Taxonomic Subsets Research Articles

Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs.

A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be analyzed has increased exponentially over the last few years. The accurate annotation of mitochondrial DNA is a prerequisite for any mitogenomic comparative analysis. To sustain with the growth of the available mitochondrial sequence data, highly efficient automatic computational methods are, hence, needed. Automatic annotation methods are typically based on databases that contain information about already annotated (and often pre-curated) mitogenomes of different species. However, the existing approaches have several shortcomings: 1) they do not scale well with the size of the database; 2) they do not allow for a fast (and easy) update of the database; and 3) they can only be applied to a relatively small taxonomic subset of all species. Here, we present a novel approach that does not have any of these aforementioned shortcomings, (1), (2), and (3). The reference database of mitogenomes is represented as a richly annotated de Bruijn graph. To generate gene predictions for a new user-supplied mitogenome, the method utilizes a clustering routine that uses the mapping information of the provided sequence to this graph. The method is implemented in a software package called DeGeCI (De Bruijn graph Gene Cluster Identification). For a large set of mitogenomes, for which expert-curated annotations are available, DeGeCI generates gene predictions of high conformity. In a comparative evaluation with MITOS2, a state-of-the-art annotation tool for mitochondrial genomes, DeGeCI shows better database scalability while still matching MITOS2 in terms of result quality and providing a fully automated means to update the underlying database. Moreover, unlike MITOS2, DeGeCI can be run in parallel on several processors to make use of modern multi-processor systems.

Aedes albopictus microbiome derives from environmental sources and partitions across distinct host tissues.

The mosquito microbiome consists of a consortium of interacting microorganisms that reside on and within culicid hosts. Mosquitoes acquire most of their microbial diversity from the environment over their life cycle. Once present within the mosquito host, the microbes colonize distinct tissues, and these symbiotic relationships are maintained by immune-related mechanisms, environmental filtering, and trait selection. The processes that govern how environmental microbes assemble across the tissues within mosquitoes remain poorly resolved. We use ecological network analyses to examine how environmental bacteria assemble to form bacteriomes among Aedes albopictus host tissues. Mosquitoes, water, soil, and plant nectar were collected from 20 sites in the Mānoa Valley, Oahu. DNA was extracted and associated bacteriomes were inventoried using Earth Microbiome Project protocols. We find that the bacteriomes of A. albopictus tissues were compositional taxonomic subsets of environmental bacteriomes and suggest that the environmental microbiome serves as a source pool that supports mosquito microbiome diversity. Within the mosquito, the microbiomes of the crop, midgut, Malpighian tubules, and ovaries differed in composition. This microbial diversity partitioned among host tissues formed two specialized modules: one in the crop and midgut, and another in the Malpighian tubules and ovaries. The specialized modules may form based on microbe niche preferences and/or selection of mosquito tissues for specific microbes that aid unique biological functions of the tissue types. A strong niche-driven assembly of tissue-specific microbiotas from the environmental species pool suggests that each tissue has specialized associations with microbes, which derive from host-mediated microbe selection.

Living and dead bivalves are congruent surrogates for whole benthic macroinvertebrate communities in Puget Sound

To integrate paleoecological data with the “whole fauna” data used in biological monitoring, analyses usually must focus on the subset of taxa that are inherently preservable, for example by virtue of biomineralized hardparts, and those skeletal remains must also be identifiable in fragmentary or otherwise imperfect condition, thus perhaps coarsening analytical resolution to the genus or family level. Here we evaluate the ability of readily preserved bivalves to reflect patterns of compositional variation from the entire infaunal macroinvertebrate fauna as typically sampled by agencies in ocean monitoring, using data from ten long-established subtidal stations in Puget Sound, Washington State. Similarity in compositional variation among these stations was assessed for five taxonomic subsets (the whole fauna, polychaetes, malacostracans, living bivalves, dead bivalves) at four levels of taxonomic resolution (species, genera, families, orders) evaluated under four numerical transformations of the original count data (proportional abundance, square root- and fourth root-transformation, presence-absence). Using the original matrix of species-level proportional abundances of the whole fauna as a benchmark of “compositional variation,” we find that living and dead bivalves had nearly identical potential to serve as surrogates of the whole fauna; they were further offset from the whole fauna than was the polychaete subset (which dominates the whole fauna), but were far superior as surrogates than malacostracans. Genus- and family-level data were consistently strong surrogates of species-level data for most taxonomic subsets, and correlations declined for all subsets with increasing severity of data transformation, although this effect lessened for subsets with high community evenness. The strong congruence of death assemblages with living bivalves, which are themselves effective surrogates of compositional variation in the whole fauna, is encouraging for using bivalve dead-shell assemblages to complement conventional monitoring data, notwithstanding strong natural environmental gradients with potential to bias shell preservation.

Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian

The mass extinction characterizing the Permian/Triassic boundary (PTB; ~ 252 Ma) corresponds to a major faunal shift between the Palaeozoic and the Modern evolutionary fauna. The temporal, spatial, environmental, and ecological dynamics of the associated biotic recovery remain highly debated, partly due to the scarce, or poorly-known, Early Triassic fossil record. Recently, an exceptionally complex ecosystem dated from immediately after the Smithian/Spathian boundary (~ 3 myr after the PTB) was reported: the Paris Biota (Idaho, USA). However, the spatiotemporal representativeness of this unique assemblage remained questionable as it was hitherto only reported from a single site. Here we describe three new exceptionally diverse assemblages of the same age as the Paris Biota, and a fourth younger one. They are located in Idaho and Nevada, and are taxonomic subsets of the Paris Biota. We show that the latter covered a region-wide area and persisted at least partially throughout the Spathian. The presence of a well-established marine fauna such as the Paris Biota, as soon as the early Spathian, indicates that the post-PTB biotic recovery and the installation of complex ecosystems probably took place earlier than often assumed, at least at a regional scale.

Drivers of parasite β-diversity among anuran hosts depend on scale, realm and parasite group.

A robust understanding of what drives parasite β-diversity is an essential step towards explaining what limits pathogens' geographical spread. We used a novel global dataset (latitude -39.8 to 61.05 and longitude -117.84 to 151.49) on helminths of anurans to investigate how the relative roles of climate, host composition and spatial distance to parasite β-diversity vary with spatial scale (global, Nearctic and Neotropical), parasite group (nematodes and trematodes) and host taxonomic subset (family). We found that spatial distance is the most important driver of parasite β-diversity at the global scale. Additionally, we showed that the relative effects of climate concerning distance increase at the regional scale when compared with the global scale and that trematodes are generally more responsive to climate than nematodes. Unlike previous studies done at the regional scale, we did not find an effect of host composition on parasite β-diversity. Our study presents a new contribution to parasite macroecological theory, evidencing spatial and taxonomic contingencies of parasite β-diversity patterns, which are related to the zoogeographical realm and host taxonomic subset, respectively. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Taxonomic resolution affects host-parasite association model performance.

Identifying the factors that structure host–parasite interactions is fundamental to understand the drivers of species distributions and to predict novel cross-species transmission events. More phylogenetically related host species tend to have more similar parasite associations, but parasite specificity may vary as a function of transmission mode, parasite taxonomy or life history. Accordingly, analyses that attempt to infer host−parasite associations using combined data on different parasite groups may perform quite differently relative to analyses on each parasite subset. In essence, are more data always better when predicting host−parasite associations, or does parasite taxonomic resolution matter? Here, we explore how taxonomic resolution affects predictive models of host−parasite associations using the London Natural History Museum's database of host–helminth interactions. Using boosted regression trees, we demonstrate that taxon-specific models (i.e. of Acanthocephalans, Nematodes and Platyhelminthes) consistently outperform full models in predicting mammal-helminth associations. At finer spatial resolutions, full and taxon-specific model performance does not vary, suggesting tradeoffs between phylogenetic and spatial scales of analysis. Although all models identify similar host and parasite covariates as important to such patterns, our results emphasize the importance of phylogenetic scale in the study of host–parasite interactions and suggest that using taxonomic subsets of data may improve predictions of parasite distributions and cross-species transmission. Predictive models of host–pathogen interactions should thus attempt to encompass the spatial resolution and phylogenetic scale desired for inference and prediction and potentially use model averaging or ensemble models to combine predictions from separately trained models.

Detecting the Signature of Body Mass Evolution in the Broad-Scale Architecture of Food Webs.

AbstractBody mass-based links between predator and prey are fundamental to the architecture of food webs. These links determine who eats whom across trophic levels and strongly influence the population abundance, flow of energy, and stability properties of natural communities. Body mass links scale up to create predator-prey mass relationships across species, but the origin of these relationships is unclear. Here I show that predator-prey mass relationships are consistent with the idea that body mass evolves to maximize a dependable supply of resource uptake. I used a global database of ~2,100 predator-prey links and a mechanistic optimization model to correctly predict the slope of the predator-prey mass scaling relationships across species generally and for nine taxonomic subsets. The model also predicted cross-group variation in the heights of the body mass relationships, providing an integrated explanation for mass relationships and their variation across taxa. The results suggest that natural selection on body mass at the local scale is detectable in ecological organization at the macro scale.

