Alexis Powell

Genetic Evidence for Early Peritoneal Spreading in Pelvic High-Grade Serous Cancer

Frontiers in oncology, 2018

Most pelvic high-grade serous (HGS) carcinomas have been proposed to arise from tubal primaries t... more Most pelvic high-grade serous (HGS) carcinomas have been proposed to arise from tubal primaries that progress rapidly to advanced disease. However, the temporal sequence of ovarian and peritoneal metastases is not well characterized. To establish the sequence of metastases, phylogenetic relationships among the ovarian and peritoneal carcinomas were determined from single-nucleotide variations (SNVs) in nine tumor regions from each patient with pelvic HGS carcinomas. Somatic SNVs from each tumor sample were used to reconstruct phylogenies of samples from each patient. Variant allele frequencies were used to reconstruct subclone phylogenies in each tumor sample. We show that pelvic HGS carcinomas are highly heterogeneous, only sharing less than 4% of somatic SNVs among all nine carcinoma implants in one patient. TP53 mutations are found in all nine carcinoma implants in each patient. The phylogenetic analyses reveal that peritoneal metastases arose from early branching events that pre...

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<strong>A revised classification of the Icteridae (Aves) based on DNA sequence data</strong>

Zootaxa, 2016

The higher-level classification of the New World blackbirds (Icteridae; Aves) has remained relati... more The higher-level classification of the New World blackbirds (Icteridae; Aves) has remained relatively stable for nearly a half-century, with most currently used classifications (e.g. Sibley &amp;amp;amp;amp;amp;amp;amp; Monroe 1990; Jaramillo &amp;amp;amp;amp;amp;amp;amp; Burke 1999; Fraga 2011; Remsen et al. 2015) following Blake&amp;amp;amp;amp;amp;amp;#39;s (1968) delimitation and sequence of genera in the Peters Check-list of Birds of the World series. Early molecular studies (e.g., Lanyon 1992, 1994; Johnson &amp;amp;amp;amp;amp;amp;amp; Lanyon 1999; Price &amp;amp;amp;amp;amp;amp;amp; Lanyon 2002; Cadena et al. 2004) produced only minor modifications.

Molecular phylogenetics of the New World blackbirds (Icteridae)

The grackles (Quiscalus spp.), together with their sister genus Euphagus, compose a clade within ... more The grackles (Quiscalus spp.), together with their sister genus Euphagus, compose a clade within the New World blackbirds (Icteridae). We used gene sequences of cytochrome b and NADH dehydrogenase subunit 2 (ND2) to reconstruct relationships within this group. A primary concern was determining the phylogenetic position and genetic distinctiveness of the extinct Slender-billed Grackle (Q. palustris)-a poorly known endemic of the Lerma Basin and the ancient lakes of the Valley of Mexico, last collected and recorded in 1910-and of the Nicaraguan Grackle (Q. nicaraguensis), which is likewise unusual among grackles for its restricted geographic range. Our analysis differs from previous efforts by inclusion of these taxa along with all other recognized grackle species, intraspecific sampling of Greater Antillean (Q. niger), Carib (Q. lugubris), and Great-tailed (Q. mexicanus) Grackles, and inclusion of additional sequence data. The recovered phylogeny reveals Slender-billed Grackle to be most closely related to one of two major haplotype clades of Great-tailed Grackle, the other being sister to Boat-tailed Grackle (Q. major). Nicaraguan Grackle appears sister to Carib Grackle (Q. lugubris). We discuss the implications of these and other relationships in the genus for species limits and biogeography. 1-1. INTRODUCTION The grackles (Quiscalus) are among the most familiar of blackbirds (Icteridae). Common in anthropogenic landscapes, they are conspicuous by virtue of their gregariousness, their habit of foraging on the ground in open areas, their iridescent black or rich rusty brown (in some females) plumages, and their long wedgeshaped tails, which they flare and keel distinctively in flight and display. The seven species currently recognized (AOU 1998) are all very similar with respect to morphology, behavior, and ecology.

