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Populations in fragmented ecosystems risk extirpation through natural disasters, which must be endured rather than avoided. Managing communities for resilience is thus critical, but details are sketchy about the capacity for resilience and its associated properties in vertebrate communities. We studied short-term resilience in a community of individually marked birds, following this community through the catastrophic destruction of its forest habitat by Hurricane Iris in Belize, Central America. We sampled for 58 d immediately before the storm, 28 d beginning 11 d after Hurricane Iris, and for 69 d approximately one year later. Our data showed that the initial capacity for resilience was strong. Many banded individuals remained after the storm, although lower post-hurricane recapture rates revealed increased turnover among individuals. Changes occurred in community dynamics and in abundances among species and guilds. Survivors and immigrants both were critical components of resilience, but in a heterogeneous, species-specific manner. Delayed effects, including higher fat storage and increased species losses, were evident one year later.

The latitudinal gradient in species richness is a nearly universal ecological phenomenon. Similarly, conspecific genetic diversity often increases towards the equator - usually explained as the consequence of post-glacial range expansion or due to the shared response of genetic diversity to processes that promote species richness. However, no study has yet examined the relationship between latitude and within-population genetic diversity in exclusively tropical species. We surveyed genetic variation in nine resident bird species co-occurring in tropical lowlands between southern Mexico and western Ecuador, where avian species richness increases with decreasing latitude. Within-population genetic variation was always highest at mid-range latitudes, and not in the most equatorial populations. Differences in demography and gene flow across species' ranges may explain some of our observations; however, much of the pattern may be due simply to geometric constraints. Our findings have implications for conservation planning and for understanding how biodiversity scales from genes to communities.

Recent literature has underestimated the number and taxonomic diversity of wild birds moving between Asia and North America. Our analyses of the major avian influenza (AI) host groups show that fully 33 species of waterfowl (Anatidae), 46 species of shorebirds (Charadriidae and Scolopacidae), and 15 species of gulls and terns (Laridae) are involved in movements from Asia to Alaska across northern oceans (Table 1). Our data suggest that about 1.5-2.9 million individuals in these important host groups move from Asia to Alaska annually. Among all of the host groups we consider most relevant for AI virus movement models in this region (waterfowl, shorebirds, and gulls and terns), it seems likely that thousands of AI-infectious birds may be involved in annual Asia-to-America migrations. Importantly, host availability in Alaska once these vectors arrive is also very high, representing at least 5-10 times more birds and infectious birds than the host populations moving from Asia to North America. Incorporating our data into a recent model of the global spread of the highly pathogenic H5N1 suggests that wild birds are a more likely source of this strain being brought into the United States than trade in domestic birds, although the latter remain a numerically more probable source of introduction into the New World. Our results should help in defining the key taxonomic, geographic, and seasonal factors involved in this complex intercontinental association of wild bird AI hosts. The next steps are to determine infection rates of low pathogenicity and highly pathogenic viruses among these hosts and to incorporate these into dynamic models.

High-latitude diversification is a process characterized by speciation and extinction due to climatically driven vicariance and dispersal events. McKay's buntings (Plectrophenax hyperboreus) are high-latitude island endemic songbirds, and their global range is restricted to Beringia. Snow buntings (P. nivalis), their closest relatives, are distributed throughout the Holarctic, breeding in available habitat surrounding the island range of McKay's buntings. We sequenced 1123 base pairs of mitochondrial DNA for 40 individuals of each species and analysed a total of 913 AFLPs for 57 individuals. Both marker types suggested weak but significant genetic differentiation. Analysis of sequence data indicated divergence occurring when the current breeding range of McKay's buntings was a hill on the Beringian steppe (approximately 18,400 to approximately 73,700 years before present), suggesting that snow buntings were restricted to lower latitudes by ice sheets. Ancestral effective population size estimates indicate a founder event in McKay's buntings followed by an expansion and then a reduction in effective size. Rising sea levels and asymmetric hybridization from McKay's buntings into the postglacially-colonizing population of snow buntings could account for this reduction. Reproductive isolation is likely maintained through differential arrival dates on breeding grounds and the high breeding density of McKay's buntings. This recent, high-latitude divergence best fits a model of founder event speciation driven by vicariance and oscillations in habitat due to climate change.

