Isolation and molecular characterization of a highly polymorphic centromeric tandem repeat in the family Falconidae

Phylogeographical analysis and phylogenetic inference based on the cytochrome b gene in the genus Caiman (Crocodylia: Alligatoridae) in Central and South America

The genus Caiman is one of the most taxonomically conflicted among crocodilians. Caiman crocodilus has four subspecies: Caiman crocodilus crocodilus, Caiman crocodilus fuscus, Caiman crocodilus chiapasius and Caiman crocodilus apaporiensis, but some studies recognize Caiman yacare as a subspecies of C. crocodilus or as a C. crocodilus–C. yacare complex. In Argentina, Caiman latirostris and C. yacare are present and included in sustainable use programmes, although they have hardly been studied at the genetic level. The present study had two main objectives: (1) to study the genetic diversity, structure and phylogeny of C. yacare and C. latirostris in Argentina; and (2) to perform a phylogenetic analysis of the genus Caiman throughout its entire distribution. The results show high haplotype diversity for both species but low nucleotide diversity for C. latirostris. Phylogenetic analysis shows a clear separation between both species but, surprisingly, a well-differentiated clade belonging to the Chaco region was observed. The phylogenetic analysis exhibited clades made up of the sequences of each Caiman species, with some inconsistencies: in the clade of C. crocodilus, one sequence of C. yacare is included, and one clade is observed including sequences from C. c. fuscus and C. c. chiapasius. These data indicate the need to undertake interdisciplinary studies to clarify the taxonomic status of these crocodilian species.

Diversity, distribution, and methodological considerations of haemosporidian infections among Galliformes in Alaska

Using samples spanning 10-degrees of latitude in Alaska, we provide the first comparative assessment of avian haemosporidia distribution of Arctic Alaska with subarctic host populations for four species of grouse and three species of ptarmigan (Galliformes). We found a high overall prevalence for at least one haemospordian genus (88%; N = 351/400), with spruce grouse (Canachites canadensis) showing the highest prevalence (100%; N = 54/54). Haemoproteus and Plasmodium lineages were only observed within grouse, while Leucocytozoon species were found within both grouse and ptarmigan. Further, different Leucocytozoon lineages were obtained from blood and tissue samples from the same individual, potentially due to the differential timing and duration of blood and tissue stages. Using different primer sets, we were able to identify different Leucocytozoon lineages within 55% (N = 44/80) of sequenced individuals, thereby detecting coinfections that may have otherwise gone undetected. The commonly used Haemoproteus/Plasmodium primers amplified Leucocytozoon for 90% (N = 103/115) of the products sequenced, highlighting the potential value of alternate primers to identify intra-genus coinfections and the importance of obtaining sequence information rather than relying solely on PCR amplification to assess parasite diversity. Overall, this dataset provides baseline information on parasite lineage distributions to assess the range expansion associated with climate change into Arctic regions and underscores methodological considerations for future studies.

Breeding origins of a uniquely regular migrant songbird in the Galápagos Islands

Little is known about the causes and consequences of alternative pathways flown by long-distance migratory birds. Bobolinks (Dolichonyx oryzivorus) breed in grasslands across northern North America and migrate from their breeding grounds toward the eastern Atlantic Coast and then proceed through the Caribbean to South America. However, a small but regular number of Bobolinks have been recorded on the Galapagos Islands. We collected genetic samples from nine Galapagos Bobolinks and performed double-digest restriction site-associated sequencing. We compared them with samples from seven locations across their breeding distribution to determine their population of origin. Galapagos Bobolinks shared the genetic structure of a cluster in the eastern portion of the breeding range that includes New Brunswick and Ontario, Canada, and Vermont, United States. Genetic assignment tests largely corroborated this finding, although slightly different results were obtained for the two methods. All individuals were assigned to the Ontario breeding population using AssignPop, while Rubias assigned six of the migrants to Ontario and three to a Midwest breeding population. Low average relatedness among Galapagos individuals indicates that they are not more related to one another than to individuals within a breeding population and are therefore likely not from a single, small isolated population. Our results do not support the probability hypothesis-that Galapagos Bobolinks originated from the region that includes the greatest proportion of their breeding range (Great Plains)-or the vagrant hypothesis-that migrants are displaced onto Galapagos due to weather events. Instead, our findings support the proximity hypothesis, where migrants originate from the geographically closest-breeding populations.

Frequency and types of alternative breeding strategies employed by nesting American black ducks in North Carolina

Although most birds are considered to be at least partially monogamous, molecular evidence continues to uncover that many species can have multiple sexual mates. Many species of Waterfowl (Order Anseriformes) consistently deploy alternative breeding strategies, and although cavity nesting species have been well studied, few attempts to understand rates of alternative breeding strategies exist in the Anatini tribe. Here, we assay mitochondrial DNA and thousands of nuclear markers across 20 broods of American black ducks (Anas rubripes; "black duck") that included 19 females and 172 offspring to study population structure as well as types and rates of secondary breeding strategies in coastal North Carolina. First, we report high levels of relatedness among nesting black ducks and offspring and while 17 (of 19) females were of pure black duck descent, three were found to be black duck x mallard (A. platyrhynchos) hybrids. Next, we evaluated for mismatched mitochondrial DNA and paternity identities across each female's clutch to determine types and frequency of alternative or secondary breeding strategies. Although we report that nest parasitism occurred in two nests, 37% (7 of 19) of the sampled nests were multi-paternal as a result of extra-pair copulation. In addition to being part of a mix of strategies used to increase fecundity by successfully breeding females, we posit nest densities providing easier alternative mate access for males also explains high rates of extra-pair copulation among our sampled black ducks. Ultimately, however, while some proportion of females of many species engage in forms of secondary breeding strategies, we conclude that the decision to do so appears to be seasonally flexible for each individual.

The evolutionary history and mechanistic basis of female ornamentation in a tropical songbird

Ornamentation, such as the showy plumage of birds, is widespread among female vertebrates, yet the evolutionary pressures shaping female ornamentation remain uncertain. In part this is due to a poor understanding of the mechanistic route to ornamentation in females. To address this issue, we evaluated the evolutionary history of ornament expression in a tropical passerine bird, the White-shouldered Fairywren, whose females, but not males, strongly vary between populations in occurrence of ornamented black-and-white plumage. We first use phylogenomic analysis to demonstrate that female ornamentation is derived and that female ornamentation evolves independently of changes in male plumage. We then use exogenous testosterone in a field experiment to induce partial ornamentation in naturally unornamented females. By sequencing the transcriptome of experimentally induced ornamented and natural feathers, we identify genes expressed during ornament production and evaluate the degree to which female ornamentation in this system is associated with elevated testosterone, as is common in males. We reveal that some ornamentation in females is linked to testosterone and that sexes differ in ornament-linked gene expression. Lastly, using genomic outlier analysis we identify a candidate melanogenesis gene that lies in a region of high genomic divergence among populations that is also differentially expressed in feather follicles of different female plumages. Taken together, these findings are consistent with sex-specific selection favoring the evolution of female ornaments and demonstrate a key role for testosterone in generating population divergence in female ornamentation through gene regulation. More broadly, our work highlights similarities and differences in how ornamentation evolves in the sexes.

