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BackgroundPopulation genetics is crucial for understanding the transmission dynamics of diseases like onchocerciasis. Landscape genetics identifies the ecological features that impact genetic variation between sampling sites. Here, we have used a landscape genetics framework to understand the relationship between environmental features and gene flow of the filarial parasiteOnchocerca volvulusand of its intermediate host and vector, blackflies in the genusSimulium. We analysed samples from the ecological transition region separating the savannah and forest ecological regions of Ghana, where the transmission ofO. volvulushas persisted despite almost half a century of onchocerciasis control efforts.MethodsWe generated a baseline microfilarial prevalence map from the point estimates of pre-ivermectin microfilarial prevalence from 47 locations in the study area. We analysed mitochondrial data from 164 parasites and 93 blackflies collected from 15 communities and four breeding sites, respectively. We estimated population genetic diversity and identified correlations with environmental variables. Finally, we compared baseline prevalence maps to movement suitability maps that were based on significant environmental variables.ResultsWe found that the resistance surfaces derived from elevation (r = 0.793, p = 0.005) and soil moisture (r = 0.507, p = 0.002) were significantly associated with genetic distance between parasite sampling locations. Similarly, for the vector populations, the resistance surfaces derived from soil moisture (r = 0.788, p = 0.0417) and precipitation (r = 0.835, p = 0.0417) were significant. The correlation between the baseline parasite prevalence map and the parasite resistance surface map was stronger than the correlation between baseline prevalence and the vector resistance surface map. The central parts of the transition region which were conducive for both the parasite and the vector gene flow were most strongly associated with high baseline onchocerciasis prevalence.ConclusionsWe present a framework for incorporating environmental, genetic, and prevalence data for identifying when ecological conditions are favourable for onchocerciasis transmission between communities. We identified areas with higher suitability for parasite and vector gene flow, which ultimately might help us gain deeper insights into defining transmission zones for onchocerciasis. Furthermore, this framework is translatable to other onchocerciasis endemic areas and to other vector-borne diseases.

BackgroundOnchocerciasis is a vector-borne disease caused by the filarial nematodeOnchocerca volvulus. Endemic countries target elimination of parasite transmission using primarily annual ivermectin mass administration. Elimination is particularly challenging in sub-Saharan Africa, where there are large contiguous areas with varying levels of endemicity and intervention history. We examined one challenge to elimination that has received little attention to date: movement of people between areas.Methodology/Principal FindingsWe extended one of the commonly used onchocerciasis transmission models, EPIONCHO, to allow modelling the effect of movement of people and/or flies between areas (“patches”). We explored the impact of humans travelling between a hypoendemic area (i.e., with low vector biting rates) with no history of interventions and a hyperendemic area (high vector biting rates) that stopped intervention (ivermectin mass administration) after infection prevalence decreased below 1.4%. Our results suggest that human travel in either direction will accelerate recrudescence in the hyperendemic area to pre-intervention levels, relative to recrudescence without travel, and can reduce the annual biting rate required for parasite transmission within hypoendemic areas.Conclusions/SignificanceOur results emphasize the importance of decisions on which hypoendemic areas to include in interventions and suggest that transmission mediated by human movement needs to be considered when planning (a) the geographic areas and sampling density for evaluations for decisions on when and where to stop interventions, (b) where, how often, and for how long to conduct post-intervention surveillance for verification of elimination of transmission and (c) where and how frequently to conduct post-elimination surveillance. Given the cost implications of stopping interventions too early or later than necessary, we encourage the development of models such as the one presented here for quantitating the impact of human and vector movement between areas on the risk and timeframe of recrudescence after interventions are stopped to inform economic analyses.Author summaryOnchocerciasis is an infectious parasitic disease that causes significant morbidity, from incessant skin itching to blindness. Onchocerciasis has also been implicated as the cause of high epilepsy rates. Efforts are underway to eliminate the parasite. Mathematical models for parasite transmission between humans via blackflies can be used to explore how interventions (e.g., mass drug administration or blackfly control) impact the percentage of people infected (infection prevalence). We extended a commonly used model to explore how people travelling between areas that differ in blackfly abundance, infection prevalence, and past interventions affects infection prevalence. We found that people travelling between an area with few blackflies (hypoendemic), low infection prevalence, and no interventions and an area with many blackflies (hyperendemic) but very low infection prevalence thanks to many years of mass drug administration which was then stopped will accelerate the increase in infection prevalence in the hyperendemic area compared to a situation where no people travel between these areas. This means that strategies for onchocerciasis elimination need to consider the effect of humans travelling.