Polytomies, or phylogenetic "bushes", are the result of a series of internodes occurring in a short period of evolutionary time (which can result in data that do not contain enough information), or data that have too much homoplasy to resolve a bifurcating branching pattern. In this study we used the Aethia auklet polytomy to explore the effectiveness of different methods for resolving polytomies: mitochondrial DNA gene choice, number of individuals per species sampled, model of molecular evolution, and AFLP loci. We recovered a fully-resolved phylogeny using NADH dehydrogenase subunit 2 (ND2) sequence data under two different Bayesian models. We were able to corroborate this tree under one model with an expanded mtDNA dataset. Effectiveness of additional intraspecific sampling varied with node, and fully 20% of the subsampled datasets failed to return a congruent phylogeny when we sampled only one or two individuals per species. We did not recover a resolved phylogeny using AFLP data. Conflict in the AFLP dataset showed that nearly all possible relationships were supported at low levels of confidence, suggesting that either AFLPs are not useful at the genetic depth of the Aethia auklet radiation (7-9% divergent in the mtDNA ND2 gene), perhaps resulting in too much homoplasy, or that the Aethia auklets have experienced incomplete lineage sorting at many nuclear loci.

Hypoxia is one of the most important factors affecting survival at high altitude, and the major hemoglobin protein is a likely target of selection. We compared population genetic structure in the alphaA and betaA hemoglobin subunits (HBA2 and HBB) of five paired lowland and highland populations of Andean dabbling ducks to unlinked reference loci. In the hemoglobin genes, parallel amino acid replacements were overrepresented in highland lineages, and one to five derived substitutions occurred at external solvent-accessible positions on the alpha and beta subunits, at alpha(1)beta(1) intersubunit contacts, or in close proximity to inositolpentaphosphate (IPP) binding sites. Coalescent analyses incorporating the stochasticity of drift and mutation indicated that hemoglobin alleles were less likely to be transferred between highland and lowland populations than unlinked alleles at five other loci. Amino acid replacements that were overrepresented in the highlands were rarely found within lowland populations, suggesting that alleles segregating at high frequency in the highlands may be maladaptive in the lowlands and vice versa. Most highland populations are probably nonmigratory and locally adapted to the Altiplano, but gene flow for several species may be sufficiently high to retard divergence at unlinked loci. Heterozygosity was elevated in the alphaA or betaA subunits of highland populations exhibiting high gene flow between the southern lowlands and the highlands and in highland species that disperse seasonally downslope to midelevation environments from the central Andean plateau. However, elevated heterozygosity occurred more frequently in the alphaA subunit but not simultaneously in both subunits, suggesting that selection may be more constrained by epistasis in the betaA subunit. Concordant patterns among multiple species with different evolutionary histories and depths of historical divergence and gene flow suggest that the major hemoglobin genes of these five dabbling duck species have evolved adaptively in response to high-altitude hypoxia in the Andes.

Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.

Low-virulence Newcastle disease viruses (loNDV) are frequently recovered from wild bird species, but little is known about their distribution, genetic diversity, or potential to cause disease in poultry. NDV isolates recovered from cloacal samples of apparently healthy waterfowl and shorebirds (WS) in the United States during 1986 to 2005 were examined for genomic diversity and their potential for virulence (n = 249). In addition 19 loNDV isolates from U.S. live bird markets (LBMs) were analyzed and found to be genetically distinct from NDV used in live vaccines but related to WS-origin NDV. Phylogenetic analysis of the fusion protein identified nine novel genotypes among the class I NDV, and new genomic subgroups were identified among genotypes I and II of the class II viruses. The WS-origin viruses exhibited broad genetic and antigenic diversity, and some WS genotypes displayed a closer phylogenetic relationship to LBM-origin NDV. All NDV were predicted to be lentogenic based upon sequencing of the fusion cleavage site, intracerebral pathogenicity index, or mean death time in embryo assays. The USDA real-time reverse transcription-PCR assay, which targets the matrix gene, identified nearly all of the class II NDV tested but failed to detect class I viruses from both LBM and WS. The close phylogenetic proximity of some WS and LBM loNDV suggests that viral transmission may occur among wild birds and poultry; however, these events may occur unnoticed due to the broad genetic diversity of loNDV, the lentogenic presentation in birds, and the limitations of current rapid diagnostic tools.

