Inferences of environmental and biotic effects on patterns of eukaryotic alpha and beta diversity for the spring systems of Ash Meadows, Nevada.

Freshwater springs are important ecosystems. In the arid regions of North America, groundwater extraction has caused the desiccation of springs and the extinction of taxa. To better describe the biodiversity of freshwater springs in the hope of establishing a sensitive approach for monitoring the predicted change in spring systems, we used high-resolution genetic methods to estimate the alpha and beta diversity of 19 springs and two reservoirs within the Ash Meadows National Wildlife Refuge in southwestern Nevada. We discovered a large number of distinct taxa based on eukaryote ribosomal gene sequences and show water temperature, spring size, and the presence or absence of non-native predators predicts alpha diversity, and temperature predicts beta diversity. Our study highlights how DNA data support inferences of environmental factors influencing community diversity and demonstrates the method may be an important tool for monitoring ecological communities.

The complete mitochondrial genome of the Warm Springs pupfish, Cyprinodon nevadensis pectoralis.

In this article we report the complete mitochondrial genome of the Warm Springs pupfish, Cyprinodon nevadensis pectoralis. The genomic DNA of a single female individual was extracted and sequenced on the Illumina HiSeq2000 platform. It contains 16,499 bp and a total of 37 genes, divided into 22 tRNA genes, 2 rRNA genes and 13 protein-coding genes. It exhibits 94% sequence similarity with the other published mitochondrion in its genus, C. rubrofluviatilis. A Tamura-Nei maximum-likelihood tree constructed from mitochondrial sequences shows expected phylogenetic relationships between C. nevadensis and sister taxa.

Constructional morphology within the head of hammerhead sharks (sphyrnidae).

The study of functional trade-offs is important if a structure, such as the cranium, serves multiple biological roles, and is, therefore, shaped by multiple selective pressures. The sphyrnid cephalofoil presents an excellent model for investigating potential trade-offs among sensory, neural, and feeding structures. In this study, hammerhead shark species were chosen to represent differences in head form through phylogeny. A combination of surface-based geometric morphometrics, computed tomography (CT) volumetric analysis, and phylogenetic analyses were utilized to investigate potential trade-offs within the head. Hammerhead sharks display a diversity of cranial morphologies where the position of the eyes and nares vary among species, with only minor changes in shape, position, and volume of the feeding apparatus through phylogeny. The basal winghead shark, Eusphyra blochii, has small anteriorly positioned eyes. Through phylogeny, the relative size and position of the eyes change, such that derived species have larger, more medially positioned eyes. The lateral position of the external nares is highly variable, showing no phylogenetic trend. Mouth size and position are conserved, remaining relatively unchanged. Volumetric CT analyses reveal no trade-offs between the feeding apparatus and the remaining cranial structures. The few trade-offs were isolated to the nasal capsule volume's inverse correlation with braincase, chondrocranial, and total cephalofoil volume. Eye volume also decreased as cephalofoil width increased. These data indicate that despite considerable changes in head shape, much of the head is morphologically conserved through sphyrnid phylogeny, particularly the jaw cartilages and their associated feeding muscles, with shape change and morphological trade-offs being primarily confined to the lateral wings of the cephalofoil and their associated sensory structures.

Fitness landscape of sympatric pupfishes a useful tool for visualizing speciation.

Arguably the most useful model of evolution emerged from the mind of Sewall Wright when he invented the fitness landscape (Wright 1932). In a recent issue of Molecular Ecology, Martin & Feinstein (2014) investigate the genetics and demographic history of an adaptive radiation of pupfish on San Salvador Island. Since the founder species colonized the island 10,000 years ago, two descendent species have appeared and in several lakes all three species (a durophage, a scale-eater, and the generalist ancestral form) coexist. The three species are thought to occupy three distinct fitness peaks. The durophage and generalists' peaks are close, whereas the scale-eater's peak is predicted to be distant and separated from the other two by a deep valley. Consistent with this view, gene flow between the two species on close fitness peaks is greater than the gene flow between these two species and the third species on a more distant peak. Correspondingly, the inferred fitness landscape predicts progress towards speciation, with more limited separation of species on close peaks, and that speciation is more complete for the scale-eater. The article provides an illustrative example of the power afforded by analysis of large numbers of SNPs for estimating key parameters underlying evolutionary divergence.

Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black-tailed prairie dogs.

Introduced diseases can cause dramatic declines in-and even the loss of-natural populations. Extirpations may be followed by low recolonization rates, leading to inbreeding and a loss of genetic variation, with consequences on population viability. Conversely, extirpations may create vacant habitat patches that individuals from multiple source populations can colonize, potentially leading to an influx of variation. We tested these alternative hypotheses by sampling 15 colonies in a prairie dog metapopulation during 7 years that encompassed an outbreak of sylvatic plague, providing the opportunity to monitor genetic diversity before, during and after the outbreak. Analysis of nine microsatellite loci revealed that within the metapopulation, there was no change in diversity. However, within extirpated colonies, patterns varied: In half of the colonies, allelic richness after recovery was less than the preplague conditions, and in the other half, richness was greater than the preplague conditions. Finally, analysis of variation within individuals revealed that prairie dogs present in recolonized colonies had higher heterozygosity than those present before plague. We confirmed plague survivorship in six founders; these individuals had significantly higher heterozygosity than expected by chance. Collectively, our results suggest that high immigration rates can maintain genetic variation at a regional scale despite simultaneous extirpations in spatially proximate populations. Thus, virulent diseases may increase genetic diversity of host populations by creating vacant habitats that allow an influx of genetic diversity. Furthermore, even highly virulent diseases may not eliminate individuals randomly; rather, they may selectively remove the most inbred individuals.

Interactions among symbionts of Oropsylla spp. (Siphonoptera: Ceratophyllidae).

We used high-throughput DNA sequencing to explore bacterial communities of three species of Oropyslla fleas [Oropsylla hirsuta (Baker), Oropsylla montana (Baker), and Oropsylla tuberculata cynomuris (Jellison)] and detected seven bacterial lineages related to known insect symbionts. No significant co-occurrence patterns were detected among bacterial lineages, but relative abundance data suggest that the two most common lineages (Bartonella and Rickettsiales) interact negatively. Furthermore, presence of these two lineages significantly reduced bacterial diversity within fleas.

Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally.

Bdelloid rotifers are important contributors to biogeochemical cycling and trophic dynamics of both aquatic and terrestrial ecosystems, but little is known about their biogeographic distribution and community structure in terrestrial environments. This lack of knowledge stems from a lack of phylogenetic information and assumptions that microbial eukaryotes are globally distributed and have very limited diversity across vast geographic distances. However, these assumptions have been based more on assessments of their morphology than any measure of their true genetic diversity and biogeographic distribution. We developed specific primers for the cytochrome c oxidase subunit 1 (cox1) gene of bdelloid rotifers and amplified and cloned sequences using a nested sampling scheme that represented local (0-10 m) to global (up to 10,000 km) scales. Using phylogenetic community analyses (UniFrac) and geospatial statistics (semivariograms, mantel tests), we were able to reject the hypothesis that communities of rotifers are the same across even fairly small geographic distances. Bdelloid communities showed highly significant spatial structuring with spatial autocorrelation ranges of 54-133 m, but beyond that distance communities were extremely dissimilar. Furthermore, we show that these spatial patterns are driven not only by changes in relative abundance of phylotypes but also by absolute changes in phylotype occurrence (richness). There is almost no overlap in phylotype [or operational taxonomic unit (OTU)] occurrence between communities at distances beyond the autocorrelation range (~133 m). Such small species ranges, combined with their ubiquity in soils, make it increasingly clear that the biodiversity of bdelloid rotifers (and other less easily dispersed microbes) is much higher than previously thought.

Population genetic structure of the prairie dog flea and plague vector, Oropsylla hirsuta.

