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Migratory birds generally divide the annual cycle between discrete breeding and nonbreeding ranges. Itinerant breeders, however, reproduce twice at different geographic locations, migrating between them. This unusual flexibility in movement ecology and breeding biology suggests that some species can rapidly modulate the conflicting physiological and behavioral traits required for migration and reproduction. The Phainopepla (Phainopepla nitens), a songbird of the southwestern USA, has long been suspected to breed first in desert habitats in spring, then migrate to woodland habitats to breed again in summer. However, direct evaluation of movement and gene flow among individuals breeding in different locations has previously been logistically intractable. We deployed GPS tags on free-flying Phainopeplas in southern California, all of which migrated to hypothesized woodland breeding habitats after desert breeding (an average distance of 232 km). GPS data also revealed previously unknown fall and spring stopover sites. Population genomic analyses revealed no genetic differentiation among desert and woodland breeding populations, indicating significant movement and gene flow across the region. Finally, we used random forest analyses to quantify substantial environmental differences among temporal stages. Our results provide direct evidence that individual Phainopeplas do indeed move between 2 drastically different breeding habitats in the same year, representing a rare and extreme example of life-history flexibility.

Infectious diseases that originate from multiple wildlife hosts can be complex and problematic to manage. A full understanding is further limited by large temporal and spatial gaps in sampling. However, these limitations can be overcome, in part, by using historical samples, such as those derived from museum collections. Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel ( Funisciurus sp.) collected across Central Africa. We found evidence of MPXV infections in host species as early as 1899, half a century earlier than the first recognized case of MPXV in 1958, supporting the suggestion that historic pox-like outbreaks in humans and non-human primates may have been caused by MPXV rather than smallpox as originally thought. MPX viral DNA was found in 93 of 1038 (9.0%) specimens from five Funisciurus species ( F. anerythrus , F. carruthersi , F. congicus , F. lemniscatus and F. pyrropus ), of which F. carruthersi and pyrropus had not previously been identified as potential MPXV hosts. We additionally documented relative prevalence rates of infection in museum specimens of Funisciurus and examined the spatial and temporal distribution of MPXV in these potential host species across nearly a hundred years (1899–1993).

Background This study aims to assess the role that Pleistocene refugia, rivers and local habitat conditions may have played in the evolutionary diversification of three central African duiker species (Cephalophus dorsalis, C. callipygus and Philantomba monticola). Genetic data from geo-referenced feces were collected from a wide range of sites across Central Africa. Historical patterns of population genetic structure were assessed using a ~ 650 bp fragment of the mitochondrial control region and contemporary patterns of genetic differentiation were evaluated using 12 polymorphic microsatellite loci. Results Mitochondrial analyses revealed that populations of C. callipygus and P. monticola in the Gulf of Guinea refugium are distinct from other populations in west central Africa. All three species exhibit signatures of past population expansion across much of the study area consistent with a history of postglacial expansion. There was no strong evidence for a riverine barrier effect in any of the three species, suggesting that duikers can readily cross major rivers. Generalized dissimilarity models (GDM) showed that environmental variation explains most of the nuclear genetic differentiation in both C. callipygus and P. monticola. The forest-savanna transition across central Cameroon and the Plateaux Batéké region in southeastern Gabon show the highest environmentally-associated turnover in genetic variability. A pattern of genetic differentiation was also evident between the coast and forest interior that may reflect differences in precipitation and/or vegetation. Conclusions Findings from this study highlight the historical impact of Pleistocene fragmentation and current influence of environmental variation on genetic structure in duikers. Conservation efforts should therefore target areas that harbor as much environmentally-associated genetic variation as possible in order to maximize species’ capacity to adapt to environmental change. Electronic supplementary material The online version of this article (10.1186/s12862-017-1054-4) contains supplementary material, which is available to authorized users.