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Interspecific Interactions between Marsh-dwelling Ammodramus Sparrows at a Migration Stopover

The Wilson Journal of Ornithology, 2007

... Interspecific Interactions between Marsh-dwelling Ammodramus Sparrows at a Migration Stopover... more

Effects of Grassland Management on Breeding Birds at the Western Edge of the Tallgrass Prairie Ecosystem in Kansas

Natural Areas Journal, 2013

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Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: An avian case study

Molecular Phylogenetics and Evolution, 2013

Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decade... more Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate heterogeneity, without discarding data, by applying separate evolutionary models to differing portions of the mitogenome. To facilitate use of complete mitogenomic sequences in phylogenetics, we (1) suggest a set of categories for dividing mitogenomic datasets into subsets, (2) explore differences in evolutionary dynamics among those subsets, and (3) apply a method for combining data subsets with similar properties to produce effective and efficient partitioning schemes. We demonstrate these procedures with a case study, using the mitogenomes of species in the grackles and allies clade of New World blackbirds (Icteridae). We found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that we tested. As hoped, we found that analyses using whole mitogenomic sequences yielded much better-resolved and more strongly-supported hypotheses of the phylogenetic history of that locus than did a conventional 2-kilobase sample (i.e. sequences of the cytochrome b and ND2 genes). Mitogenomes have much untapped potential for phylogenetics, especially of birds, a taxon for which they have been little exploited except in investigations of ordinal-level relationships.

A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae)

Molecular Phylogenetics and Evolution, 2014

The New World blackbirds (Icteridae) are among the best known songbirds, serving as a model clade... more The New World blackbirds (Icteridae) are among the best known songbirds, serving as a model clade in comparative studies of morphological, ecological, and behavioral trait evolution. Despite wide interest in the group, as yet no analysis of blackbird relationships has achieved comprehensive species-level sampling or found robust support for most intergeneric relationships. Using mitochondrial gene sequences from all ∼108 currently recognized species and six additional distinct lineages, together with strategic sampling of four nuclear loci and whole mitochondrial genomes, we were able to resolve most relationships with high confidence. Our phylogeny is consistent with the strongly-supported results of past studies, but it also contains many novel inferences of relationship, including unexpected placement of some newly-sampled taxa, resolution of relationships among major clades within Icteridae, and resolution of genus-level relationships within the largest of those clades, the grackles and allies. We suggest taxonomic revisions based on our results, including restoration of Cacicus melanicterus to the monotypic Cassiculus, merging the monotypic Ocyalus and Clypicterus into Cacicus, restoration of Dives atroviolaceus to the monotypic Ptiloxena, and naming Curaeus forbesi to a new genus, Anumara. Our hypothesis of blackbird phylogeny provides a foundation for ongoing and future evolutionary analyses of the group.

Status of the regal fritillary (Speyeria idalia) and effects of fire management on its abundance in northeastern Kansas, USA

Journal of Insect Conservation, 2007

... Alexis FLA Powell Æ William H. Busby Æ Kelly Kindscher ... Abstract The Regal Fritillary (Spe... more

A Complete Species-Level Phylogeny of the Grackles ( Quiscalus SPP.), Including the Extinct Slender-Billed Grackle, Inferred from Mitochondrial Dna

The Condor, 2008

The grackles (Quiscalus spp.), together with their sister genus Euphagus, compose a clade within ... more The grackles (Quiscalus spp.), together with their sister genus Euphagus, compose a clade within the New World blackbirds (Icteridae). We used gene sequences of cytochrome b and NADH dehydrogenase subunit 2 (ND2) to reconstruct relationships within this group. A primary concern was determining the phylogenetic position and genetic distinctiveness of the extinct Slender-billed Grackle (Q. palustris)-a poorly known endemic of the Lerma Basin and the ancient lakes of the Valley of Mexico, last collected and recorded in 1910-and of the Nicaraguan Grackle (Q. nicaraguensis), which is likewise unusual among grackles for its restricted geographic range. Our analysis differs from previous efforts by inclusion of these taxa along with all other recognized grackle species, intraspecific sampling of Greater Antillean (Q. niger), Carib (Q. lugubris), and Great-tailed (Q. mexicanus) Grackles, and inclusion of additional sequence data. The recovered phylogeny reveals Slender-billed Grackle to be most closely related to one of two major haplotype clades of Great-tailed Grackle, the other being sister to Boat-tailed Grackle (Q. major). Nicaraguan Grackle appears sister to Carib Grackle (Q. lugubris). We discuss the implications of these and other relationships in the genus for species limits and biogeography.