Oropsylla hirsuta is the primary flea of the black-tailed prairie dog and is a vector of the plague bacterium, Yersinia pestis. We examined the population genetic structure of O. hirsuta fleas collected from 11 prairie dog colonies, 7 of which had experienced a plague-associated die-off in 1994. In a sample of 332 O. hirsuta collected from 226 host individuals, we detected 24 unique haplotype sequences in a 480 nucleotide segment of the cytochrome oxidase II gene. We found significant overall population structure but we did not detect a signal of isolation by distance, suggesting that O. hirsuta may be able to disperse relatively quickly at the scale of this study. All 7 colonies that were recently decimated by plague showed signs of recent population expansion, whereas 3 of the 4 plague-negative colonies showed haplotype patterns consistent with stable populations. These results suggest that O. hirsuta populations are affected by plague-induced prairie dog die-offs and that flea dispersal among prairie dog colonies may not be dependent exclusively on dispersal of prairie dogs. Re-colonization following plague events from plague-free refugia may allow for rapid flea population expansion following plague epizootics.

Antipodean white sharks on a Mediterranean walkabout? Historical dispersal leads to genetic discontinuity and an endangered anomalous population.

The provenance of white sharks (Carcharodon carcharias) in the Mediterranean is both a conundrum and an important conservation issue. Considering this species's propensity for natal philopatry, any evidence that the Mediterranean stock has little or no contemporary immigration from the Atlantic would suggest that it is extraordinarily vulnerable. To address this issue we sequenced the mitochondrial control region of four rare Mediterranean white sharks. Unexpectedly, the juvenile sequences were identical although collected at different locations and times, showing little genetic differentiation from Indo-Pacific lineages, but strong separation from geographically closer Atlantic/western Indian Ocean haplotypes. Historical long-distance dispersal (probably a consequence of navigational error during past climatic oscillations) and potential founder effects are invoked to explain the anomalous relationships of this isolated 'sink' population, highlighting the present vulnerability of its nursery grounds.

Phylogeny of hammerhead sharks (Family Sphyrnidae) inferred from mitochondrial and nuclear genes.

Hammerhead sharks (Family Sphyrnidae) get their name from their laterally expanded, dorsal-ventrally compressed head, a structure referred to as the cephalofoil. Species within the family vary for head size and shape and for body size in ways that are functionally significant. Here we infer the phylogeny for all species within the family based on analysis of mitochondrial and nuclear genes amounting to 6292 base pairs. Mixed model Bayesian analysis of the concatenated data and Bayesian estimation of the species tree (BEST) converged on the same topology of the relationships. Shimodaira-Hasegawa tests revealed that all previously proposed hypotheses could be refuted by the data. The new hypothesis for the group suggests that the ancestor of all extant sharks was large (>200 cms) and that small body size probably evolved twice at different times and places. Moreover, the results suggest that once the cephalofoil evolved, it underwent divergent evolution in different lineages presumably in response to unique selective regimes.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009.

This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.

Bacterial communities of disease vectors sampled across time, space, and species.

A common strategy of pathogenic bacteria is to form close associations with parasitic insects that feed on animals and to use these insects as vectors for their own transmission. Pathogens interact closely with other coexisting bacteria within the insect, and interactions between co-occurring bacteria may influence the vector competency of the parasite. Interactions between particular lineages can be explored through measures of alpha-diversity. Furthermore, general patterns of bacterial community assembly can be explored through measures of beta-diversity. Here, we use pyrosequencing (n=115,924 16S rRNA gene sequences) to describe the bacterial communities of 230 prairie dog fleas sampled across space and time. We use these communinty characterizations to assess interactions between dominant community members and to explore general patterns of bacterial community assembly in fleas. An analysis of co-occurrence patterns suggests non-neutral negative interactions between dominant community members (P<0.001). Furthermore, bacterial communities of fleas shift dramatically across years (phylotype-based: R=0.829, P<0.001; phylogenetic-based: R=0.612-0.753, P<0.001), but they also significantly differ across space (phylotype-based: R=0.418, P<0.001; phylogenetic-based: R=0.290-0.328, P<0.001) and between flea species (phylotype-based: R=0.160, P=0.011; phylogenetic-based: not significant). Collectively, our results show that flea-associated bacterial communities are not random assemblages; rather, an individual flea's bacterial community is governed by interactions between bacterial lineages and by the flea's place in space and time.

Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers.

BACKGROUND: The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms.Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly from soil. Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers. RESULTS: The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by both the BLAST similarity searches and phylogenetic analyses. Tardigrades showed much better phylogenetic resolution than bdelloids. Both groups of organisms exhibited varying levels of endemism. CONCLUSION: The development of clade-specific primers for characterizing eutardigrades and bdelloid rotifers from environmental samples should greatly increase our ability to characterize the composition of these taxa in environmental samples. Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. Our non-cultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence, absence and diversity of Bdelloidea and Eutardigrada in a variety of soils.

Flight metabolic rate and Pgi genotype influence butterfly dispersal rate in the field.

Dispersal is a key life-history trait, especially in species inhabiting fragmented landscapes. The process of dispersal is affected by a suite of morphological, physiological, and behavioral traits, all of which have a more or less complex genetic basis and are affected by the prevailing environmental conditions. To be able to identify genetic and phenotypic effects on dispersal, movements have to be recorded over relevant spatial and temporal scales. We used harmonic radar to track free-flying Glanville fritillary butterflies (Melitaea cinxia) released in the field and reconstructed their flight tracks for several hours. Flight track lengths for individual butterflies ranged from tens of meters to several kilometers. Butterflies were most mobile at midday and in intermediate temperatures. Flight metabolic rate (MR), measured prior to the tracking, explained variation in mobility at all scales studied. One-third of the variation in the distance moved in one hour could be attributed to variation in flight MR. Heterozygous individuals at a single nucleotide polymorphism in the phosphoglucose isomerase (Pgi) gene moved longer distances in the morning and at lower ambient temperatures than homozygous individuals. A similar genotype x temperature interaction was found to affect the metabolic rate. Our results establish connections from molecular variation in a single gene to flight physiology and movement behavior at the landscape level. These results indicate a fitness advantage to the heterozygous genotype in low temperatures and suggest a mechanism by which varying environmental conditions maintain genetic polymorphism in populations.

Tracking butterfly movements with harmonic radar reveals an effect of population age on movement distance.

We used harmonic radar to track freely flying Glanville fritillary butterfly (Melitaea cinxia) females within an area of 30 ha. Butterflies originated from large and continuous populations in China and Estonia, and from newly established or old (> 5 years) small local populations in a highly fragmented landscape in Finland. Caterpillars were raised under common garden conditions and unmated females were tested soon after eclosion. The reconstructed flight paths for 66 individuals comprised a total distance of 51 km with high spatial resolution. Butterflies originating from large continuous populations and from old local populations in Finland exhibited similar movement behaviors, whereas butterflies originating from newly established local populations in the fragmented landscape in Finland moved significantly more than the others. There was no difference in the lengths of individual flight bouts, but the new-population females flew more frequently, resulting in longer daily movement tracks. The flight activity of all individuals was affected by environmental conditions, peaking at 19-23 degrees C (depending on population type), in the early afternoon, and during calm weather. Butterflies from all population types showed a strong tendency to follow habitat edges between the open study area and the neighboring woodlands.

Insights and inferences about integron evolution from genomic data.