A trophic radiation in the South-American annual killifish genus Austrolebias has led to the evolution of large specialized piscivores from small generalized carnivores. It has been proposed that this occurred in a single series of vicariant speciation events. An alternative hypothesis is denoted giant-dwarf speciation: piscivores would have evolved in sympatry by character displacement and cannibalism. We test the plausibility of both scenarios using size measures combined with distributional data and new phylogenetic trees based on mitochondrial and nuclear molecular markers.Our analysis uses historical biogeography models and Ornstein-Uehlenbeck processes describing trait evolution across the posterior distributions of phylogenetic trees. Large species most likely evolved three times from small ones. For the clade containing A. elongatus, we argue that vicariance was not involved in the origin of these large and specialized piscivores. They experience stabilizing selection with an optimum shifted towards larger bodies and longer jaws. The branch leading to this clade has the fastest evolving jaw lengths across the phylogeny, in agreement with expectations for giant-dwarf speciation. For A. wolterstorffi, the support for giant-dwarf speciation is weaker. When the species is placed at the root of Austrolebias, ancestral reconstructions are unreliable and vicariance cannot be ruled out. For the remaining large species, we can reject vicariance and giant dwarf speciation. Our results give rise to two new additional scenarios for the evolution of specialized piscivores. In the first, two successive speciation events in sympatry or parapatry produced large and piscivorous species. In the second, the immigration of a different annual killifish genus (Cynopoecilus) in the Patos area of endemism has contributed to in-situ diversification of Austrolebias species.

Studies of both vertebrates and invertebrates have suggested that specialists, as compared to generalists, are likely to suffer more serious declines in response to environmental change. Less is known about the effects of environmental conditions on specialist versus generalist parasites. Here, we study the evolutionary strategies of malaria parasites (Plasmodium spp.) among different bird host communities. We determined the parasite diversity and prevalence of avian malaria in three bird communities in the lowland forests in Cameroon, highland forests in East Africa and fynbos in South Africa. We calculated the host specificity index of parasites to examine the range of hosts parasitized as a function of the habitat and investigated the phylogenetic relationships of parasites. First, using phylogenetic and ancestral reconstruction analyses, we found an evolutionary tendency for generalist malaria parasites to become specialists. The transition rate at which generalists become specialists was nearly four times as great as the rate at which specialists become generalists. We also found more specialist parasites and greater parasite diversity in African lowland rainforests as compared to the more climatically variable habitats of the fynbos and the highland forests. Thus, with environmental changes, we anticipate a change in the distribution of both specialist and generalist parasites with potential impacts on bird communities.

In the debate over modes of vertebrate diversification in tropical rainforests, two competing hypotheses of speciation predominate: those that emphasize the role of geographical isolation during glacial periods and those that stress the role of ecology and diversifying selection across ecotones or environmental gradients. To investigate the relative roles of selection versus isolation in refugia, we contrasted genetic and morphologic divergence of the olive sunbird (Cyanomitra olivacea) at 18 sites (approximately 200 individuals) across the forest-savanna ecotone of Central Africa in a region considered to have harboured three hypothesized refugia during glacial periods. Habitats were characterized using bioclimatic and satellite remote-sensing data. We found relatively high levels of gene flow between ecotone and forest populations and between refugia. Consistent with a pattern of divergence-with-gene-flow, we found morphological characters to be significantly divergent across the gradient [forest versus ecotone (mean ± SD): wing length 60.47 ± 1.81 mm versus 62.18 ± 1.35 mm; tarsus length 15.51 ± 0.82 mm versus 16.00 ± 0.57 mm; upper mandible length 21.77 ± 1.09 mm versus 23.19 ± 0.98 mm, respectively]. Within-habitat comparisons across forest and ecotone sites showed no significant differences in morphology. The results show that divergence in morphological traits is tied to environmental variables across the gradient and is occurring despite gene flow. The pattern of divergence-with-gene-flow found is similar to that described for other rainforest species across the gradient. These results suggest that neither refugia, nor isolation-by-distance have played a major role in divergence in the olive sunbird, although ecological differences along the forest and savanna ecotone may impose significant selection pressures on the phenotype and potentially be important in diversification.

