Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST ) and absolute (dXY ) estimates of divergence. In contrast, the ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.
LETTERSUndercover. Many Alpheidae shrimps live deep in the reef and are impossible to collect nonlethally. Published by AAAS
Flagship species are charismatic species that serve as a symbol and rallying point to stimulate conservation awareness and action but are often used synonymously as de facto umbrella species to delineate reserve boundaries. We tested the extent to which the presence of a flagship species would protect other 'background species' at the local scale at which practical decisions about small reserves are often made. Using long term sightings, we identified four 1 km 2 sites that are frequently visited by jaguars and by tapirs (flagship species), and by white-lipped peccaries and spider monkeys (non-flagship species) in neotropical rainforest in Belize. We then made inventories of five vertebrate taxonomic groups at each site. We found no consistent differences in species richness or abundances of frogs, phyllostomid bats, terrestrial mammals, scansorial mammals or birds across the four sites, except that frog diversity and abundance was higher close to a river at the flagship site where tapirs were found. Since these classic Latin American flagship species fail to encompass particularly high numbers or abundances of vertebrate species at a local scale, they appear to be a poor conservation tool when co-opted as umbrella species for delineating the location of very small reserves in the neotropics.
Since 1989, we have conducted a large-scale ecological experiment in semiarid thorn scrub of a national park in north-central Chile. Initially, we focused on the role of biotic interactions including predation, interspecific competition, and herbivory in small mammal and plant components of the community. We utilized a reductionist approach with replicated 0.56 ha fenced grids that selectively excluded vertebrate predators and/or larger small mammal herbivores such as the degu, Octodon degus. Although we detected small transitory effects of predator exclusions on degu survival and numbers, other species failed to show responses. Similarly, interspecific competition (i.e., degus with other small mammals) had no detectable numerical effects (although some behavioral responses occurred), and degu-exclusions had relatively small effects on various plant components. Modeling approaches indicate that abiotic factors play a determining role in the dynamics of principal small mammal species such as O. degus and the leaf-eared mouse (Phyllotis darwini). In turn, these are mainly related to aperiodic pulses of higher rainfall (usually during El Niño events) which trigger ephemeral plant growth; a food addition experiment in 1997-2000 verified the importance of precipitation as a determinant of food availability. Since 2004, we have expanded long-term monitoring efforts to other important community components including birds and insects in order to understand effects of abiotic factors on them; we report some of the first results of comprehensive surveys on the former in this region. Finally, we recently shifted focus to documenting effects of exotic lagomorphs in the park. We installed additional treatments selectively excluding small mammals, lagomorphs, or both, from replicated grids in order to evaluate putative herbivore impacts. In conjunction with increased annual rainfall since 2000, we predict that introduced lagomorphs will have increasing impacts in this region, and that more frequent El Niños in conjunction with global climatic change may lead to marked changes in community dynamics. The importance of long-term experimental studies is underscored by the fact that only now after 20 years of work are some patterns becoming evident.
Hawaiian ducks (Anas wyvilliana), or koloa, are endemic to the Hawaiian Islands and are listed as a federal and state endangered species. Hybridization between koloa and introduced mallards (A. platyrhynchos) is believed to be a primary threat to the recovery of koloa. We evaluated the utility of two sets of nuclear markers (microsatellite loci and amplified fragment length polymorphisms) and a variable portion of the mitochondrial DNA control region to distinguish among koloa, mallards, and hybrids. We show that microsatellite and AFLP markers can be used to distinguish between koloa and mallard-koloa hybrids with a high degree of confidence. For all but one of the putative koloa in our sample, the posterior probability of belonging to the koloa category was [0.90. Similarly all but one of the mallard-koloa hybrids were assigned to the hybrid category with posterior probabilities [0.98. Subsets of markers led to poorer resolution among koloa, mallard and hybrid categories. Among a sample of 61 koloa, hybrids and mallards, we found 25 different mtDNA haplotypes, belonging to two groups of haplotypes (A and B) identified previously in mallards and their relatives. All putative koloa samples exhibited group B haplotypes, of which 65% comprised one haplotype, while the rest were divided among four haplotypes. All Hawai'i mallard samples exhibited haplotypes that belonged to group A. Hybrids and California mallards exhibited haplotypes belonging to both groups, but a majority were of group A, suggesting that hybridization may more commonly involve mating between Hawai'i mallard females and koloa males.
Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create complex signals of phylogenetic relationships, especially among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian duck (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (Anas platyrhynchos) and Laysan duck (Anas laysanensis). Whereas mtDNA clearly shows a sister relationship between Hawaiian duck and mallard, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan duck and mallard. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the predefined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene-Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian subfossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin and support the hypothesis that the Hawaiian duck may represent a young hybrid species.
Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation in hybrid prevalence in populations throughout the main Hawaiian Islands, using genomic data to characterize population structure of koloa, quantify the extent of hybridization, and compare hybrid proportions over time. To accomplish this, we genotyped 3,308 double‐digest restriction‐site‐associated DNA (ddRAD) loci in 425 putative koloa, mallards, and hybrids from populations across the main Hawaiian Islands. We found that despite a population decline in the last century, koloa genetic diversity is high. There were few hybrids on the island of Kauaʻi, home to the largest population of koloa. By contrast, we report that sampled populations outside of Kauaʻi can now be characterized as hybrid swarms, in that all individuals sampled were of mixed koloa × mallard ancestry. Further, there is some evidence that these swarms are stable over time. These findings demonstrate spatial variation in the extent and consequences of interspecific hybridization, and highlight how islands or island‐like systems with small population sizes may be especially prone to genetic extinction when met with a congener that is not reproductively isolated.
The Florida mottled duck (Anas fulvigula fulvigula) is threatened by introgression through hybridization with feral mallards (A. platyrhynchos). An essential component in managing this threat is the ability to accurately distinguish mottled ducks from mallards and hybrids in the wild. We provide a genetically cross‐validated phenotype key that accurately identifies mottled ducks. We collected data on structural and plumage traits from museum specimens of Florida, USA, mottled ducks and mallards to identify morphological traits useful in this process. We performed extensive comparisons and discriminant function analysis to identify traits informative in distinguishing the 2 species. We used these traits to preliminarily assign 168 contemporary birds as putative mottled duck, mallard, or hybrid. We collected tissue samples from each contemporary specimen and amplified and genotyped associated DNA. We used microsatellite markers to determine posterior probability species assignments for the 168 specimens. We then performed recursive partitioning of phenotypic traits and posterior genotype assignments to create identification keys based on the most informative traits separating mottled ducks from mallards and hybrids. Finally, we cross‐validated the keys by comparing assignments made using the key to those from genotyping for 339 wild ducks. The keys were >90% accurate, which suggests that their adoption will increase the ability of managers to address the threat of hybridization by mallards by allowing mottled ducks to be distinguished from other ducks in Florida. Our research provides a methodology to develop genetically cross‐validated identification keys for other species threatened by genetic introgression. © 2016 The Wildlife Society.
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