Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini)

Pervasive gene flow despite strong and varied reproductive barriers in swordtails

The evolution of reproductive barriers leads to the formation of new species. However, recent research has demonstrated that hybridization has been pervasive across the tree of life even in the presence of strong barriers. Using swordtail fishes (genus Xiphophorus), an emerging model system, we document overlapping mechanisms that act as barriers to gene flow between Xiphophorus birchmanni and Xiphophorus cortezi by combining genomic sequencing from natural hybrid populations, experimental laboratory crosses, behavioural assays, sperm measures and developmental studies. We show that assortative mating plays a role in maintaining subpopulations with distinct ancestry within natural hybrid populations. Using F2 hybrids we identify several genomic regions that strongly impact hybrid viability. Strikingly, two of these regions underlie genetic incompatibilities in hybrids between X. birchmanni and its sister species Xiphophorus malinche. Our results demonstrate that ancient hybridization has played a role in the origin of this shared genetic incompatibility. Moreover, ancestry mismatch at these incompatible regions has remarkably similar consequences for phenotypes and hybrid survival in X. cortezi × X. birchmanni hybrids as in X. malinche × X. birchmanni hybrids. Our findings identify varied reproductive barriers that shape genetic exchange between naturally hybridizing species and highlight the complex evolutionary outcomes of hybridization.

Mitochondrial genome of the Indian spot-billed duck and its phylogenetic and conservation implications

The Indian spot-billed duck, Anas poecilorhyncha is a large dabbling and non-migratory breeding bird. The identification and phylogenetic relationship of A. poecilorhyncha remain uncertain due to the presence of overlapping meristic characters and hybridization with closely related species. Molecular data aids when there are challenges in morphological identification. However, genetic characterization of A. poecilorhyncha has been paid less attention. Apart from their functional and physiological role, mitochondrial genome can also be used for various purposes, including species identification, phylogenetic analysis, understanding the domestication history of species etc. Therefore, the present study aimed to sequence the mitochondrial genome of A. poecilorhyncha and its closely related domestic species A. platyrhynchos (mallard duck) to understand their mitochondrial genome structure and phylogenetic relationships. The length of mitochondrial genome of A. poecilorhyncha and A. platyrhynchos was 16,608 and 16,604 bp respectively. Mitochondrial genome contained 37 genes and a non-coding control region. Overall, the characteristics of mitochondrial genome of both species were found to be conserved. The phylogenetic tree exhibited seven major clades (A to G) with a high bootstrap support. Notably, the Indian A. poecilorhyncha population formed a distinct clade (C) whereas the A. poecilorhyncha that were probably sampled from China grouped along with A. zonorhyncha (clade B). Besides, one of the A. poecilorhyncha probably sampled from China was placed in the clade A, which predominantly consisted of A. platyrhynchos. It suggests that Indian A. poecilorhyncha population is genetically different from Chinese A. poecilorhyncha population. Further, it sheds light on the importance of conducting a comprehensive phylogenetic study on these species. The newly sequenced mitochondrial genome of A. poecilorhyncha and A. platyrhynchos would be useful not only to have a better understanding of the phylogeny and evolution of Anas species but also to help in the conservation of A. poecilorhyncha which is under constant threat from rapid urbanization, interspecific hybridization and other human activities.

Population connectivity and size reductions in the Anthropocene: the consequence of landscapes and historical bottlenecks in white forsythia fragmented habitats

BACKGROUND

White forsythia (Abeliophyllum distichum) is an endangered Korean Peninsula endemic that has been subjected to recent population genomics studies using SNPs via RAD sequencing. Here, we primarily employed the often underutilized haplotype information from RAD loci to further describe the species' previously uninvestigated haplotype-based genomic variation and structure, and genetic-geographic characteristics and gene flow patterns among its five earlier identified genetic groups. We also inferred the time of past events that may have impacted the effective population size of these groups, as well as the species' potential future distribution amidst the warming climate and anthropogenic threats.

RESULTS

Our findings emphasized the recognition of the species' regional patterns of genetic structure, and the role of topography and its associated gene flow patterns as some of the possible factors that may have influenced the species' present-day fragmented population distribution. The inferred bottleneck events during the Anthropocene, some of which aligned with the time of historical catastrophic events on the Peninsula (e.g., the Korean War), were revealed to have contributed to the generally low effective population size of its five lineages, particularly those with marginal distributional range. Future distribution under both optimistic and pessimistic climatic scenarios suggests unlikely suitable habitats for these populations to expand from their current range limits, at least in the next 80 years.