To better understand how environment shapes phenotypic and genetic variation, we explore the relationship between environmental variables across Ecuador and genetic and morphological variation in the wedge-billed woodcreeper (Glyphorynchus spirurus), a common Neotropical rainforest bird species. Generalized dissimilarity models show that variation in amplified fragment length polymorphism markers was strongly associated with environmental variables on both sides of the Andes, but could also partially be explained by geographic distance on the western side of the Andes. Tarsus, wing, tail, and bill lengths and bill depth were well explained by environmental variables on the western side of the Andes, whereas only tarsus length was well explained on the eastern side. Regions that comprise the highest rates of genetic and phenotypic change occur along steep elevation gradients in the Andes. Such environmental gradients are likely to be particularly important for maximizing adaptive diversity to minimize the impacts of climate change. Using a framework for conservation prioritization based on preserving ecological and evolutionary processes, we found little overlap between currently protected areas in Ecuador and regions we predicted to be important in maximizing adaptive variation.

Several swiftlet species echolocate to navigate in the darkness of their nesting caves. We investigated whether swiftlets’ echo clicks and social vocalizations differed among species and whether they could be used in phylogenetic inference. We incorporated echo clicks of eight swiftlet species and social vocalizations of 27 echolocating and nonecholocating swifts and swiftlets. Characters in the frequency and time domain were used and analysed using nonparametric multivariate analysis of variance and stepwise discriminant analysis. We performed maximum parsimony analyses and character mapping to investigate phylogenetic signal and evolutionary patterns of swiftlet vocalizations. Echo clicks were species-specific. As well as in navigation, they may be used in recognition of conspecifics. Social vocalizations were species-specific also. However, the vocalizations contained no phylogenetic interpretable information. Maximum parsimony trees of echo clicks and of social vocalizations were almost completely unresolved. Moreover, resolved branches showed no congruence to a DNA-based tree that had been obtained previously. Mapping of the vocalization characters on the DNA-based tree revealed no consistent phylogenetic patterns. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88, 631–643.

Due to a lack of distinctive morphological characters, swift taxonomy and phylogeny has always been an area of disagreement. To shed more light on this subject, we reconstructed swift(let) phylogeny based on 1143 bp of mitochondrial cytochrome-b DNA sequence. Although this is not the first attempt to reconstruct swift phylogeny using molecular data, our results show higher support for many of the branches due to our much longer sequences. However, placement of Hydrochous is still unexpected. Implementation of more conservative genetic regions and sampling of more taxa could solve this problem. Most importantly, the Collocaliini resolve as a monophyletic group. The internal structure of the group shows that non-echolocating Collocalia and echolocating Aerodramus form two distinct clades. This is in congruence with earlier classifications based on morphological characters, but in contrast with more recent classifications. (C) 2003 Elsevier Science (USA). All rights reserved.

The adaptive significance of zebra stripes has thus far eluded understanding. Many explanations have been suggested, including social cohesion, thermoregulation, predation evasion and avoidance of biting flies. Identifying the associations between phenotypic and environmental factors is essential for testing these hypotheses and substantiating existing experimental evidence. Plains zebra striping pattern varies regionally, from heavy black and white striping over the entire body in some areas to reduced stripe coverage with thinner and lighter stripes in others. We examined how well 29 environmental variables predict the variation in stripe characteristics of plains zebra across their range in Africa. In contrast to recent findings, we found no evidence that striping may have evolved to escape predators or avoid biting flies. Instead, we found that temperature successfully predicts a substantial amount of the stripe pattern variation observed in plains zebra. As this association between striping and temperature may be indicative of multiple biological processes, we suggest that the selective agents driving zebra striping are probably multifarious and complex.

Since first introduced to North America in 1999, West Nile virus (WNV) has spread rapidly across the continent, threatening wildlife populations and posing serious health risks to humans. While WNV incidence has been linked to environmental factors, particularly temperature and rainfall, little is known about how future climate change may affect the spread of the disease. Using available data on WNV infections in vectors and hosts collected from 2003-2011 and using a suite of 10 species distribution models, weighted according to their predictive performance, we modeled the incidence of WNV under current climate conditions at a continental scale. Models were found to accurately predict spatial patterns of WNV that were then used to examine how future climate may affect the spread of the disease. Predictions were accurate for cases of human WNV infection in the following year (2012), with areas reporting infections having significantly higher probability of presence as predicted by our models. Projected geographic distributions of WNV in North America under future climate for 2050 and 2080 show an expansion of suitable climate for the disease, driven by warmer temperatures and lower annual precipitation that will result in the exposure of new and naive host populations to the virus with potentially serious consequences. Our risk assessment identifies current and future hotspots of West Nile virus where mitigation efforts should be focused and presents an important new approach for monitoring vector-borne disease under climate change.

