Hybridization or the interbreeding of genetically discrete populations or species can occur where ranges of genetically distinct units overlap. Golden-winged warblers Vermivora chrysoptera, a species that has been in steady decline for decades, highlight the potential population-level consequences of hybridization. A major factor implicated in their decline is hybridization with their sister species, the blue-winged warbler Vermivora cyanoptera, which has likely been exacerbated by historic and current land-use practices. We examined habitat associations of golden-winged...

The Cerulean Warbler is a declining Nearctic-Neotropical migrant species of concern that breeds in hardwood forests of the eastern United States and Canada. While much knowledge has been gained about the nesting period of this canopy species, little is known about the post-fledging period. During the 2014 and 2015 breeding seasons, after locating and monitoring nests within a matrix of habitat conditions created by various forest management strategies in NW Pennsylvania, USA, we captured fledglings...

The Cerulean Warbler (Setophaga cerulea) is a declining Nearctic-Neotropical migratory species of conservation concern. Implementing full annual cycle conservation strategies to facilitate recovery has been difficult because we know little about the migratory period or connectivity between North American breeding regions and South American non-breeding regions. Between 2014–2017, we deployed geolocators on 282 males at 13 study sites throughout the species’ range with the objectives of a) evaluating the strength of connectivity between breeding and...

Additional file 4: Relationship between probability of identity (PID), probability of identity between siblings (PIDsib) and the number of genotyped SNP or microsatellite loci.

1.The extent to which environmental context mediates the bioaccumulation of biotransported contaminants by stream-resident organisms is poorly understood. For example, it is unclear the extent to which contaminant type, instream characteristics, or resident fish identity interact to influence the uptake of contaminants deposited by Pacific salmon (Oncorhynchus spp.) during their spawning runs. 2.To address this uncertainty, we sampled four stream-resident fish species from 13 watersheds of the Laurentian Great Lakes in locations with and without...

Extensive range loss for the Golden-winged Warbler (Vermivora chrysoptera) has occurred in areas of intrusion by the Blue-winged Warbler (V. cyanoptera) potentially related to their close genetic relationship. We compiled data on social pairing from nine studies for 2,679 resident Vermivora to assess evolutionary divergence. Hybridization between pure phenotypes occurred with 1.2% of resident males for sympatric populations. Pairing success rates for Golden-winged Warblers was 83% and for Blue-winged Warblers was 77%. Pairing success for...

Background: Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, Allegheny woodrat populations have experienced population declines throughout their range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small,...

Additional file 2: Summary statistics associated with nuclear genome sequencing, assembly and annotation.

Additional file 1: Microsatellite genotypes of woodrats sampled in 2009, 2011 and 2012 in the Palisades, NJ. The spreadsheets labeled “Raw Data” and “data GenAlEx” include the genotypes for twenty-eight individuals genotyped at 11 microsatellite loci. These individuals had relatively low genetic variability, as indicated by number of alleles (spreadsheets AFP and AGL), observed heterozygosity and expected heterozygosity (spreadsheet HFP).

Additional file 1: Microsatellite genotypes of woodrats sampled in 2009, 2011 and 2012 in the Palisades, NJ. The spreadsheets labeled “Raw Data” and “data GenAlEx” include the genotypes for twenty-eight individuals genotyped at 11 microsatellite loci. These individuals had relatively low genetic variability, as indicated by number of alleles (spreadsheets AFP and AGL), observed heterozygosity and expected heterozygosity (spreadsheet HFP).

Additional file 5: Comparison of microsatellite- and SNP-based genetic variation.

Abstract Background Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species’ range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of...

Our understanding of songbird habitat needs during the breeding season stems largely from studies of nest success. However, growing evidence shows that nesting habitat and post-fledging habitat often differ. Management guidelines for declining species need to be revaluated and updated to account for habitat shifts that may occur across the full breeding cycle. The Golden-winged Warbler (Vermivora chrysoptera) is a declining songbird species for which best management practices (BMPs) are based overwhelmingly on nesting habitat....

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g. cryptic species), differences in criteria of species concepts, and discordance between gene topologies (e.g. mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to...

Eastern deciduous forests are changing in species composition and diversity outside of classical successional trajectories. Three disturbance mechanisms appear central to this phenomenon: fire frequency is reduced, canopy gaps are smaller, and browsers are more abundant. Which factor is most responsible is a matter of great debate and remains unclear, at least partly because few studies have simultaneously investigated more than one process. We conducted a large-scale experiment in mesophytic forests of West Virginia, USA,...

Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear...

Fishers (Pekania pennanti) are often associated with the coniferous and mixed forests of the northern United States and central Canada, and their ecology has been studied extensively in portions of their distributional range. Recently, natural range expansion and reintroductions have led to recolonization by fishers of portions of the central Appalachian Mountains, USA, where deciduous forest is the dominant vegetation type. We used noninvasive hair snare surveys and microsatellite genetic analysis to detect fishers in...

Additional file 5: Comparison of microsatellite- and SNP-based genetic variation.

Additional file 2: Summary statistics associated with nuclear genome sequencing, assembly and annotation.

Throughout Amazonia, overfishing has decimated populations of fruit-eating fishes, especially the largebodied characid, Colossoma macropomum. During lengthy annual floods, frugivorous fishes enter vast Amazonian floodplains, consume massive quantities of fallen fruits and egest viable seeds. Many tree and liana species are clearly specialized for icthyochory, and seed dispersal by fish may be crucial for the maintenance of Amazonian wetland forests. Unlike frugivorous mammals and birds, little is known about seed dispersal effectiveness of fishes. Extensive...

Southern Ocean paleoceanography provides key insights into how iron fertilization and oceanic productivity developed through Pleistocene ice-ages and their role in influencing the carbon cycle. We report the first high-resolution record of dust deposition and ocean productivity for the Antarctic Zone, close to the main dust source, Patagonia. Our deep-ocean records cover the last 1.5 Ma, thus doubling that from Antarctic ice-cores. We find a ≥10-fold increase in dust deposition during glacials and a ≤5-fold...

Abstract Background Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species’ range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of...

Additional file 3: SNP genotypes of woodrats sampled in Indiana, New Jersey, Ohio and Pennsylvania. The spreadsheet labeled “Raw Data” includes the genotypes for 318 individuals genotyped at 134 SNP loci.

Additional file 3: SNP genotypes of woodrats sampled in Indiana, New Jersey, Ohio and Pennsylvania. The spreadsheet labeled “Raw Data” includes the genotypes for 318 individuals genotyped at 134 SNP loci.

Additional file 4: Relationship between probability of identity (PID), probability of identity between siblings (PIDsib) and the number of genotyped SNP or microsatellite loci.