Genetic mapping of the female mimic morph locus in the ruff.

BACKGROUND: Ruffs (Aves: Philomachus pugnax) possess a genetic polymorphism for male mating behaviour resulting in three permanent alternative male reproductive morphs: (i) territorial 'Independents', (ii) non-territorial 'Satellites', and (iii) female-mimicking 'Faeders'. Development into independent or satellite morphs has previously been shown to be due to a single-locus, two-allele autosomal Mendelian mode of inheritance at the Satellite locus. Here, we use linkage analysis to map the chromosomal location of the Faeder locus, which controls development into the Faeder morph, and draw further conclusions about candidate genes, assuming shared synteny with other birds. RESULTS: Segregation data on the Faeder locus were obtained from captive-bred pedigrees comprising 64 multi-generation families (N = 381). There was no evidence that the Faeder locus was linked to the Satellite locus, but it was linked with microsatellite marker Ppu020. Comparative mapping of ruff microsatellite markers against the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes places the Ppu020 and Faeder loci on a region of chromosome 11 that includes the Melanocortin-1 receptor (MC1R) gene, which regulates colour polymorphisms in numerous birds and other vertebrates. Melanin-based colouration varies with life-history strategies in ruffs and other species, thus the MC1R gene is a strong candidate to play a role in alternative male morph determination. CONCLUSION: Two unlinked loci appear to control behavioural development in ruffs. The Faeder locus is linked to Ppu020, which, assuming synteny, is located on avian chromosome 11. MC1R is a candidate gene involved in alternative male morph determination in ruffs.

A dominant allele controls development into female mimic male and diminutive female ruffs.

Maintaining polymorphisms for genes with effects of ecological significance may involve conflicting selection in males and females. We present data from a captive population of ruffs (Philomachus pugnax) showing that a dominant allele controls development into both small, 'female mimic' males ('faeders'), and a previously undescribed class of small 'female faeders'. Most male ruffs have elaborate breeding plumage and display behaviour, but 0.5-1.5% are faeders, which lack both. Females from a captive population previously lacking faeders were bred with two founder faeder males and their faeder sons. The faeders' offspring had a quadrimodal size distribution comprising normal-sized males and females, faeders and atypically small females. By contrast, ornamented males fathered only normal-sized offspring. We conclude that both founding faeders were heterozygous for a faeder allele absent from the original population. This allele is dominant to previously described genes that determine development into independent versus satellite ornamented males. Unlike those genes, the faeder allele is clearly expressed in females. Small body size is a component of the male faeder mating strategy, but provides no obvious benefit to females. Bisexual expression of the gene provides the opportunity to quantify the strength of sexually antagonistic selection on a Mendelian trait.

Interclutch variability in egg characteristics in two species of rail: Is maternal identity encoded in eggshell patterns?

Maternal signatures are present in the eggs of some birds, but quantifying interclutch variability within populations remains challenging. Maternal assignment of eggs with distinctive appearances could be used to non-invasively identify renesting females, including hens returning among years, as well as to identify cases of conspecific brood parasitism. We explored whether King Rail (Rallus elegans) eggs with shared maternity could be matched based on eggshell pattern. We used NaturePatternMatch (NPM) software to match egg images taken in the field in conjunction with spatial and temporal data on nests. Since we had only a small number of marked breeders, we analyzed similar clutch images from a study of Eurasian Common Moorhens (Gallinula chloropus chloropus) with color-banded breeders for which parentage at many nests had been verified genetically to validate the method. We ran 66 King Rail clutches (n = 338 eggs) and 58 Common Moorhen clutches (n = 364 eggs) through NPM. We performed non-metric multidimensional scaling and permutational analysis of variance using the best egg match output from NPM. We also explored whether eggs could be grouped by clutch using a combination of egg dimensions and pattern data derived from NPM using linear discriminant analyses. We then scrutinized specific matches returned by NPM for King Rail eggs to determine whether multiple matches between the same clutches might reveal maternity among nests and inform our understanding of female laying behavior. To do this, we ran separate NPM analyses for clutches photographed over several years from two spatially distant parts of the site. With these narrower datasets, we were able to identify four instances where hens likely returned to breed among years, four likely cases of conspecific brood parasitism, and a within-season re-nesting attempt. Thus, the matching output was helpful in identifying congruent egg patterns among clutches when used in conjunction with spatial and temporal data, revealing previously unrecognized site fidelity, within-season movements, and reproductive interference by breeding females. Egg pattern data in combination with nest mapping can be used to inform our understanding of female reproductive effort, success, and longevity in King Rails. These methods may also be applied to other secretive birds and species of conservation concern.