Although the incidence of human monkeypox has greatly increased in Central Africa over the last decade, resources for surveillance remain extremely limited. We conducted a geospatial analysis using existing data to better inform future surveillance efforts. Using active surveillance data collected between 2005 and 2007, we identified locations in Sankuru district, Democratic Republic of Congo (DRC) where there have been one or more cases of human monkeypox. To assess what taxa constitute the main reservoirs of monkeypox, we tested whether human cases were associated with (i) rope squirrels (Funisciurus sp.), which were implicated in monkeypox outbreaks elsewhere in the DRC in the 1980s, or (ii) terrestrial rodents in the genera Cricetomys and Graphiurus, which are believed to be monkeypox reservoirs in West Africa. Results suggest that the best predictors of human monkeypox cases are proximity to dense forests and associated habitat preferred by rope squirrels. The risk of contracting monkeypox is significantly greater near sites predicted to be habitable for squirrels (OR = 1.32; 95% CI 1.08–1.63). We recommend that semi-deciduous rainforests with oil-palm, the rope squirrel’s main food source, be prioritized for monitoring. Electronic supplementary material The online version of this article (doi:10.1007/s10393-010-0355-5) contains supplementary material, which is available to authorized users.

Studies on the burden of human monkeypox in the Democratic Republic of the Congo (DRC) were last conducted from 1981 to 1986. Since then, the population that is immunologically naïve to orthopoxviruses has increased significantly due to cessation of mass smallpox vaccination campaigns. To assess the current risk of infection, we analyzed human monkeypox incidence trends in a monkeypox-enzootic region. Active, population-based surveillance was conducted in nine health zones in central DRC. Epidemiologic data and biological samples were obtained from suspected cases. Cumulative incidence (per 10,000 population) and major determinants of infection were compared with data from active surveillance in similar regions from 1981 to 1986. Between November 2005 and November 2007, 760 laboratory-confirmed human monkeypox cases were identified in participating health zones. The average annual cumulative incidence across zones was 5.53 per 10,000 (2.18–14.42). Factors associated with increased risk of infection included: living in forested areas, male gender, age < 15, and no prior smallpox vaccination. Vaccinated persons had a 5.2-fold lower risk of monkeypox than unvaccinated persons (0.78 vs. 4.05 per 10,000). Comparison of active surveillance data in the same health zone from the 1980s (0.72 per 10,000) and 2006–07 (14.42 per 10,000) suggests a 20-fold increase in human monkeypox incidence. Thirty years after mass smallpox vaccination campaigns ceased, human monkeypox incidence has dramatically increased in rural DRC. Improved surveillance and epidemiological analysis is needed to better assess the public health burden and develop strategies for reducing the risk of wider spread of infection.

Background Avian influenza virus (AIV) is an important public health issue because pandemic influenza viruses in people have contained genes from viruses that infect birds. The H5 and H7 AIV subtypes have periodically mutated from low pathogenicity to high pathogenicity form. Analysis of the geographic distribution of AIV can identify areas where reassortment events might occur and how high pathogenicity influenza might travel if it enters wild bird populations in the US. Modelling the number of AIV cases is important because the rate of co-infection with multiple AIV subtypes increases with the number of cases and co-infection is the source of reassortment events that give rise to new strains of influenza, which occurred before the 1968 pandemic. Aquatic birds in the orders Anseriformes and Charadriiformes have been recognized as reservoirs of AIV since the 1970s. However, little is known about influenza prevalence in terrestrial birds in the order Passeriformes. Since passerines share the same habitat as poultry, they may be more effective transmitters of the disease to humans than aquatic birds. We analyze 152 passerine species including the American Robin (Turdus migratorius) and Swainson's Thrush (Catharus ustulatus). Methods We formulate a regression model to predict AIV cases throughout the US at the county scale as a function of 12 environmental variables, sampling effort, and proximity to other counties with influenza outbreaks. Our analysis did not distinguish between types of influenza, including low or highly pathogenic forms. Results Analysis of 13,046 cloacal samples collected from 225 bird species in 41 US states between 2005 and 2008 indicates that the average prevalence of influenza in passerines is greater than the prevalence in eight other avian orders. Our regression model identifies the Great Plains and the Pacific Northwest as high-risk areas for AIV. Highly significant predictors of AIV include the amount of harvested cropland and the first day of the year when a county is snow free. Conclusions Although the prevalence of influenza in waterfowl has long been appreciated, we show that 22 species of song birds and perching birds (order Passeriformes) are influenza reservoirs in the contiguous US.

