Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data.

AIM: We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines. LOCATION: Oceania, greater Indonesia, and the Philippines. TAXON: Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species. RESULTS: Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples. MAIN CONCLUSIONS: Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.

Sustained plumage divergence despite weak genomic differentiation and broad sympatry in sister species of Australian woodswallows (Artamus spp.).

Plumage divergence can function as a strong premating barrier when species come into secondary contact. When it fails to do so, the results are often genome homogenization and phenotypic hybrids at the zone of contact. This is not the case in the largely sympatric masked woodswallow and white-browed woodswallow species (Passeriformes: Artamidae: Artamus spp) complex in Australia where phenotypic integrity is sustained despite no discernible mitochondrial structure in earlier work. This lack of structure may suggest recent divergence, ongoing gene flow or both, and phenotypic hybrids are reported albeit rarely. Here, we further assessed the population structure and differentiation across the species' nuclear genomes using ddRAD-seq. As found in the mitochondrial genome, no structure or divergence within or between the two species was detected in the nuclear genome. This coarse sampling of the genome nonetheless revealed peaks of differentiation around the genes SOX5 and AXIN1. Both are involved in the Wnt/ß-catenin signalling pathway, which regulates feather development. Reconstruction of demographic history and estimation of parameters supports a scenario of secondary contact. Our study informs how divergent plumage morphs may arise and be sustained despite whole-genome homogenization and reveals new candidate genes potentially involved in plumage divergence.

Adaptive introgression of the beta-globin cluster in two Andean waterfowl.

Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb ß-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the ß-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these ß-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution.

Prevalence and Coinfection of Three Tick-Borne Pathogens in Questing Adult Blacklegged Ticks Ixodes scapularis (Vilas County, Wisconsin).

Introduction: In North America, the blacklegged tick (Ixodes scapularis) is a vector of several human pathogens, and tick-borne disease incidence is increasing. Objectives: We estimated the prevalence of questing blacklegged ticks vectoring three zoonotic pathogens in Vilas County, Wisconsin. Materials and Methods: We collected 461 adult blacklegged ticks and used PCR to screen for the presence of pathogens that cause Lyme disease (Borrelia burgdorferi), human granulocytic anaplasmosis (HGA, Anaplasma phagocytophilum), and babesiosis (Babesia microti). Results: We found that 52.5% of ticks carried at least one pathogen. The estimated infection prevalence in the tick population was 17.4% (Lyme disease), 14.3% (HGA), and 6.5% (babesiosis). Multiple pathogens were present in 14.3% of ticks surveyed. Conclusion: About half of questing ticks tested in this study carried at least one zoonotic pathogen. Coinfection was common in our study area and, if not properly recognized, leads to greater risk of underdiagnosis.

Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands.

Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation in hybrid prevalence in populations throughout the main Hawaiian Islands, using genomic data to characterize population structure of koloa, quantify the extent of hybridization, and compare hybrid proportions over time. To accomplish this, we genotyped 3,308 double-digest restriction-site-associated DNA (ddRAD) loci in 425 putative koloa, mallards, and hybrids from populations across the main Hawaiian Islands. We found that despite a population decline in the last century, koloa genetic diversity is high. There were few hybrids on the island of Kaua'i, home to the largest population of koloa. By contrast, we report that sampled populations outside of Kaua'i can now be characterized as hybrid swarms, in that all individuals sampled were of mixed koloa × mallard ancestry. Further, there is some evidence that these swarms are stable over time. These findings demonstrate spatial variation in the extent and consequences of interspecific hybridization, and highlight how islands or island-like systems with small population sizes may be especially prone to genetic extinction when met with a congener that is not reproductively isolated.

Old divergence and restricted gene flow between torrent duck (Merganetta armata) subspecies in the Central and Southern Andes.

AIM: To investigate the structure and rate of gene flow among populations of habitat-specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction. LOCATION: Peruvian and Argentine Andes. TAXON: Two subspecies of torrent duck (Merganetta armata). METHODS: We sampled 156 individuals in Peru (M. a. leucogenis; Chillón River, n = 57 and Pachachaca River, n = 49) and Argentina (M. a. armata; Arroyo Grande River, n = 33 and Malargüe River, n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine-scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, n = 10 and Argentina, n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z-linked double-digest restriction-associated DNA sequences. RESULTS: Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species-level differences (ΦST mtDNA = 0.82; ΦST autosomal = 0.30; ΦST Z chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using ∂a∂i (isolation-with-migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal ∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well-differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country. MAIN CONCLUSIONS: We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.

ddRAD-seq data reveal significant genome-wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America.

Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi-locus data requires substantial genomic coverage. In this study, we used ddRAD-seq to sample the genomes of five recently diverged, New World "mallards" (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD-seq loci and 177 loci from the Z-chromosome. In contrast to previous studies, the ddRAD-seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD-seq data were sufficient to identify previously unknown outlier regions across the Z-chromosome and several autosomal chromosomes that may have been involved in the diversification of species in this recent radiation.

Host community heterogeneity and the expression of host specificity in avian haemosporidia in the Western Cape, South Africa.

Similar patterns of parasite prevalence in animal communities may be driven by a range of different mechanisms. The influences of host heterogeneity and host-parasite interactions in host community assemblages are poorly understood. We sampled birds at 27 wetlands in South Africa to compare four hypotheses explaining how host community heterogeneity influences host specificity in avian haemosporidia communities: the host-neutral hypothesis, the super-spreader hypothesis, the host specialist hypothesis and the heterogeneity hypothesis. A total of 289 birds (29%) were infected with Plasmodium, Haemoproteus and/or Leucocytozoon lineages. Leucocytozoon was the most diverse and generalist parasite genus, and Plasmodium the most conservative. The host-neutral and host specialist hypotheses received the most support in explaining prevalence by lineage (Leucocytozoon) and genus (Plasmodium and Haemoproteus), respectively. We observed that haemosporidian prevalence was potentially amplified or reduced with variation in host and/or parasitic taxonomic levels of analysis. Our results show that Leucocytozoon host abundance and diversity was influential to parasite prevalence at varying taxonomic levels, particularly within heterogeneous host communities. Furthermore, we note that prevalent mechanisms of infection can potentially act as distinct roots for shaping communities of avian haemosporidia.

Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations.

Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA, all individuals were assigned to their respective species with >0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations (F2-F10) of backcrossing. F1 hybrids and F2, F3 and most F4 backcrosses were clearly distinguishable from pure individuals, but evidence of admixed histories was effectively lost after the fourth generation. Thus, we conclude that low interspecific assignment probabilities (0.011-0.043) for two lesser and nineteen greater scaup were consistent with admixed histories beyond the F3 generation. These results indicate that the propensity of these species to hybridize in the wild is low and largely asymmetric. When applied to species-specific cases, our approach offers powerful utility for examining concerns of hybridization in conservation efforts, especially for determining the generational time until admixed histories are effectively lost through backcrossing.

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards.

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (ΦST  = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST  = 0.017) but comparable to mtDNA (ΦST  = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST ) and absolute (dXY ) estimates of divergence. In contrast, the ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST  = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.

Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas).

Many species have Holarctic distributions that extend across Europe, Asia and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared with the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause increased mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation and that more holistic approaches are needed for species delimitation.

Host specificity and co-speciation in avian haemosporidia in the Western Cape, South Africa.

Host and pathogen ecology are often closely linked, with evolutionary processes often leading to the development of host specificity traits in some pathogens. Host specificity may range from 'generalist', where pathogens infect any available competent host; to 'specialist', where pathogens repeatedly infect specific host species or families. Avian malaria ecology in the region remains largely unexplored, despite the presence of vulnerable endemic avian species. We analysed the expression of host specificity in avian haemosporidia, by applying a previously developed host specificity index to lineages isolated from wetland passerines in the Western Cape, South Africa. Parasite lineages were isolated using PCR and identified when possible using matching lineages deposited in GenBank and in MalAvi. Parasitic clades were constructed from phylogenetic trees consisting of Plasmodium and Haemoproteus lineages. Isolated lineages matched some strains of Plasmodium relictum, P. elongatum, Haemoproteus sylvae and H. lanii. Plasmodium lineages infected a wide range of hosts from several avian families in a generalist pattern of infection. Plasmodium spp. also exhibited an infection trend according to host abundance rather than host species. By contrast, Haemoproteus lineages were typically restricted to one or two host species or families, and displayed higher host fidelity than Plasmodium spp. The findings confirm that a range of host specificity traits are exhibited by avian haemosporidia in the region. The traits show the potential to not only impact infection prevalence within specific host species, but also to affect patterns of infection at the community level.

Phylogenetics of a recent radiation in the mallards and allies (Aves: Anas): inferences from a genomic transect and the multispecies coalescent.

