Barcoding of the cytochrome oxidase I (COI) indicates a recent introduction of Ciona savignyi into New Zealand and provides a rapid method for Ciona species discrimination

Mitochondrial cytochrome oxidase I (COI) gene sequencing (DNA barcoding) of Ciona specimens from New Zealand (NZ) led to the first record of the solitary ascidian Ciona savignyi in the Southern Hemisphere. We sought to quantify C. savignyi COI genetic diversity around the NZ archipelago and to compare this with diversity within C. savignyi's native range in the north-west Pacific. Ciona savignyi specimens were collected from two NZ sites and from three sites around Japan. COI sequences (595 bp) were amplified and measures of genetic diversity were calculated. Based on differences between their COI sequences we developed a PCR-based assay to distinguish C. savignyi from the morphologically similar C. intestinalis. A total of 12 C. savignyi COI haplotypes were recovered from the 76 samples. Of the four haplotypes observed in NZ, two were unique. From the 10 haplotypes observed in the Japan samples, eight were unique. The C. savignyi populations in Japan were found to contain higher haplotype diversity when compared with those in NZ. The NZ samples contained only a small subset of the haplotype variation of the Japan samples, however, NZ samples did harbor two haplotypes not observed in the Japan samples. A PCR-based assay developed from the COI sequences was able to reliably discriminate the two Ciona species. The low COI genetic diversity within the two NZ C. savignyi populations sampled is consistent with a founder effect associated loss of genetic diversity. The robust PCR-based assay for distinguishing C. savignyi and C. intestinalis may find application in ecological and taxonomic studies and can be applied to both archival materials and live animals

Evidence for increased olfactory receptor gene repertoire size in two nocturnal bird species with well-developed olfactory ability

<p>Abstract</p> <p>Background</p> <p>In vertebrates, the molecular basis of the sense of smell is encoded by members of a large gene family, namely olfactory receptor (OR) genes. Both the total number of OR genes and the proportion of intact OR genes in a genome may indicate the importance of the sense of smell for an animal. There is behavioral, physiological, and anatomical evidence that some bird species, in particular nocturnal birds, have a well developed sense of smell. Therefore, we hypothesized that nocturnal birds with good olfactory abilities have evolved (i) more OR genes and (ii) more intact OR genes than closely related and presumably less 'olfaction-dependent' day-active avian taxa.</p> <p>Results</p> <p>We used both non-radioactive Southern hybridization and PCR with degenerate primers to investigate whether two nocturnal bird species that are known to rely on olfactory cues, the brown kiwi (<it>Apteryx australis</it>) and the kakapo (<it>Strigops habroptilus</it>), have evolved a larger OR gene repertoire than their day-active, closest living relatives (for kiwi the emu <it>Dromaius novaehollandiae</it>, rhea <it>Rhea americana</it>, and ostrich <it>Struthio camelus </it>and for kakapo the kaka <it>Nestor meridionalis </it>and kea <it>Nestor notabilis</it>). We show that the nocturnal birds did not have a significantly higher proportion of intact OR genes. However, the estimated total number of OR genes was larger in the two nocturnal birds than in their relatives.</p> <p>Conclusion</p> <p>Our results suggest that ecological niche adaptations such as daily activity patterns may have shaped avian OR gene repertoires.</p

No evidence for an association between <i>Clock</i> gene allelic variation and migration timing in a long-distance migratory shorebird (<i>Limosa lapponica baueri</i>)

