in body size and plumage diversity that is characterized by 12 genera, 53 species, and 78 subspecies. Previous phylogenetic work has suggested relationships among several species are unclear or unknown, and that nearly half of the genera may not be monophyletic. To infer phylogenetic relationships among the lories and lorikeets, we sequenced ultraconserved elements (UCEs) from > 95 of the described taxa (species and subspecies) and collected thousands of loci from modern and historical DNA samples. We performed phylogenetic analyses and obtained resolved relationships throughout the tree and confirmed the nonmonophyly of several genera. We will present a time-calibrated phylogeny for Loriini and discuss the challenges of estimating phylogenetic relationships from historical and modern DNA samples.

 

[Peter Kovalik]

Catharus minimus, C. bicknelli

A. FitzGerald & J. Kirchman. Phylogeography of the Gray-cheeked Thrush (Catharus minimus)/ Bicknell’s Thrush (C. bicknelli) species complex.

During periods of Pleistocene glaciation when northern habitats were completely icecovered, boreal forest habitats were fragmented and pushed southward. Historical biogeographic studies show that boreal forest birds generally have patterns of genetic divergence that are consistent with a single “boreal” clade in northern and eastern North America whereas any genetic structure or morphological differences, if present, are found in the western portions of their range. However, the Catharus bicknelli/minimus clade shows a well-defined species break in the east between the Bicknell’s Thrush and Gray-cheeked Thrush. Using a phylogeographic approach that combines population genetics with species distribution models (SDMs), we examine the evolutionary history of this boreal species complex. Sequence divergence (2.33%) between the Bicknell’s Thrush (n=187) and Gray-cheeked Thrush (n=78) based on the mitochondrial gene ND2 was an order of magnitude greater than divergence within each species. Graycheeked Thrushes had greater genetic diversity than the threatened Bicknell’s Thrush. One individual captured in Southern Labrador, phenotypically a Gray-cheeked Thrush, carried a widespread and common Bicknell’s Thrush haplotype. We also sequenced the nuclear intron ADAMTS6 on the Z-chromosome from a subset of 74 thrushes, but there was essentially no variation at this locus in our sample. SDMs of the Last Glacial Maximum revealed that the species both had suitable habitat in two or three distinct eastern refugia; the Graycheeked Thrush also had a western refugium. Coalescent analyses show that the divergence between the Bicknell’s Thrush and Gray-cheeked Thrush was mid-Pleistocene, and divergence may have been maintained by residence in different late-Pleistocene refugia

.

 

[Peter Kovalik]

Suboscine birds

T. Chesser, E. Derryberry, R. Brumfield, A. Cuervo, G. Derryberry, J. Cracraft, R. Moyle, A. Aleixo, G. Bravo, F. Sheldon & M. Harvey. A UCE-based genus-level phylogeny of suboscine birds.

Suboscine birds form one of two major groups of passerines and consist of roughly 1300 species, or about one-eighth of extant birds. Suboscines are a predominantly New World group and account for more than 30% of the world’s richest avifauna, that of the Neotropics. Some 50 species of suboscines are also found in the Old World, where they form a phenotypically striking part of the avifauna. Using a next-generation approach, we sequenced 2500 nuclear loci, including exons and ultraconserved elements and their flanking sequence (UCEs), for >98% of suboscine species and >99% of suboscine genera. For this talk, phylogenetic analyses were conducted on a subset of nearly 600 suboscine individuals, including representatives of all genera in the dataset and including more than one species for genera of questionable monophyly. Our results supported previous conclusions regarding monophyly of all suboscines, Old World suboscines (including Sapayoa aenigma), and New World suboscines. Monophyly of most families and subfamilies, including many only recently recognized as clades, was also supported, although relationships among groups differed in some cases. Our phylogeny also tallied well with recent Sanger-based species-level phylogenies (e.g., that of the Furnariiidae) in the furnarioid suboscines, but many genera in the tyrannoid suboscines, species-level phylogenies of which have not generally been published, were found to be para- or polyphyletic, even given our limited sampling. This indicates the degree to which specieslevel phylogenies will likely rewrite our understanding of the lower-level systematics of birds generally.

