RESUMO
The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.
Assuntos
Águias , Genoma , Animais , Águias/genética , Feminino , Elementos de DNA Transponíveis/genética , Filogenia , Evolução Molecular , Retroelementos/genética , Genômica/métodosRESUMO
We explore the potential factors that affect clutch initiation in four Neotropical large raptors (Harpy eagle-HE, Crested eagle-CE, Ornate hawk-eagle-OHE, and Black hawk-eagle-BHE) by analyzing 414 clutch events mostly obtained from captive individuals. Differences in how clutch initiation is associated with changes in photoperiod were found between HE and both hawk-eagles, and between CE and BHE. Changes in temperature at the time of clutch initiation only differed between HE and OHE, whereas changes in precipitation varied between BHE and all other species. Principal Component Analysis of these environmental cues showed that ellipses in the dataset of each species overlap, but only ellipses from CE and OHE had the same variation trends. This means that although these species live under similar ecological conditions, they exhibit three different patterns of response to environmental cues. Apparently, these patterns are not associated with phylogenetic relatedness because species belonging to the same clade do not show the same response pattern. Diet diversity analysis revealed that HE has the least varied diet, and CE and OHE the most varied diet. The fact that species who fit the same reproductive timing response to environmental cues show similar diets leads us to hypothesize that breeding in these eagles was most likely shaped by food availability.
Assuntos
Águias , Humanos , Animais , Águias/genética , Filogenia , Florestas , Dieta , AlimentosRESUMO
Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest.
Assuntos
Águias/genética , Floresta Úmida , Animais , Brasil , Espécies em Perigo de Extinção , Deriva Genética , Variação Genética , Repetições de MicrossatélitesRESUMO
The white-bellied sea eagle, Haliaeetus leucogaster, displays reversed sexual size dimorphism and is monomorphic for adult plumage coloration. Early attempts to identify sex in sexually monomorphic birds were based on morphological or chromosomal characters, but since avian W-specific DNA sequences were identified, PCR amplification has become commonly used for molecular sexing. We used a PCR test employing primers that amplify two homologous fragments of both the CHD-W gene, unique to females, and the CHD-Z gene, occurring in both sexes. This test was applied to five individuals of H. leucogaster from the Malacca Zoo and to male and female domestic chickens, Gallus domesticus, for comparison. All individuals were sexed successfully with high reproducibility. We conclude that this PCR-based test with feathers as the DNA source is a reliable sexing method for H. leucogaster. This sexing technique is objective and non-invasive and could be used to test sex ratio theories, as well as to help improve conservation and management actions for captive breeding program of this species in Malaysia.
Assuntos
Proteínas Aviárias/genética , Proteínas de Ligação a DNA/genética , Águias/genética , Plumas , Caracteres Sexuais , Cromossomos Sexuais/genética , Animais , Tamanho Corporal/genética , Feminino , Masculino , Pigmentação/genéticaRESUMO
We report the characterization and optimization of 45 heterologous microsatellite loci, and the development of a new set of molecular sex markers for the conservation and management of the Neotropical harpy eagle (Harpia harpyja L. 1758). Of the 45 microsatellites tested, 24 were polymorphic, six monomorphic, 10 uncharacterizable due to multiple bands and five did not amplify. The observed gene diversity of the analyzed sample of H. harpyja was low and similar to that of other threatened Falconiformes. While a high proportion of the microsatellite markers were highly variable, individuals of H. harpyja could be differentiated by a joint analysis of just three (p = 2.79 x 10-4) or four markers (p = 2.89 x 10-5). Paternity could be rejected with 95.23 percent and 97.83 percent probabilities using the same three and four markers, respectively. The sex determination markers easily and consistently differentiated males from females even with highly degraded DNA extracted from naturally shed feathers. The markers reported in this study potentially provide an excellent set of molecular tools for the conservation and management of wild and captive H. harpyja and they may also prove useful for the enigmatic Neotropical crested eagle (Morphnus guianensis Daudin 1800).
Assuntos
Animais , Águias/genética , Conservação dos Recursos Naturais , Repetições de Microssatélites , Variação Genética , Genética Populacional , Aves Predatórias , Fatores SexuaisRESUMO
Like various other diurnal birds of prey, the world's largest eagle, the Harpy (Harpia harpyja), presents an atypical bird karyotype with 2n=58 chromosomes. There is little knowledge about the dramatic changes in the genomic reorganization of these species compared to other birds. Since recently, the chicken provides a "default map" for various birds including the first genomic DNA sequence of a bird species. Obviously, the gross division of the chicken genome into relatively gene-poor macrochromosomes and predominantly gene-rich microchromosomes has been conserved for more than 150 million years in most bird species. Here, we present classical features of the Harpy eagle karyotype but also chromosomal homologies between H. harpyja and the chicken by chromosome painting and comparison to the chicken genome map. We used two different sets of painting probes: (1) chicken chromosomes were divided into three size categories: (a) macrochromosomes 1-5 and Z, (b) medium-sized chromosomes 6-10, and (c) 19 microchromosomes; (2) combinatorially labeled chicken chromosome paints 1-6 and Z. Both probe sets were visualized on H. harpyja chromosomes by multicolor fluorescence in situ hybridization (FISH). Our data show how the organization into micro- and macrochromosomes has been lost in the Harpy eagle, seemingly without any preference or constraints.