Toward accurate species-level metabarcoding of arthropod communities from the tropical forest canopy.

Metabarcoding of arthropod communities can be used for assessing species diversity in tropical forests but the methodology requires validation for accurate and repeatable species occurrences in complex mixtures. This study investigates how the composition of ecological samples affects the accuracy of species recovery.Starting with field‐collected bulk samples from the tropical canopy, the recovery of specimens was tested for subsets of different body sizes and major taxa, by assembling these subsets into increasingly complex composite pools. After metabarcoding, we track whether richness, diversity, and most importantly composition of any size class or taxonomic subset are affected by the presence of other subsets in the mixture.Operational taxonomic units (OTUs) greatly exceeded the number of morphospecies in most taxa, even under very stringent sequencing read filtering. There was no significant effect on the recovered OTU richness of small and medium‐sized arthropods when metabarcoded alongside larger arthropods, despite substantial biomass differences in the mixture. The recovery of taxonomic subsets was not generally influenced by the presence of other taxa, although with some exceptions likely due to primer mismatches. Considerable compositional variation within size and taxon‐based subcommunities was evident resulting in high beta‐diversity among samples from within a single tree canopy, but this beta‐diversity was not affected by experimental manipulation.We conclude that OTU recovery in complex arthropod communities, with sufficient sequencing depth and within reasonable size ranges, is not skewed by variable biomass of the constituent species. This could remove the need for time‐intensive manual sorting prior to metabarcoding. However, there remains a chance of taxonomic bias, which may be primer‐dependent. There will never be a panacea primer; instead, metabarcoding studies should carefully consider whether the aim is broadscale turnover, in which case these biases may not be important, or species lists, in which case separate PCRs and sequencing might be necessary. OTU number inflation remains an issue in metabarcoding and requires bioinformatic development, particularly in read filtering and OTU clustering, and/or greater use of species‐identifying sequences generated outside of bulk sequencing.

Using SQL Databases for Sequence Similarity Searching and Analysis.

Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc.

“Pollard-walk” Butterfly Survey does not Warrant the Equity of Sampling-completeness among Butterfly Families: A Case Study with Tropical Butterfly Fauna in Bhutan

Complete or even sub-complete inventories of biodiversity often remain well out of reach, especially when dealing with speciose taxonomic groups, such as insects in general and butterfly fauna in particular. Moreover, it is even uncertain that similar completeness levels may be reached among taxonomic subsets within a same surveyed taxonomic group. For example, one can wonder whether sampling butterfly fauna according to the commonly implemented Pollard walk consistently ensure a similar recording efficiency (i.e. similar sampling completeness) according to the different butterfly families. To address this issue and quantify the possible unevenness of sampling completeness between five main butterfly families, we consider a Pollard walk butterfly survey of tropical butterfly fauna, carried out along Sankosh River (Bhutan) by Arun P. Singh. Reasonably accurate estimates of the true total species richness and the corresponding sampling completeness were derived, for each butterfly family, by implementing the recently developed procedure of least-biased extrapolation of the species accumulation curve. Whereby, a reliable evaluation of the level of sampling completeness is obtained for each butterfly family. For the inventory under consideration, a significant scatter of sampling completeness levels between the five families is highlighted: sampling completeness levels range from 65% for Lycaenidae to quasi exhaustivity for Papilionidae, with intermediate levels for the other three families. 2 These findings revealed that Pollard walk survey may lead to appreciable differences of sampling completeness level among the different butterfly families. Besides, this study provides a reliable estimate of the total species richness of butterfly fauna in the surveyed ecosystem, amounting to no less than 280 species concentrated in a rather reduced area along Sankosh River.

Mapping the space of genomic signatures.

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to k (herein k = 9) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and that the sequence most different from it in this dataset belongs to a cucumber.