Over 892 million people in 48 countries are at risk of infection by nematodes that cause lymphatic filariasis. As part of the Global Programme to Eliminate Lymphatic Filariasis, mass drug administration is distributed to communities until surveillance indicates infection rates are below target prevalence thresholds. In some countries, including American Samoa, lymphatic filariasis transmission persists despite years of mass drug administration and/or has resurged after cessation. Nothing is known about the population genetics of Wuchereria bancrofti worms in Polynesia, or whether local transmission is persisting and/or increasing due to inadequate mass drug administration coverage, expansion from residual hotspots, reintroduction from elsewhere, or a combination. We extracted DNA from microfilariae on blood slides collected during prevalence surveys in 2014 and 2016, comprising 31 pools of five microfilariae from 22 persons living in eight villages. We sequenced 1104 bp across three mitochondrial markers (ND4, COI, CYTB). We quantified parasite genetic differentiation using variant calls and estimated haplotypes using principal components analysis, F-statistics, and haplotype networks. Of the variants called, all but eight were shared across the main island of Tutuila, and three of those were from a previously described hotspot village, Fagali’i. Genotypic data did not support population genetic structure among regions or villages in 2016, although differences were observed between worms collected in Fagali’i in 2014 and those from 2016. Because estimated haplotype frequency varied between villages, these statistics suggested genetic differentiation, but were not consistent among villages. Finally, haplotype networks demonstrated American Samoan sequence clusters were related to previously published sequences from Papua New Guinea. These are, to our knowledge, the first reports of W. bancrofti genetic variation in Polynesia. The resurgent parasites circulating on the main island of American Samoa represent a single population. This study is the first step towards investigating how parasite population structure might inform strategies to manage resurgence and elimination of lymphatic filariasis.

“Occasional” sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species.

Background Onchocerciasis is a neglected tropical and filarial disease transmitted by the bites of blackflies, causing blindness and severe skin lesions. The change in focus for onchocerciasis management from control to elimination requires thorough mapping of pre-control endemicity to identify areas requiring interventions and to monitor progress. Onchocerca volvulus infection prevalence in sub-Saharan Africa is spatially continuous and heterogeneous, and highly endemic areas may contribute to transmission in areas of low endemicity or vice-versa. Ethiopia is one such onchocerciasis-endemic country with heterogeneous O. volvulus infection prevalence, and many districts are still unmapped despite their potential for O. volvulus infection transmission. Methodology/Principle findings A Bayesian geostatistical model was fitted for retrospective pre-intervention nodule prevalence data collected from 916 unique sites and 35,077 people across Ethiopia. We used multiple environmental, socio-demographic, and climate variables to estimate the pre-intervention prevalence of O. volvulus infection across Ethiopia and to explore their relationship with prevalence. Prevalence was high in southern and northwestern Ethiopia and low in Ethiopia's central and eastern parts. Distance to the nearest river (-0.015, 95% BCI: -0.025 - -0.005), precipitation seasonality (-0.017, 95% BCI: -0.032 - -0.001), and flow accumulation (-0.042, 95% BCI: -0.07 - -0.019) were negatively associated with O. volvulus infection prevalence, while soil moisture (0.0216, 95% BCI: 0.014 - 0.03) was positively associated. Conclusions/Significance Infection distribution was correlated with habitat suitability for vector breeding and associated biting behavior. The modeled pre-intervention prevalence can be used as a guide for determining priority for intervention in regions of Ethiopia that are currently unmapped, most of which have comparatively low infection prevalence.

Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Where program duration, treatment coverage, and compliance are sufficiently high, elimination is achievable for both parasites within defined geographic areas. However, transmission has re-emerged after apparent elimination in some areas, and in others has continued despite years of mass drug treatment. A critical question is whether this re-emergence and/or persistence of transmission is due to persistence of local parasites—i.e., the result of insufficient duration or drug coverage, poor parasite response to the drugs, or inadequate methods of assessment and/or criteria for determining when to stop treatment—or due to re-introduction of parasites via human or vector movement from another endemic area. We review recent genetics-based research exploring these questions in Onchocerca volvulus, the filarial nematode that causes onchocerciasis, and Wuchereria bancrofti, the major pathogen for lymphatic filariasis. We focus in particular on the combination of genomic epidemiology and genome-wide associations to delineate transmission zones and distinguish between local and introduced parasites as the source of resurgence or continuing transmission, and to identify genetic markers associated with parasite response to chemotherapy. Our ultimate goal is to assist elimination efforts by developing easy-to-use tools that incorporate genetic information about transmission and drug response for more effective mass drug distribution, surveillance strategies, and decisions on when to stop interventions to improve sustainability of elimination.

Ticks are important vectors of a broad range of pathogens in Australia. Many tick species are morphologically similar and are therefore difficult to identify using morphology alone, particularly when collected in the larval and nymphal life stages. We report here the application of molecular methods to examine the species diversity of ixodid ticks at two sites in southern New South Wales, Australia. Our taxon sampling included six morphologically characterised adult stage voucher specimens of Ixodes trichosuri, Ixodes tasmani, Ixodes fecialis and Ixodes holocyclus (the paralysis tick) and ~250 field collected specimens that were in the larva or nymph stage and thus not morphologically identifiable. One nuclear and two mitochondrial amplicons were sequenced using a combination of Sanger and Illumina MiSeq sequencing. Phylogenetic relationships were estimated using both maximum likelihood and Bayesian methods. Two clades with strong bootstrap and Bayesian support were observed across trees estimated from each of three markers and from an analysis of the concatenated sequences. One voucher specimen of I. trichosuri was located in one of these clades, while the other I. trichosuri voucher specimen was in a second clade with the remaining three identified species, suggesting these morphologically similar ticks may represent different cryptic species. Unidentified specimens were found across both clades, and molecular divergence of many of these is equal to or greater than that observed between identified species, suggesting additional unidentified species may exist. Further studies are required to understand the taxonomic status of ticks in Australia, and how this species diversity impacts disease risk for livestock, domestic animals, wildlife and humans., Graphical abstract Image 1, Highlights • Ticks genetically closely related had distinct morphological features. • Remarkable genetic diversity of tick species collected. • Rapid evolution of morphological characters in Ixodes. • Understanding tick relationships could improve control of disease risk.

