A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years.

The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.

Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex.

The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca-nimia, crecca-carolinensis, and carolinensis-flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M âˆ¼0.1-0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca-nimia), parapatric (crecca-carolinensis), and (mostly) allopatric (carolinensis-flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.

Estimating Movement Rates Between Eurasian and North American Birds That Are Vectors of Avian Influenza.

Avian influenza (AI) is a zoonotic disease that will likely be involved in future pandemics. Because waterbird movements are difficult to quantify, determining the host-specific risk of Eurasian-origin AI movements into North America is challenging. We estimated relative rates of movements, based on long-term evolutionary averages of gene flow, between Eurasian and North American waterbird populations to obtain bidirectional baseline rates of the intercontinental movements of these AI hosts. We used population genomics and coalescent-based demographic models to obtain these gene-flow-based movement estimates. Inferred rates of movement between these continental populations varies greatly among species. Within dabbling ducks, gene flow, relative to effective population size, varies from ∼3 to 24 individuals/generation between Eurasian and American wigeons (Mareca penelope and Mareca americana) to ∼100-300 individuals/generation between continental populations of northern pintails (Anas acuta). These are evolutionary long-term averages and provide a solid foundation for understanding the relative risks of each of these host species in potential intercontinental AI movements. We scale these values to census size for evaluation in that context. In addition to being AI hosts, many of these bird species are also important in the subsistence diets of Alaskans, increasing the risk of direct bird-to-human exposure to Eurasian-origin AI virus. We contrast species-specific rates of intercontinental movements with the importance of each species in Alaskan diets to understand the relative risk of these taxa to humans. Assuming roughly equivalent AI infection rates among ducks, greater scaup (Aythya marila), mallard (Anas platyrhynchos), and northern pintail (Anas acuta) were the top three species presenting the highest risks for intercontinental AI movement both within the natural system and through exposure to subsistence hunters. Improved data on AI infection rates in this region could further refine these relative risk assessments. These directly comparable, species-based intercontinental movement rates and relative risk rankings should help in modeling, monitoring, and mitigating the impacts of intercontinental host and AI movements.

Estimación de las tasas de movimiento entre aves euroasiáticas y norteamericanas que son vectores de la influenza aviar. La influenza aviar es una enfermedad zoonótica que probablemente estará involucrada en futuras pandemias. Debido a que los movimientos de aves acuáticas son difíciles de cuantificar, La determinación del riesgo específico de hospedador de los movimientos de influenza aviar de origen euroasiático en América del Norte es un desafío. Se estimaron las tasas relativas de movimientos, sobre la base de promedios evolutivos a largo plazo del flujo de genes, entre las poblaciones de aves acuáticas euroasiáticas y norteamericanas para obtener tasas de referencia bidireccionales de los movimientos intercontinentales de estos huéspedes de influenza aviar. Se utilizó genómica de poblaciones y modelos demográficos basados en la teoría de la coalescencia para obtener estas estimaciones de movimiento basadas en el flujo de genes. Las tasas inferidas de movimiento entre estas poblaciones continentales varían mucho entre especies. Dentro de los patos chapuceros, el flujo de genes, en relación con el tamaño efectivo de la población, varía aproximadamente de 3 a 24 individuos/generación entre los silbones europeos y americanos (Mareca penelope y Mareca americana) hasta aproximadamente entre 100 a 300 individuos/generación entre poblaciones continentales de ánades rabudos (Anas acuta). Estos son promedios evolutivos a largo plazo y proporcionan una base sólida para comprender los riesgos relativos de cada una de estas especies hospedadoras en posibles movimientos intercontinentales de la influenza aviar. Se evaluaron estos valores al tamaño del censo para evaluarlos en ese contexto. Además de ser huéspedes de influenza aviar, muchas de estas especies de aves también son importantes en las dietas de subsistencia de los habitantes de Alaska, lo que aumenta el riesgo de exposición directa de las aves al ser humano por el virus de la influenza aviar de origen euroasiático. Se contrastaron las tasas específicas de especies de movimientos intercontinentales con la importancia de cada especie en las dietas de personas en Alaska para comprender el riesgo relativo de estos taxones para los humanos. Suponiendo tasas de infección por influenza aviar aproximadamente equivalentes entre patos, el porrón bastardo o pato boludo mayor (Aythya marila), el ánade real (Anas platyrhynchos) y el ánade rabudo eran las tres especies principales que presentaban los mayores riesgos para el movimiento de influenza aviar intercontinental tanto dentro del sistema natural como a través de la exposición a cazadores de subsistencia. La mejora de los datos sobre las tasas de infección por influenza aviar en esta región podría mejorar aún más estas evaluaciones de riesgo relativo. Estas tasas de movimiento intercontinental directamente comparables, basadas en especies, y clasificaciones de riesgo relativo deberían ayudar a modelar, monitorear y mitigar los impactos de los movimientos intercontinentales de huéspedes y de la influenza aviar.

An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data.

Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6-8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4N refµ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used.

Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds.

Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split-migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST ), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves:Turdidae).

New World thrushes in the genus Catharus are small, insectivorous or omnivorous birds that have been used to explore several important questions in avian evolution, including the evolution of seasonal migration and plumage variation. Within Catharus, members of a clade of obligate long-distance migrants (C. fuscescens, C. minimus, and C. bicknelli) have also been used in the development of heteropatric speciation theory, a divergence process in which migratory lineages (which might occur in allopatry or sympatry during portions of their annual cycle) diverge despite low levels of gene flow. However, research on Catharus relationships has thus far been restricted to the use of small genetic datasets, which provide limited resolution of both phylogenetic and demographic histories. We used a large, multi-locus dataset from loci containing ultraconserved elements (UCEs) to study the demographic histories of the migratory C. fuscescens-minimus-bicknelli clade and to resolve the phylogeny of the migratory species of Catharus. Our dataset included more than 2000 loci and over 1700 variable genotyped sites, and analyses supported our prediction of divergence with gene flow in the fully migratory clade, with significant gene flow among all three species. Our phylogeny of the genus differs from past work in its placement of C. ustulatus, and further analyses suggest historic gene flow throughout the genus, producing genetically reticulate (or network) phylogenies. This raises questions about trait origins and suggests that seasonal migration and the resulting migratory condition of heteropatry is likely to promote hybridization not only during pairwise divergence and speciation, but also among non-sisters.