Find research datasets worth reusing

opencc-by-4.0Dec 2009View details →

Figure 6 in Recent advances in phylogeny and taxonomy of Near and Middle Eastern Vipers – an update

Figure 6. Montivipera wagneri

opencc-by-4.0Dec 2009View details →

Figure 7 in Recent advances in phylogeny and taxonomy of Near and Middle Eastern Vipers – an update

Figure 7. Macrovipera lebetina obtusa

opencc-by-4.0Jun 2010View details →

Figure 6 in Revision and phylogeny of the Caribbean weevil genus Apotomoderes Dejean, 1834 (Coleoptera, Curculionidae, Entiminae)

Figure 6. Terminalia of A. lateralis, female: A sternum VIII B coxites and styli C spermatheca.

opencc-by-3.0Mar 2017View details →

Fig. 1. Part 2 in Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea), with implications for taxonomy and evolutionary scenarios

Fig. 1. Part 2. See legend on preceding page.

opencc-by-3.0Feb 2017View details →

Appendix 1 in Biodiversity and phylogeny of Ammotheidae (Arthropoda: Pycnogonida)

Appendix 1. CO1 and 18S sequences used for this study, including GenBank accession numbers.

opencc-by-3.0Dec 2015View details →

Fig. 5 in Revision, phylogeny, and microhabitat shifts in the Southeast Asian spider genus Aetana (Araneae, Pholcidae)

Fig. 5. Known distributions of the Aetana kinabalu (Borneo) and A. omayan (Philippines) groups.

Fig. 19 in Uncovering hidden diversity: phylogeny and taxonomy of Physoderinae (Reduviidae, Heteroptera), with emphasis on Physoderes Westwood in the Oriental and Australasian regions

Fig. 19. Dorsal view of the phallus in species of Physoderes Westwood, 1845 (partial).

Fig. 20 in Uncovering hidden diversity: phylogeny and taxonomy of Physoderinae (Reduviidae, Heteroptera), with emphasis on Physoderes Westwood in the Oriental and Australasian regions

Fig. 20. Distribution map for species of Physoderes Westwood, 1845 (partial).

Fig. 12 in Uncovering hidden diversity: phylogeny and taxonomy of Physoderinae (Reduviidae, Heteroptera), with emphasis on Physoderes Westwood in the Oriental and Australasian regions

Fig. 12. Distribution map for species of Macrophysoderes gen. nov.

Fig. 5 in Uncovering hidden diversity: phylogeny and taxonomy of Physoderinae (Reduviidae, Heteroptera), with emphasis on Physoderes Westwood in the Oriental and Australasian regions

Fig. 5. Ventral habitus images for species of Breviphysoderes gen. nov. Scale bars = 2 mm.

Fig. 6 in Uncovering hidden diversity: phylogeny and taxonomy of Physoderinae (Reduviidae, Heteroptera), with emphasis on Physoderes Westwood in the Oriental and Australasian regions

Fig. 6. Distribution map for species of Breviphysoderes gen. nov.

openother-openJul 2020View details →

LAR phylogeny for Güngör et al. 2020: The complete analysis and dataset

Fixing this repository as version 1.00.00 while the corresponding revised manuscript was submitted to new phytologist.

opencc-zeroJul 2020View details →

A Hirnantian holdover from the late Ordovician mass extinction: phylogeny and biogeography of a new Anthracocrinid crinoid from Estonia

Relatively few Hirnantian (Late Ordovician) crinoids are known, and none have been previously described from the palaeocontinent of Baltica. This has impaired our ability to understand patterns of extinction and biogeographic dispersal surrounding the Late Ordovician mass extinction, which triggered a major turnover in crinoid faunas. Here, we describe Tallinnicrinus toomae gen. et sp. nov., an anthracocrinid diplobathrid from the Hirnantian of northern Estonia. Tallinnicrinus is the youngest member of the Anthracocrinidae and the first representative of the family to occur in Baltica. Morphologically, Tallinnicrinus is unusual in that the radial and basal plates are in a single circlet of ten plates, similar to the anthracocrinid Rheocrinus Haugh, 1979 from the Katian of Laurentia. Phylogenetic analysis further confirms a close relationship between Tallinnicrinus and Laurentian anthracocrinids, suggesting biogeographic dispersal of the lineage from Laurentia to Baltica during the late Katian or early Hirnantian. The occurrence of this new taxon establishes that the family Anthracocrinidae survived the first pulse of the Late Ordovician mass extinction. However, the lineage remained a "dead clade walking" as it failed to diversify in the wake of the end-Katian extinction and ultimately went extinct itself by the end of the Ordovician.

opencc-zeroJun 2020View details →

Data from: Bacterial phylogeny predicts volatile organic compound composition and olfactory response of an aphid parasitoid

