For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternativemore »
A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism
The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods more »
- Award ID(s):
- 2010898
- Publication Date:
- NSF-PAR ID:
- 10308663
- Journal Name:
- PeerJ
- Volume:
- 9
- ISSN:
- 2167-8359
- Sponsoring Org:
- National Science Foundation
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Abstract Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the anchored hybrid enrichment markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, inmore »
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Stomatopoda, commonly known as mantis shrimps, are notable for their enlarged second maxillipeds encompassing the raptorial claw. The form of the claw can be used to divide them into two basic groups: smashers and spearers. Previous phylogenetic studies of Stomatopoda have focused on morphology or a few genes, though there have been whole mitochondrial genomes published for 15 members of Stomatopoda. However, the sampling has been somewhat limited with key taxa not included. Here, nine additional stomatopod mitochondrial genomes were generated and combined with the other available mitogenomes for a phylogenetic analysis. We used the 13 protein coding genes, as well as 12S rRNA, 16S rRNA genes, and included nuclear 18S rRNA gene sequences. Different rooting options were used for the analyses: (1) single and multiple outgroups from various eumalocostracan relatives and (2) a stomatopod-only dataset, with Hemisquilla californiensis used to root the topologies, based on the current hypothesis that Hemisquilla is the sister group to the rest of Stomatopoda. The eumalocostracan-rooted analyses all showed H. californiensis nested within Stomatopoda, raising doubts as to previous hypotheses as to its placement. Allowing for the rooting difference, the H. californiensis outgroup datasets had the same tree topology as the eumalocostracan outgroup datasetsmore »
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Pupko, Tal (Ed.)Abstract Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplicationsmore »
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Abstract Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updatedmore »
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Accepted Manuscript1.0
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- https://doi.org/10.7717/peerj.12034
