Population assignment reveals low migratory connectivity in a weakly structured songbird

Museum genomics provide insight into the extinction of a specialist North American warbler species

Museum genomics provide an opportunity to investigate population demographics of extinct species, especially valuable when research prior to extinction was minimal. The Bachman's warbler (Vermivora bachmanii) is hypothesized to have gone extinct due to loss of its specialized habitat. However, little is known about other potential contributing factors such as natural rarity or changes to connectivity following habitat fragmentation. We examined mitochondrial DNA (mtDNA) and genome-wide SNPs using specimens collected from breeding and migration sites across the range of the Bachman's warbler. We found no signals of strong population structuring across the breeding range of Bachman's warblers in both mtDNA and genome-wide SNPs. Thus, long-term population isolation did not appear to be a significant contributor to the extinction of the Bachman's warbler. Instead, our findings support the theory that Bachman's warblers underwent a rapid decline likely driven by habitat destruction, which may have been exacerbated by the natural rarity, habitat specificity and low genetic diversity of the species.

A synthesis of recent tools and perspectives in migratory connectivity studies

Migration movements connect breeding and non-breeding bird populations over the year. Such links, referred to as migratory connectivity, have important implications for migratory population dynamics as they dictate the consequences of localised events for the whole population network. This calls for concerted efforts to understand migration processes for large-scale conservation. Over the last 20 years, the toolbox to investigate connectivity patterns has expanded and studies now consider migratory connectivity over a broader range of species and contexts. Here, we summarise recent developments in analysing migratory connectivity, focusing on strategies and challenges to pooling various types of data to both optimise and broaden the scope of connectivity studies. We find that the different approaches used to investigate migratory connectivity still have complementary strengths and weaknesses, whether in terms of cost, spatial and temporal resolution, or challenges in obtaining large sample sizes or connectivity estimates. Certain recent developments offer particularly promising prospects: robust quantitative models for banding data, improved precision of geolocators and accessibility of telemetry tracking systems, and increasingly precise probabilistic assignments based on genomic markers or large-scale isoscapes. In parallel, studies have proposed various ways to combine the information of different datasets, from simply comparing the connectivity patterns they draw to formally integrating their analyses. Such data combinations have proven to be more accurate in estimating connectivity patterns, particularly for integrated approaches that offer promising flexibility. Given the diversity of available tools, future studies would benefit from a rigorous comparative evaluation of the different methodologies to guide data collection to complete migration atlases: where and when should data be collected during the migratory cycle to best describe connectivity patterns? Which data are most favourable to combine, and under what conditions? Are there methods for combining data that are better than others? Can combination methods be improved by adjusting the contribution of the various data in the models? How can we fully integrate connectivity with demographic and environmental data? Data integration shows strong potential to deepen our understanding of migratory connectivity as a dynamic ecological process, especially if the gaps can be bridged between connectivity, population and environmental models.

Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Novel insights into symbiont population structure: Globe-trotting avian feather mites contradict the specialist-generalist variation hypothesis

Researchers often examine symbiont host specificity as a species-level pattern, but it can also be key to understanding processes occurring at the population level, which are not as well understood. The specialist-generalist variation hypothesis (SGVH) attempts to explain how host specificity influences population-level processes, stating that single-host symbionts (specialists) exhibit stronger population genetic structure than multi-host symbionts (generalists) because of fewer opportunities for dispersal and more restricted gene flow between populations. However, this hypothesis has not been tested in systems with highly mobile hosts, in which population connectivity may vary temporally and spatially. To address this gap, we tested the SGVH on proctophyllodid feather mites found on migratory warblers (family Parulidae) with contrasting host specificities, Amerodectes protonotaria (a host specialist of Protonotaria citrea) and A. ischyros (a host generalist of 17 parulid species). We used a pooled-sequencing approach and a novel workflow to analyse genetic variants obtained from whole genome data. Both mite species exhibited fairly weak population structure overall, and contrary to predictions of the SGVH, the generalist was more strongly structured than the specialist. These results may suggest that specialists disperse more freely among conspecifics, whereas generalists sort according to geography. Furthermore, our results may reflect an unexpected period for mite transmission - during the nonbreeding season of migratory hosts - as mite population structure more closely reflects the distributions of hosts during the nonbreeding season. Our findings alter our current understanding of feather mite biology and highlight the potential for studies to explore factors driving symbiont diversification at multiple evolutionary scales.

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

Evolutionary stability inferred for a free ranging lizard with sex-reversal

The sex of vertebrates is typically determined genetically, but reptile sex can also be determined by developmental temperature. In some reptiles, temperature interacts with genotype to reverse sex, potentially leading to transitions from a chromosomal to a temperature‐dependent sex determining system. Transitions between such systems in nature are accelerated depending on the frequency and fitness of sex‐reversed individuals. The Central Bearded Dragon, Pogona vitticeps, exhibits female heterogamety (ZZ/ZW) but can have its sex reversed from ZZ male to ZZ female by high incubation temperatures. The species exhibits sex‐reversal in the wild and it has been suggested that climate change and fitness of sex‐reversed individuals could be increasing the frequency of reversal within the species range. Transitions to temperature‐dependent sex determination require low levels of dispersal and high (>50%) rates of sex‐reversal. Here, we combine genotype‐by‐sequencing, identification of phenotypic and chromosomal sex, exhaustive field surveys, and radio telemetry to examine levels of genetic structure, rates of sex‐reversal, movement, space use, and survival of P. vitticeps in a location previously identified as a hot spot for sex‐reversal. We find that the species exhibits low levels of population structure (FST ~0.001) and a modest (~17%) rate of sex‐reversal, and that sex‐reversed and nonsex‐reversed females have similar survival and behavioural characteristics to each other. Overall, our data indicate this system is evolutionary stable, although we do not rule out the prospect of a more gradual transition in sex‐determining mechanisms in the future in a more fragmented landscape and as global temperatures increase.