Background Samoa conducted eight nationwide rounds of mass drug administration (MDA) for lymphatic filariasis (LF) between 1999 and 2011, and two targeted rounds in 2015 and 2017 in North West Upolu (NWU), one of three evaluation units (EUs). Transmission Assessment Surveys (TAS) were conducted in 2013 (failed in NWU) and 2017 (all three EUs failed). In 2018, Samoa was the first in the world to distribute nationwide triple-drug MDA using ivermectin, diethylcarbamazine, and albendazole. Surveillance and Monitoring to Eliminate LF and Scabies from Samoa (SaMELFS Samoa) is an operational research program designed to evaluate the effectiveness of triple-drug MDA on LF transmission and scabies prevalence in Samoa, and to compare the usefulness of different indicators of LF transmission. This paper reports results from the 2018 baseline survey and aims to i) investigate antigen (Ag) prevalence and spatial epidemiology, including geographic clustering; ii) compare Ag prevalence between two different age groups (5–9 years versus ≥10 years) as indicators of areas of ongoing transmission; and iii) assess the prevalence of limb lymphedema in those aged ≥15 years. Methods A community-based cluster survey was conducted in 30 randomly selected and five purposively selected clusters (primary sampling units, PSUs), each comprising one or two villages. Participants were recruited through household surveys (age ≥5 years) and convenience surveys (age 5–9 years). Alere Filariasis Test Strips (FTS) were used to detect Ag, and prevalence was adjusted for survey design and standardized for age and gender. Adjusted Ag prevalence was estimated for each age group (5–9, ≥10, and all ages ≥5 years) for random and purposive PSUs, and by region. Intraclass correlation (ICC) was used to quantify clustering at regions, PSUs, and households. Results A total of 3940 persons were included (1942 children aged 5–9 years, 1998 persons aged ≥10 years). Adjusted Ag prevalence in all ages ≥5 years in randomly and purposively selected PSUs were 4.0% (95% CI 2.8–5.6%) and 10.0% (95% CI 7.4–13.4%), respectively. In random PSUs, Ag prevalence was lower in those aged 5–9 years (1.3%, 95% CI 0.8–2.1%) than ≥10 years (4.7%, 95% CI 3.1–7.0%), and poorly correlated at the PSU level (R-square = 0.1459). Adjusted Ag prevalence in PSUs ranged from 0% to 10.3% (95% CI 5.9–17.6%) in randomly selected and 3.8% (95% CI 1.3–10.8%) to 20.0% (95% CI 15.3–25.8%) in purposively selected PSUs. ICC for Ag-positive individuals was higher at households (0.46) compared to PSUs (0.18) and regions (0.01). Conclusions Our study confirmed ongoing transmission of LF in Samoa, in accordance with the 2017 TAS results. Ag prevalence varied significantly between PSUs, and there was poor correlation between prevalence in 5–9 year-olds and older ages, who had threefold higher prevalence. Sampling older age groups would provide more accurate estimates of overall prevalence, and be more sensitive for identifying residual hotspots. Higher prevalence in purposively selected PSUs shows local knowledge can help identify at least some hotspots., Author summary Lymphatic filariasis (LF), a disease caused by infection with worms transmitted by mosquitoes, has long been present in Samoa. Since the 1960s, Samoa has attempted to control the disease through many rounds of annual administration of two deworming drugs to the whole population. However, Samoa recently observed that LF transmission was still occurring, prompting mass drug administration (MDA) with three drugs in 2018. Here, we report the baseline survey of an operational research program to evaluate the triple-drug MDA. The survey assessed prevalence and geographical distribution of LF in the population, compared prevalence by age groups, and investigated the burden of elephantiasis (swollen limbs caused by long-term LF infection). The study confirmed ongoing transmission, with 4% of those aged ≥5 years showing antigen in their blood as evidence of infection. Antigen prevalence was more than three times higher in those aged ≥10 years (4.7%) than in 5–9 year-old children (1.3%). Infection was highly clustered within households and villages, with up to 20% of residents infected in known hotspot villages. Future surveillance strategies should consider that i) testing older age groups would provide more accurate indication of LF transmission, and ii) local knowledge can help identify transmission hotspots.

In 2012, the reduction inOnchocerca volvulusinfection prevalence through long-term mass ivermectin distribution in African meso- and hyperendemic areas motivated expanding control of onchocerciasis (river blindness) as a public health problem to elimination of parasite transmission. Given the large contiguous hypo-, meso- and hyperendemic areas with an estimated population of 204 million, sustainable elimination requires an understanding of the geographic, and in turn genetic, boundaries of different parasite populations to ensure interventions are only stopped where the risk of re-introduction of the parasite through vector or human migration from areas with ongoing transmission is acceptable. These boundaries, which define the transmission zones of the parasite, may be delineated by characterising the parasite genetic population structure within and between potential zones. We analysed whole mitochondrial genome sequences of 189O. volvulusadults to determine the pattern of genetic similarity across three West African countries: Ghana, Mali, and Côte d’Ivoire. Population structure measures indicate that parasites from the Pru, Daka and Black Volta/Tombe river basins in central Ghana belong to one parasite population, showing that different river basins cannot be assumed to constitute independent transmission zones. This research forms the basis for developing tools for elimination programs to delineate transmission zones, to estimate the risk of parasite re-introduction via vector or human movement when mass ivermectin administration is stopped in one area while transmission is ongoing in others, to identify the origin of infections detected post-treatment cessation, and to investigate whether migration contributes to persisting prevalence levels during interventions.