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A complete species-level phylogeny of the Grackles (Quiscalus spp.), including the extinct slender-billed Grackle, inferred from mitochondrial DNA

The Condor, 2008

The grackles (Quiscalus spp.), together with their sister genus Euphagus, compose a clade within ... more The grackles (Quiscalus spp.), together with their sister genus Euphagus, compose a clade within the New World blackbirds (Icteridae). We used gene sequences of cytochrome b and NADH dehydrogenase subunit 2 (ND2) to reconstruct relationships within this group. A primary concern was determining the phylogenetic position and genetic distinctiveness of the extinct Slender-billed Grackle (Q. palustris)-a poorly known endemic of the Lerma Basin and the ancient lakes of the Valley of Mexico, last collected and recorded in 1910-and of the Nicaraguan Grackle (Q. nicaraguensis), which is likewise unusual among grackles for its restricted geographic range. Our analysis differs from previous efforts by inclusion of these taxa along with all other recognized grackle species, intraspecific sampling of Greater Antillean (Q. niger), Carib (Q. lugubris), and Great-tailed (Q. mexicanus) Grackles, and inclusion of additional sequence data. The recovered phylogeny reveals Slender-billed Grackle to be most closely related to one of two major haplotype clades of Great-tailed Grackle, the other being sister to Boat-tailed Grackle (Q. major). Nicaraguan Grackle appears sister to Carib Grackle (Q. lugubris). We discuss the implications of these and other relationships in the genus for species limits and biogeography.

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Effects of Prescribed Burns and Bison (Bos Bison) Grazing on Breeding Bird Abundances in Tallgrass Prairie

The Auk, 2006

AяѠѡџюѐѡ.-Grassland birds have declined more than any other avian assemblage in North America, wi... more AяѠѡџюѐѡ.-Grassland birds have declined more than any other avian assemblage in North America, with nearly every species showing negative population trends. In the Flint Hills of Kansas, the largest remnant of the tallgrass prairie biome, annual spring burning of rangeland has recently replaced burning every 2-3 years. I examined eff ects of diff erent burning and bison (Bos bison) grazing regimes on June abundances of seven bird species using a 23-year data set from the Konza Prairie Biological Station. Fire signifi cantly aff ected the abundances of six of the seven species. Eff ects varied among species but, notably, four grass-dependent species-Grasshopper Sparrow (Ammodramus savannarum), Henslow's Sparrow (A. henslowii), Dickcissel (Spiza americana), and Eastern Meadowlark (Sturnella magna)and the shrub-dependent Bell's Vireo (Vireo bellii)-were least abundant or absent at sites in the breeding season immediately following burning. Upland Sandpipers (Bartramia longicauda) were most abundant at sites in the season following burning, whereas Brown-headed Cowbirds (Molothrus ater) exhibited no signifi cant response. Bison grazing increased abundance of Upland Sandpiper and Grasshopper Sparrow, nearly eliminated Henslow's Sparrow, and (in combination with recent fi re) lowered the abundance of Dickcissel. Although fi re and grazing are natural forces that maintain tallgrass prairie, their action was, until recently, intermiĴ ent and patchy, providing grassland birds with a variety of levels of disturbance. If the vast Flint Hills prairie is to serve as a grassland bird stronghold, the region-wide practice of annual burning with intensive grazing must be replaced with alternatives that restore heterogeneity to the landscape.

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Effects of prescribed burns and bison (Bos bison) grazing on breeding bird abundances in tallgrass prairie

The Auk, 2006

AяѠѡџюѐѡ.-Grassland birds have declined more than any other avian assemblage in North America, wi... more AяѠѡџюѐѡ.-Grassland birds have declined more than any other avian assemblage in North America, with nearly every species showing negative population trends. In the Flint Hills of Kansas, the largest remnant of the tallgrass prairie biome, annual spring burning of rangeland has recently replaced burning every 2-3 years. I examined eff ects of diff erent burning and bison (Bos bison) grazing regimes on June abundances of seven bird species using a 23-year data set from the Konza Prairie Biological Station. Fire signifi cantly aff ected the abundances of six of the seven species. Eff ects varied among species but, notably, four grass-dependent species-Grasshopper Sparrow (Ammodramus savannarum), Henslow's Sparrow (A. henslowii), Dickcissel (Spiza americana), and Eastern Meadowlark (Sturnella magna)and the shrub-dependent Bell's Vireo (Vireo bellii)-were least abundant or absent at sites in the breeding season immediately following burning. Upland Sandpipers (Bartramia longicauda) were most abundant at sites in the season following burning, whereas Brown-headed Cowbirds (Molothrus ater) exhibited no signifi cant response. Bison grazing increased abundance of Upland Sandpiper and Grasshopper Sparrow, nearly eliminated Henslow's Sparrow, and (in combination with recent fi re) lowered the abundance of Dickcissel. Although fi re and grazing are natural forces that maintain tallgrass prairie, their action was, until recently, intermiĴ ent and patchy, providing grassland birds with a variety of levels of disturbance. If the vast Flint Hills prairie is to serve as a grassland bird stronghold, the region-wide practice of annual burning with intensive grazing must be replaced with alternatives that restore heterogeneity to the landscape.

