Interspecific networks in ground beetle (Coleoptera: Carabidae) assemblages

Although changes to interspecific relationships can significantly alter the composition of insect assemblages, they are often ignored when assessing impacts of environmental change. Long-term ground beetle data were used in this study to analyse ecological networks from three habitats at two sites in Scotland. A Bayesian Network inference algorithm was used to reveal interspecific relationships. The significance and strength of relationships between species (nodes) were estimated along with other network properties. Links were identified as positive relationships if co-occurrences of beetles correlated positively, and as negatives relationships if there was a negative correlation between the occurrences of the species. Most of the species had few links and only 10% of the nodes were connected with several links. Calathus fuscipes, a common carabid in the samples, was the most connected, with nine links to other species. More interspecific relationships were found to be positive than negative, with 48 and 23 links, respectively. The modular structure of the network was assessed and eight separate sub-networks were found. Habitat preferences of the species were clearly represented in the structure of the sets of those five sub-networks containing more than one species and were in line with the findings of the indicator species analysis. In our study, we showed that generated Bayesian networks can model interspecific relationships between carabid species. Due to the relative ease of the collection of field data and the high information content of the results, this method could be incorporated into everyday ecological analysis.     

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.     

A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora

To critically examine the relationship between species recognized by phylogenetic and reproductive compatibility criteria, we applied phylogenetic species recognition (PSR) to the fungus in which biological species recognition (BSR) has been most comprehensively applied, the well-studied genus Neurospora. Four independent anonymous nuclear loci were characterized and sequenced from 147 individuals that were representative of all described outbreeding species of Neurospora. We developed a consensus-tree approach that identified monophyletic genealogical groups that were concordantly supported by the majority of the loci, or were well supported by at least one locus but not contradicted by any other locus. We recognized a total of eight phylogenetic species, five of which corresponded with the five traditional biological species, and three of which were newly discovered. Not only were phylogenetic criteria superior to traditional reproductive compatibility criteria in revealing the full species diversity of Neurospora, but also significant phylogenetic subdivisions were detected within some species. Despite previous suggestions of hybridization between N. crassa and N. intermedia in nature, and the fact that several putative hybrid individuals were included in this study, no molecular evidence in support of recent interspecific gene flow or the existence of true hybrids was observed. The sequence data from the four loci were combined and used to clarify how the species discovered by PSR were related. Although species-level clades were strongly supported, the phylogenetic relationships among species remained difficult to resolve, perhaps due to conflicting signals resulting from differential lineage sorting.     

Overall concordance correlation coefficient for evaluating agreement among multiple observers

Accurate and precise measurement is an important component of any proper study design. As elaborated by Lin (1989, Biometrics 45, 255-268), the concordance correlation coefficient (CCC) is more appropriate than other indices for measuring agreement when the variable of interest is continuous. However, this agreement index is defined in the context of comparing two fixed observers. In order to use multiple observers in a study involving large numbers of subjects, there is a need to assess agreement among these multiple observers. In this article, we present an overall CCC (OCCC) in terms of the interobserver variability for assessing agreement among multiple fixed observers. The OCCC turns out to be equivalent to the generalized CCC (King and Chinchilli, 2001, Statistics in Medicine 20, 2131-2147; Lin, 1989; Lin, 2000, Biometrics 56, 324-325) when the squared distance function is used. We evaluated the OCCC through generalized estimating equations (Barnhart and Williamson, 2001, Biometrics 57, 931-940) and U-statistics (King and Chinchilli, 2001) for inference. This article offers the following important points. First, it addresses the precision and accuracy indices as components of the OCCC. Second, it clarifies that the OCCC is the weighted average of all pairwise CCCs. Third, it is intuitively defined in terms of interobserver variability. Fourth, the inference approaches of GEE and the U-statistics are compared via simulations for small samples. Fifth, we illustrate the use of the OCCC by two medical examples with the GEE, U-statistics, and bootstrap approaches.     

Do coral-reef fish faunas have a distinctive taxonomic structure?