“Occasional” sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species.

BackgroundWolbachia are important endosymbionts of filarial parasites. The Wolbachia of Onchocerca volvulus, the filarial pathogen responsible for the human disease onchocerciasis, is implicated in the immunopathology of the disease and may be associated with disease severity dependent on the density of Wolbachia. However, little is known in regards to the density and heterogeneity of Wolbachia in microfilariae, the life stage that is thought to be responsible for the pathology.ResultsWe used a real-time qPCR relative copy number assay to estimate the number of Wolbachia genome(s) per nuclear genome of skin microfilariae (Mf), vector L1 and iL3, and nodulectomy adult male and female O. volvulus worms sampled in Ghana and the Democratic Republic of the Congo. Relatively low median Wolbachia copy numbers and variation was observed in the Mf and vector stages, in contrast to significantly higher median and more variable Wolbachia copy number from the iL3 stage to the adult worm stages.ConclusionsThis study provides the first insight into variation in Wolbachia density between the major life stages of the parasite. The relatively invariant ratios observed for Mf and vector stages is in strong contrast to the high degree of variability of Wolbachia to nuclear ratios in adults and may indicate that the mutualistic relationship between the nematode and Wolbachia in these earlier stages is regulated differently, and certainly more stringently, than the relationship in adults.

Among the asexual reproductive modes, androgenesis is probably one of the most astonishing and least studied mechanisms. In this ‘paternal monopolization', the maternal nuclear genome fails to participate in zygote development and offspring are paternal nuclear clones. Obligate androgenesis is known in only a few organisms, including multiple species of clam in the genus Corbicula. Corbicula is a good system to review the evolutionary consequences of this ‘all-male asexuality' because the cytological mechanisms of androgenetic reproduction have been described. In Corbicula, sperm are unreduced and, after fertilization, the maternal nuclear chromosomes are extruded as two polar bodies. Hermaphroditic lineages of Corbicula have a worldwide distribution and seem to reproduce through androgenesis, whereas their sexual relatives have restricted ranges. The invasive success of these androgenetic Corbicula lineages may be linked to their asexual mode of reproduction. We review the phenomenon of androgenesis, focusing on evolutionary perspectives, using the genus Corbicula as an exemplar system.

The long-term persistence of completely asexual species is unexpected. Although asexuality has short-term evolutionary advantages, a lack of genetic recombination leads to the accumulation over time of deleterious mutations. The loss of individual fitness as a result of accumulated deleterious mutations is expected to lead to reduced population fitness and possible lineage extinction. Persistent lineages of asexual, all-female clones (parthenogenetic and gynogenetic species) avoid the negative effects of asexual reproduction through the production of rare males, or otherwise exhibit some degree of genetic recombination. Another form of asexuality, known as androgenesis, results in offspring that are clones of the male parent. Several species of the Asian clam genus Corbicula reproduce via androgenesis. We compared gene trees of mitochondrial and nuclear loci from multiple sexual and androgenetic species across the global distribution of Corbicula to test the hypothesis of long-term clonality of the androgenetic species. Our results indicate that low levels of genetic capture of maternal nuclear DNA from other species occur within otherwise androgenetic lineages of Corbicula . The rare capture of genetic material from other species may allow androgenetic lineages of Corbicula to mitigate the effects of deleterious mutation accumulation and increase potentially adaptive variation. Models comparing the relative advantages and disadvantages of sexual and asexual reproduction should consider the possibility of rare genetic recombination, because such events seem to be nearly ubiquitous among otherwise asexual species.