Asian-origin avian influenza (AI) viruses are spread in part by migratory birds. In Alaska, diverse avian hosts from Asia and the Americas overlap in a region of intercontinental avifaunal mixing. This region is hypothesized to be a zone of Asia-to-America virus transfer because birds there can mingle in waters contaminated by wild-bird-origin AI viruses. Our 7 years of AI virus surveillance among waterfowl and shorebirds in this region (1998-2004; 8,254 samples) showed remarkably low infection rates (0.06%). Our findings suggest an Arctic effect on viral ecology, caused perhaps by low ecosystem productivity and low host densities relative to available water. Combined with a synthesis of avian diversity and abundance, intercontinental host movements, and genetic analyses, our results suggest that the risk and probably the frequency of intercontinental virus transfer in this region are relatively low.

The taxonomic challenge posed by cryptic species (two or more distinct species classified as a single species) has been recognized for nearly 300 years, but the advent of relatively inexpensive and rapid DNA sequencing has given biologists a new tool for detecting and differentiating morphologically similar species. Here, we synthesize the literature on cryptic and sibling species and discuss trends in their discovery. However, a lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups. The discovery of cryptic species is likely to be non-random with regard to taxon and biome and, hence, could have profound implications for evolutionary theory, biogeography and conservation planning.

Apart from an outbreak in commercial poultry in Chile in 2002, there have been few reports of avian influenza in South America. However, surveillance in free-flying birds has been limited. An avian influenza virus was isolated from a Cinnamon Teal (Anas cyanoptera) in Bolivia in 2001 from samples collected for an avian influenza virus and avian paramyxovirus surveillance study. This isolate was determined to be an H7N3 virus by gene sequencing. Analysis of all eight genes revealed that five genes were most closely related to the H7N3 in Chile in 2002. Two genes were most closely related to North American wild aquatic bird virus lineages and one gene was most closely related to an equine influenza virus from South America.

The postglacial recolonization of northern North America was heavily influenced by the Pleistocene glaciation. In the Pacific Northwest, there are two disjunct regions of mesic temperate forest, one coastal and the other interior. The chestnut-backed chickadee is one of the species associated with this distinctive ecosystem. Using seven microsatellite markers we found evidence of population structure among nine populations of chestnut-backed chickadees. High levels of allelic variation were found in each of the populations. Northern British Columbia and central Alaska populations contained a large number of private alleles compared to other populations, including those from unglaciated regions. The disjunct population in the interior was genetically distinct from the coastal population. Genetic and historical records indicate that the interior population originated from postglacial inland dispersal. Population structuring was found within the continuous coastal population, among which the peripheral populations, specifically those on the Queen Charlotte Islands and the central Alaska mainland, were genetically distinct. The pattern of population structure among contemporary chickadee populations is consistent with a pioneer model of recolonization. The persistence of genetic structure in western North American chestnut-backed chickadees may be aided by their sedentary behaviour, linear distribution, and dependence on cedar-hemlock forests.

An H7N3 avian influenza virus (AIV) was isolated from a Cinnamon Teal (Anas cyanoptera) (A/CinnamonTeal/Bolivia/4537/01) during a survey of wild waterfowl in Bolivia in 2001. The NA and M genes had the greatest identity with North American wild bird isolates, the NS was most closely related to an equine virus, and the remaining genes were most closely related to isolates from an outbreak of H7N3 in commercial poultry in Chile in 2002. The HA protein cleavage site and the results of pathogenesis studies in chickens were consistent with a low-pathogenicity virus, and the infective dose was 10(5) times higher for chickens than turkeys.