 

[Peter Kovalik]

Phasianidae

N. Wang, P. Hosner, B. Liang, E. Braun & R. Kimball. Phylogenomics and mitogenomics place enigmatic phasianids (Aves: Galliformes).

The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, positions for a number of taxa, e.g., Blood Pheasant (Ithaginis cruentus), Snow Partridge (Lerwa lerwa), and Long-billed Partridge (Rhizothera longirostris), remain enigmatic. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them cannot be inferred. Although Rhizothera was originally placed in Perdix (true partridges), a partial CYTB sequence suggests it is sister to Pucrasia (Koklass Pheasant). To test these hypotheses, we used 3692 ultra-conserved element (UCE) loci and complete mitogenomes from 19 species selected to represent previous hypotheses and the major phasianid clades. Toepads were used for poorly studied taxa. All UCE analyses strongly supported placing Lerwa sister to Ithaginis plus a large clade including turkey, typical pheasants, tragopans, Pucrasia, and Perdix. Rhizothera was in this clade, sister to a large group including Perdix, typical pheasants, Pucrasia, turkey and grouse. The results of mitogenomic analyses differed, supporting a sister relationship between Ithaginis and Lerwa, rather than a grade. The position of Rhizothera using mitogenomes depended upon analyses, with unpartitioned and codon-based analyses placing Rhizothera sister to a tragopan clade, whereas partitioned DNA model was congruent with the UCE data. In all mitogenome analyses, Pucrasia was sister to a clade comprising Perdix and the typical pheasants with high support, in contrast to UCEs and published nuclear intron data. Overall, we have been able to place these enigmatic, poorly-studied, phasianid taxa with strong support.

 

[Peter Kovalik]

Newtonia

J. Younger, L. Strozier, J. Maddox, S. Goodman, M. Raherilalao & S. Reddy. Cryptic diversification within the Newtonia of Madagascar: evidence from ultraconserved elements, nuclear introns and mitochondrial sequences.

Despite its reputation as a biodiversity hotspot, the full genetic breadth of Madagascar’s avifauna remains poorly understood. Newtonia are a genus of putatively four species of forest-dwelling birds originally classified as Old World Warblers, but recently placed within the monophyletic Vanginae radiation. Two of the species, N. amphichroa and N. brunneicauda, have widespread distributions. To explore relationships within Newtonia we sequenced mitochondrial genes, nuclear introns and over 3000 ultra-conserved element (UCE) loci for N. amphichroa, N. brunneicauda and N. archboldi. We used maximum likelihood phylogenetic inference to confirm monophyly of the three species. For the two widespread species we conducted further intraspecific analyses to assess the possibility of cryptic speciation. Our study included 45 specimens of N. amphichroa from five study sites spanning the latitudinal breadth of Madagascar, and 96 specimens of N. brunneicauda, covering both eastern and western populations of the species. We analysed these datasets for phylogeographic patterns using both maximum likelihood phylogenetic inference and dated Bayesian (BEAST) methods.Within N. amphicroa we discovered three highly distinct, monophyletic clades. The three clades are isolated in geographically disjunct montane regions. Our estimation of divergence times indicated that one lineage has been isolated for ca. 1.2 million years and the remaining two separated around 0.5 million years ago. We propose that these three lineages represent cryptic diversification and possibly two new species, further expanding the remarkably diverse Vanginae radiation.

 

[Peter Kovalik]

Meliphagidae

B. Benz & R. Moyle. Phylogenetic relationships of myzomelid honeyeaters reveal contrasting patterns of diversification in Australasia.

The myzomelid honeyeaters (Myzomela, Meliphagidae) comprise 77 named taxa in 30 species, and are ubiquitous across much of the Australasian tropics. Despite their small size, most myzomelids exhibit a strong capacity for long-distance dispersal, which has enabled successful colonization of remote islands throughout Wallacea, Micronesia, and western Polynesia. Although several recent studies have brought significant advances in resolving higher-level meliphagid phylogenetic relationships, limited representation within Myzomela has precluded detailed biogeographic inference within the group. In this study, we developed a multilocus dataset with comprehensive taxon sampling to examine the diversification history and species-limits of myzomelid honeyeaters throughout their distribution. Maximum likelihood and Bayesian inference analyses recovered a well resolved phylogeny indicating that myzomelid honeyeaters likely arose in the Bismarck Archipelago during the late Miocene, followed by early waves of diversification in New Guinea, Australia, and eastern Wallacea. Secondary pulses of rapid diversification are evident in the Solomon Islands, Wallacea, Micronesia and western Polynesia, which account for over half of the myzomelid species diversity. The evolutionary history of Myzomela is considerably more complex within archipelagos of Wallacea by comparison with Melanesian and Polynesia counterparts, a pattern that is consistent with other Australasian bird groups. Our molecular phylogenetic results also clarified several important aspects of myzomelid plumage evolution and taxonomy, revealing paraphyly in four currently recognized species complexes and confirming labile plumage evolution throughout the group.