Negligible evidence for detrimental effects of Leucocytozoon infections among Emperor Geese (Anser canagicus) breeding on the Yukon-Kuskokwim Delta, Alaska

Emperor Geese (Anser canagicus) are iconic waterfowl endemic to Alaska and adjacent areas of northeastern Russia that are considered to be near threatened by the International Union for Conservation. This species has been identified as harboring diverse viruses and parasites which have, at times, been associated with disease in other avian taxa. To better assess if disease represents a vulnerability for Emperor Geese breeding on the Yukon-Kuskokwim Delta, Alaska, we evaluated if haemosporidian parasites were associated with decreased mass or survival among adult female nesting birds captured during 2006-2016. Through molecular analyses, we detected genetically diverse Leucocytozoon, Haemoproteus, and Plasmodium parasites in 28%, 1%, and 1% of 607 blood samples screened in triplicate, respectively. Using regression analysis, we found evidence for a small effect of Leucocytozoon infection on the mass of incubating adult female Emperor Geese. The estimated mass of infected individuals was approximately 43 g (95% CI: 20-67 g), or approximately 2%, less than uninfected birds when captured during the second half of incubation (days 11-25). We did not, however, find support for an effect of Leucocytozoon infection on survival of adult female nesting Emperor Geese using a multi-state hidden Markov framework to analyze mark-resight and recapture data. Using parasite mitochondrial DNA cytochrome b sequences, we identified 23 haplotypes among infected Emperor Geese. Leucocytozoon haplotypes clustered into three phylogenetically supported clades designated as 'L. simondi clade A', 'L. simondi clade B', and 'other Leucocytozoon'. We did not find evidence that parasites assigned to any of these clades were associated with differential mass measures among nesting adult female Emperor Geese. Collectively, our results provide negligible evidence for Leucocytozoon parasites as causing detrimental effects to adult female Emperor Geese breeding on the Yukon-Kuskokwim Delta.

A comprehensive overview of the genetic diversity in Thylamys elegans (Didelphimorphia: Didelphidae): establishing the phylogeographic determinants

Background

For the genus Thylamys, the rivers have been reported as barriers to dispersal, limiting current and historical distribution of its lineages. We hypothesized that the Maipo river has affected the genetic structure of northern and southern lineages of Thylamys elegans, recovering a phylogenetic relationships with reciprocally monophyletic sister groups on opposite river banks. We evaluated the role of other rivers in the Mediterranean zone of Chile as historical and recent modulators of the biogeographic processes of this species.

Methods

We applied a phylogeographic approach, using the cytochrome-b mitochondrial gene for 93 individuals of T. elegans, from 37 localities in a latitudinal gradient between 21°25’ and 35˚56’S, encompassing a geographic area between the Atacama Desert and most of the Mediterranean Chilean zone.

Results

The phylogenetics results recovered six lineages within T. elegans: Thylamys elegans elegans, Thylamys elegans coquimbensis, the Loa lineage and three other lineages not described previously (Aconcagua, South 1 and South 2). We suggest that following rivers play a role like primary barrier: the Maipo river in the genetic differentiation of northern and southern ancestral lineages, and the Mataquito river and its tributary Teno river for the South 1 and South 2 lineages. On the other hand, the Quilimarí river preserve the genetic divergence in T. e. coquimbensis and Aconcagua lineage and the Aconcagua river in Aconcagua lineage and T. e. elegans acting like secondary barriers.

Conclusions

We concluded that the genetic diversity and biogeographic history of T. elegans was shaped by mountain glaciers, changes in river water levels during the Pleistocene glaciations and hyperaridity, promoting the differentiation and persistance of the T. elegans lineages.

Are you my baby? Testing whether paternity affects behavior of cobreeder male acorn woodpeckers

Natural selection is expected to favor males that invest more in offspring they sire. We investigated the relationship between paternity and male behavior in the acorn woodpecker (Melanerpes formicivorus), a cooperative breeder that lives in family groups including offspring that remain on their natal territory, sometimes for years, and cobreeders of both sexes. Regardless of group composition, only one communal nest is attended at a time. Whereas cobreeding females share maternity equally, one male usually sires the majority of young in the group’s communal nest. Copulations are rarely observed, and thus it has not been possible to link paternity to sexual behavior. There were no differences among cobreeder males that did or did not sire young in their propensity to roost in the nest cavity at night. However, cobreeder males that attended females continuously prior to egg-laying were more likely to successfully sire young than males that did not, and the relative share of feeding visits and time spent at the subsequent nest were positively related to a male’s realized paternity. These differences in male behavior were partly due to differences among males and partly to plasticity in male behavior covarying with paternity share. Feedings by males successfully siring young also involved a larger proportion of nutritionally valuable insect prey. Males are aware of their paternity success, apparently because of their relative access to females prior to egg laying, and provide more paternal care at nests in which they are more likely to have sired young.

Lifetime reproductive benefits of cooperative polygamy vary for males and females in the acorn woodpecker (Melanerpes formicivorus)

Cooperative breeding strategies lead to short-term direct fitness losses when individuals forfeit or share reproduction. The direct fitness benefits of cooperative strategies are often delayed and difficult to quantify, requiring data on lifetime reproduction. Here, we use a longitudinal dataset to examine the lifetime reproductive success of cooperative polygamy in acorn woodpeckers (Melanerpes formicivorus), which nest as lone pairs or share reproduction with same-sex cobreeders. We found that males and females produced fewer young per successful nesting attempt when sharing reproduction. However, males nesting in duos and trios had longer reproductive lifespans, more lifetime nesting attempts and higher lifetime reproductive success than those breeding alone. For females, cobreeding in duos increased reproductive lifespan so the lifetime reproductive success of females nesting in duos was comparable to those nesting alone and higher than those nesting in trios. These results suggest that for male duos and trios, reproductive success alone may provide sufficient fitness benefits to explain the presence of cooperative polygamy, and the benefits of cobreeding as a duo in females are higher than previously assumed. Lifetime individual fitness data are crucial to reveal the full costs and benefits of cooperative polygamy.