The gene Clock is a key part of the Core Circadian Oscillator, and the length of the polyglutamine (poly-Q) repeat sequence in Clock (ClkpolyQcds) has been proposed to be associated with the timing of annual cycle events in birds. We tested whether variation in ClkpolyQcds corresponds to variation in migration timing in the bar-tailed godwit (Limosa lapponica baueri), a species in which individuals show strong annual consistency in their migration timing despite the New Zealand population migrating across a 5-week period. We describe allelic variation of the ClkpolyQcds in 135 godwits over-wintering in New Zealand (N.Z.) and investigate whether polymorphism in this region is associated with northward migration timing (chronophenotype) from N.Z. or (for 32 birds tracked by geolocator) after the primary stopover in Asia. Six Clock alleles were detected (Q(7)-Q(12)) and there was substantial variation between individuals (heterozygosity of 0.79). There was no association between ClkpolyQcds polymorphism and migration timing from N.Z. The length of the shorter Clock allele was related to migration timing from Asia, though this relationship arose largely from just a few northern-breeding birds with longer alleles. Other studies show no consistent associations between ClkpolyQcds and migration timing in birds, although Clock may be associated with breeding latitude in some species (as an adaptation to photoperiodic regime). Apparent relationships with migration timing could reflect latitude-related variation in migration timing, rather than Clock directly affecting migration timing. On current evidence, ClkpolyQcds is not a strong candidate for driving migration timing in migratory birds generally

Drd4 gene polymorphisms are associated with personality variation in a passerine bird

Polymorphisms in several neurotransmitter-associated genes have been associated with variation in human personality traits. Among the more promising of such associations is that between the human dopamine receptor D4 gene (Drd4) variants and novelty-seeking behaviour. However, genetic epistasis, genotype–environment interactions and confounding environmental factors all act to obscure genotype–personality relationships. Such problems can be addressed by measuring personality under standardized conditions and by selection experiments, with both approaches only feasible with non-human animals. Looking for similar Drd4 genotype–personality associations in a free-living bird, the great tit (Parus major), we detected 73 polymorphisms (66 SNPs, 7 indels) in the P. major Drd4 orthologue. Two of the P. major Drd4 gene polymorphisms were investigated for evidence of association with novelty-seeking behaviour: a coding region synonymous single nucleotide polymorphism (SNP830) and a 15 bp indel (ID15) located 5′ to the putative transcription initiation site. Frequencies of the three Drd4 SNP830 genotypes, but not the ID15 genotypes, differed significantly between two P. major lines selected over four generations for divergent levels of ‘early exploratory behaviour’ (EEB). Strong corroborating evidence for the significance of this finding comes from the analysis of free-living, unselected birds where we found a significant association between SNP830 genotypes and differing mean EEB levels. These findings suggest that an association between Drd4 gene polymorphisms and animal personality variation predates the divergence of the avian and mammalian lineages. Furthermore, this work heralds the possibility of following microevolutionary changes in frequencies of behaviourally relevant Drd4 polymorphisms within populations where natural selection acts differentially on different personality types

Effects of temperature and salinity stress on DNA methylation in a highly invasive marine invertebrate, the colonial ascidian Didemnum vexillum

Environmentally induced epigenetic changes may contribute to phenotypic plasticity, increase adaptive potential in changing environments, and play a key role in the establishment and spread of invasive species in new habitats. In this study, we used methylation-sensitive amplified polymorphism (MSAP) to assess environmentally induced DNA methylation changes in a globally invasive clonal ascidian, Didemnum vexillum. We tested the effect of increasing temperature (19, 25 and 27 °C) and decreasing salinity (34, 32, 30, 28 and 26 practical salinity units (PSU)) on global DNA methylation, growth and survival rates. Exposure to 27 °C resulted in significant changes in DNA methylation over time. Growth also decreased in colonies exposed to high temperatures, suggesting they were under thermal stress. In contrast, no differences in growth nor DNA methylation patterns were observed in colonies exposed to a decreasing salinity gradient, potentially due to prior adaptation. The results of this study show that environmental stress can induce significant global DNA methylation changes in an invasive marine invertebrate on very rapid timescales, and that this response varies depending on the type, magnitude, and duration of the stressor. Changes in genomic DNA methylation and the rate of growth may act to ‘buy survival time’ under stressful conditions, expanding the distribution limits of this globally invasive species