A surprising number of recent Bayesian phylogenetic analyses contain branch-length estimates that are several orders of magnitude longer than corresponding maximum-likelihood estimates. The levels of divergence implied by such branch lengths are unreasonable for studies using biological data and are known to be false for studies using simulated data. We conducted additional Bayesian analyses and studied approximate-posterior surfaces to investigate the causes underlying these large errors. We manipulated the starting parameter values of the Markov chain Monte Carlo (MCMC) analyses, the moves used by the MCMC analyses, and the prior-probability distribution on branch lengths. We demonstrate that inaccurate branch-length estimates result from either 1) poor mixing of MCMC chains or 2) posterior distributions with excessive weight at long tree lengths. Both effects are caused by a rapid increase in the volume of branch-length space as branches become longer. In the former case, both an MCMC move that scales all branch lengths in the tree simultaneously and the use of overdispersed starting branch lengths allow the chain to accurately sample the posterior distribution and should be used in Bayesian analyses of phylogeny. In the latter case, branch-length priors can have strong effects on resulting inferences and should be carefully chosen to reflect biological expectations. We provide a formula to calculate an exponential rate parameter for the branch-length prior that should eliminate inference of biased branch lengths in many cases. In any phylogenetic analysis, the biological plausibility of branch-length output must be carefully considered.

Androgenesis is a rare form of asexual male reproduction found in disparate taxa across the Tree of Life. Phylogenetic analyses of mitochondrial genes suggest that androgenesis has arisen repeatedly in the Asian clam genus Corbicula. Two of these androgenetic species have been introduced to North America. Multiple lines of genetic evidence suggest that although nuclear recombination between these two species is rare, mitochondrial genome capture is a frequent consequence of androgenetic parasitism of heterospecific eggs. Egg parasitism may also rarely result in partial nuclear genome capture between closely related species of Corbicula, which provides a mechanism for the otherwise clonal species to avoid the deleterious effects of asexuality. Egg parasitism among congeners may explain why androgenesis has been maintained in Corbicula after fixation and has not yet led to population extinction. This mechanism also provides an explanation for the apparent multiple origins of androgenesis in Corbicula as seen on the mitochondrial DNA phylogeny. We suggest that a single androgenetic lineage may have repeatedly captured mitochondrial genomes (as well as portions of nuclear genomes) from various sexual species, resulting in several distinct androgenetic species with distantly related mtDNA genomes and divergent morphologies.

We used microsatellite loci to examine rangewide population structure and interpopulation gene flow in the federally threatened Coachella Valley fringe-toed lizar d( Uma inornata). Our results indicate low population differentiation consistent with high gene flow, recent colonization and range expansion, and/ or frequent local extirpation/recolonization events. Given high historical gene flow among populations and current isolation of remaining populations, conservation planning for this species should include monitoring of potential deleterious effects that may result from reduction in gene flow, such as inbreeding and loss of genetic variation, to ensure maintenance of ecological and evolutionary population processes adequate for long-term survival of the species.

