Geology topics

Terry Chesser

Publications and source records attributed to Terry Chesser.

10 recordsLinked to original sources

USGS2020

Conservative plumage masks extraordinary phylogenetic diversity in the Grallaria rufula (Rufous Antpitta) complex of the humid Andes

The Grallaria rufula complex is currently considered to consist of 2 species, G. rufula (Rufous Antpitta) and G. blakei (Chestnut Antpitta). However, it has been suggested that the complex, populations of which occur in humid montane forests from Venezuela to Bolivia, comprises a suite of vocally distinct yet morphologically cryptic species. We sequenced nuclear and mitochondrial DNA for 80 individuals from across the distribution of the complex to determine the extent of genetic variation between and within described taxa. Our results revealed 18 geographically coherent clades separated by substantial genetic divergence: 14 within rufula, 3 within blakei, and 1 corresponding to G. rufocinerea (Bicolored Antpitta), a species with distinctive plumage found to be nested within the complex. Neither G. rufula nor G. blakei as presently defined was monophyletic. Although 6 of the 7 recognized subspecies of G. rufula were monophyletic, several subspecies contained substantial genetic differentiation. Genetic variation was largely partitioned across recognized geographic barriers, especially across deep river valleys in Peru and Colombia. Coalescent modeling identified 17 of the 18 clades as significantly differentiated lineages, whereas analyses of vocalizations delineated 16 biological species within the complex. The G. rufula complex seems unusually diverse even among birds of the humid Andes, a prime location for cryptic speciation; however, the extent to which other dispersal-limited Andean species groups exhibit similar degrees of cryptic differentiation awaits further study.

Auk↗

USGS2020

Taxonomic evaluation of the Grallaria rufula (Rufous Antpitta) complex (Aves: Passeriformes: Grallariidae) distinguishes sixteen species

Populations in the Rufous Antpitta ( Grallaria rufula ) complex occupy humid montane forests of the Andes from northern Colombia and adjacent Venezuela to central Bolivia. Their tawny to cinnamon-colored plumages are generally uniform, featuring subtle variation in hue and saturation across this range. In contrast to their conservative plumage, substantial vocal differences occur among geographically isolated or parapatric populations. Working within the framework of a comprehensive molecular phylogeny, we reexamined species limits in the G. rufula complex, basing taxonomic recommendations on diagnostic differences in vocalizations and considering identifiable differences in plumage where pertinent. We identified 16 populations for species designation, including seven populations previously described as subspecies and, remarkably, six new species described herein. Within one of these species, we identified less robust vocal differences between populations that we designate as subspecies. Geographic variation exists within another species, but its critical evaluation requires additional material. Taxonomic revisions of groups consisting of cryptic species, like the Grallaria rufula complex, are imperative for their conservation. Rather than widespread species as currently defined, these complexes can comprise many range-restricted taxa at higher risk of extinction given the continuing human pressures on their habitats.

Zootaxa↗

USGS2020

The evolution of a tropical biodiversity hotspot

The role of the environment in the origin of new species has long been debated. Harvey et al. examined the evolutionary history and species diversity of suboscine birds in the tropics (see the Perspective by Morlon). Contrary to expectations that the tropics have higher rates of speciation, the authors observed that higher and more constant speciation rates occur in harsh environments relative to the tropics. Thus, for this group of birds, diversification in temperate to Arctic regions followed by the movement and retention of species in the tropics results in their higher local levels of species diversity.

Science↗

USGS2019

A phylogenomic supertree of birds

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally-efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used this to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

Diversity↗

USGS2019

Earth history and the passerine superradiation

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records, suggest that passerines originated on the Australian landmass ~47 Ma, and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

PNAS↗

USGS2018

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6 , three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.

Mitochondrial DNA Part A↗

USGS2018

Spatial organization of the gastrointestinal microbiota in urban Canada geese

Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose ( Branta canadensis ). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes , Proteobacteria , and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.

Scientific Reports↗

USGS2018

Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae)

Phylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura . Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified using plumage characters. However, our genetic data, when considered in combination with phenotypic data, appear to be at odds with the current classification of some species of Chaetura . We recommend that C. viridipennis , currently generally treated as specifically distinct from C. chapmani , be returned to its former status as C. chapmani viridipennis , and that C. andrei , now generally regarded as synonymous with C. vauxi aphanes , again be recognized as a valid species. Widespread Neotropical species C. spinicaudus is paraphyletic with respect to more range-restricted species C. fumosa , C. egregia , and C. martinica . Geographically structured genetic variation within some other species of Chaetura , especially notable in C. cinereiventris , suggests that future study may lead to recognition of additional species in this genus. Biogeographic analysis indicated that Chaetura originated in South America and identified several dispersal events to Middle and North America following the formation of the Isthmus of Panama.

Molecular Phylogenetics and Evolution↗

USGS2017

Fifty-eighth supplement to the American Ornithologists' Union: Check-list of North American Birds

This is the 17th supplement since publication of the 7th edition of the Check-list of North American Birds (American Ornithologists' Union [AOU] 1998). It summarizes decisions made between April 15, 2016, and April 15, 2017, by the AOS's Committee on Classification and Nomenclature—North and Middle America. The Committee has continued to operate in the manner outlined in the 42nd Supplement

The Auk↗

USGS2016

Recurrent hybridization and recent origin obscure phylogenetic relationships within the ‘white-headed’ gull (Larus sp.) complex

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/ canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Molecular Phylogenetics and Evolution↗