Quantitative acoustic differentiation of cryptic species illustrated with King and Clapper rails.

Reliable species identification is vital for survey and monitoring programs. Recently, the development of digital technology for recording and analyzing vocalizations has assisted in acoustic surveying for cryptic, rare, or elusive species. However, the quantitative tools that exist for species differentiation are still being refined. Using vocalizations recorded in the course of ecological studies of a King Rail (Rallus elegans) and a Clapper Rail (Rallus crepitans) population, we assessed the accuracy and effectiveness of three parametric (logistic regression, discriminant function analysis, quadratic discriminant function analysis) and six nonparametric (support vector machine, CART, Random Forest, k-nearest neighbor, weighted k-nearest neighbor, and neural networks) statistical classification methods for differentiating these species by their kek mating call. We identified 480 kek notes of each species and quantitatively characterized them with five standardized acoustic parameters. Overall, nonparametric classification methods outperformed parametric classification methods for species differentiation (nonparametric tools were between 57% and 81% accurate, parametric tools were between 57% and 60% accurate). Of the nine classification methods, Random Forest was the most accurate and precise, resulting in 81.1% correct classification of kek notes to species. This suggests that the mating calls of these sister species are likely difficult for human observers to tell apart. However, it also implies that appropriate statistical tools may allow reasonable species-level classification accuracy of recorded calls and provide an alternative to species classification where other capture- or genotype-based survey techniques are not possible.

Genetic analyses reveal cryptic introgression in secretive marsh bird populations.

Hybridization is common in bird populations but can be challenging for management, especially if one of the two parent species is of greater conservation concern than the other. King rails (Rallus elegans) and clapper rails (R. crepitans) are two marsh bird species with similar morphologies, behaviors, and overlapping distributions. The two species are found along a salinity gradient with the king rail in freshwater marshes and the clapper in estuarine marshes. However, this separation is not absolute; they are occasionally sympatric, and there are reports of interbreeding. In Virginia, USA, both king and clapper rails are identified by the state as Species of Greater Conservation Need, although clappers are thought to be more abundant and king rails have a higher priority ranking. We used a mitochondrial DNA marker and 13 diagnostic nuclear single nucleotide polymorphisms (SNPs) to identify species, classify the degree of introgression, and explore the evolutionary history of introgression in two putative clapper rail focal populations along a salinity gradient in coastal Virginia. Genetic analyses revealed cryptic introgression with site-specific rates of admixture. We identified a pattern of introgression where clapper rail alleles predominate in brackish marshes. These results suggest clapper rails may be displacing king rails in Virginia coastal waterways, most likely as a result of ecological selection. As introgression can result in various outcomes from outbreeding depression to local adaptation, continued monitoring of these populations would allow further exploration of hybrid fitness and inform conservation management.

Seasonal home range dynamics and sex differences in habitat use in a threatened, coastal marsh bird.