The global distribution of diet breadth in insect herbivores

Understanding variation in resource specialization is important for progress on issues that include coevolution, community assembly, ecosystem processes, and the latitudinal gradient of species richness. Herbivorous insects are useful models for studying resource specialization, and the interaction between plants and herbivorous insects is one of the most common and consequential ecological associations on the planet. However, uncertainty persists regarding fundamental features of herbivore diet breadth, including its relationship to latitude and plant species richness. Here, we use a global dataset to investigate host range for over 7,500 insect herbivore species covering a wide taxonomic breadth and interacting with more than 2,000 species of plants in 165 families. We ask whether relatively specialized and generalized herbivores represent a dichotomy rather than a continuum from few to many host families and species attacked and whether diet breadth changes with increasing plant species richness toward the tropics. Across geographic regions and taxonomic subsets of the data, we find that the distribution of diet breadth is fit well by a discrete, truncated Pareto power law characterized by the predominance of specialized herbivores and a long, thin tail of more generalized species. Both the taxonomic and phylogenetic distributions of diet breadth shift globally with latitude, consistent with a higher frequency of specialized insects in tropical regions. We also find that more diverse lineages of plants support assemblages of relatively more specialized herbivores and that the global distribution of plant diversity contributes to but does not fully explain the latitudinal gradient in insect herbivore specialization.

NEW DIRECTIONS IN VERTEBRATE PALEONTOLOGICAL RESEARCH IN THE TRANSANTARCTIC MOUNTAINS, ANTARCTICA

The emphasis on record setting during the Heroic Age of Antarctic exploration meant that the scientific accomplishments of these expeditions often went overlooked (Larson, 2012). Many people know the story of the ill-fated (and second-place) return of Robert Falcon Scott from the South Pole, but few people are aware that 45 kg of Permian Glossopteris fossils were found with him and his deceased colleagues. Refusal to jettison the material suggests their recognition of its importance for understanding past life on the frozen continent. Since that time, great advances have been made in understanding the ancient life and environments of Antarctica. Here, I review some of these developments in the context of recent vertebrate paleontological research in the Transantarctic Mountains. In 1967 the first terrestrial vertebrate from the central Transantarctic Mountains, a small amphibian jaw, was discovered in Lower Triassic rocks at Graphite Peak (Barrett et al., 1968). Subsequent work has yielded three distinct Mesozoic faunas from the region. Early Triassic vertebrates have been collected at numerous localities in the lower Fremouw Formation around the Beardmore and Shackleton glaciers (Barrett et al., 1968). The Beardmore Glacier region has also produced an early Middle Triassic assemblage at two localities in the upper Fremouw Formation (Hammer et al., 1987; Sidor et al., 2007), and an Early Jurassic assemblage from the Hanson Formation on Mt. Kirkpatrick (Hammer and Hickerson, 1994). Early discoveries from the lower Fremouw Formation (Fig. 1) prompted comparisons to similar faunas from the Karoo Basin of South Africa, and the presence of taxa such as Lystrosaurus provided compelling support for the nascent theory of plate tectonics (Elliot et al., 1970). Antarctic faunas were often considered to represent taxonomic subsets of those found in the Karoo Basin, …

Bergmann′s rule in mammals: a cross‐species interspecific pattern

Although Bergmann’s rule – stating that among closely related species, the bigger ones will inhabit the colder climates/higher latitudes – was formulated for inter‐specific comparisons, most analyses that tested this pattern in mammals were on an intra‐specific level. To date, no large‐scale taxonomy‐driven cross‐species evaluation of the pattern predicted by Bergmann exists. Here we show, in a dataset comprising 3561 mammal species from 26 orders, that while there is no significant correlation between latitude and body mass using conventional methods, this correlation is highly significant when the phylogenetic structure of the dataset is accounted for, thus supporting Bergmann’s claim that the rule only applies to closely related species. Analyses of different subsets indicate that the Bergmann’s rule is evident across a variety of latitude ranges. In many taxonomic subsets, when analysed alone, there is no significant correlation between body mass and latitude. In combination with both the significant relationship in the overall dataset and with results of intra‐specific analyses from the literature, this suggests that Bergmann’s rule describes a fundamental principle within mammals, but that its expression has been modified by a variety of factors during mammalian diversification yet to be resolved.

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present-day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher-level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family-level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher-level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo-Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo-Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology-based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family- and subfamily-level molecular clades [previously identified as XVII−XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine-shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle-shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well-developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67-species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower-level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166, 465–529.