Account and Utilization of Blood Lipid Profiles: Lipid Levels Predicted Hemosporidian Infection in Migrating Northern Saw-Whet Owls of Eastern North America

Noting lipidomic changes following the parasitism of migrating birds, the metabolic needs of which are primarily fueled by lipids, can deepen our understanding of host-parasite interactions. We identified lipids of migrating Northern saw-whet owls (Aegolius acadicus) using collision-induced dissociation mass spectrometry, compared the lipidomic signatures of hemoparasite-infected and noninfected individuals, and performed cross-validation analyses to reveal associations between parasite infection and lipid levels. We found significantly lower levels of lipid classes phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidylserine (PS), phosphatidylethanolamine (PE), phosphatidylcholine (PC), and sphingomyelin (SM) in infected Northern saw-whet owls than in the noninfected individuals. Conversely, we found higher levels for certain lysoPS and lysoPE species, and variable lipid level changes for free fatty acid (FFA) species. Reporting lipidomic changes observed between hemosporidian-infected and noninfected Northern saw-whet owls can strengthen our understanding of the mechanisms governing parasite proliferation in this species. Furthermore, our analysis indicated that lipidomic signatures are better predictors of parasite infection than the log-adjusted mass/wing chord body index, a metric commonly used to assess the influence of hemosporidia infection on the health of birds. Establishing a lipidomic profile for Northern saw-whet owls that provides baseline lipid levels during fall migration may assist future studies assessing causes of reductions in breeding brought about from subtle differences in behaviors such as delayed migration.

Impact of Annual Bacterial Epizootics on Albatross Population on a Remote Island

The reduced species richness typical of oceanic islands provides an interesting environmental setup to examine in natura the epidemiological dynamics of infectious agents with potential implications for public health and/or conservation. On Amsterdam Island (Indian Ocean), recurrent die-offs of Indian yellow-nosed albatross (Thalassarche carteri) nestlings have been attributed to avian cholera, caused by the bacterium Pasteurella multocida. In order to help implementing efficient measures for the control of this disease, it is critical to better understand the local epidemiology of P. multocida and to examine its inter- and intra-annual infection dynamics. We evaluated the infection status of 264 yellow-nosed albatrosses over four successive breeding seasons using a real-time PCR targeting P. multocida DNA from cloacal swabs. Infection prevalence patterns revealed an intense circulation of P. multocida throughout the survey, with a steady but variable increase in infection prevalence within each breeding season. These epizootics were associated with massive nestling dies-offs, inducing very low fledging successes (≤ 20%). These results suggest important variations in the transmission dynamics of this pathogen. These findings and the developed PCR protocol have direct applications to guide future research and refine conservation plans aiming at controlling the disease.

Use of genetic mark-recapture to estimate breeding site fidelity and philopatry in a threatened sea duck population, Alaska-breeding Steller’s eiders

The Steller’s eider Polysticta stelleri is a sea duck that breeds in Arctic tundra regions of Russia and Alaska (USA). The Alaska-breeding population is listed as ‘threatened’ under the US Endangered Species Act because of a perceived contraction of the breeding range in North America. Understanding demography of the listed population is critical for evaluating measures that can lead to increased abundance and thus, long-term viability. Specifically, estimates of return rates to breeding areas by adult females and natal areas by juvenile females are needed for planning effective recovery actions. We used a suite of polymorphic loci to genotype individuals and generated genetic profiles of nesting females and female offspring from nest materials collected between 1995 and 2016 in a ~170 km2 study area near Utqiagvik, Alaska. We analyzed capture histories of genetically identified individuals to estimate breeding site fidelity, temporary emigration, and philopatry. From a sample of 365 nests, we found that breeding site fidelity of adult females was high (0.91 ± 0.07 SE), and temporary emigration was also high (0.77 ± 0.06) and annually variable (range 0.34-0.97). From egg shell remains of 124 hatched females, we observed 9 recaptures as nesting adults, suggesting that philopatry was also high (range 0.6-1.0). Given the relatively high rates of adult female breeding site fidelity and female philopatry that we estimated, management actions that reduce mortality of adult females and increase annual productivity are likely to help maintain the population of a few hundred breeding Steller’s eiders on the Arctic Coastal Plain of Alaska.

Assessing the blood meal hosts of Culex quinquefasciatus and Aedes taeniorhynchus in Isla Santa Cruz, Galápagos

Background

Blood meal host selection by mosquito vectors is an important component in understanding disease dynamics of pathogens that threaten endemic fauna in isolated islands such as Galápagos. Research on the feeding behavior of mosquitoes can provide clues to the hosts and vectors involved in disease transmission. This information is particularly critical for endemic wildlife fauna in island systems that have evolved without resistance to novel diseases such as avian malaria. The aims of this study were to determine the blood-feeding patterns of two species of mosquitoes found in Galápagos and discuss how their feeding behavior may influence the transmission of pathogens such as avian malaria.

Methods

In the summer of 2015, we sampled two mosquito species (Aedes taeniorhynchus and Culex quinquefasciatus) across 18 different sites on Isla Santa Cruz, which is the second largest island in Galápagos and has the largest human population. We trapped mosquitoes using CDC light traps and CDC gravid traps and identified sources of blood meals for engorged mosquitoes by sequencing a portion of the vertebrate mitochondrial cytochrome b gene.

Results

Out of 947 female mosquitoes captured, 320 were blood-fed, and PCR amplifications were successful for 301 of the blood meals. Results revealed that both Aedes taeniorhynchus and Culex quinquefasciatus feed from a variety of vertebrate taxa, numerically dominated by humans on Isla Santa Cruz.

Conclusions

The high proportion of mammalian blood meals could represent locally available and abundant hosts on Santa Cruz. However, host surveys and estimates of relative abundances of vertebrate species will need to accompany mosquito trapping studies on non-inhabited and inhabited islands in Galápagos to further validate this.

Prevalence and diversity of avian blood parasites in a resident northern passerine

BACKGROUND

Climate-related changes are expected to influence the prevalence and distribution of vector-borne haemosporidian parasites at northern latitudes, although baseline information about resident birds is still lacking. In this study, we investigated prevalence and genetic diversity of Plasmodium, Haemoproteus, and Leucocytozoon parasites infecting the northwestern crow (Corvus caurinus), a non-migratory passerine with unique life-history characteristics. This species occupies both intertidal and forested habitats and is subject to high prevalence of avian keratin disorder (AKD), a disease that causes gross beak deformities. Investigation of avian blood parasites in northwestern crows at sites broadly distributed across coastal Alaska provided an opportunity to evaluate specific host factors related to parasite infection status and assess geographical patterns of prevalence.

RESULTS

We used molecular methods to screen for haemosporidian parasites in northwestern crows and estimated genus-specific parasite prevalence with occupancy modeling that accounts for imperfect detection of parasite infection. We observed considerable geographical and annual variation in prevalence of Plasmodium, Haemoproteus, and Leucocytozoon, but these patterns were not correlated with indices of local climatic conditions. Our models also did not provide support for relationships between the probability of parasite infection and body condition or the occurrence of co-infections with other parasite genera or clinical signs of AKD. In our phylogenetic analyses, we identified multiple lineages of each parasite genus, with Leucocytozoon showing greater diversity than Plasmodium or Haemoproteus.