 

[Peter Kovalik]

Aves

S. Reddy, R. Kimball, A. Pandey, P. Hosner, M. Braun, Kin-Lan Han, J. Harshman, S. Hackett, C. Huddleston, S. Kingston, B. Marks, K. Miglia, W. Moore, F. Sheldon, C. Witt, T. Yuri & E. Braun. The impact of taxon sampling and data type on difficult problems in phylogenomics: Birds in a bush revisited?

Resolving deep relationships of modern birds has challenged avian systematics and despite enormous efforts, much conflict remains across studies. Recent phylogenomic analyses using different strategies – whole genome sequencing for a limited taxon set (Jarvis et al. 2014. Science 346: 1320-31) or sequence capture with more extensive taxonomic coverage (Prum et al. 2015. Nature 526: 569-73) – have resulted in very different topologies. Using an independent data set with coverage comparable to Prum et al. (235 taxa and 54 loci, mainly introns), we tested whether this incongruence is due to biases such as taxon sampling, signal in data, or analytical methods. Our analyses show that taxon sampling improves support for a set of interordinal relationships that are recovered across most analyses. However, in comparing our data to published analyses, conflict in the deep internodes of birds appears to depend more upon differences in data type (coding versus non-coding). Some biases in data–type, such as base compositional biases that violate the assumptions of existing substitution models, are more problematic in coding regions than non-coding sequences, indicating that these coding regions may not be ideal to use with existing models. Although the avian tree of life has made tremendous advances in the last 10 years in reaching consilience in several relationships, some deeper nodes may be unresolvable given limitation of the analytical tools and the inherent signal in avian genomes.

 

[Jim LeNomenclatoriste]

W. Mauck, M. Andersen, B. Benz & B. Smith. Phylogenomics of Lories and Lorikeets (Order: Psittaciformes)

I'm so enthusiastic !!!

 

[Peter Kovalik]

Atthis

F. Rodríguez-Gómez, E. Zarza, W. Tsai & J. McCormack. Using phylogenomic markers to test the taxonomy and evolution of Atthis hummingbirds spanning the Isthmus of Tehuantepec in Mexico.

The Isthmus of Tehuantepec (IT) is one of the major biogeographic barriers of Mexico, with many sister species found in highlands on either side of this lowland area. In the case of Atthis hummingbirds, however, divergence between forms on either side of the IT appears weak, with evidence for ongoing gene flow and misidentifications. Our aim was to clarify the phylogenetic relationships between the currently described species, the Bumblebee Hummingbird (A. heloisa) with populations in the west of IT and Winethroated Hummingbird(A. ellioti)with population in the east of IT and to associate divergence processes with past geological and climatic fluctuations in Mesoamerica. We used ultraconserved elements (UCEs) from museum specimens to collect a set of loci and informative single nucleotide polymorphisms for phylogenetic and population genetic analysis. Phylogenies based on UCEs and those from mtDNA collected as “by-catch” show two weakly supported clades on either side of the IT. With regard to phenotype, the two species lacked clear morphological differences. Analysis of their niches using niche models based on climate data and habitat variables suggest little evidence for ecological divergence and a pattern more in keeping with niche conservatism, as has been demonstrated for other sister groups that span the IT. In sum, the IT does not appear to be a strong barrier to genetic Exchange between the two species. Further research is needed to determine their taxonomic status and quantification of the level of current gene flow.

 

[Peter Kovalik]

Sporophila torqueola

N. Mason, A. Olvera-Vital & A. Navarro-Sigüenza. Endemism in the Pacific lowlands of Mexico: Phylogeography of the Whitecollared Seedeater (Sporophila torqueola).

