Homologues of the engrailed gene from five molluscan classes

AbstractWe used the polymerase chain reaction (PCR) to amplify, clone, and sequence 10 engrailed homeodomains from 8 species in the five major molluscan classes, including the serially organized chiton (Polyplacophora) lineage. The Drosophila melanogaster gene engrailed (en) is one of several genes involved in embyonic segment polarity determination. Studies of engrailed sequence and expression in molluscs are of interest due to questions regarding the evolution and homology of segmentation in these taxa. Nucleotide and deduced amino acid sequence comparisons reflect evolutionary conservation within helices of the en homeodomain and ancient divergences in the region 3′ to the homeodomain

The founding charter of the Genomic Observatories Network

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.Neil Davies ... Andrew J Lowe ... et al. and GOs-CO

Distribution and habitat preferences of tiger beetles (Coleoptera: Cicindelidae) of the riverine ecosystems of Sri Lanka

Tiger beetles have been observed in many riverine ecosystems of Sri Lanka. However, current locations, species, distribution of species, habitat preferences and possible interactions between species are unknown. The present study intends to investigate these details and provide information that can be used in further studies. Tiger beetles are sampled from 15 riverine locations and examined for identification, body weight and body length. The riverine locations are analysed for locational, climatic and soil parameters and microhabitat details are recorded. Statistical analysis using One-Way Analysis of Variance and Tukey’s pair comparison method of Minitab 16.0 statistical software package is conducted to compare the body sizes of species. Further, a statistical comparison between the climatic and soil parameters of the locations of Cylindera (Ifasina) labioaenea and that of other species are carried out. The study reveals five tiger beetle species Cylindera (Ifasina) labioaenea Horn, Cylindera (Ifasina) willeyi Horn, Cylindera (Ifasina) waterhousei Horn, Calomera cardoni Fleutiaux, Calomera angulata Fabricius, from the riverine ecosystems of Sri Lanka. Cylindera labioaenea is the most common species; C. willeyi and C. waterhousei are endemic to Sri Lanka. Cylindera labioaenea, C. willeyi and C. waterhousei are small, while Calomera cardoni and Calomera angulata are medium in size. Cylindera labioaenea is significantly smaller than C. willeyi and C. waterhousei, and resides in locations with significantly higher air temperatures, solar radiations and significantly lower relative humidity than the other two species. An optimal temperature range for the riverine tiger beetles is suggested and their preferences to soil moisture, soil temperature, soil colour and soil salinity are discussed. The occurrence of C. labioaenea as a single species population while the fact that other species co-exist may be due to a defensive strategy

Revisiting the insect mitochondrial molecular clock: The mid-aegean trench calibration

Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My -1, but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My-1 for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources. © The Author 2010

Comparative phylogeography of tenebrionid beetles in the Aegean archipelago: The effect of dispersal ability and habitat preference

Comparative phylogeographical studies in island archipelagos can reveal lineage-specific differential responses to the geological and climatic history. We analysed patterns of genetic diversity in six codistributed lineages of darkling beetles (Tenebrionidae) in the central Aegean archipelago which differ in wing development and habitat preferences. A total of 600 specimens from 30 islands and eight adjacent mainland regions were sequenced for mitochondrial cytochrome oxidase I and nuclear Muscular protein 20. Individual gene genealogies were assessed for the presence of groups that obey an independent coalescent process using a mixed Yule coalescent model. The six focal taxa differed greatly in the number of coalescent groups and depth of lineage subdivision, which was closely mirrored by the degree of geographical structuring. The most severe subdivision at both mitochondrial DNA and nuclear DNA level was found in flightless lineages associated with presumed stable compact-soil habitats (phrygana, maquis), in contrast to sand-obligate lineages inhabiting ephemeral coastal areas that displayed greater homogeneity across the archipelago. A winged lineage, although associated with stable habitats, showed no significant phylogenetic or geographical structuring. Patterns of nucleotide diversity and local genetic differentiation, as measured using ΦSTand hierarchical amova, were consistent with high levels of ongoing gene flow in the winged taxon; frequent local extinction and island recolonisation for flightless sand-obligate taxa; and very low gene flow and geographical structure largely defined by the palaeogeographical history of the region in flightless compact-soil taxa. These results show that differences in dispersal rate, mediated by habitat persistence, greatly influence the levels of phylogeographical subdivision in lineages that are otherwise subjected to the same geological events and palaeoclimatic changes. © 2009 Blackwell Publishing Ltd

Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate

10.1186/s12983-016-0150-4Frontiers in Zoology13

Testing the species-genetic diversity correlation in the Aegean archipelago: Toward a haplotype-based macroecology?

positive correlation between species diversity and genetic diversity has been proposed, consistent with neutral predictions in macroecology.We assessed the species-genetic diversity correlation in tenebrionid beetle communities of the Aegean archipelago on 15 islands of different sizes, distances to mainland, and ages of isolation. Alpha and beta diversity of species and haplotypes were assessed using sequences of 11,000 individuals (mitochondrial cytochrome oxidase 1 and nuclear muscular protein 20). We show that (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland is factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated on the basis of species, nuclear, and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sanddwelling lineages compared with less dispersive lineages that are not sand obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting largescale biodiversity patterns based on genetic inventories of local samples. © 2011 by The University of Chicago