CONCLUSIONS

Results from this study expand our knowledge about the prevalence and diversity of avian blood parasites in northern resident birds as well as corvids worldwide. We detected all three genera of avian haemosporidians in northwestern crows in Alaska, although only Leucocytozoon occurred at all sites in both years. Given the strong geographical and annual variation in parasite prevalence and apparent lack of correlation with climatic variables, it appears that there are other key factors responsible for driving transmission dynamics in this region. Thus, caution is warranted when using standard climatic or geographical attributes in a predictive framework. Our phylogenetic results demonstrate lower host specificity for some lineages of Leucocytozoon than is typically reported and provide insights about genetic diversity of local haemosporidian parasites in Alaska.

Development and characterization of polymorphic microsatellite markers in northern fulmar, Fulmarus glacialis (Procellariiformes), and cross-species amplification in eight other seabirds

BACKGROUND

In the North Pacific, northern fulmar (Fulmarus glacialis) forms extensive colonies in few locales, which may lead to limited gene flow and locale-specific population threats. In the Atlantic, there are thousands of colonies of varying sizes and in Europe the species is considered threatened. Prior screens and classical microsatellite development in fulmar failed to provide a suite of markers adequate for population genetics studies.

OBJECTIVES

The objective of this study was to isolate a suite of polymorphic microsatellite loci with sufficient variability to quantify levels of gene flow, population affinity, and identify familial relationships in fulmar. We also performed a cross-species screening of these markers in eight other species.

METHODS

We used shotgun sequencing to isolate 26 novel microsatellite markers in fulmar to screen for variability using individuals from two distinct regions: the Pacific (Chagulak Island, Alaska) and the Atlantic (Hafnarey Island, Iceland).

RESULTS

Polymorphism was present in 24 loci in Chagulak and 23 in Hafnarey, while one locus failed to amplify in either colony. Polymorphic loci exhibited moderate levels of genetic diversity and this suite of loci uncovered genetic structuring between the regions. Among the other species screened, polymorphism was present in one to seven loci.

CONCLUSION

The loci yielded sufficient variability for use in population studies and estimation of familial relationships; as few as five loci provide resolution to determine individual identity. These markers will allow further insight into the global population dynamics and phylogeography of fulmars. We also demonstrated some markers are transferable to other species.

Habitat Saturation Results in Joint-Nesting Female Coalitions in a Social Bird

Joint nesting by females and cooperative polyandry-cooperatively breeding groups with a male-biased breeder sex ratio-are little-understood, rare breeding systems. We tested alternative hypotheses of factors potentially driving these phenomena in a population of joint-nesting acorn woodpeckers (Melanerpes formicivorus). During periods of high population density and thus low independent breeding opportunities, acorn woodpecker females formed joint-nesting coalitions with close kin. Coalitions were typically associated with groups with a male bias. We found strong evidence for both inter- and intrasexual conflict, as joint nesting conferred a fitness benefit to some males, a significant fitness cost to females, and no gain in per capita reproductive output for either sex. Such conflict, particularly the cost to females, may be an important reason why joint nesting is rare among cooperatively breeding taxa.

Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.

Haemosporidian parasite community in migrating bobolinks on the Galapagos Islands

Bobolinks (Dolichonyx oryzivorus) migrate from their breeding grounds in North America to their wintering grounds in South America during the fall each year. A small number of Bobolinks stop temporarily in Galapagos, and potentially carry parasites. On the North American breeding grounds, Bobolinks carry a least two of the four Plasmodium lineages recently detected in resident Galapagos birds. We hypothesized that Bobolinks carried these parasites to Galapagos, where they were bitten by mosquitoes that then transmitted the parasites to resident birds. The haemosporidian parasite community in 44% of the Bobolinks we captured was consistent with those on their breeding grounds. However, the lineages were not those found in Galapagos birds. Our results provide a parasite community key for future monitoring.

Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection

BACKGROUND

Avian keratin disorder (AKD) is an epizootic of debilitating beak deformities, first documented in black-capped chickadees (Poecile atricapillus) in Alaska during the late 1990s. Similar deformities have now been recorded in dozens of species of birds across multiple continents. Despite this, the etiology of AKD has remained elusive, making it difficult to assess the impacts of this disease on wild populations. We previously identified an association between infection with a novel picornavirus, Poecivirus, and AKD in a small cohort of black-capped chickadees.

METHODS

To test if the association between Poecivirus and AKD holds in a larger study population, we used targeted PCR followed by Sanger sequencing to screen 124 symptomatic and asymptomatic black-capped chickadees for Poecivirus infection. We further compared the efficacy of multiple non-terminal field sampling methods (buccal swabs, cloacal swabs, fecal samples, and blood samples) for Poecivirus screening. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to determine if virus is actively replicating in beak tissue.

RESULTS

Poecivirus was detected in 28/28 (100%) individuals with AKD, but only 9/96 (9.4%) asymptomatic individuals with apparently normal beaks (p < 0.0001). We found that cloacal swabs are the most sensitive of these sample types for detecting Poecivirus in birds with AKD, but that buccal swabs should be combined with cloacal swabs in evaluating the infection status of asymptomatic birds. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to provide evidence of active viral replication.

CONCLUSION

The data presented here show a strong, statistically significant relationship between Poecivirus infection and AKD, and provide evidence that Poecivirus is indeed an avian virus, infecting and actively replicating in beak tissue of AKD-affected BCCH. Taken together, these data corroborate and extend the evidence for a potential causal association between Poecivirus and AKD in the black-capped chickadee. Poecivirus continues to warrant further investigation as a candidate agent of AKD.

Mating System of Caiman yacare (Reptilia: Alligatoridae) Described from Microsatellite Genotypes

The yacare caiman (Caiman yacare) is a reptile from South America and 1 of the 2 crocodilian species present in Argentina. The degradation of their natural habitat and strong hunting pressure led to a sharp numerical decline of wild populations. Nowadays, C. yacare is included in Appendix II of CITES, and ranching practices in some areas in Argentina are helping hatching success. In this context, it is important to better understand the population structure and mating system of the species. To do this, we amplified 10 microsatellite markers (SSRs) in 148 individuals of 13 C. yacare nests. All of the markers were polymorphic with 2–12 alleles per locus, with allelic sizes ranging between 154 and 400 bp and medium levels of polymorphism (Ho = 0.152–0.551 and He = 0.221–0.621). We were able to determine the maternal genotype in 9 out of 13 nests. In 6 of them we found more than 1 paternal genotype, with a maximum of 3 fathers for a single nest. This study is the first to provide evidence of multiple paternity behavior. These findings will be useful to improve management and conservation strategies for the species.