Resolving the evolutionary and ecological factors that generate and maintain avian biodiversity is a central goal of ornithology. The Pacific lowlands of Mexico are biodiverse but understudied with respect to spatial patterns of genealogical and phenotypic diversity. We examine genetic and phenotypic variation of the widespread Whitecollared Seedeater (Sporophila torqueola), a granivorous songbird. We use highthroughput sequencing of ultraconserved elements to reconstruct the evolutionary history of populations from the Pacific and Atlantic lowlands of Mexico and Central America. Leveraging over 1000 nuclear loci and whole mitochondrial genomes from 72 individuals sampled throughout the species’ range, we report that the Pacific lowlands populations (S. t. torqueola group) are genetically differentiated from the remaining populations (S. t. morelletti group). The two lineages are reciprocally monophyletic with ~7.5% divergence in mitochondrial DNA. Using coalescent models, we find little evidence of gene flow between the two lineages, while ecological niche models suggest multiple glacial refugia during the last glacial maximum. Additionally, there is extensive phenotypic differentiation within the complex: the western S. t. torqueola group has a cinnamon rump and crissum with no wing bars, while the eastern S. t. morelletti group has wing bars combined with a white rump and crissum. Our study provides evidence of strong phenotypic and genetic differentiation within the S. torqueola complex, suggesting a possible taxonomic split. These findings highlight the Pacific lowlands of Mexico as a biodiverse—yet understudied—region of avian endemism.

 

[Peter Kovalik]

Common Chaffinches

U. Perktas, A. Townsend Peterson & D. Dyer. Integrating morphology, phylogeography, and ecological niche modeling to explore population differentiation in North African Common Chaffinches.

Diagnosing discrete evolutionary taxa requires careful assessment of genetic, morphological, ecological, and behavioral variation within and among populations. In this study, data on phenotype (mensural and coloration characters) and genotype [mitochondrial DNA (mtDNA) control-region sequences], and distributional projections derived from ecological niche models (ENMs), were used to investigate population differentiation of North African Common Chaffinches. Results showed substantial genetic variation among populations, mostly (~56%) distributed between Libyan populations and other North African populations, rather than within populations. Isolation-by-distance analyses, together with spatial genetic structure analyses, indicated severely restricted gene flow between populations. Historical demographic analyses indicate that population expansion began before the Last Glacial Maximum (LGM), which is concordant with ecological niche model paleoprojections; interestingly, the differentiation of the Libyan population apparently did not take place under the last glacial conditions. Hence, although its taxonomic status must await robust testing using multilocus DNA data, this population is an important element in the conservation of bird diversity in North Africa.

 

[Peter Kovalik]

Atlapetes albinucha complex

A. Rocha-Mendez, E. Arbel ez-Cortes & Senchez-Gonz lez. When molecules do not follow morphology: Phylogeography of the Atlapetes albinucha complex (Aves, Emberizidae).

The white-naped brush finch (Atlapetes albinucha) complex comprises eight subspecies identified based mainly in the color pattern (gray vs. yellow belly) and geographic distribution. Yellow and gray bellied forms were long considered two different species (A. albinucha and A. gutturalis). Previous studies in Atlapetes have shown that the phylogeny is usually not congruent with characters like coloration, ecology, and distributional patterns. Herein, we analyzed the phylogeography and phylogenetic relationships in A. albinucha using two mitochondrial and one nuclear markers from samples including 28 different localities along the whole distribution, from the mountains in eastern Mexico to Colombia, and were divided for the analyses into six populations according to their geographical distribution. Topologies recovered by means of Bayesian inference and Maximum Likelihood analyses revealed no geographic structure within populations in the complex, however both recovered a major Colombian clade. Molecular diversity indices in both mitochondrial markers were analyzed and showed low diversity between geographically distant populations. The results provided by the haplotype network structure suggest a recent process of expansion after a bottleneck event with a cryptic speciation scenario thanks to a differentiation owed to a glacial refugia event. This type of hard polytomies, maintained even with the use of alternative data sets, may reflect a simultaneous lineage diversification.

 

[Peter Kovalik]

Polyplectron

H. Miranda, D. Brooks, T. Quach & B. Caballero. Mitogenomic Phylogeography of the Peacock-Pheasants Polyplectron of Southeast Asia.