Background Bees are the primary pollinators of angiosperms throughout the world. There are more than 16,000 described species, with broad variation in life history traits such as nesting habitat, diet, and social behavior. Despite their importance as pollinators, the evolution of bee biodiversity is understudied: relationships among the seven families of bees remain controversial, and no empirical global-level reconstruction of historical biogeography has been attempted. Morphological studies have generally suggested that the phylogeny of bees is rooted near the family Colletidae, whereas many molecular studies have suggested a root node near (or within) Melittidae. Previous molecular studies have focused on a relatively small sample of taxa (~150 species) and genes (seven at most). Public databases contain an enormous amount of DNA sequence data that has not been comprehensively analysed in the context of bee evolution. Results We downloaded, aligned, concatenated, and analysed all available protein-coding nuclear gene DNA sequence data in GenBank as of October, 2011. Our matrix consists of 20 genes, with over 17,000 aligned nucleotide sites, for over 1,300 bee and apoid wasp species, representing over two-thirds of bee genera. Whereas the matrix is large in terms of number of genes and taxa, there is a significant amount of missing data: only ~15% of the matrix is populated with data. The placement of the root as well as relationships between Andrenidae and other bee families remain ambiguous, as several alternative maximum-likelihood estimates fall within the statistically credible set. However, we recover strong bootstrap support for relationships among many families and for their monophyly. Ancestral geographic range reconstruction suggests a likely origin of bees in the southern hemisphere, with Melittidae ancestrally located within Africa, and Halictidae, Colletidae, and Apidae within the New World. Conclusions Our study affirms the monophyly of each bee family, sister-taxa relationships between Apidae and Megachilidae (the ‘long-tongued bees’), between Colletidae and Stenotritidae, and between Colletidae + Stenotritidae and Halictidae. Our analyses reject a Colletidae-basal hypothesis for family-level relationships and instead support Melittidae as sister to the remaining bees. Southern hemisphere vicariance likely played an important role in early diversification within many bee families.

Pollinators such as bees are essential to the functioning of terrestrial ecosystems. However, despite concerns about a global pollinator crisis, long-term data on the status of bee species are limited. We present a long-term study of relative rates of change for an entire regional bee fauna in the northeastern United States, based on >30,000 museum records representing 438 species. Over a 140-y period, aggregate native species richness weakly decreased, but richness declines were significant only for the genus Bombus . Of 187 native species analyzed individually, only three declined steeply, all of these in the genus Bombus . However, there were large shifts in community composition, as indicated by 56% of species showing significant changes in relative abundance over time. Traits associated with a declining relative abundance include small dietary and phenological breadth and large body size. In addition, species with lower latitudinal range boundaries are increasing in relative abundance, a finding that may represent a response to climate change. We show that despite marked increases in human population density and large changes in anthropogenic land use, aggregate native species richness declines were modest outside of the genus Bombus . At the same time, we find that certain ecological traits are associated with declines in relative abundance. These results should help target conservation efforts focused on maintaining native bee abundance and diversity and therefore the important ecosystems services that they provide.

Estimated phylogenies of evolutionarily diverse taxa will be well supported and more likely to be historically accurate when the analysis contains large amounts of data-many genes sequenced across many taxa. Inferring such phylogenies for non-model organisms is challenging given limited resources for whole-genome sequencing. We take advantage of genomic data from a single species to test the limits of hybridization-based enrichment of hundreds of exons across frog species that diverged up to 250 million years ago. Enrichment success for a given species depends greatly on the divergence time between it and the reference species, and the resulting alignment contains a significant proportion of missing data. However, our alignment generates a well-supported phylogeny of frogs, suggesting that this technique is a practical solution towards resolving relationships across deep evolutionary time.

WOS: 000313051500058 PubMed ID: 23285178 Insecticide resistance is a model phenotype that can be used to investigate evolutionary processes underlying the spread of alleles across a global landscape, while offering valuable insights into solving the problems that resistant pests present to human health and agriculture. Pyrethroids are one of the most widely used classes of insecticides world-wide and they exert their toxic effects through interactions with the voltage-sensitive sodium channel (Vssc). Specific mutations in Vssc (kdr, kdr-his and super-kdr) are known to cause resistance to pyrethroid insecticides in house flies. In order to determine the number of evolutionary origins of kdr, kdr-his and super-kdr, we sequenced a region of Vssc from house flies collected in the USA, Turkey and China. Our phylogenetic analysis of Vssc unequivocally supports the hypothesis of multiple independent origins of kdr, super-kdr and kdr-his on an unprecedented geographic scale. The implications of these evolutionary processes on pest management are discussed. Hatch projectUnited States Department of Agriculture (USDA) [139 7416] This work was supported by Hatch project 139 7416. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