The matrix (M) (98 isolates), nucleoprotein (NP) (67 isolates), non-structural (NS) (107 isolates), H4 subtype HA1 (21 isolates) and H6 (38 isolates) subtype HA1 region of the hemagglutinin (HA) gene were sequenced from avian influenza viruses isolated from North American wild aquatic birds between 1969 and 2003. Sequences were compared phylogenetically with all available wild aquatic bird isolate sequences and sequences from isolates from gallinaceous poultry and mammalian host species. Among the wild aquatic bird isolates the NS subtype B NS1 and subtype B NS2 proteins were the most conserved with minimum amino acid identities of 98.0 and 99.0%, respectively. The H6 HA1, M and NS subtype A genes were more divergent; both nucleotide and amino acid divergence levels were similar to those of the same genes from gallinaceous poultry and mammalian origin type A influenza isolates. Phylogenetically none of the genes assorted geographically (within North America), chronologically or by species of origin, unlike isolates from non-natural host species, suggesting that selection pressure is low. A lack of clear temporal or spatial grouping shows that multiple lineages of virus co-circulate and precludes the development of an epidemiological map for influenza virus from these species.

Post-Pleistocene avian colonization of deglaciated North America occurred from multiple refugia, including a coastal refugium in the northwest. The location of a Pacific Coastal refugium is controversial; however, multiple lines of evidence suggest that it was located near the Queen Charlotte Islands (also known as Haida Gwaii). The Queen Charlotte Islands contain a disproportionately large number of endemic plants and animals including the Steller's jay Cyanocitta stelleri carlottae. Using five highly variable microsatellite markers, we studied population structure among eight populations of Steller's jay (N = 150) from geographical areas representing three subspecies in western North America: C. s. carlottae, C. s. stelleri and C. s. annectens. Microsatellite analyses revealed genetic differentiation between each of the three subspecies, although more extensive sampling of additional C. s. annectens populations is needed to clarify the level of subspecies differentiation. High levels of population structure were found among C. s. stelleri populations with significant differences in all but two pairwise comparisons. A significant isolation by distance pattern was observed amongst populations in the Pacific Northwest and Alaska. In the C. s. carlottae population, there was evidence of reduced genetic variation, higher number of private alleles than northern C. s. stelleri populations and higher levels of divergence between Queen Charlotte Island and other populations. We were unable to reject the hypothesis that the Queen Charlotte Islands served as a refugium during the Pleistocene. Steller's jay may have colonized the Queen Charlotte Islands near the end of the last glaciation or persisted throughout the Pleistocene, and this subspecies may thus represent a glacial relic. The larger number of private alleles, despite reduced genetic variation, morphological distinctiveness and high divergence from other populations suggests that the Queen Charlotte Island colonization pre-dates that of the mainland. Furthermore, our results show rapid divergence in Steller's jay populations on the mainland following the retreat of the ice sheets.

Two genetic consequences are often considered evidence of a founder effect: substantial loss in genetic diversity and rapid divergence between source and founder populations. Single-step founder events have been studied for these effects, but with mixed results, causing continued controversy over the role of founder events in divergence. Experiments of serial bottlenecks have shown losses of diversity, increased divergence, and rapid behavioural changes possibly leading to reproductive isolation between source and final populations. The few studies conducted on natural, sequentially founded systems show some evidence of these effects. We examined a natural vertebrate system of sequential colonization among northwestern song sparrows (Melospiza melodia). This system has an effectively linear distribution, it was probably colonized within the last 10,000 years, there are morphological and behavioural differences among populations, and the westernmost populations occur in atypical habitats for the species. Eight microsatellite loci from eight populations in Alaska and British Columbia (n = 205) showed stepwise loss of genetic diversity, genetic evidence for strong population bottlenecks, and increased population divergence. The endpoint population on Attu Island has extremely low diversity (H(E) = 0.18). Our study shows that sequential bottlenecks or founder events can have powerful genetic effects in reducing diversity, possibly leading to rapid evolutionary divergence.

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.

Based on our observations and those of others from the literature, we construct a graphical model of habitat use in territorial species at high densities relative to optimal habitat availability. This model ignores differences in abundance among habitats, and, together with other models of habitat use, predicts that there should be greater stability (lower turnover rates) among individuals occupying optimal habitat than among those in suboptimal habitat(s). Future studies assessing quality among habitats might take advantage of this by comparing individual turnover rates among habitat types using standard mark-recapture methodology. As an illustrative example, we present a case in wintering wood thrushes (Catharus mustelinus; Muscicapidae: Turdinae) in which relative abundance and habitat quality were inversely related. Many individuals of this nearctic-neotropic migrant species hold nonbreeding territories in the seemingly crowded rainforest of southern Veracruz, Mexico.