Systematics within Gyps vultures: a clade at risk

BACKGROUND: Populations of the Oriental White-backed Vulture (Gyps bengalensis) have declined by over 95% within the past decade. This decline is largely due to incidental consumption of the non-steroidal anti-inflammatory veterinary pharmaceutical diclofenac, commonly used to treat domestic livestock. The conservation status of other Gyps vultures in southern Asia is also of immediate concern, given the lack of knowledge regarding status of their populations and the continuing existence of taxonomic uncertainties. In this study, we assess phylogenetic relationships for all recognized species and the majority of subspecies within the genus Gyps. The continuing veterinary use of diclofenac is an unknown but potential risk to related species with similar feeding habits to Gyps bengalensis. Therefore, an accurate assessment of the phylogenetic relationships among Gyps vultures should aid in their conservation by clarifying taxonomic uncertainties, and enabling inference of their respective relatedness to susceptible G. bengalensis. RESULTS: Phylogenetic results using mitochondrial cytB, ND2 and control region sequence data indicate a recent and rapid diversification within the genus Gyps. All recognized species formed monophyletic groups with high statistical support, with the exception of the Eurasian Vulture, for which specimens identified as subspecies G. fulvus fulvescens appear closely related to the Himalayan Vulture (G. himalayensis). In all analyses, the earliest divergence separated the Oriental White-backed Vulture from other Gyps taxa, with the next diverging taxon being either the African White-backed Vulture (G. africanus), or the Himalayan Vulture. All analyses supported a sister relationship between the Eurasian Vulture (G. f. fulvus), and Rüppell's Vulture (G. rueppellii), with this clade being sister to another consisting of the two taxa of "Long-billed" Vulture (G. indicus indicus and G. i. tenuirostris), and the Cape Vulture (G. coprotheres). These molecular phylogenies strongly support the treatment of indicus and tenuirostris as separate species, as does morphological data showing that these two taxa of similar overall size differ in proportions, especially in rostral, alar, and pedal characters. In addition, grouping of bengalensis and africanus together in the genus Pseudogyps, as historically proposed, is not upheld based on mitochondrial data. CONCLUSION: Both molecular and morphological data provide strong support for considering the "Long-billed" Vulture to be comprised of two species (G. indicus and G. tenuirostris), and further analysis is warranted to determine the taxonomic distinctiveness of G. f. fulvescens. Our phylogenetic analyses and conservative estimates suggest the diversification of Gyps taxa to be within the past 6 million years. Diclofenac susceptibility has been previously demonstrated for four Gyps species (G. indicus, G. fulvus, G. africanus, G. bengalensis), and the phylogenetic position of these species each forming a sister relationship with at least one of the remaining species, support concern that other Gyps taxa may be susceptible as well. Determining genetic and evolutionary distinctiveness for Gyps lineages is increasingly important as a breeding program is being established to prevent extinction

It\u27s not too Late for the Harpy Eagle (Harpia harpyja): High Levels Of Genetic Diversity and Differentiation Can Fuel Conservation Programs

Background: The harpy eagle (Harpia harpyja) is the largest Neotropical bird of prey and is threatened by human persecution and habitat loss and fragmentation. Current conservation strategies include local education, captive rearing and reintroduction, and protection or creation of trans-national habitat blocks and corridors. Baseline genetic data prior to reintroduction of captive-bred stock is essential for guiding such efforts but has not been gathered previously. Methodology/Findings: We assessed levels of genetic diversity, population structure and demographic history for harpy eagles using samples collected throughout a large portion of their geographic distribution in Central America (n = 32) and South America (n = 31). Based on 417 bp of mitochondrial control region sequence data, relatively high levels of haplotype and nucleotide diversity were estimated for both Central and South America, although haplotype diversity was significantly higher for South America. Historical restriction of gene flow across the Andes (i.e. between our Central and South American subgroups) is supported by coalescent analyses, the haplotype network and significant FST values, however reciprocally monophyletic lineages do not correspond to geographical locations in maximum likelihood analyses. A sudden population expansion for South America is indicated by a mismatch distribution analysis, and further supported by significant (p,0.05) negative values of Fu and Li’s DF and F, and Fu’s FS. This expansion, estimated at approximately 60 000 years BP (99 000–36 000 years BP 95% CI), encompasses a transition from a warm and dry time period prior to 50 000 years BP to an interval of maximum precipitation (50 000–36 000 years BP). Notably, this time period precedes the climatic and habitat changes associated with the last glacial maximum. In contrast, a multimodal distribution of haplotypes was observed for Central America suggesting either population equilibrium or a recent decline. Significance: High levels of mitochondrial genetic diversity in combination with genetic differentiation among subgroups within regions and between regions highlight the importance of local population conservation in order to preserve maximal levels of genetic diversity in this species. Evidence of historically restricted female-mediated gene flow is an important consideration for captive-breeding programs

Evolutionary biology for the 21st century

New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.Molecular and Cellular BiologyOrganismic and Evolutionary Biolog

Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani

<p>Abstract</p> <p>Background</p> <p>Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of <it>Buteo jamaicensis harlani </it>to other <it>B. jamaicensis </it>subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations.</p> <p>Results</p> <p>To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor (<it>Mc1r</it>) to investigate molecular genetic differentiation among three <it>B. jamaicensis </it>subspecies (<it>B. j. borealis</it>, <it>B. j. calurus</it>, <it>B. j. harlani</it>). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between <it>B. j. harlani </it>and <it>B. j. borealis</it>. Differences observed between <it>B. j. harlani </it>and <it>B. j. borealis </it>in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, <it>B. j. borealis </it>and <it>B. j. calurus</it>, and estimates of migration rates among all three subspecies were high. No consistent differences were observed in <it>Mc1r </it>data between <it>B. j. harlani </it>and other <it>B. jamaicensis </it>subspecies or between light and dark color morphs within <it>B. j. calurus</it>, suggesting that <it>Mc1r </it>does not play a significant role in <it>B. jamaicensis </it>melanism.</p> <p>Conclusions</p> <p>These data suggest recent interbreeding and gene flow between <it>B. j. harlani </it>and the other <it>B. jamaicensis </it>subspecies examined, providing no support for the historical designation of <it>B. j. harlani </it>as a distinct species.</p

The Use of Genetics for the Management of a Recovering Population: Temporal Assessment of Migratory Peregrine Falcons in North America

Background: Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (FST and DEST), and effective population size (Ne). The primary goal of any recovery effort is to produce a longterm self-sustaining population, and these genetic measures provide a metric by which we can gauge our progress and help make important management decisions. Methodology/Principal Findings: The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci suggest limited differentiation that can be attributed to an isolation by distance relationship and warrant no delineation of these two subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985–2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean Ne were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods. Conclusions/Significance: These results, including those from simulations to assess the power of each method to estimate Ne, suggest a stable or growing population, which is consistent with ongoing field-based monitoring surveys. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful with no indication of recent decline, at least from the northern latitude range-wide perspective. The results also further highlight the importance of archiving samples and their use for continual assessment of population recovery and long-term viability

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates

Big data and data repurposing – using existing data to answer new questions in vascular dementia research

Introduction: Traditional approaches to clinical research have, as yet, failed to provide effective treatments for vascular dementia (VaD). Novel approaches to collation and synthesis of data may allow for time and cost efficient hypothesis generating and testing. These approaches may have particular utility in helping us understand and treat a complex condition such as VaD. Methods: We present an overview of new uses for existing data to progress VaD research. The overview is the result of consultation with various stakeholders, focused literature review and learning from the group’s experience of successful approaches to data repurposing. In particular, we benefitted from the expert discussion and input of delegates at the 9th International Congress on Vascular Dementia (Ljubljana, 16-18th October 2015). Results: We agreed on key areas that could be of relevance to VaD research: systematic review of existing studies; individual patient level analyses of existing trials and cohorts and linking electronic health record data to other datasets. We illustrated each theme with a case-study of an existing project that has utilised this approach. Conclusions: There are many opportunities for the VaD research community to make better use of existing data. The volume of potentially available data is increasing and the opportunities for using these resources to progress the VaD research agenda are exciting. Of course, these approaches come with inherent limitations and biases, as bigger datasets are not necessarily better datasets and maintaining rigour and critical analysis will be key to optimising data use

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

Abstract: Background: Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. Results: Here, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identify common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems, such as loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems that are convergent with other nocturnal avian orders. Additionally, we find that a suite of genes associated with vision and circadian rhythm are differentially expressed in blood tissue between nocturnal and diurnal raptors, possibly indicating adaptive expression change during the transition to nocturnality. Conclusions: Overall, raptor genomes show genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators

Health impact assessment of waste management facilities in three European countries

<p>Abstract</p> <p>Background</p> <p>Policies on waste disposal in Europe are heterogeneous and rapidly changing, with potential health implications that are largely unknown. We conducted a health impact assessment of landfilling and incineration in three European countries: Italy, Slovakia and England.</p> <p>Methods</p> <p>A total of 49 (Italy), 2 (Slovakia), and 11 (England) incinerators were operating in 2001 while for landfills the figures were 619, 121 and 232, respectively. The study population consisted of residents living within 3 km of an incinerator and 2 km of a landfill. Excess risk estimates from epidemiological studies were used, combined with air pollution dispersion modelling for particulate matter (PM₁₀) and nitrogen dioxide (NO₂). For incinerators, we estimated attributable cancer incidence and years of life lost (YoLL), while for landfills we estimated attributable cases of congenital anomalies and low birth weight infants.</p> <p>Results</p> <p>About 1,000,000, 16,000, and 1,200,000 subjects lived close to incinerators in Italy, Slovakia and England, respectively. The additional contribution to NO₂levels within a 3 km radius was 0.23, 0.15, and 0.14 μg/m³, respectively. Lower values were found for PM₁₀. Assuming that the incinerators continue to operate until 2020, we are moderately confident that the annual number of cancer cases due to exposure in 2001-2020 will reach 11, 0, and 7 in 2020 and then decline to 0 in the three countries in 2050. We are moderately confident that by 2050, the attributable impact on the 2001 cohort of residents will be 3,621 (Italy), 37 (Slovakia) and 3,966 (England) YoLL. The total exposed population to landfills was 1,350,000, 329,000, and 1,425,000 subjects, respectively. We are moderately confident that the annual additional cases of congenital anomalies up to 2030 will be approximately 2, 2, and 3 whereas there will be 42, 13, and 59 additional low-birth weight newborns, respectively.</p> <p>Conclusions</p> <p>The current health impacts of landfilling and incineration can be characterized as moderate when compared to other sources of environmental pollution, e.g. traffic or industrial emissions, that have an impact on public health. There are several uncertainties and critical assumptions in the assessment model, but it provides insight into the relative health impact attributable to waste management.</p