The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species-level phylogenies

Most aquatic beetles in the family Dytiscidae are tightly associated either with running (lotic) or stagnant (lentic) water bodies. The range size of lotic species is known to be, on average, much smaller than that of lentic species, presumably as a result of differences in dispersal strategies in each habitat type. We explored possible effects of these differences on clade evolution and speciation rates by comparing species-level phylogenies based on cytochrome oxidase I (COI) and 16S rRNA mitochondrial genes for two genera, the lentic Ilybius and the lotic Deronectes. The expectation that species turnover is higher in lotic lineages due to their lower dispersal propensity compared to lentic species was not strongly supported. Deronectes displays a higher frequency of recent splits than Ilybius, consistent with the hypothesis, but the difference was not significant compared to expected patterns under a constant speciation rate null model. Similarly, when the degree of sympatry was plotted against relative node age, more allopatric splits were evident in the lentic Deronectes, suggesting a slower rate of range movement since speciation, but the differences were not significant. We discuss two explanations for our failure to detect differences between the two clades. First, current methods for analysing species-level phylogenies may be sensitive to taxonomic and sampling artefacts. Second, lentic and lotic clades may indeed display similar levels of species turnover despite occupying very different habitats at different spatial scales. More work is needed to investigate the effects of population level processes and spatial scale on macroevolutionary dynamics.     

Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007

Background Yersinia pestis is the causative agent of human plague and is endemic in various African, Asian and American countries. In Madagascar, the disease represents a significant public health problem with hundreds of human cases a year. Unfortunately, poor infrastructure makes outbreak investigations challenging.Conclusions/SignificancePlague in Madagascar is caused by numerous distinct types of Y. pestis. Genotyping method choice should be based upon the discriminatory power needed, expense, and available data for any desired comparisons. We conclude that genotyping should be a standard tool used in epidemiological investigations of plague outbreaks.     

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf‐feeding monkey (Pygathrix nemaeus)

Faecal samples are of great value as a non‐invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red‐shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~10 000 (0.014%) and ~44 000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast ‘barcodes’ for angiosperms. The results were compared with ‘metabarcoding’ using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.     

Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.     

Deep mtDNA subdivision within Linnean species in an endemic radiation of tiger beetles from New Zealand (genus Neocicindela)

The invertebrate fauna of New Zealand is of great interest as a geologically tractable model for the study of species diversification, but direct comparisons with closely related lineages elsewhere are lacking. Integrating population-level analyses with studies of taxonomy and clade diversification, we performed mtDNA analysis on Neocicindela (Cicindelidae, tiger beetles) for a broad sample of populations from 11 of 12 known species and 161 specimens (three loci, 1883 nucleotides), revealing 123 distinct haplotypes. Phylogenetic reconstruction recovered two main lineages, each composed of 5-6 Linnean species whose origin was dated to 6.66 and 7.26 Mya, while the Neocicindela stem group was placed at 10.82 ± 0.48 Mya. Species delimitation implementing a character-based (diagnostic) species concept recognized 19 species-level groups that were in general agreement with Linnean species but split some of these into mostly allopatric subgroups. Tree-based methods of species delimitation using a mixed Yule-coalescence model were inconclusive, and recognized 32-51 entities (including singletons), splitting existing species into up to 8 partially sympatric groups. These findings were different from patterns in the Australian sister genus Rivacindela, where character-based and tree-based methods were previously shown to produce highly congruent groupings. In Neocicindela, the pattern of mtDNA variation was characterized by high intra-population and intra-species haplotype divergence, the coexistence of divergent haplotypes in sympatry, and a poor correlation of genetic and geographic distance. These observations combined suggest a scenario of phylogeographic divergence and secondary contact driven by orogenetic and climatic changes of the Pleistocene/Pliocene. The complex evolutionary history of most species of Neocicindela due to the relative instability of the New Zealand biota resulted in populations of mixed ancestry but not in a general loss of genetic variation.     

Hypoosmotic and glutamate‐induced swelling of bipolar cells in the rat retina: comparison with swelling of Müller glial cells

Regulation of cellular volume is of great importance to avoid changes in neuronal excitability resulting from a decrease in the extracellular space volume. We compared the volume regulation of retinal glial (Müller) and neuronal (bipolar) cells under hypoosmotic and glutamate‐stimulated conditions. Freshly isolated slices of the rat retina were superfused with a hypoosmotic solution (60% osmolarity; 4 min) or with a glutamate (1 mM)‐containing isoosmotic solution (15 min), and the size changes of Müller and bipolar cell somata were recorded. Bipolar cell somata, but not Müller cell somata, swelled under hypoosmotic conditions and in the presence of glutamate. The hypoosmotic swelling of bipolar cell somata might be mediated by sodium flux into the cells, because it was not observed under extracellular sodium‐free conditions, and was induced by activation of metabotropic glutamate receptors and sodium‐dependent glutamate transporters. The glutamate‐induced swelling of bipolar cell somata was mediated by sodium chloride flux into the cells induced by activation of NMDA‐ and non‐NMDA glutamate receptors, glutamate transporters, and voltage‐gated sodium channels. The glutamate‐induced swelling of bipolar cell somata was abrogated by adenosine and γ‐aminobutyric acid, but not by vascular endothelial growth factor and ATP. The data may suggest that Müller cells, in contrast to bipolar cells, possess endogenous mechanisms which tightly regulate the cellular volume in response to hypoosmolarity and prolonged glutamate exposure. Inhibitory retinal transmission may regulate the volume of bipolar cells, likely by inhibition of the excitatory action of glutamate.