From Galapagos doves to passerines: Spillover of Haemoproteus multipigmentatus

Haemoproteus (Haemoproteus) multipigmentatus, a haemosporidian parasite thought to be specific to columbiform birds, was detected in passeriform birds on Santiago Island in the Galapagos archipelago. We surveyed birds along an altitudinal gradient on the islands of Santa Cruz, Isabela and Santiago between June 2013 and July 2015. Molecular screening of 2254 individuals from 25 species of endemic and introduced birds revealed clusters of passerine birds positive for H. multipigmentatus on Santiago Island that coincide with captures of Galapagos doves at sampled sites. Of 507 individuals from 10 species of endemic passerines sampled on Santiago, 58 individuals from 6 species were found positive (11% prevalence). However, no gametocytes were found in the blood smears of positive passerines, suggesting that these species are not competent hosts for the parasite. All 31 doves captured were positive and gametocytes were found upon microscopic examination of all thin blood smears (averaging 357 gametocytes per 10,000 erythrocytes). These findings indicate parasite spillover from doves to passerines, but that passerines are possibly not competent hosts for further parasite transmission. The endemic Galapagos dove acts as a reservoir host for the introduced H. multipigmentatus, however the effect of this parasite on passerines has not been studied. We report on these findings because parasites can have large effects on individual host populations and on the ecology of a community, but may go undetected.

Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes

Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20^th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–F. p. tundrius, anatum, and pealei–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20^th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping (pealei) and a boreal/Arctic grouping (currently anatum and tundrius)–each comprised of discrete populations that are variously intra-regionally connected.

Genetic implications of bottleneck effects of differing severities on genetic diversity in naturally recovering populations: An example from Hawaiian coot and Hawaiian gallinule

The evolutionary trajectory of populations through time is influenced by the interplay of forces (biological, evolutionary, and anthropogenic) acting on the standing genetic variation. We used microsatellite and mitochondrial loci to examine the influence of population declines, of varying severity, on genetic diversity within two Hawaiian endemic waterbirds, the Hawaiian coot and Hawaiian gallinule, by comparing historical (samples collected in the late 1800s and early 1900s) and modern (collected in 2012–2013) populations. Population declines simultaneously experienced by Hawaiian coots and Hawaiian gallinules differentially shaped the evolutionary trajectory of these two populations. Within Hawaiian coot, large reductions (between −38.4% and −51.4%) in mitochondrial diversity were observed, although minimal differences were observed in the distribution of allelic and haplotypic frequencies between sampled time periods. Conversely, for Hawaiian gallinule, allelic frequencies were strongly differentiated between time periods, signatures of a genetic bottleneck were detected, and biases in means of the effective population size were observed at microsatellite loci. The strength of the decline appears to have had a greater influence on genetic diversity within Hawaiian gallinule than Hawaiian coot, coincident with the reduction in census size. These species exhibit similar life history characteristics and generation times; therefore, we hypothesize that differences in behavior and colonization history are likely playing a large role in how allelic and haplotypic frequencies are being shaped through time. Furthermore, differences in patterns of genetic diversity within Hawaiian coot and Hawaiian gallinule highlight the influence of demographic and evolutionary processes in shaping how species respond genetically to ecological stressors.

No evidence for a link between forest herbicides and offspring sex ratio in a migratory songbird using high-throughput molecular sexing

Many species that use or require early-successional forest are of conservation concern, including a number of songbirds that have experienced long-term population declines. In this study, our initial goal was to test whether herbicide application intensity was linked to offspring sex ratio in the White-crowned Sparrow (Zonotrichia leucophrys), a species that requires early-successional forest within forested landscapes. However, a rapid and accurate method using direct PCR to sex a large sample of birds (n > 1000 individuals) was unavailable, so our secondary goal was to develop a new approach for rapidly determine offspring sex. We obtained blood samples from sparrow young during the 2013-2014 breeding seasons in regenerating conifer plantations that were treated with one of four treatments (i.e. light, moderate, and intensive herbicide application, or no-spray control). We then optimized a protocol that used a commercially available, direct PCR kit to amplify sex-specific fragments of the CHD (chromo-helicase-DNA-binding) genes directly from whole blood stored in lysis buffer. Using this approach, we found no evidence that offspring sex ratio was linked to herbicide application intensity or to food availability across herbicide treatments. Our molecular sexing technique was 100% accurate when validated on known-sex adults, and 99.9% of our blood samples amplified successfully after being stored in lysis buffer stored for up to 3 years. The application of direct PCR for sexing birds eliminated the need for DNA extraction and substantially reduced sample processing time, cost, and the opportunity for errors during the extraction step. We conclude that forest herbicide application intensity does not influence sparrow offspring sex ratio in our study system, and that our approach provides a rapid, accurate, and tractable method for sexing birds that can facilitate studies that require processing of a large number of samples.

Genetic structure among greater white-fronted goose populations of the Pacific Flyway

An understanding of the genetic structure of populations in the wild is essential for long‐term conservation and stewardship in the face of environmental change. Knowledge of the present‐day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white‐fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine‐scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long‐lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population‐specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white‐fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.

Inferring the timing of long-distance dispersal between Rail metapopulations using genetic and isotopic assignments

The stochastic and infrequent nature of long-distance dispersal often makes it difficult to detect. We quantified the frequency, distance, and timing of long-distance dispersal in a nonmigratory, secretive wetland bird, the California Black Rail (Laterallus jamaicensis coturniculus), between an inland and a coastal metapopulation separated by greater than 100 km. Using 15 microsatellites in conjunction with stable carbon, nitrogen, and sulfur isotopes, we classified Rails as residents of their capture population, recent migrants that dispersed to their capture population less than one year before capture, established migrants that dispersed to their capture population more than one year before capture, and seasonal migrants that dispersed away from their capture population to forage, but returned the next season. Most Rails (195 of 204, or 95.6%) were classified as residents, but we detected two established migrants that had moved >100 km more than a year before capture. Seven Rails appeared to be seasonal migrants, but comparisons of feather isotope values with isotope values from wetland soils indicated that the isotope values in the feathers of these Rails likely resulted from natural environmental variation (e.g., source element effects) rather than long-distance dispersal of individuals. Thus, these seven Rails were most likely misassigned by isotopic population assignments due to small-scale variation in the isoscape. Using genetic data in conjunction with isotopic data allowed us to not only infer the timing of long-distance dispersal events, but to successfully track long-distance movements of nonmigratory Rails between metapopulations even when environmental variation of isotopes occurred across small spatial scales.

Novel Picornavirus Associated with Avian Keratin Disorder in Alaskan Birds

Avian keratin disorder (AKD), characterized by debilitating overgrowth of the avian beak, was first documented in black-capped chickadees (Poecile atricapillus) in Alaska. Subsequently, similar deformities have appeared in numerous species across continents. Despite the widespread distribution of this emerging pathology, the cause of AKD remains elusive. As a result, it is unknown whether suspected cases of AKD in the afflicted species are causally linked, and the impacts of this pathology at the population and community levels are difficult to evaluate. We applied unbiased, metagenomic next-generation sequencing to search for candidate pathogens in birds affected with AKD. We identified and sequenced the complete coding region of a novel picornavirus, which we are calling poecivirus. Subsequent screening of 19 AKD-affected black-capped chickadees and 9 control individuals for the presence of poecivirus revealed that 19/19 (100%) AKD-affected individuals were positive, while only 2/9 (22%) control individuals were infected with poecivirus. Two northwestern crows (Corvus caurinus) and two red-breasted nuthatches (Sitta canadensis) with AKD-consistent pathology also tested positive for poecivirus. We suggest that poecivirus is a candidate etiological agent of AKD.