BACKGROUND: Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. Here, we provide a systematic analysis of the distribution and diversity of integron intI genes and integron-containing bacteria. RESULTS: We found integrons in 103 different pathogenic and non-pathogenic bacteria, in six major phyla. Integrons were widely scattered, and their presence was not confined to specific clades within bacterial orders. Nearly 1/3 of the intI genes that we identified were pseudogenes, containing either an internal stop codon or a frameshift mutation that would render the protein product non-functional. Additionally, 20% of bacteria contained more than one integrase gene. dN/dS ratios revealed mutational hotspots in clades of Vibrio and Shewanella intI genes. Finally, we characterized the gene cassettes associated with integrons in Methylobacillus flagellatus KT and Dechloromonas aromatica RCB, and found a heavy metal efflux gene as well as genes involved in protein folding and stability. CONCLUSION: Our analysis suggests that the present distribution of integrons is due to multiple losses and gene transfer events. While, in some cases, the ability to integrate and excise foreign DNA may be selectively advantageous, the gain, loss, or rearrangment of gene cassettes could also be deleterious, selecting against functional integrases. Thus, such a high fraction of pseudogenes may suggest that the selective impact of integrons on genomes is variable, oscillating between beneficial and deleterious, possibly depending on environmental conditions.

Hybridization dynamics between Colorado's native cutthroat trout and introduced rainbow trout.

Newly formed hybrid populations provide an opportunity to examine the initial consequences of secondary contact between species and identify genetic patterns that may be important early in the evolution of hybrid inviability. Widespread introductions of rainbow trout (Oncorhynchus mykiss) into watersheds with native cutthroat trout (Oncorhynchus clarkii) have resulted in hybridization. These introductions have contributed to the decline of native cutthroat trout populations. Here, we examine the pattern of hybridization between introduced rainbow trout and 2 populations of cutthroat trout native to Colorado. For this study, we utilized 7 diagnostic, codominant nuclear markers and a diagnostic mitochondrial marker to investigate hybridization in a population of greenback cutthroat trout (Oncorhynchus clarkii stomias) and a population of Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). We infer that cutthroat-rainbow trout hybrid swarms have formed in both populations. Although a mixture of hybrid genotypes was present, not all genotype combinations were detected at expected frequencies. We found evidence that mitochondrial DNA introgression in hybrids is asymmetric and more likely from rainbow trout than from cutthroat trout. A difference in spawning time of the 2 species or differences in the fitness between the reciprocal crosses may explain the asymmetry. Additionally, the presence of intraspecific cytonuclear associations found in both populations is concordant with current hypotheses regarding coevolution of mitochondrial and nuclear genomes.

Bacterial communities of Bartonella-positive fleas: diversity and community assembly patterns.

We investigated the bacterial communities of nine Bartonella-positive fleas (n = 6 Oropsylla hirsuta fleas and n = 3 Oropsylla montana fleas), using universal primers, clone libraries, and DNA sequencing. DNA sequences were used to classify bacteria detected in a phylogenetic context, to explore community assembly patterns within individual fleas, and to survey diversity patterns in dominant lineages.

Bumblebee flight distances in relation to the forage landscape.

1. Foraging range is a key aspect of the ecology of 'central place foragers'. Estimating how far bees fly under different circumstances is essential for predicting colony success, and for estimating bee-mediated gene flow between plant populations. It is likely to be strongly influenced by forage distribution, something that is hard to quantify in all but the simplest landscapes; and theories of foraging distance tend to assume a homogeneous forage distribution. 2. We quantified the distribution of bumblebee Bombus terrestris L. foragers away from experimentally positioned colonies, in an agricultural landscape, using two methods. We mass-marked foragers as they left the colony, and analysed pollen from foragers returning to the colonies. The data were set within the context of the 'forage landscape': a map of the spatial distribution of forage as determined from remote-sensed data. To our knowledge, this is the first time that empirical data on foraging distances and forage availability, at this resolution and scale, have been collected and combined for bumblebees. 3. The bees foraged at least 1.5 km from their colonies, and the proportion of foragers flying to one field declined, approximately linearly, with radial distance. In this landscape there was great variation in forage availability within 500 m of colonies but little variation beyond 1 km, regardless of colony location. 4. The scale of B. terrestris foraging was large enough to buffer against effects of forage patch and flowering crop heterogeneity, but bee species with shorter foraging ranges may experience highly variable colony success according to location.