CONCLUSIONS

The small effective population size and landscape-driven limited gene flow among white forsythia populations will remain a big challenge for the conservation management of the species' already fragmented population distribution. To help mitigate these impacts, the merging of various research approaches and the use of genomic data to their full potential is recommended to provide the optimized knowledge-based tools for the conservation of this endangered species, and other similar plants under pressure.

Consistent changes in muscle phenotype and mitochondrial abundance underlie dive performance across multiple lineages of diving ducks

Diving animals must sustain high muscle activity with finite oxygen (O2) to forage underwater. Studies have shown that some diving mammals exhibit changes in the metabolic phenotype of locomotory muscles compared with non-divers, but the pervasiveness of such changes across diving animals is unclear, particularly among diving birds. Here, we examined whether changes in muscle phenotype and mitochondrial abundance are associated with dive capacity across 17 species of ducks from three distinct evolutionary clades (tribes) in the subfamily Anatinae: the longest diving sea ducks, the mid-tier diving pochards and the non-diving dabblers. In the gastrocnemius (the primary swimming and diving muscle), mitochondrial volume density in both oxidative and glycolytic fiber types was 70% and 30% higher in sea ducks compared with dabblers, respectively. These differences were associated with preferential proliferation of the subsarcolemmal subfraction, the mitochondria adjacent to the cell membrane and nearest to capillaries, relative to the intermyofibrillar subfraction. Capillary density and capillary-to-fiber ratio were positively correlated with mitochondrial volume density, with no variation in the density of oxidative fiber types across tribes. In the pectoralis, sea ducks had greater abundance of oxidative fiber types than dabblers, whereas pochards were intermediate between the two. These data suggest that skeletal muscles of sea ducks have a heightened capacity for aerobic metabolism and an enhanced ability to utilize O2 stores in the blood and muscle while diving.

Pervasive gene flow despite strong and varied reproductive barriers in swordtails

One of the mechanisms that can lead to the formation of new species occurs through the evolution of reproductive barriers. However, recent research has demonstrated that hybridization has been pervasive across the tree of life even in the presence of strong barriers. Swordtail fishes (genus Xiphophorus) are an emerging model system for studying the interface between these barriers and hybridization. We document overlapping mechanisms that act as barriers between closely related species, X. birchmanni and X. cortezi, by combining genomic sequencing from natural hybrid populations, artificial crosses, behavioral assays, sperm performance, and developmental studies. We show that strong assortative mating plays a key role in maintaining subpopulations with distinct ancestry in natural hybrid populations. Lab experiments demonstrate that artificial F1 crosses experience dysfunction: crosses with X. birchmanni females were largely inviable and crosses with X. cortezi females had a heavily skewed sex ratio. Using F2 hybrids we identify several genomic regions that strongly impact hybrid viability. Strikingly, two of these regions underlie genetic incompatibilities in hybrids between X. birchmanni and its sister species X. malinche. Our results demonstrate that ancient hybridization has played a role in the origin of this shared genetic incompatibility. Moreover, ancestry mismatch at these incompatible regions has remarkably similar consequences for phenotypes and hybrid survival in X. cortezi × X. birchmanni hybrids as in X. malinche × X. birchmanni hybrids. Our findings identify varied reproductive barriers that shape genetic exchange between naturally hybridizing species and highlight the complex evolutionary outcomes of hybridization.

Consistent changes in muscle metabolism underlie dive performance across multiple lineages of diving ducks

Diving animals must sustain high activity with limited O2 stores to successfully capture prey. Studies suggest that increasing body O2 stores supports breath-hold diving, but less is known about metabolic specializations that underlie underwater locomotion. We measured maximal activities of 10 key enzymes in locomotory muscles (gastrocnemius and pectoralis) to identify biochemical changes associated with diving in pathways of oxidative and substrate-level phosphorylation and compared them across three groups of ducks-the longest diving sea ducks (eight spp.), the mid-tier diving pochards (three spp.) and the non-diving dabblers (five spp.). Relative to dabblers, both diving groups had increased activities of succinate dehydrogenase and cytochrome c oxidase, and sea ducks further showed increases in citrate synthase (CS) and hydroxyacyl-CoA dehydrogenase (HOAD). Both diving groups had relative decreases in capacity for anaerobic metabolism (lower ratio of lactate dehydrogenase to CS), with sea ducks also showing a greater capacity for oxidative phosphorylation and lipid oxidation (lower ratio of pyruvate kinase to CS, higher ratio of HOAD to hexokinase). These data suggest that the locomotory muscles of diving ducks are specialized for sustaining high rates of aerobic metabolism, emphasizing the importance of body O2 stores for dive performance in these species.