Reconstructing species trees by incorporating information from many independent gene trees reduces the confounding influence of stochastic lineage sorting. Such analyses are particularly important for taxa that share polymorphisms due to incomplete lineage sorting or introgressive hybridization. We investigated phylogenetic relationships among 14 closely related taxa from the mallard (Anas spp.) complex using the multispecies coalescent and 20 nuclear loci sampled from a genomic transect. We also examined how treating recombining loci and hybridizing species influences results by partitioning the data using various protocols. In general, topologies were similar among the various species trees, with major clades consistently composed of the same taxa. However, relationships among these clades and among taxa within clades changed among partitioned data sets. Posterior support generally decreased when filtering for recombination, whereas excluding mallards (Anas platyrhynchos) increased posterior support for taxa known to hybridize with them. Furthermore, branch lengths decreased substantially for recombination-filtered data. Finally, concordance between nuclear and morphometric topologies conflicted with those in the mitochondrial tree, particularly with regard to the placement of the Hawaiian duck (A. wyvilliana), Philippine duck (A. luzonica), and two spot-billed ducks (A. zonorhyncha and A. poecilorhyncha). These results demonstrate the importance of maximizing sequence length and taxon sampling when inferring taxonomic relationships that are confounded by extensive allele sharing.

Coalescent analyses show isolation without migration in two closely related tropical orioles: the case of Icterus graduacauda and Icterus chrysater.

The Isthmus of Tehuantepec has played an important role in shaping the avian diversity of Mexico, as well as the rest of the Western Hemisphere. It has been both a barrier and a land connector between North and South America for many groups of birds. Furthermore, climatic change over the Pleistocene has resulted in ecological fluctuations that led to periods of connection and isolation of the highlands in this area. Here we studied the divergence of two species of orioles whose distribution in the highlands is separated by the lowlands of the Isthmus of Tehuantepec: Icterus graduacauda (west of the Isthmus) and Icterus chrysater (east of the Isthmus). We sequenced multiple loci (one mitochondrial gene and six nuclear introns) and performed coalescent analyses (Isolation with Migration) to test whether their divergence resulted from prior occupancy of the ancestral area followed by a vicariant event or recent dispersal from one side or the other of this Isthmus. Results strongly indicate a vicariant event roughly 300,000 years ago in the Pleistocene followed by little or no gene flow. Both mitochondrial and nuclear genes show that the Isthmus of Tehuantepec is a strong barrier to gene flow. Thus, these two species appear to not exchange genes despite their recent divergence and the close geographic proximity of their ranges.

Heteropatric speciation in a duck, Anas crecca.

Heteropatric differentiation is a mode of speciation with gene flow in which divergence occurs between lineages that are in sympatry and allopatry at different times during cyclic spatial movements. Empirical evidence suggests that heteropatric differentiation may prove to be common among seasonally migratory organisms. We examined genetic differentiation between the sedentary Aleutian Islands population of green-winged teal (Anas crecca-nimia) and its close migratory relative, the Eurasian, or Old World (OW), Anas c. crecca population, a portion of which passes through the range of nimia during its seasonal migrations. We also examined its relationship with the parapatric North American, New World (NW), A. c. carolinensis population. Sequence data from eight nuclear introns and the mtDNA control region showed that the nimia-crecca divergence occurred much more recently than the deeper crecca-carolinensis split (~83 000 years vs. ~1.1 Myr). Despite considerable spatial overlap between crecca and nimia during seasonal migration, three key predictions of heteropatric differentiation are supported: significant genetic divergence (overall mean Φst  = 0.07), low gene flow (2Ne m ~ 1.8), and an effective population size in nimia that is not especially low (Ne  ~ 80 000 individuals). Similar levels of gene flow have come into nimia from carolinensis, but no detectable nuclear gene flow has gone out of nimia into either OW (crecca) or NW (carolinensis) populations. We infer that adaptations of these populations to local optima in different places (e.g. each matching their reproductive effort to different resource blooms) promote genetic isolation and divergence despite periods of sympatry between them, as the heteropatric model predicts.

Genetic structure of the endangered northeastern bulrush (Scirpus ancistrochaetus) in Pennsylvania, USA, using information from RAPD and SNPs.