A comprehensive understanding of spatiotemporal ecology is needed to develop conservation strategies for declining species. The king rail (Rallus elegans) is a secretive marsh bird whose range historically extended across the eastern United States. Inland migratory populations have been greatly reduced with most remaining populations inhabiting the coastal margins. Our objectives were to determine the migratory status of breeding king rails on the mid-Atlantic coast and to characterize home range size, seasonal patterns of movement, and habitat use. Using radiotelemetry, we tracked individual king rails among seasons, and established that at least a segment of this breeding population is resident. Mean (±SE) home range size was 19.8 ± 5.0 ha (95% kernel density) or 2.5 ± 0.9 (50% kernel density). We detected seasonal variation and sex differences in home range size and habitat use. In the nonbreeding season, resident male home ranges coincided essentially with their breeding territories. Overwintering males were more likely than females to be found in natural emergent marsh with a greater area of open water. Females tended to have larger home ranges than males during the nonbreeding season. We report for the first time the use of wooded natural marsh by overwintering females. Brood-rearing king rails led their young considerable distances away from their nests (average maximum distance: ~600 ± 200 m) and used both wooded natural and impounded marsh. King rails moved between natural marsh and managed impoundments during all life stages, but the proximity of these habitat types particularly benefitted brood-rearing parents seeking foraging areas with shallower water in proximity to cover. Our results demonstrate the importance of interspersion of habitat types to support resident breeders. Summer draining of impounded wetlands that are seasonally flooded for wintering waterfowl allows regrowth of vegetation and provides additional habitat at a critical time for wading birds.

A supergene determines highly divergent male reproductive morphs in the ruff.

Three strikingly different alternative male mating morphs (aggressive 'independents', semicooperative 'satellites' and female-mimic 'faeders') coexist as a balanced polymorphism in the ruff, Philomachus pugnax, a lek-breeding wading bird. Major differences in body size, ornamentation, and aggressive and mating behaviors are inherited as an autosomal polymorphism. We show that development into satellites and faeders is determined by a supergene consisting of divergent alternative, dominant and non-recombining haplotypes of an inversion on chromosome 11, which contains 125 predicted genes. Independents are homozygous for the ancestral sequence. One breakpoint of the inversion disrupts the essential CENP-N gene (encoding centromere protein N), and pedigree analysis confirms the lethality of homozygosity for the inversion. We describe new differences in behavior, testis size and steroid metabolism among morphs and identify polymorphic genes within the inversion that are likely to contribute to the differences among morphs in reproductive traits.

Conspecific brood parasitism in the tropics: an experimental investigation of host responses in common moorhens and American purple gallinules.

Species occupying a broad latitudinal range may show greater phenotypic plasticity in behavior than species with smaller ranges or more specific habitat requirements. This study investigates for the first time the occurrence of conspecific brood parasitism (CBP) in sympatric tropical populations of the common moorhen (Gallinula chloropus pauxilla Bangs) and the American purple gallinule (Porphyrula martinica L.). CBP occurred in at least 20% (N = 76) of common moorhen nests on the Rio Chagres in Panama. Half (N = 20) of the parasitic eggs were accepted, but 10 were destroyed or ejected from host nests. Introductions of experimental eggs into nests revealed hosts were more likely to accept parasitism later in the host's laying period and during incubation, consistent with expectation of an adaptive response. CBP was not detected in a small sympatric population of American purple gallinules. Members of this population did not eject experimental eggs, suggesting a lack of experience with costly CBP. Contrasting ecological factors help explain why these two species of rail (Family Rallidae) differ in regard to CBP. Purple gallinule territories were sparse, owing to the distribution of preferred habitat. Moorhens flocked outside of the breeding season. They nested more synchronously, at higher densities, and primarily in ephemeral floating vegetation. Further, moorhens suffered a rate of nest loss nearly double that of American purple gallinules, and this increased over the course of the breeding season. Moorhen clutches were larger on average, and more variable in size than those of purple gallinules. Reproductive effort and rate (seasonality) constitute important life history differences between these species that may constrain the evolution of reproductive tactics. Comparing these sympatric populations, and others differing in life-history traits and ecological constraints, highlights the role of risk management in the evolution of CBP.