Avian keratin disorder (AKD) is an increasingly common disease of wild birds. This disease, characterized by beak overgrowth, was first described in the late 1990s and has been spreading rapidly both geographically and in terms of host species affected. AKD decreases host fitness and can be fatal. However, the cause of the disease has remained elusive, and its impact on host populations is poorly understood. We found a novel and divergent picornavirus in 19/19 AKD-affected black-capped chickadees that we examined but in only 2/9 control cases. We also found this virus in 4 individuals of 2 other passerine species that exhibited symptoms consistent with AKD. Our data suggest that this novel picornavirus warrants further investigation as the causative agent of AKD.

Haemosporidian parasite prevalence, parasitemia, and diversity in three resident bird species at a shrubland dominated landscape of the Mexican highland plateau

Background

Studies of avian haemosporidians allow understanding how these parasites affect wild bird populations, and if their presence is related to factors such as habitat loss, degradation and fragmentation, and climate change. Considering the importance of the highland Plateau of Mexico as part of the North American bird migratory route and as a region containing important habitat for numerous bird species, the purpose of this study was to document haemosporidian species richness and how habitat degradation, bird body condition, and distance from water sources correlate with bird parasitemia.

Methods

We assessed the presence of avian haemosporidians in three resident bird species through microscopy and PCR amplification of a fragment of the haemosporidian cytochrome b gene. Average parasitemia was estimated in each species, and its relationship with habitat degradation through grazing, bird body condition and distance from water bodies was assessed.

Results

High levels of parasitemia were recorded in two of the three bird species included in this study. Four lineages of haemosporidians were identified in the study area with nearly 50 % prevalence. Areas with highly degraded shrublands and villages showed higher parasitemia relative to areas with moderately degraded shrublands. No strong relationship between parasitemia and distance from water bodies was observed. There were no significant differences in prevalence and parasitemia between the two bird species infected with the parasites. Two of the sequences obtained from the fragments of the parasite’s cytochrome b gene represent a lineage that had not been previously reported.

Conclusions

Haemosporidian diversity in arid zones of the Mexican highland plateau is high. Shrubland habitat degradation associated to the establishment of small villages, as well as tree extraction and overgrazing in the surroundings of these villages, significantly enhances parasitemia of birds by haemosporidians.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1569-3) contains supplementary material, which is available to authorized users.

Genetic, spatial, and social relationships among adults in a group of howler monkeys (Alouatta palliata) from Barro Colorado Island, Panama

Kinship plays an important role in the social behavior of many primate species, including patterns of intra-group affiliation and cooperation. Within social groups, kinship is strongly affected by dispersal patterns, with the degree of relatedness among group-mates expected to decrease as the tendency to disperse increases. In primate species characterized by bisexual dispersal, relatedness among adult group-mates is predicted to be low, with social interactions shaped largely by factors other than kinship. To date, however, few studies have examined the role of kinship in social interactions in bisexually dispersing species. Accordingly, we collected genetic, spatial and behavioral data on all adult members (three males, six females) in a group of free-ranging mantled howler monkeys (Alouatta palliata)--a bisexually dispersing species of atelid primate--from Barro Colorado Island (BCI), Panama. Analyses of microsatellite variation revealed that relatedness was greater among adult males in this group (mean pairwise relatedness = 0.32 for males versus 0.09 for females). Relatedness among individuals, however, was not associated with either spatial proximity or frequency of social interactions. Instead, sex was a better predictor of both of these aspects of social behavior. While relatedness among adults had no discernible effect on the intra-group social interactions documented in this study, we postulate that kinship may facilitate affiliative and cooperative behaviors among male group-mates when interacting competitively with neighboring howler groups over access to food or potential mates.

Paternal behaviour in a socially monogamous but sexually promiscuous passerine bird

We documented parental behaviour and paternity of eastern kingbirds (Tyrannus tyrannus) to test the predictions that paternal care would decline with increasing loss of paternity, increasing nesting density (a proxy for probability of paternity loss), male quality, and number of fertile females available in the population. Extra-pair young were found in 58% of 45 nests for which behaviour was recorded and a higher proportion of young were extra-pair as nesting density increased. Male feeding rate declined with increasing nesting density and male quality, but neither feeding rate nor a composite measure of paternal behaviour varied with number of fertile females or paternity. Although alternative explanations exist, one interpretation of the reduced paternal care at high nesting density was that it was a response to perceived threats of paternity loss. The ultimate basis for the lower paternal effort of higher quality males is unclear but we discuss several possible explanations.

Geographic variation and genetic structure in the Bahama Oriole (Icterus northropi), a critically endangered synanthropic species

Bird species may exhibit unexpected population structuring over small distances, with gene flow restricted by geographic features such as water or mountains. The Bahama Oriole (Icterus northropi) is a critically endangered, synanthropic island endemic with a declining population of fewer than 300 individuals. It now remains only on Andros Island (The Bahamas), which is riddled with waterways that past studies assumed did not hinder gene flow. We examined 1,858 base pairs of mitochondrial DNA sequenced from four gene regions in 14 birds (roughly 5% of the remaining population) found on the largest land masses of Andros Island (North Andros and Mangrove Cay/South Andros). We sought to discern genetic structuring between the remaining subpopulations and its relationship to current conservation concerns. Four unique haplotypes were identified, with only one shared between the two subpopulations. Nucleotide and haplotype diversity were higher for the North Andros subpopulation than for the Mangrove Cay/South Andros subpopulation. Analysis of molecular variance (AMOVA) yielded a Wright's fixation index (F st) of 0.60 (P Fst = 0.016), with 40.2% of the molecular variation explained by within-population differences and 59.8% by among-population differences. Based on the mitochondrial regions examined in this study, we suggest the extant subpopulations of Bahama Oriole exhibit significant population structuring over short distances, consistent with some other non-migratory tropical songbird species.

