Integrated Specimen-Based Studies of Philippine Birds and Avian Influenza: Applications in Conservation, Taxonomy, Wildlife Enforcement, and Disease

Conservation is practiced in many ways, but often overlooked is the role of specimens in conservation biological research. With increasingly powerful phylogenetic analyses necessary to describe dwindling genetic diversity, the preservation of biodiversity can only be as successful as the infrastructure of specimens available. Taxonomic units of biodiversity may not completely reflect true genetic diversity, so new phylogenetic tools useful for the recognition of biodiversity require specimen-based resources to be as complete as possible. Here, we discuss how specimen-based, integrated research has multiple goals, and how conservation biology remains a key focus and outcome of these studies. Our sample archiving methods are among the most comprehensive in the discipline, and critical for quality research in conservation, phylogenetics, taxonomy, wildlife enforcement, and avian influenza studies. Although we have not isolated any avian influenza from Philippine samples, we have learned much from these negative results about avian influenza in the Philippines, and our methodology is producing quality multidisciplinary science

Estimating the unbiased estimator θ for population genetic survey data

We consider a method of approximating Weir and Cockerham\u27s θ, an unbiased estimator of genetic population structure, using values readily available from published studies using biased estimators (Wright\u27s FST or Nei\u27s GST). The estimation algorithm is shown to be useful for both model populations and real-world avian populations. However, the correlation between Wright\u27s FST and Weir and Cockerham\u27s θ is strong when compared among 39 empirical avian datasets. Thus, the advantage of approximating an unbiased estimator is unclear considering the small actual effect of θ\u27s bias-removing power on empirical datasets

BIOMONITORING OF CONTAMINANTS IN BIRDS FROM TWO TROPHIC LEVELS IN THE NORTH PACIFIC

Abstract-The presence and accumulation of persistent contaminants at high latitudes from long-range transport is an important environmental issue. Atmospheric transport has been identified as the source of pollutants in several arctic ecosystems and has the potential to severely impact high-latitude populations. Elevated levels of contaminants in Aleutian Island avifauna have been documented, but the great distance from potential industrial sources and the region's complex military history have confounded identification of contaminant origins. We sampled bird species across the natural longitudinal transect of the Aleutian Archipelago to test three contaminant source hypotheses. We detected patterns in some polychlorinated biphenyl congeners and mercury that indicate abandoned military installations as likely local point sources. Carbon isotopes were distinct among island groups, enabling us to rule out transfer through migratory prey species as a contaminant source. The long-range transport hypothesis was supported by significant west-to-east declines in contaminant concentrations for most detected organochlorines and some trace metals. Although relatively low at present, concentrations may increase in Aleutian fauna as Asian industrialization increases and emitted contaminants are atmospherically transported into the region, necessitating continued monitoring in this unique ecosystem

A phylogeographic and population genetic analysis of a widespread, sedentary North American bird: The Hairy Woodpecker (Picoides villosus)

The Hairy Woodpecker (Picoides villosus) has one of the broadest breeding distributions of any North American bird and is also one of the most morphologically variable with as many as 21 described subspecies. This wide distribution and high degree of phenotypic diversity suggests the presence of underlying genetic structure. We used ND2 sequence from 296 individuals from 89 localities throughout the Hairy Woodpecker distribution to address this question and to explore this species’ evolutionary history. Phylogenetic analyses identified three main Hairy Woodpecker clades, each ~1.5% divergent from one another. One clade was comprised of birds from boreal and eastern zones of North America (N&E); the second, of birds from western and southwestern North America (S&W), and the third included only birds from a disjunct population in Costa Rica and Panama. Population genetic analyses and climatic niche models indicated that the N&E and S&W clades have very different recent evolutionary histories. Populations in the N&E are characterized by a lack of genetic structure and a genetic signature of recent population expansion. In contrast, S&W populations are highly structured and relative population stability was inferred. The S&W clade is further structured into three additional geographically and genetically isolated groups: Pacific Coast ranges, interior ranges, and southern Mexico. The continental scale patterns of genetic variation observed suggest that the complex topography of the montane west has probably been more important than latitude in generating phylogenetic diversity within this species

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths

Decadal changes and delayed avian species losses due to deforestation in the northern Neotropics

How avifauna respond to the long-term loss and fragmentation of tropical forests is a critical issue in biodiversity management. We use data from over 30 years to gain insights into such changes in the northernmost Neotropical rainforest in the Sierra de Los Tuxtlas of southern Veracruz, Mexico. This region has been extensively deforested over the past half-century. The Estación de Biología Tropical Los Tuxtlas, of the Universidad Nacional Autónoma de México (UNAM), protects a 640 ha tract of lowland forest. It became relatively isolated from other forested tracts between 1975 and 1985, but it retains a corridor of forest to more extensive forests at higher elevations on Volcán San Martín. Most deforestation in this area occurred during the 1970s and early 1980s. Forest birds were sampled on the station and surrounding areas using mist nets during eight non-breeding seasons from 1973 to 2004 (though in some seasons netting extended into the local breeding season for some species). Our data suggested extirpations or declines in 12 species of birds subject to capture in mist nets. Six of the eight species no longer present were captured in 1992–95, but not in 2003–2004. Presence/absence data from netting and observational data suggested that another four low-density species also disappeared since sampling began. This indicates a substantial time lag between the loss of habitat and the apparent extirpation of these species. Delayed species loss and the heterogeneous nature of the species affected will be important factors in tropical forest management and conservation