Latitudinal variation in morphological traits of the genus Pinus and its relation to environmental and phylogenetic signals

Background: Broad-scale analysis of interspecific trait variation is a fundamental approach in comparative ecology to investigate general species–environment relationships, but inferences from environmental and phylogenetic signals are still controversially discussed. Aims: The aim of this study was to globally analyse the genus Pinus and the interspecific variation of morphological traits with latitude as a surrogate of broad-scale environmental changes, and to compare latitudinal trait correlations with biogeographic, environmental and phylogenetic signals in trait variation. Methods: Based on native range maps of 103 Pinus species, the latitudinal correlations of nine morphological traits, including needle characters, cone length and tree height were calculated. Principal component analysis was used to explore trait covariation. Variation partitioning was applied to disentangle environmental and phylogenetic signals in trait variation. Results: Strong latitudinal correlations were detected for traits, such as needle length:width ratio or needle longevity, with similar trends for different taxonomic species subsets and geographic regions. Strong latitudinal correlations were related to a decrease in the pure phylogenetic signal and to an increase in the phylogenetically structured environmental variation (PSEV), whereas the pure environmental signal was almost negligible. Conclusions: Besides a ranking of traits that differ in environmental and phylogenetic signals, our results showed a general relationship between increasing latitudinal trait correlation and an increase in PSEV, which indicates phylogenetic niche conservatism. Thus, for the investigated morphological traits of the genus Pinus both environmental and phylogenetic signals are directly linked by PSEV to broad-scale spatial patterns in trait variation.

Global analysis of thermal tolerance and latitude in ectotherms.

A tenet of macroecology is that physiological processes of organisms are linked to large-scale geographical patterns in environmental conditions. Species at higher latitudes experience greater seasonal temperature variation and are consequently predicted to withstand greater temperature extremes. We tested for relationships between breadths of thermal tolerance in ectothermic animals and the latitude of specimen location using all available data, while accounting for habitat, hemisphere, methodological differences and taxonomic affinity. We found that thermal tolerance breadths generally increase with latitude, and do so at a greater rate in the Northern Hemisphere. In terrestrial ectotherms, upper thermal limits vary little while lower thermal limits decrease with latitude. By contrast, marine species display a coherent poleward decrease in both upper and lower thermal limits. Our findings provide comprehensive global support for hypotheses generated from studies at smaller taxonomic subsets and geographical scales. Our results further indicate differences between terrestrial and marine ectotherms in how thermal physiology varies with latitude that may relate to the degree of temperature variability experienced on land and in the ocean.

Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer events

To investigate the evolutionary origins of proteins encoded by the Poxviridae family of viruses, we examined all poxvirus protein coding genes using a method of characterizing and visualizing the similarity between these proteins and taxonomic subsets of proteins in GenBank. Our analysis divides poxvirus proteins into categories based on their relative degree of similarity to two different taxonomic subsets of proteins such as all eukaryote vs. all virus (except poxvirus) proteins. As an example, this allows us to identify, based on high similarity to only eukaryote proteins, poxvirus proteins that may have been obtained by horizontal transfer from their hosts. Although this method alone does not definitively prove horizontal gene transfer, it allows us to provide an assessment of the possibility of horizontal gene transfer for every poxvirus protein. Potential candidates can then be individually studied in more detail during subsequent investigation. Results of our analysis demonstrate that in general, proteins encoded by members of the subfamily Chordopoxvirinae exhibit greater similarity to eukaryote proteins than to proteins of other virus families. In addition, our results reiterate the important role played by host gene capture in poxvirus evolution; highlight the functions of many genes poxviruses share with their hosts; and illustrate which host-like genes are present uniquely in poxviruses and which are also present in other virus families.

Estimating species diversity in a guild of Neotropical skippers (Lepidoptera: Hesperiidae) with artificial lures is a sampling problem

Abstract. Butterflies are frequently used to investigate Neotropical diversity, but the family Hesperiidae is almost never employed as a focal group. Sampling Hesperiidae with artificial lures has been used to assist in species richness estimates of males that use bird droppings as a resource, but its effectiveness for estimating total hesperiid site diversity is unknown. This study characterises species richness and abundance in a diverse assemblage of Hesperiidae sampled at artificial lures. Sampled and estimated richness among taxonomic subsets were compared to the known site richness. These comparisons are used to assess artificial lures as a method for sampling total richness of Hesperiidae. We tested for potential differences in attraction in lures placed with and without the presence of army ant swarms. Five years of intermittent sampling with lures recovered 65% of the known Hesperiidae species richness at the study site. We found the subfamilies were differentially attracted to lures, where 86% of Eudaminae, 56% of Hesperiinae and 55% of Pyrginae species known from the site were recovered by lures. Species accumulation and taxonomic diversity differed among lures placed alone, and those placed in the presence of army ants. Our results suggest that sampling with artificial lures can be used to estimate diversity of Neotropical Eudaminae and a few tribes of Hesperiinae at some sites. Available evidence indicates that Hesperiidae feeding at bird droppings is predominately a Neotropical phenomenon. Finally, we conclude that estimating diversity in Neotropical Hesperiidae will require long‐term studies that use multiple sampling techniques.

RrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.