Establishing the evolutionary compatibility of potential sources of colonizers for overfished stocks: a population genomics approach

Identifying fish stock structure is fundamental to pinpoint stocks that might contribute colonizers to overfished stocks. However, a stock's potential to contribute to rebuilding hinges on demographic connectivity, a challenging parameter to measure. With genomics as a new tool, fisheries managers can detect signatures of natural selection and thus identify fishing areas likely to contribute evolutionarily compatible colonizers to an overfished area (i.e. colonizers that are not at a fitness disadvantage in the overfished area and able to reproduce at optimal rates). Identifying evolutionarily compatible stocks would help narrow the focus on establishing demographic connectivity where it matters. Here, we genotype 4723 SNPs in 616 orange roughy (Hoplostethus atlanticus) across five fishing areas off the Tasmanian coast in Australia. We ask whether these areas form a single genetic unit, and test for signatures of local adaptation. Results from amova, structure, discriminant analysis of principal components, BAYESASS and isolation by distance suggest that sampled locations are subjected to geneflow amounts that are above what is needed to establish 'drift connectivity'. However, it remains unclear whether there is a single panmictic population or several highly connected populations. Most importantly, we did not find any evidence of local adaptation, suggesting that the examined orange roughy stocks are evolutionarily compatible. The data have helped test an assumption of the orange roughy management programme and to formulate hypotheses regarding stock demographic connectivity. Overall, our results demonstrate the potential of genomics to inform fisheries management, even when evidence for stock structure is sparse.

Serological evidence for the circulation of flaviviruses in seabird populations of the western Indian Ocean

Birds play a central role in the epidemiology of several flaviviruses of concern for public and veterinary health. Seabirds represent the most abundant and widespread avifauna in the western Indian Ocean and may play an important role as host reservoirs and spreaders of arthropod-borne pathogens such as flaviviruses. We report the results of a serological investigation based on blood samples collected from nine seabird species from seven islands in the Indian Ocean. Using a commercial competitive enzyme-linked immunosorbent assay directed against the prototypic West Nile flavivirus, antibodies against flaviviruses were detected in the serum of 47 of the 855 seabirds tested. They were detected in bird samples from three islands and from four bird species. Seroneutralization tests on adults and chicks suggested that great frigatebirds (Fregata minor) from Europa were infected by West Nile virus during their non-breeding period, and that Usutu virus probably circulated within bird colonies on Tromelin and on Juan de Nova. Real-time polymerase chain reactions performed on bird blood samples did not yield positive results precluding the genetic characterization of flavivirus using RNA sequencing. Our findings stress the need to further investigate flavivirus infections in arthropod vectors present in seabird colonies.

A real-time, quantitative PCR protocol for assessing the relative parasitemia of Leucocytozoon in waterfowl

Microscopic examination of blood smears can be effective at diagnosing and quantifying hematozoa infections. However, this method requires highly trained observers, is time consuming, and may be inaccurate for detection of infections at low levels of parasitemia. To develop a molecular methodology for identifying and quantifying Leucocytozoon parasite infection in wild waterfowl (Anseriformes), we designed a real-time, quantitative PCR protocol to amplify Leucocytozoon mitochondrial DNA using TaqMan fluorogenic probes and validated our methodology using blood samples collected from waterfowl in interior Alaska during late summer and autumn (n=105). By comparing our qPCR results to those derived from a widely used nested PCR protocol, we determined that our assay showed high levels of sensitivity (91%) and specificity (100%) in detecting Leucocytozoon DNA from host blood samples. Additionally, results of a linear regression revealed significant correlation between the raw measure of parasitemia produced by our qPCR assay (Ct values) and numbers of parasites observed on blood smears (R(2)=0.694, P=0.003), indicating that our assay can reliably determine the relative parasitemia levels among samples. This methodology provides a powerful new tool for studies assessing effects of haemosporidian infection in wild avian species.

Biomarkers of animal health: integrating nutritional ecology, endocrine ecophysiology, ecoimmunology, and geospatial ecology

Diverse biomarkers including stable isotope, hormonal, and ecoimmunological assays are powerful tools to assess animal condition. However, an integrative approach is necessary to provide the context essential to understanding how biomarkers reveal animal health in varied ecological conditions. A barrier to such integration is a general lack of awareness of how shared extraction methods from across fields can provide material from the same animal tissues for diverse biomarker assays. In addition, the use of shared methods for extracting differing tissue fractions can also provide biomarkers for how animal health varies across time. Specifically, no study has explicitly illustrated the depth and breadth of spacial and temporal information that can be derived from coupled biomarker assessments on two easily collected tissues: blood and feathers or hair. This study used integrated measures of glucocorticoids, stable isotopes, and parasite loads in the feathers and blood of fall-migrating Northern saw-whet owls (Aegolius acadicus) to illustrate the wealth of knowledge about animal health and ecology across both time and space. In feathers, we assayed deuterium (δD) isotope and corticosterone (CORT) profiles, while in blood we measured CORT and blood parasite levels. We found that while earlier migrating owls had elevated CORT levels relative to later migrating birds, there was also a disassociation between plasma and feather CORT, and blood parasite loads. These results demonstrate how these tissues integrate time periods from weeks to seasons and reflect energetic demands during differing life stages. Taken together, these findings illustrate the potential for integrating diverse biomarkers to assess interactions between environmental factors and animal health across varied time periods without the necessity of continually recapturing and tracking individuals. Combining biomarkers from diverse research fields into an integrated framework hold great promise for advancing our understanding of environmental effects on animal health.

Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric repetitive sequences in New World quails

Many families of centromeric repetitive DNA sequences isolated from Struthioniformes, Galliformes, Falconiformes, and Passeriformes are localized primarily to microchromosomes. However, it is unclear whether chromosome size-correlated homogenization is a common characteristic of centromeric repetitive sequences in Aves. New World and Old World quails have the typical avian karyotype comprising chromosomes of two distinct sizes, and C-positive heterochromatin is distributed in centromeric regions of most autosomes and the whole W chromosome. We isolated six types of centromeric repetitive sequences from three New World quail species (Colinus virginianus, CVI; Callipepla californica, CCA; and Callipepla squamata, CSQ; Odontophoridae) and one Old World quail species (Alectoris chukar, ACH; Phasianidae), and characterized the sequences by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. The 385-bp CVI-MspI, 591-bp CCA-BamHI, 582-bp CSQ-BamHI, and 366-bp ACH-Sau3AI fragments exhibited tandem arrays of the monomer unit, and the 224-bp CVI-HaeIII and 135-bp CCA-HaeIII fragments were composed of minisatellite-like and microsatellite-like repeats, respectively. ACH-Sau3AI was a homolog of the chicken nuclear membrane repeat sequence, whose homologs are common in Phasianidae. CVI-MspI, CCA-BamHI, and CSQ-BamHI showed high homology and were specific to the Odontophoridae. CVI-MspI was localized to microchromosomes, whereas CVI-HaeIII, CCA-BamHI, and CSQ-BamHI were mapped to almost all chromosomes. CCA-HaeIII was localized to five pairs of macrochromosomes and most microchromosomes. ACH-Sau3AI was distributed in three pairs of macrochromosomes and all microchromosomes. Centromeric repetitive sequences may be homogenized in chromosome size-correlated and -uncorrelated manners in New World quails, although there may be a mechanism that causes homogenization of centromeric repetitive sequences primarily between microchromosomes, which is commonly observed in phasianid birds.