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Status of the regal fritillary (Speyeria idalia) and effects of fire management on its abundance in northeastern Kansas, USA

Journal of Insect Conservation, 2007

... Alexis FLA Powell Æ William H. Busby Æ Kelly Kindscher ... Abstract The Regal Fritillary (Spe... more

Responses of breeding birds in tallgrass prairie to fire and cattle grazing

Journal of Field Ornithology, 2008

No other group of North American birds has declined as precipitously and over so large an area as... more No other group of North American birds has declined as precipitously and over so large an area as has the grassland assemblage. In the Flint Hills of Kansas, the largest extant region of tallgrass prairie, annual spring burning of rangeland has largely replaced traditional regimes and natural patterns with longer intervals between burns. I examined effects of burning and low-intensity cattle grazing on abundances of seven bird species at Konza Prairie Research Natural Area in June 2002 and 2003. Every species was affected by fire, with Upland Sandpipers (Bartramia longicauda) more abundant, and six species-Grasshopper Sparrow (Ammodramus savannarum), Henslow's Sparrow (A. henslowii), Dickcissel (Spiza americana), Eastern Meadowlark (Sturnella magna), Brown-headed Cowbird (Molothrus ater), and Bell's Vireo (Vireo bellii)-either less abundant or absent at sites in the breeding season following a fire. These results demonstrate that annual burning limits the potential of much of the Flint Hills prairie to harbor high breeding densities of many grassland birds. On the other hand, I found a trade-off between immediate and longer-term effects of burning for several grass-dependent species. Grasshopper Sparrows, Henslow's Sparrows, and Eastern Meadowlarks, although more numerous in areas that were not burned the preceding spring, were less abundant at sites burned every 4 yrs than those burned at shorter intervals. In contrast, shrub-dependent Bell's Vireos were more abundant at sites burned every 4 yrs. Upland Sandpipers, Grasshopper Sparrows, and Eastern Meadowlarks were more abundant in grazed areas. Use of alternatives to annual burning could increase habitat heterogeneity by transforming the Flint Hills into a mosaic of regularly, but asynchronously, burned pastures that would better meet the diverse habitat needs of the region's grassland birds. SINOPSIS. Respuesta de aves, que se reproducen en yerbazales de praderas, a fuegos y al pastoreo Ningún otro grupo de aves de norteamérica se ha reducido en número de forma tan precipitada y sobre uń area tan extensiva, que las aves de yerbazales. En las colinas Flint de Kansas, la extención más grande de pradera con yerbas altas, la quema primaveral y el pastoreo del ganado han remplazado los regímenes, más tradicionales y naturales, con intérvalos más amplios entre quemas. Examiné el efecto de fuegos y pastoreo de baja intensidad con la abundancia de siete especies en elárea Experimental Natural de la Pradera de Konza. El estudio se llevó a cabo entre 2002 y 2003. Cada especie fue afectada por el fuego. El playero Bartramia longicauda, incrementé en números. Sin embargo, otras seis especies, Ammodramus savannarum, A. henslowii, Spiza americana, Sturnella magna, Molothrus ater y Vireo bellii, se redujeron o desaparecieron luego de la quema. Estos resultados demuestran que la quema anual limita el potencial de mantener densidades reproductivas altas de dichas aves en las praderas de Flint Hill. De otra parte, encontré un intercambio entre los efectos a corto y largo plazo de la quema en varias de las especies que dependen de dichos yerbazales. A. savannarum, A. henslowii, y S. magna, aunque resultaron más numerosos eń areas que no fueron quemadas la primavera anterior, resultaron menos abundantes en lugares que se quemaron en lapsos de cuatro años que en aquellos que se quemaron a intérvalos más cortos. En contraste, aves como V. bellii, que dependen de matorrales oáreas arbustivas, resultaron más abundantes enáreas que se quemaron cada cuatro años. Bartramia longicauda, Ammodramus savannarum y S. magna resultaron más abundantes en lugares en donde hubo pastoreo. El uso de alternativas a la quema anual puede incrementar la heterogeneidad del hábitat transformando a Flint Hills en un mosaico de patizales quemados, regulares pero asincrónicos, que provee las necesidades de un hábitat más diverso para las aves de hierbazales de la región.

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