Widespread gene flow following range expansion in Anna's Hummingbird.

Anthropogenic changes have altered the historical distributions of many North American taxa. As environments shift, ecological and evolutionary processes can combine in complex ways to either stimulate or inhibit range expansion. Here, we examined the role of evolution in a rapid range expansion whose ecological context has been well-documented, Anna's Hummingbird (Calypte anna).

Visualizing population structure with variational autoencoders.

Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs)-generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data-for visualizing population genetic variation. VAEs incorporate nonlinear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP.

Predicting geographic location from genetic variation with deep neural networks.

Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here, we describe a deep learning method, which we call Locator, to accomplish this task faster and more accurately than existing approaches.

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data.

Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here, we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies (GWAS).

Evidence of linked selection on the Z chromosome of hybridizing hummingbirds.

Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen's Hummingbirds during the Holocene.

Ecological Release of the Anna's Hummingbird during a Northern Range Expansion.

During range expansions, species can experience rapid population growth if changes in climate or interspecific interactions remove limits on growth rates in novel habitats. Here I document a century of range expansion in the Anna's hummingbird () and investigate the causes of its recent abundance through a combination of demographic, climatic, and phenological analyses. Christmas Bird Count records indicate that populations have been growing in California since the early twentieth century.

Minor allele frequency thresholds strongly affect population structure inference with genomic data sets.

A common method of minimizing errors in large DNA sequence data sets is to drop variable sites with a minor allele frequency (MAF) below some specified threshold. Although widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical single nucleotide polymorphism data set to demonstrate the impacts of MAF thresholds on inference of population structure-often the first step in analysis of population genomic data.

A Migratory Divide in the Painted Bunting (Passerina ciris).

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.

Cryptic speciation and gene flow in a migratory songbird Species Complex: Insights from the Red-Eyed Vireo (Vireo olivaceus).

Migratory species that alternate between sympatry and allopatry over the course of an annual cycle are promising subjects for studies seeking to understand the process of speciation in the absence of strict geographic isolation. Here we sought to identify cryptic species and assess rates of gene flow in a clade of neotropical migrant songbirds in which geography and taxonomy are currently out of sync: the Red-Eyed Vireo (V. olivaceus) Species Complex.

A multilocus phylogeny of a major New World avian radiation: the Vireonidae.

The family Vireonidae represents one of the most widespread and well-known New World avian radiations, but a robust species-level phylogeny of the group is lacking. Here, we infer a phylogeny of Vireonidae using multilocus data obtained from 221 individuals from 46 of 52 vireonid species (representing all four genera) and five "core Corvoidea" outgroups. Our results show Vireonidae to be monophyletic, consistent with a single colonization of the New World by an Asian ancestor.

Characterization of post-hospital infections in adults requiring home parenteral nutrition.

Objective: Limited data are available on the incidence and risk factors for infection in patients requiring home parenteral nutrition (HPN).

Methods: A retrospective study was conducted in 101 consecutive adults (63 female, 38 male) discharged on HPN from the Emory University Hospital, Atlanta, GA. New bloodstream infections (BSIs) requiring rehospitalization and other infections were evaluated.

Efficacy of parenteral nutrition supplemented with glutamine dipeptide to decrease hospital infections in critically ill surgical patients.

Background: Nosocomial infections are an important cause of morbidity and mortality in the surgical intensive care unit (SICU). Clinical benefits of glutamine-supplemented parenteral nutrition may occur in hospitalized surgical patients, but efficacy data in different surgical subgroups are lacking. The objective was to determine whether glutamine-supplemented parenteral nutrition differentially affects nosocomial infection rates in selected subgroups of SICU patients.

Intravenous erythromycin facilitates bedside placement of postpyloric feeding tubes in critically ill adults: a double-blind, randomized, placebo-controlled study.

Unlabelled: OBJECTIVE To evaluate the efficacy of intravenous erythromycin as a method to facilitate feeding tube placement into the small intestine in critically ill patients. DESIGN Double blind, randomized, controlled trial. SETTING Medical and surgical intensive care units in an academic medical center.