Haemoproteus iwa in Great Frigatebirds (Fregata minor) in the Islands of the Western Indian Ocean

Blood parasites of the sub-genus Haemoproteus have been reported in seabirds, in particular in species in the Suliformes order. These parasites are transmitted by hippoboscid flies of the genus Olfersia; strong specificity has been suggested between the vector and its vertebrate host. We investigated the prevalence of Haemoproteus infection in Suliformes and hippoboscid flies in two oceanic islands of the Western Indian Ocean: Europa and Tromelin. In total, 209 blood samples were collected from great frigatebirds (Fregata minor), masked boobies (Sula dactylatra) and red-footed boobies (Sula sula). Forty-one hippoboscid flies were also collected from birds. Seventeen frigatebirds and one fly collected on Europa tested positive for the presence of Haemoproteus parasites by polymerase chain reaction. Phylogenetic analyses based on partial sequences of the Cytochrome b gene showed that parasites were closely related to Haemoproteus iwa reported from frigatebirds in the Pacific Ocean and in the Caribbean. Plasmodium was also detected in a frigatebird on Europa; however, its placement on the phylogenetic tree could not be resolved. We provide strong support for transmission of blood parasites in seabirds in the Western Indian Ocean and suggest that migrations between the Pacific and the Indian oceans could favor the large-scale distribution of Haemoproteus iwa in frigatebird populations.

Monitoring jaguar populationsPanthera oncawith non-invasive genetics: a pilot study in Brazilian ecosystems

The global population of jaguarsPanthera oncahas decreased significantly since the beginning of the 20th century. Given the scarcity of demographic and biological information, estimating population parameters is critical for the design of conservation measures. The jaguar's elusive behaviour makes it impossible to estimate and monitor populations by direct observation. We propose a non-invasive genetic sampling approach and demonstrate its potential for large-scale monitoring. Sex identification was optimized for faecal samples of jaguars and other felids. We also optimized a set of 11 microsatellite markers for reliable identification of individuals. We estimated the effectiveness of faecal sample genotyping in two distinct Brazilian biomes: the Pantanal and the semi-arid Caatinga. Almost 90% of the samples that were molecularly identified as jaguar (n = 90) were successfully genotyped and were assigned to 30 individuals. Genetic diversity was generally high but was significantly lower in the Caatinga population. We show that non-invasive genetic sampling can be a reliable tool to study population parameters and to monitor the genetic status of jaguar populations in different habitats. It may also be useful for future surveys of jaguars that address ecological, behavioural and conservation issues, and could provide a baseline for non-invasive genetic studies of other wild felid populations.

Kinship and social behavior of lowland tapirs (Tapirus terrestris) in a central Amazon landscape

We tested the hypothesis that tapirs tolerate individuals from adjacent and overlapping home ranges if they are related. We obtained genetic data from fecal samples collected in the Balbina reservoir landscape, central Amazon. Samples were genotyped at 14 microsatellite loci, of which five produced high quality informative genotypes. Based on an analysis of 32 individuals, we inferred a single panmictic population with high levels of heterozygosity. Kinship analysis identified 10 pairs of full siblings or parent-offspring, 10 pairs of half siblings and 25 unrelated pairs. In 10 cases, the related individuals were situated on opposite margins of the reservoir, suggesting that tapirs are capable of crossing the main river, even after damming. The polygamous model was the most likely mating system for Tapirus terrestris. Moran's I index of allele sharing between pairs of individuals geographically close (<3 km) was similar to that observed between individual pairs at larger distances (>3 km). Confirming this result, the related individuals were not geographically closer than unrelated ones (W = 188.5; p = 0.339). Thus, we found no evidence of a preference for being close to relatives and observed a tendency for dispersal. The small importance of relatedness in determining spatial distribution of individuals is unusual in mammals, but not unheard of. Finally, non-invasive sampling allowed efficient access to the genetic data, despite the warm and humid climate of the Amazon, which accelerates DNA degradation.

Physiological and fitness correlates of experimentally altered hatching asynchrony magnitude in chicks of a wild seabird

Nest-bound chicks depend entirely on their parents for food, often leading to high sibling competition. Asynchronous hatching, resulting from the onset of incubation before clutch completion, facilitates the establishment of within-nest hierarchy, with younger chicks being subject to lower feeding and growth rates. Because social and nutritional stresses affect baseline stress hormone levels in birds, younger chicks are expected to have higher levels of corticosterone than their siblings. As previous studies showed that hatching asynchrony magnitude influences the course of sibling competition, it should also affect baseline corticosterone. We measured baseline corticosterone at age 5 days in nestling black-legged kittiwakes (Rissa tridactyla) in 3 types of experimental broods: synchronous, asynchronous, and highly asynchronous. Sexual dimorphism takes place during chick-rearing and might also influence baseline corticosterone, we thus included chick sex in our analyses and also monitored chick growth and survival. Baseline corticosterone did not differ among A-chicks, but was higher in B-chicks from highly asynchronous broods compared with the other brood types, in line with the presumed increase in nutritional stress. In asynchronous broods, A-chicks had higher baseline corticosterone than their siblings, contrary to our expectations. We interpret that result as a cost of dominance among A-chicks. In line with previous studies, mass gain was negatively correlated with baseline corticosterone levels. We found that baseline corticosterone predicted survival in a sex-specific way. Regardless of hatching rank, males with higher baseline corticosterone suffered higher mortality, suggesting that males were more sensitive to high level of stress, independently of its cause.

Identifying parentage using molecular markers: improving accuracy of studbook records for a captive flock of marabou storks (Leptoptilos crumeniferus)

Extra-pair copulations (EPCs) leading to extra-pair fertilization (EPF) are common in avian mating systems, despite the prevalence of observed social monogamy in many species. Colonially breeding birds are interesting species to investigate the prevalence of EPCs and EPF because they show nesting habits including close proximity of nest sites and sexual partners, which are proposed to promote alternative reproductive tactics. Endemic to Africa, the colonial marabou stork (Leptoptilos crumeniferus) is one of the most commonly held avian species in North American zoos. The aims of this study were to use genetic information to verify parentage in a population of marabou stork housed at Disney's Animal Kingdom® based on five microsatellite loci and to investigate reproductive behavior. We compared genetic analyses of parents and offspring to studbook data collected through behavioral observations of parental behavior at the nest. Using genetic analyses to reconstruct the pedigree of the marabou stork flock using the program COLONY led to improvement of studbook records by determining parentage of an individual that had previously unknown parentage, and identified one individual that had a sire that differed genetically from studbook records. An important contribution of our analyses was the identification and verification of the most likely parents for offspring hatched in this colony and improving incorrect or undocumented parentage in the studbook. Additionally, the colonial nature of this species makes it difficult to observe and understand reproductive behavior. Gaining better understanding of the mating system of a species is essential for successful breeding and captive management.