The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards

The translocation of individuals around the world is leading to rising incidences of anthropogenic hybridization, particularly between domestic and wild congeners. We apply a landscape genomics approach for thousands of mallard (Anas platyrhynchos) samples across continental and island populations to determine the result of over a century of supplementation practices. We establish that a single domestic game-farm mallard breed is the source for contemporary release programs in Eurasia and North America, as well as for established feral populations in New Zealand and Hawaii. In particular, we identify central Europe and eastern North America as epicenters of ongoing anthropogenic hybridization, and conclude that the release of game-farm mallards continues to affect the genetic integrity of wild mallards. Conversely, self-sustaining feral populations in New Zealand and Hawaii not only show strong differentiation from their original stock, but also signatures of local adaptation occurring in less than a half-century since game-farm mallard releases have ceased. We conclude that 'wild' is not singular, and that even feral populations are capable of responding to natural processes. Although considered paradoxical to biological conservation, understanding the capacity for wildness among feral and feral admixed populations in human landscapes is critical as such interactions increase in the Anthropocene.

Interspecific forced copulations generate most hybrids in broadly sympatric ducks

Although rare, hybrids are more common in broadly sympatric waterfowl than in any other avian family; yet, the behavioral ecology explaining their generation has remained controversial. Leading hypotheses are forced interspecific copulations, mis-imprinting caused by mixed broods, and scarcity of conspecific mates. Using a large sample of hybrid ducks solicited from North American hunters we evaluated these hypotheses by genetically determining the mother and father species of F₁ hybrids. Based on abundances in areas where their breeding ranges overlap, the frequency of hybrids varied greatly from expectations, with hybrids between species within recently derived clades being much more frequent than those between more divergent clades. Forced copulations, as measured by large phallus-length asymmetries between parentals, strongly predicted the father species of most F₁ hybrids. Thus, most Anas acuta x A. platyrhynchos (Northern Pintail x Mallard) F₁s were sired by A. acuta, and most A. platyrhynchos x Mareca strepera (Mallard x Gadwall) F₁s were sired by A. platyrhynchos. Siring asymmetries were consistent with phallus length asymmetries in five additional parental combinations, but none had samples large enough to be individually statistically significant. The exception to this trend was our sample of nine A. platyrhynchos x Mareca americana (Mallard x Gadwall) F₁s, for which a large phallus asymmetry failed to predict the father species. Hybrids were rare in brood parasitic species, suggesting mis-imprinting to be an unlikely cause of most hybrids; however, our samples of hybrids from regular brood parasites were inadequate to strongly address this hypothesis. We could test the scarcity of mates hypothesis for only a single hybrid combination and it contradicted our prediction: most F₁M. Penelope x M. americana (Eurasian x American Wigeon) were sired by M. penelope, strongly contradicting our prediction that female M. penelope wintering in enormous flocks of M. americana (American Wigeon) on the west coast of North America would have difficulty finding conspecific mates. In general, our results support interspecific forced copulations as the predominant behavioral mechanism generating hybrids in North temperate waterfowl.

Evolutionary and Ecological Drivers of Local Adaptation and Speciation in a North American Avian Species Complex

Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for non-model organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in a climate refugia arising during a glacial period in in a southwestern North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that likely reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.

No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference

A recent article in Ecology and Evolution featured the discovery of hybrid snowcocks (Tetraogallus) and speculated on the hybrid origin of an extant species (T. altaicus). Comprehensive re-analyses of original data from the latter paper reliably refute the phylogenetic hypothesis taken as firm evidence of a past hybridization event in these birds. The new re-analyses showed that there is no evidence of hybridization in these snowcocks from the data available so far.