Search Results - "Maley, James M."

hzar: hybrid zone analysis using an R software package by Derryberry, Elizabeth P, Derryberry, Graham E, Maley, James M, Brumfield, Robb T

“…We present a new software package (hzar) that provides functions for fitting molecular genetic and morphological data from hybrid zones to classic equilibrium…”
Get full text

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats by Song, Se Jin, Sanders, Jon G, Delsuc, Frédéric, Metcalf, Jessica, Amato, Katherine, Taylor, Michael W, Mazel, Florent, Lutz, Holly L, Winker, Kevin, Graves, Gary R, Humphrey, Gregory, Gilbert, Jack A, Hackett, Shannon J, White, Kevin P, Skeen, Heather R, Kurtis, Sarah M, Withrow, Jack, Braile, Thomas, Miller, Matthew, McCracken, Kevin G, Maley, James M, Ezenwa, Vanessa O, Williams, Allison, Blanton, Jessica M, McKenzie, Valerie J, Knight, Rob

“…Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all…”
Get full text

A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry by Medina, Joshua J, Maley, James M, Sannapareddy, Siddharth, Medina, Noah N, Gilman, Cyril M, McCormack, John E

“…Natural history collections are yielding more information as digitization brings specimen data to researchers, connects specimens across museums, and as new…”
Get full text

Interpreting negative results with taxonomic and conservation implications: Another look at the distinctness of coastal California Gnatcatchers by McCormack, John E, Maley, James M

“…A recent study by Zink et al. (2013) raises questions about how to interpret negative results in studies when the distinctness of a species of conservation…”
Get full text

Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog ( Sarcohyla ; Hylidae) by Zarza, Eugenia, Connors, Elizabeth M, Maley, James M, Tsai, Whitney L E, Heimes, Peter, Kaplan, Moises, McCormack, John E

“…Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this…”
Get full text

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species by Harvey, Michael G, Judy, Caroline Duffie, Seeholzer, Glenn F, Maley, James M, Graves, Gary R, Brumfield, Robb T

“…Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted impacts of divergence, gene flow and selection…”
Get full text

More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens by Tsai, Whitney L. E., Schedl, Margaret E., Maley, James M., McCormack, John E.

“…Next‐generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum…”
Get full text

Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands by Tsai, Whitney L.E., Mota-Vargas, Claudio, Rojas-Soto, Octavio, Bhowmik, Ravi, Liang, Emily Y., Maley, James M., Zarza, Eugenia, McCormack, John E.

“…[Display omitted] •We use historical specimen DNA to explore biogeography of Dendrortyx wood-partridges.•Phylogenies reveal divergences from the Pliocene…”
Get full text

Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird by Venkatraman, Madhvi X, Deraad, Devon A, Tsai, Whitney L E, Zarza, Eugenia, Zellmer, Amanda J, Maley, James M, Mccormack, John E

“…Abstract The highlands of Mesoamerica harbour some of the highest biodiversity in the world, especially in cloud forests, but the landscape drivers of this…”
Get full text

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences by McCormack, John E., Maley, James M., Hird, Sarah M., Derryberry, Elizabeth P., Graves, Gary R., Brumfield, Robb T.

“…[Display omitted] ► We demonstrate a way to generate multilocus DNA data using next-generation sequencing. ► The method produces thousands of loci and hundreds…”
Get full text

Diversification at high latitudes: speciation of buntings in the genus Plectrophenax inferred from mitochondrial and nuclear markers by Maley, James M, Winker, Kevin

“…High-latitude diversification is a process characterized by speciation and extinction due to climatically driven vicariance and dispersal events. McKay's…”
Get full text

Mitochondrial and Next-Generation Sequence Data Used to Infer Phylogenetic Relationships and Species Limits in the Clapper/King Rail Complex by Maley, James M., Brumfield, Robb T.

“…The family Rallidae is a distinct, species-rich group of birds, many of which are exceptional at long-distance colonization. Six of the ten species in the…”
Get full text

Phenotypic clines across an unstudied hybrid zone in Woodhouse's Scrub-Jay (Aphelocoma woodhouseii) by DeRaad, Devon A, Maley, James M, Tsai, Whitney L. E, McCormack, John E

“…Woodhouse's Scrub-Jay (Aphelocoma woodhouseii) comprises 7 subspecies, ranging from the Rocky Mountains to southern Mexico. We quantified the phenotype of…”
Get full text

Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact by Gowen, Fiona C, Maley, James M, Cicero, Carla, Peterson, A Townsend, Faircloth, Brant C, Warr, T Caleb, McCormack, John E

“…Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between…”
Get full text

Evidence from the Genetics of Landbirds for a Forested Pleistocene Glacial Refugium in the Haida Gwaii Area by Pruett, Christin L, Topp, Carrie M, Maley, James M, McCracken, Kevin G, Rohwer, Sievert, Birks, Sharon, Sealy, Spencer G, Winker, Kevin

“…Pleistocene refugia likely contributed to the modern biodiversity of northern areas. Using the mitochondrial DNA cytochrome-b gene, we compared 11…”
Get full text

Paraphyly of Cinclodes fuscus (Aves: Passeriformes: Furnariidae): Implications for taxonomy and biogeography by Sanín, Camilo, Cadena, Carlos Daniel, Maley, James M., Lijtmaer, Darío A., Tubaro, Pablo L., Chesser, R. Terry

“…The Andes are a hotspot of global avian diversity, but studies on the historical diversification of Andean birds remain relatively scarce. Evolutionary studies…”
Get full text

Characterization of microsatellite loci for a threatened species, the King Rail, Rallus elegans, using a next-generation sequencing protocol by Brackett, Carol L., Maley, James M., Brumfield, Robb T., McRae, Susan B.

“…The King Rail Rallus elegans (Audubon) has experienced population declines of 4.6 % per year on average since the 1960s. Wetland loss, most severely affecting…”
Get full text

USE OF JUVENAL PLUMAGE IN DIAGNOSING SPECIES LIMITS: AN EXAMPLE USING BUNTINGS IN THE GENUS PLECTROPHENAX by Maley, James M, Winker, Kevin

“…Species limits in the genus Plectrophenax have been difficult to assess. McKay’s Buntings (Plectrophenax hyperboreus) are very similar both morphologically and…”
Get full text

Diversification at high latitudes: speciation of buntings in the genus Plectrophenax inferred from mitochondrial and nuclear markers: DIVERSIFICATION AT HIGH LATITUDES by MALEY, JAMES M., WINKER, KEVIN

Get full text

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats by Song, Se Jin, Sanders, Jon G, Delsuc, Frédéric, Metcalf, Jessica, Amato, Katherine, Taylor, Michael W, Mazel, Florent, Lutz, Holly L, Winker, Kevin, Graves, Gary R, Humphrey, Gregory, Gilbert, Jack A, Hackett, Shannon J, White, Kevin P, Skeen, Heather R, Kurtis, Sarah M, Withrow, Jack, Braile, Thomas, Miller, Matthew, Mccracken, Kevin G, Maley, James M, Ezenwa, Vanessa O, Williams, Allison, Blanton, Jessica M, Mckenzie, Valerie J, Knight, Rob

“…Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all…”
Get full text