Low Variation in the Polymorphic Clock Gene Poly-Q Region Despite Population Genetic Structure across Barn Swallow (Hirundo rustica) Populations

Recent studies of several species have reported a latitudinal cline in the circadian clock gene, Clock, which influences rhythms in both physiology and behavior. Latitudinal variation in this gene may hence reflect local adaptation to seasonal variation. In some bird populations, there is also an among-individual association between Clock poly-Q genotype and clutch initiation date and incubation period. We examined Clock poly-Q allele variation in the Barn Swallow (Hirundo rustica), a species with a cosmopolitan geographic distribution and considerable variation in life-history traits that may be influenced by the circadian clock. We genotyped Barn Swallows from five populations (from three subspecies) and compared variation at the Clock locus to that at microsatellite loci and mitochondrial DNA (mtDNA). We found very low variation in the Clock poly-Q region, as >96% of individuals were homozygous, and the two other alleles at this locus were globally rare. Genetic differentiation based on the Clock poly-Q locus was not correlated with genetic differentiation based on either microsatellite loci or mtDNA sequences. Our results show that high diversity in Clock poly-Q is not general across avian species. The low Clock variation in the background of heterogeneity in microsatellite and mtDNA loci in Barn Swallows may be an outcome of stabilizing selection on the Clock locus

Do users’ reading skills and difficulty ratings for texts affect choices and evaluations?

In our contribution, we consider how corpus data can be used as a proxy for the written language environment around us in constructing offline studies of native-speaker intuition and usage. We assume a broadly emergent perspective on language: in other words, the linguistic competence of individuals is not identical or hardwired but forms gradually through exposure and coalescence of patterns of production and reaction. We hypothesize that while users presumably all in theory have access to the same linguistic material, their actual exposure to it and their ability to interpret it may differ, which will result in differing judgments and choices. Our study looks at the interaction between corpus frequency and two possible indicators of individual difference: attitude towards reading tasks and performance on reading tasks. We find a small but consistent effect of task performance on respondents’ judgments but do not confirm any effects on respondents’ production tasks

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

Background International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. Methods We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15–49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. Findings Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4–7·3) of transmissions occurred within lakeside areas, 89·2% (86·0–91·8) within inland areas, 1·3% (0·6–2·6) from lakeside to inland areas, and 3·7% (2·3–5·8) from inland to lakeside areas. Interpretation Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. Funding The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention

Increased Inter-Colony Fusion Rates Are Associated with Reduced COI Haplotype Diversity in an Invasive Colonial Ascidian Didemnum vexillum

Considerable progress in our understanding of the population genetic changes associated with biological invasions has been made over the past decade. Using selectively neutral loci, it has been established that reductions in genetic diversity, reflecting founder effects, have occurred during the establishment of some invasive populations. However, some colonial organisms may actually gain an ecological advantage from reduced genetic diversity because of the associated reduction in inter-colony conflict. Here we report population genetic analyses, along with colony fusion experiments, for a highly invasive colonial ascidian, Didemnum vexillum. Analyses based on mitochondrial cytochrome oxidase I (COI) partial coding sequences revealed two distinct D. vexillum clades. One COI clade appears to be restricted to the probable native region (i.e., north-west Pacific Ocean), while the other clade is present in widely dispersed temperate coastal waters around the world. This clade structure was supported by 18S ribosomal DNA (rDNA) sequence data, which revealed a one base-pair difference between the two clades. Recently established populations of D. vexillum in New Zealand displayed greatly reduced COI genetic diversity when compared with D. vexillum in Japan. In association with this reduction in genetic diversity was a significantly higher inter-colony fusion rate between randomly paired New Zealand D. vexillum colonies (80%, standard deviation ±18%) when compared with colonies found in Japan (27%, standard deviation ±15%). The results of this study add to growing evidence that for colonial organisms reductions in population level genetic diversity may alter colony interaction dynamics and enhance the invasive potential of newly colonizing species