The Oilbird and many Swiftlet species are unique among birds for their ability to echolocate. Echolocaters may benefit from improved hearing sensitivity. Therefore, morphological adaptations to echolocation might be present in echolocating birds’ middle ears. We studied the functional morphology of the tympano–ossicular chain of seven specimens of four echolocating Swiftlet species and one specimen each of five non-echolocating species. Three dimensional (3D) reconstructions were made from micro-Computer-Tomographic (μCT) scans. The reconstructions were used in functional morphological analyses and model calculations. A two dimensional (2D) rigid rod model with fixed rotational axes was developed to study footplate output-amplitudes and to describe how changes in the arrangement of the tympano–ossicular chain affect its function. A 3D finite element model was used to predict ossicular-chain movement and to investigate the justification of the 2D approach. No morphological adaptations towards echolocation were found in the middle-ear lever system or in the mass impedance of the middle ear. A wide range of middle-ear configurations result in maximum output-amplitudes and all investigated species are congruent with these predicted best configurations. Echolocation is unlikely to depend on adaptations in the middle ear tympano–ossicular chain.

We recently reconstructed the troublesome swiftlet phylogeny using cytochrome- b mitochondrial DNA sequences. The relationship of the giant swiftlet ( Hydrochous gigas ) with swiftlets of the genus Aerodramus was, however, unresolved. In an attempt to clarify this issue, we now incorporated mitochondrial 12S rRNA and nuclear β-fibrinogen intron 7 nuclear DNA sequences with the cyt- b sequences of six swiftlet, two swift, and one hummingbird outgroup species. A partition homogeneity (PH) test, used to determine the congruence of phylogenetic signal between two sets of sequences, suggested that cyt- b and Fib7 sequences were incongruent and therefore should not be combined. However, further analyses revealed that the apparent incongruence was probably due to the high amount of variation in cyt- b sequences. Separate and combined analyses of the three sequences unambiguously placed H. gigas as the sister-group of Aerodramus and supported monophyly of the swiftlets. These results were supported by analyses of combined NADH dehydrogenase subunit-2 (ND2) and cyt- b sequences of H. gigas in combination with sequences previously published by other workers. Recently, it was shown that the pygmy swiftlet ( C. troglodytes )—in our phylogenetic analyses consistently placed with other, non-echolocating, Collocalia species—is in fact able to echolocate. Echolocation thereby lost its value to distinguish between different swiftlet genera. Furthermore, the phylogenetic distribution of echolocation can be explained either by its single evolution at the base of the swiftlets, with subsequent loss, or by independent evolution in Aerodramus and C. troglodytes . Because yet unpublished data suggest that only the auditory nuclei in swiftlet brains show adaptations to echolocation, the latter explanation seems the more likely one.

Myzomela honeyeaters are distributed from eastern Austalia and Indonesia throughout the islands of the tropical Pacific, a biodiversity hotspot that is particularly vulnerable due to small population sizes, habitat destruction, and high levels of isolation between islands. We developed fourteen microsatellite loci for Myzomela honeyeaters from the tropical Pacific. Microsatellites were tested for polymorphism on a panel of 104 individuals. The number of alleles ranged from 3 to 23, observed heterozygosity from 0.067 to 0.913, and the fixation index from −0.143 to 0.634. Cross-amplification was tested in 18 different species and subspecies in the genus Myzomela from throughout the Pacific, Australia, and eastern Indonesian archipelago. These new microsatellites could potentially be useful in making informed conservation decisions regarding Myzomela honeyeaters on the islands of the tropical Pacific.

Background The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations. Results We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti. Conclusions We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.