Hierarchical genetic structure and implications for conservation of the world's largest salmonid, Hucho taimen

Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.

Bergmann's rule is followed at multiple stages of postembryonic development in a long-distance migratory songbird

Bergmann’s rule is a well‐established, ecogeographical principle that states that body size varies positively with latitude, reflecting the thermoregulatory benefits of larger bodies as temperatures decline. However, this principle does not seem to easily apply to migratory species that are able to avoid the extreme temperatures during winter at higher latitudes. Further, little is known about the ontogeny of this relationship across life stages or how it is influenced by ongoing global climate change. To address these knowledge gaps, we assessed the contemporary relationship between latitude and body size in a long‐distance migratory species, the prothonotary warbler (Protonotaria citrea) across life stages (egg to adult) on their breeding grounds. We also measured historic eggs (1865‐1961) to assess if the relationship between latitude and size during this life stage has changed over time. In accordance with Bergmann’s rule, we found a positive relationship between latitude and body mass during all post‐embryonic life stages, from early nestling stage through adulthood. We observed this same predicted pattern with historic eggs, but contemporary eggs exhibited the reverse (negative) relationship. We suggest that these results indicate a genetic component to this pattern and speculate that selection for larger body size in altricial nestlings as latitude increases may possibly drive the pattern in migratory species as even rare extreme cold weather events may cause mortality during early life stages. Furthermore, the opposite relationships observed in eggs, dependent on time period, may be related to the rapidly warming environments of higher latitudes that is associated with climate change. Although it is unclear what mechanism(s) would allow for this recent reversal in eggs (but still allow for its maintenance in later life stages). This evidence of a reversal suggests that anthropogenic climate change may be in the process of altering one of the longest‐standing principles in ecology.

Using multiple natural tags provides evidence for extensive larval dispersal across space and through time in summer flounder

Dispersal sets the fundamental scales of ecological and evolutionary dynamics and has important implications for population persistence. Patterns of marine dispersal remain poorly understood, partly because dispersal may vary through time and often homogenizes allele frequencies. However, combining multiple types of natural tags can provide more precise dispersal estimates, and biological collections can help to reconstruct dispersal patterns through time. We used single nucleotide polymorphism genotypes and otolith core microchemistry from archived collections of larval summer flounder (Paralichthys dentatus, n = 411) captured between 1989 and 2012 at five locations along the US East coast to reconstruct dispersal patterns through time. Neither genotypes nor otolith microchemistry alone were sufficient to identify the source of larval fish. However, microchemistry identified clusters of larvae (n = 3-33 larvae per cluster) that originated in the same location, and genetic assignment of clusters could be made with substantially more confidence. We found that most larvae probably originated near a biogeographical break (Cape Hatteras) and that larvae were transported in both directions across this break. Larval sources did not shift north through time, despite the northward shift of adult populations in recent decades. Our novel approach demonstrates that summer flounder dispersal is widespread throughout their range, on both intra- and intergenerational timescales, and may be a particularly important process for synchronizing population dynamics and maintaining genetic diversity during an era of rapid environmental change. Broadly, our results reveal the value of archived collections and of combining multiple natural tags to understand the magnitude and directionality of dispersal in species with extensive gene flow.

Habitat-dependent occupancy and movement in a migrant songbird highlights the importance of mangroves and forested lagoons in Panama and Colombia

Climate change is predicted to impact tropical mangrove forests due to decreased rainfall, sea-level rise, and increased seasonality of flooding. Such changes are likely to influence habitat quality for migratory songbirds occupying mangrove wetlands during the tropical dry season. Overwintering habitat quality is known to be associated with fitness in migratory songbirds, yet studies have focused primarily on territorial species. Little is known about the ecology of nonterritorial species that may display more complex movement patterns within and among habitats of differing quality. In this study, we assess within-season survival and movement at two spatio-temporal scales of a nonterritorial overwintering bird, the prothonotary warbler (Protonotaria citrea), that depends on mangroves and tropical lowland forests. Specifically, we (a) estimated within-patch survival and persistence over a six-week period using radio-tagged birds in central Panama and (b) modeled abundance and occupancy dynamics at survey points throughout eastern Panama and northern Colombia as the dry season progressed. We found that site persistence was highest in mangroves; however, the probability of survival did not differ among habitats. The probability of warbler occupancy increased with canopy cover, and wet habitats were least likely to experience local extinction as the dry season progressed. We also found that warbler abundance is highest in forests with the tallest canopies. This study is one of the first to demonstrate habitat-dependent occupancy and movement in a nonterritorial overwintering migrant songbird, and our findings highlight the need to conserve intact, mature mangrove, and lowland forests.