Do the highly diverse fish faunas that associate with coral reefs have distinguishing taxonomic and ecological characteristics, as proposed by Choat and Bellwood (1991) and Bellwood (1996)? Does a 50?my old (Eocene) fossil fish fauna from Italy represent a coral-reef fish assemblage that provides unique information about the evolution of such assemblages, as claimed by Bellwood (1996)? I compared the structure of the reef fish faunas of adjacent tropical regions rich and poor in coral reefs, in both America and Polynesia, and found that they exhibit no substantive differences in relative species richness among families of typical “coral-reef” fishes. While coral-rich regions have larger reef fish faunas, a variety of factors probably contribute to such differences. Thus coral-reef fish faunas may lack a distinctive taxonomic structure. A similar comparative approach would be useful for assessing whether assemblages of fishes on coral reefs have distinctive ecological characteristics. Based on patterns of habitat use by modern tropical shorefishes, the Italian Eocene fauna includes few definite reef fishes, and may well consist primarily of non-reef fishes preserved in a non-reef habitat. Until we know more about the environment in which those fossils were preserved, that fauna can contribute little to understanding how coral reef fish assemblages have evolved.     

Longitudinal patterns of fish assemblages in small unregulated subbasins: evaluating reach- and watershed-scale parameters

Fish assemblage relationships with environmental parameters were studied in four small unregulated subbasins in the speciose Upper Green River Basin of central Kentucky, USA. One subbasin drains into a tributary of the Green River and produced the lowest species (28) richness. The three other subbasins drain directly into the Green River and supported 41−59 species. Parameters were partitioned into watershed- and reach-scale spatial categories. Watershed area per stream segment and stream-size related environmental parameters at the reach scale produced the highest loadings of a principle components analysis (PCA), and both PCA Axes 1 and 2 for all subbasins were reflective either of watershed area or stream-size parameters. Small loadings were produced by all watershed-scale land-use parameters and all reach-scale water chemistry parameters. Fish richness and diversity were positively correlated with watershed area for the two largest subbasins and for the three Upper Green River subbasins combined. The lack of a linear relationship, however, between the residuals of multiple linear regression models between richness and diversity versus stream width, percent bedrock, percent pool and percent fine substrates indicated that a simple species area relationship was not operating. A detrended correspondence analysis (DCA) performed for each subbasin showed that several fish species were associated mainly either with small, upland segments or conversely the largest, deeper segments, and each subbasin yielded significant correlations between the environmental PCA loadings and fish assemblage DCA site scores. These results indicated that within the regional scale, and in absence of steep disturbance gradients, stream fish assemblages can reflect natural hydrologic and geomorphic gradients.     

Tests of phenotypic and genetic concordance and their application to the conservation of Panamanian golden frogs (Anura, Bufonidae)

Evolutionarily significant units (ESUs) differ in the extent to which they capture, or even consider, adaptive variation, and most such designations are based solely on neutral genetic differences that may not capture variation relevant to species' adaptabilities to changing environmental conditions. While concordant patterns of divergence among data sets (i.e. neutral and potentially non-neutral characters) can strengthen ESU designations, determining whether such criteria are met for highly variable taxa is especially challenging. This study tests whether previously defined ESUs for endangered Panamanian golden frogs (Atelopus varius and Atelopus zeteki) exhibit concordant variation among multiple phenotypic traits and mitochondrial DNA sequences, and the extent to which such divergence corresponds to environmental differences. Multivariate analyses identify phenotypic and genetic differentiation consistent with proposed ESUs and support the status of A. varius and A. zeteki as separate species. Moreover, the significant association detected between ESU co-membership and genetic similarity, which remained strong after removing the effect of geographic distance, also indicates that genetic differences are not simply due to isolation by distance. Two phenotypic characters (body size and the extent of dorsal black patterning) that differ among ESUs also co-vary with environmental differences, suggesting that to the extent that these phenotypic differences are heritable, variation may be associated with adaptive divergence. Lastly, discriminant function analyses show that the frogs can be correctly assigned to ESUs based on simultaneous analysis of multiple characters. The study confirms the merit of conserving the previously proposed golden frog ESUs as well as demonstrates the utility and feasibility of combined analyses of ecological, morphological and genetic variation in evaluating ESUs, especially for highly variable taxa.