The northeastern bulrush, Scirpus ancistrochaetus, is a federally endangered wetland plant species found primarily in Pennsylvania, USA. Data on the population genetic structure of this species are needed by conservation managers to prioritize conservation efforts. In this study, we used two genetic marker systems to examine diversity and structure of this species in populations throughout Pennsylvania. The first simple and inexpensive approach utilized RAPD primers; our second, more detailed approach relied on DNA sequencing of single nucleotide polymorphisms. We found genetic variation using both RAPDs and sequencing and found some overlap in information between the two methods, including clusters of related populations and the identification of a genetically unique population. Future studies will seek to examine variation across the full geographic range of the species.

Genetic and phenotypic divergence between low- and high-altitude populations of two recently diverged cinnamon teal subspecies.

Spatial variation in the environment can lead to divergent selection between populations occupying different parts of a species' range, and ultimately lead to population divergence. The colonization of new areas can thus facilitate divergence in beneficial traits, yet with little differentiation at neutral genetic markers. We investigated genetic and phenotypic patterns of divergence between low- and high-altitude populations of cinnamon teal inhabiting normoxic and hypoxic regions in the Andes and adjacent lowlands of South America. Cinnamon teal showed strong divergence in body size (PC1; P(ST) = 0.56) and exhibited significant frequency differences in a single nonsynonymous α-hemoglobin amino acid polymorphism (Asn/Ser-α9; F(ST) = 0.60) between environmental extremes, despite considerable admixture of mtDNA and intron loci (F(ST) = 0.004-0.168). Inferences of strong population segregation were further supported by the observation of few mismatched individuals in either environmental extreme. Coalescent analyses indicated that the highlands were most likely colonized from lowland regions but following divergence, gene flow has been asymmetric from the highlands into the lowlands. Multiple selection pressures associated with high-altitude habitats, including cold and hypoxia, have likely shaped morphological and genetic divergence within South American cinnamon teal populations.

Host associations, biogeography, and phylogenetics of avian malaria in southern African waterfowl.

The relevance of spatial variation in the environment and host communities for parasite community composition is poorly documented, creating a need for additional case studies from which general principles can be developed. Avian malaria in southern African waterfowl has not previously been studied. As a first step towards documenting and understanding its biogeography, we used PCR and molecular sequencing techniques to analyse 454 blood samples from Afrotropical ducks from 5 different locations (spread around the subregion) for avian malaria. Fifty-five blood samples were positive for one or more genera of haematozoa. The regional infection rate across all sites and sampling periods was 12·1%. Nine individuals carried dual infections containing multiple haematozoa. Fifteen different cytochrome b haplotypes among 52 positives (3 samples failed to sequence) and 61 total sequences were found. Eleven haplotypes closely matched Plasmodium, whereas 4 were more similar to Haemoproteus. Five distinct haematozoan clades were identified. Haemoproteus parasites appeared to be more host-specific than Plasmodium, which occurred at every sampling location and in every host species examined. There were no significant differences in overall parasite prevalence attributable to either site or species, although Plasmodium and Haemoproteus occurrences differed by site-species combination and the borderline significance of our test for between-site variation (P < 0·06) implied that with a larger sample size, differences in parasite prevalence among locations might be detectable.

Landscape structure influences avian malaria ecology in the Western Cape, South Africa.

A central theme in landscape ecology is that of understanding the consequences of landscape heterogeneity for ecological processes. The effects of landscape heterogeneity on parasite communities are poorly understood, although it has been shown that anthropogenic impacts may contribute to outbreaks of both parasites and pathogens. We tested for effects of landcover type, composition, configuration, and urbanisation on avian diversity and avian malaria prevalence in 26 communities of wetland-associated passerines in the Western Cape of South Africa. We predicted that avian malaria prevalence would be influenced by the pattern of farmland and urban areas in the surrounding landscapes and the sizes of the wetlands in which birds were sampled. We quantified landscape pattern using a six-class simplification of the National Landcover data set at 35 × 35 m resolution and five extents of between 1 and 20 km from each wetland. The bird community was sampled using point counts and we collected blood samples from birds at each site. We screened these for malaria using PCR and molecular techniques. Passerine species richness and infection prevalence varied significantly between different landcover types. Host richness and parasite prevalence were highest in viticultural and cropping sites respectively and lowest in urban sites. Wetlands located in indigenous vegetation had intermediate numbers of bird species and intermediate parasite prevalence. Landscape composition and habitat type surrounding wetlands emerged as useful correlates of infection prevalence. Anthropogenic landscape modification appears to have both direct and indirect effects on avian communities and their associated parasite assemblages, with attendant consequences for avian health.