There is increasing evidence that microorganisms emit a wide range of volatile compounds (mVOCs, microbial volatile organic compounds) that act as insect semiochemicals, and therefore play an important role in insect behaviour. Although it is generally believed that phylogenetically closely related microbes tend to have similar phenotypic characteristics and therefore may elicit similar responses in insects, currently little is known about whether the evolutionary history and phylogenetic relationships among microorganisms have an impact on insect-microbe interactions. In this study, we tested the hypothesis that phylogenetic relationships among 40 Bacillus strains isolated from diverse environmental sources predicted mVOC composition and the olfactory response of the generalist aphid parasitoid Aphidius colemani. Results revealed that phylogenetically closely related Bacillus strains emitted similar blends of mVOCs and elicited a comparable olfactory response of A. colemani in Y-tube olfactometer bioassays, varying between attraction and repellence. Analysis of the chemical composition of the mVOC blends showed that all Bacillus strains produced a highly similar set of volatiles, but often in different concentrations and ratios. Benzaldehyde was produced in relatively high concentrations by strains that repel A. colemani, while attractive mVOC blends contained relatively higher amounts of acetoin, 2,3-butanediol, 2,3-butanedione, eucalyptol and isoamylamine. Overall, these results indicate that bacterial phylogeny had a strong impact on mVOC compositions and as a result on the olfactory responses of insects.

opencc-zeroJul 2020View details →

Data from: Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari

High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455–552 Mya), while the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.

Data from: Assessing support for Blaberoidea phylogeny suggests optimal locus

Phylogenomics seeks to use next-generation data to robustly infer an organism's evolutionary history. Yet, the practical caveats of phylogenomics motivates investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in Blaberoidea. We examine locus substitution rate, saturation, evolutionary divergence, rate heterogeneity, stabilizing selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species. Loci with high substitution rate, low saturation, low sequence distance, low rate heterogeneity, and strong stabilizing selection derive more support for phylogenetic relationships. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori. We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction, improved statistical support, and potential 4-6x improvements to computation time. Supported by phylogenetic and morphological evidence, we erect three newly named clades (Anallactinae Evangelista & Wipfler subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, & Béthoux, and Hemithyrsocerini Evangelista tribe nov.) and propose other taxonomic modifications. The diagnosis of Pseudophyllodromiidae Grandcolas, 1996 is modified to accommodate Anallactinae and Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel morphological characters.

Shared geographic histories and dispersal contribute to congruent phylogenies between amphipods and their microsporidian parasites at regional and global scales

In parasites that strongly rely on a host for dispersal, geographic barriers that act on the host will simultaneously influence parasite distribution as well. If their association persists over macroevolutionary time it may result in congruent phylogenetic and phylogeographic patterns due to shared geographic histories. Here, we investigated the level of congruent evolutionary history at a regional and global scale in a highly specialised parasite taxon infecting hosts with limited dispersal abilities: the microsporidians Dictyocoela spp. and their amphipod hosts. Dictyocoela can be transmitted both vertically and horizontally and is the most common microsporidian genus occurring in amphipods in Eurasia. However, little is known about its distribution elsewhere. We started by conducting molecular screening to detect microsporidian parasites in endemic amphipod species in New Zealand; based on phylogenetic analyses, we identified nine species-level microsporidian taxa including six belonging to Dictyocoela. With a distance-based cophylogenetic analysis at the regional scale, we identified overall congruent phylogenies between Paracalliope, the most common New Zealand freshwater amphipod taxon, and their Dictyocoela parasites. Also, hosts and parasites showed similar phylogeographic patterns suggesting shared biogeographic histories. Similarly, at a global scale, phylogenies of amphipod hosts and their Dictyocoela parasites showed broadly congruent phylogenies. The observed patterns may have resulted from covicariance and/or codispersal, suggesting that the intimate association between amphipods and Dictyocoela may have persisted over macroevolutionary time. We highlight that shared biogeographic histories could play a role in the codiversification of hosts and parasites at a macroevolutionary scale.

opencc-by-4.0Sep 2015View details →

Figure 5 in A new species and the phylogeny of the South American genus Gromphas Brullé, 1837 (Coleoptera: Scarabaeidae: Scarabaeinae: Phanaeini)

Figure 5. Updated distribution of the six species of Gromphas.

Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals

Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage <a href="http://www.iqtree.org/doc/Rootstrap">http://www.iqtree.org/doc/Rootstrap</a>. In addition, a python script is available at <a href="https://github.com/suhanaser/Rootstrap">https://github.com/suhanaser/Rootstrap</a>

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior onBayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effectof the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyze datasets containing both populations and species variation when its computational-efficiency is needed.