Several phylogenies for Polyplectorn has been proposed over several decades. We sequenced the whole mitochondrial genomes of six Polyplectron, integrated existing single gene sequence data, and conducted phylogenetic analyses in an attempt to track the historical pattern of speciation. Our analysis strongly suggests the Sundaic origin of Polyplecton with P. schleiermacheri (Borneo) and P. malacense (Peninsular Malaysia) and P. napoleonis (Palawan) forming the basal clade and P. bicalcaratum, P. chalcurum and P. inopinatum as terminal taxa. The P. inopinatum of peninsular Malaysia and P. chalcurum of Sumatra sister-taxa relationship suggests allopatry, or secondary colonization to Sumatra, by ancestral P. inopinatum. The coexistence of P. inopinatum and P. malacense in the same region does not suggest sympatry, but may have resulted from that secondary colonization event of the montane habitat during the Last Glacial Maxima. The isolation of P. chalcurum population in Sumatra and P. inopinatum of Peninsular Malaysia occurred following sea level rise and upland contraction of the montane vegetation at the end of the Pleistocene. Our analysis supports the Sunda shelf origin then spreading to the highland/montane region of mainland Asia. We suspect climate change and the rising sea levels during the Pleistocene drove this speciation pattern.

 

[Peter Kovalik]

Aves

J. Cracraft & S. Claramunt. Global avian biogeography: a test of two
worldviews.

For the last 45 years there has been a clash of worldviews over the biogeographic history of modern birds. One the one hand, multiple avian paleontologists have proposed that modern birds arose primarily in the Northern Hemisphere and then spread to the Southern continents, or are relictual to those areas following climate deterioration in the mid-Miocene. A second worldview, inferred from phylogenetic studies, proposed that many clades, including a large number near the base of Neornithes, suggest that birds arose on the continental fragments of Gondwana. This often-intense debate has been perpetuated because of reasons well understood in the history of science: entrenched belief systems over evidence as well as over methods. In this case it has involved the primacy of fossil evidence in biogeographic analysis and the relevance of quantitative analytical methods in historical biology (phylogenetics, biogeography). To resolve this problem we constructed a global timetree and phylogenetic analysis of 202 avian families of birds using a large suite of fossil taxa for time-calibration. Our analysis shows that Neornithes arose and diversified on Gondwana, primarily in South America and West Antarctica around the K-Pg boundary, and became cosmopolitan by ~55-50 Ma (Claramunt and Cracraft Sci. Adv. 2015;1:e1501005). This result is robust to phylogenetic uncertainty at the base of birds as well as to methods of analysis. We contend the 45 year-old debate is solved.

 

[Peter Kovalik]

Pachyramphus

L. Musher & J. Cracraft. Phylogenomic analysis using ultraconserved elements reveals cryptic diversity in the complex Neotropical genus Pachyramphus.

Phylogeographic studies within the Neotropics continue to uncover cryptic diversity, the extent of which remains unknown. Molecular studies of suboscine birds, in particular are producing evidence that diversity is substantially underestimated. One group of Neotropical suboscine birds, the becards (genus: Pachyramphus), ranges from Argentina through northern Mexico and the Caribbean. Within the 16 currently recognized species, 55 taxa have been described. Their taxonomic relationships have been confusing and controversial. The genus has bounced around a number of suboscine families and been considered incertae sedis repeatedly. Within-genus taxonomy has also been complex, as certain named taxa have been designated to multiple species-groups. Previous analyses (Barber and Rice, 2007) found evidence of paraphyly in one species, P. castaneus, but all prior studies have been both taxonomically and phylogeographically under-sampled. We sequenced mitochondrial DNA for 255 individuals of 50 taxa, including all recognized species, in the genus Pachyramphus, and used target capture and massively parallel sequencing of ultraconserved elements for 41 individuals of 29 taxa, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. While some discordance between genetrees and species trees for diagnosable taxa may be attributable to incomplete lineage sorting or gene flow at recent timescales, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches, nonmonophyletic taxa, and a high number of reciprocally monophyletic intraspecific lineages across the tree suggest that diversity is underestimated and the evolutionary history has been misunderstood.