In many organisms, gene trees based on nuclear mark ers and those based on cytoplasmic markers (chloroplasts or mitochondria) sometimes indicate quite different re lationships among the species being studied (e.g., Rieseberg and Soltis 1991; Rieseberg et al. 1996; Cathey et al. 1998; Bergthorsson et al. 2003; Avise 2004; Croucher et al. 2004; Sullivan et al. 2004; Chan and Levin 2005; Fehrer et al. 2007; Linnen and Farrell 2007). This in congruence is normally attributed to incomplete lineage sorting (when two al?eles coalesce prior to speciation and do not track the species phylogeny), introgression (interspecific hybridization followed by unidirectional backcrossing), horizontal gene transfer, or errors in phy logenetic reconstruction. Although the usual explanations for cytoplasmic nuclear incongruence are well documented, these expla nations are often assumed rather than demonstrated in

The debate about whether phylogenetic accuracy is most efficiently increased by sampling more charac ters or more taxa is certainly not new (e.g., Kim, 1996; Graybeal, 1998; Poe, 1998a,b; Rannala et al., 1998; Poe and Swofford, 1999; Pollock and Bruno, 2000; Rosenburg and Kumar, 2001; Pollock et al., 2002; Zwickl and Hillis, 2002; Rosenberg and Kumar, 2003; Hillis et al., 2003). However, the recent increase of whole genomic sequences available from an assortment of distantly related taxa makes this debate highly relevant to researchers across fields of bi ology. Recently, Rokas et al. (2003) argued that the true species tree can be recovered despite conflicting phylo genetic signal between genes if enough genes are used in the analysis. Using the bootstrap proportion (BP) as a measure of phylogenetic accuracy, they concluded that approximately 20 genes are needed to ensure a robustly supported tree (>95% BP) for their study group of eight yeast taxa. From these empirical results, they generalized that most molecular phylogenetic studies have probably included insufficient numbers of genes to confidently re solve relationships within their respective focal groups. This approach to measuring accuracy can be sensitive to method inconsistency, or the failure to converge on the correct tree as the data set becomes infinitely large. When a method is inconsistent, measures of support such as nonparametric bootstrapping can increase as more se quence data are added?but in support of the wrong phy logeny (Phillips et al., 2004; Collins et al., 2005; Delsuc et al., 2005). Although most methods perform well over most of tree space (Huelsenbeck, 1995; Poe, 2003), regions of inconsistency have been identified in the literature for all of the most commonly used phylogenetic meth ods. For example, compositional bias can affect the accu racy of minimum evolution (Phillips et al., 2004), model misspecification may affect parametric methods such as maximum likelihood (ML) (Poe, 2003; Philippe et al, 2005; Collins et al., 2005), and branch-length asymme try can lead to inconsistency in maximum parsimony (Felsenstein, 1978; Hendy and Penny, 1989). Parsimony is particularly prone to long-branch attraction (LBA), an analytical artifact in which two taxa on long branches are incorrectly placed as sister taxa (Felsenstein, 1978; Hendy and Penny, 1989; Huelsenbeck and Hillis, 1993). Although there are many reasons for conflicting phylo genetic signal between genes, one relevant reason could be related to method inconsistency: differing rates of evo lution between genes could cause a particular method to be inconsistent for some genes and not for others. We argue that by addressing this source of conflict between genes, fewer genes may be needed to return an accu rate phylogeny. One source of conflict in the Rokas et al. (2003) data set may be nonstationarity: taxa that differ from the others in their base compositional bias may be erroneously drawn together as sister taxa (Collins et al., 2005). Here, we show that an additional source of conflict between the 106 genes in the Rokas et al. data set may be branch-length asymmetry. Using simulations of 106 genes from the Rokas et al. data set on a 79-taxon yeast phylogeny, we additionally show that when genes are added to a data set, support for the wrong reconstruc tion can increase when there is LBA. However, when taxa are added to the analysis, support for the correct reconstruction increases, and fewer genes are needed to achieve accuracy.