Site specific rates of mitochondrial genomes and the phylogeny of eutheria

BACKGROUND: Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3(rd )codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand). We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs. RESULTS: Mitochondrial genomic data for 78 eutherian mammals, 8 metatherians, and 3 monotremes were analyzed with a Bayesian analysis and our site specific rate model. The resultant phylogeny revealed strong support for most nodes and was highly congruent with more recent phylogenies based on nuclear DNA sequences. In addition, many of the conflicting relationships observed by earlier mitochondrial-based analyses were resolved without need for the exclusion of large subsets of the data. CONCLUSION: Rather than exclusion of data to minimize presumed noise associated with non-protein encoding genes in the mitochondrial genome, our results indicate that selection of an appropriate model that accommodates rate heterogeneity across data partitions and proper treatment of RNA genes can result in a mitochondrial genome-based phylogeny of eutherian mammals that is reasonably congruent with recent phylogenies derived from nuclear genes

Associating Larvae and Adults of Chinese Hydropsychidae Caddiflies (Insecta:Trichoptera) using DNA Sequences

The utility of hydropsychid (Trichoptera:Hydropsychidae) caddisfly larvae for freshwater biomonitoring has been demonstrated, but the major impediment to its implementation has been the lack of species-level larval descriptions and illustrations. A rapid and reliable molecular protocol that also uses morphology is proposed because conventional approaches to associating undescribed larvae with adults have been slow and problematic. Male adults were identified before DNA sequence analyses were used. These identifications established morphospecies boundaries that were mapped on phylograms constructed from 2 independent gene fragments: mitochondrial cytochrome c oxidase subunit I (COI) and large subunit (28S) nuclear ribosomal DNA expansion fragment D2 (D2). Species boundaries were confirmed if they were monophyletic on both molecular phylograms. Larval associations were made with reference to the phylogenetic analyses under 2 criteria: sequence identity across both genes or nested placement within a reference species boundary. A total of 133 individuals belonging to Chinese Hydropsyche sensu lato group (including Hydropsyche [Hydropsyche], Hydropsyche [Occutanspsyche], Ceratopsyche, Mexipsyche, Hydatomanicus, and Herbertorossia) were included in our study to test the new protocol. D2 sequences (all individuals) and COI sequences (101 individuals) were obtained, and 2 independent phylograms were constructed using neighbor joining. Both fragments provided enough nucleotide changes to differentiate independently most Hydropsyche sensu lato species, with ambiguity in only a few species that eventually could be resolved with additional sequences and specimens. COI diverges significantly within some species, suggesting a need for caution when applying typical genetic divergence thresholds in species diagnoses. The study enabled us to establish a procedure for delimiting species boundaries and associating larvae and adults using DNA sequences and morphological evidence. Ideal sampling strategies for larval–adult association are suggested. Associating larvae and adults of hydropsychids using DNA sequences appears to be promising in terms of both reliability and speed

Defining the Genus Hydropsyche (Trichoptera:Hydropsychidae) Based on DNA and Morphological Evidence

In this paper, we review the history of Hydropsychinae genus-level classification and nomenclature and present new molecular evidence from mitochondrial cytochrome c oxidase subunit I (COI) and nuclear large subunit ribosomal ribonucleic acid (28S) markers supporting the monophyly of the genus Hydropsyche. Both molecular and morphological characters support a broad conservative definition of Hydropsyche. Caledopsyche, Hydatomanicus, and Occutanspsyche are synonymized with Hydropsyche. The following species groups are established: Hydropsyche bronta Group (generally corresponding with Ceratopsyche and Hydropsyche morosa and newae Groups), Hydropsyche colonica Group (generally corresponding with Orthopsyche), Hydropsyche instabilis Group (generally corresponding with Hydropsyche s.s.), and Hydropsyche naumanni Group (generally corresponding with Occutanspsyche). Molecular data recovered Hydromanicus as paraphyletic, and Cheumatopsyche and Potamyia as sister taxa. The genus names Plectropsyche and Streptopsyche are reinstated

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

<p>Abstract</p> <p>Background</p> <p>Failure to account for covariation patterns in helical regions of ribosomal RNA (rRNA) genes has the potential to misdirect the estimation of the phylogenetic signal of the data. Furthermore, the extremes of length variation among taxa, combined with regional substitution rate variation can mislead the alignment of rRNA sequences and thus distort subsequent tree reconstructions. However, recent developments in phylogenetic methodology now allow a comprehensive integration of secondary structures in alignment and tree reconstruction analyses based on rRNA sequences, which has been shown to correct some of these problems. Here, we explore the potentials of RNA substitution models and the interactions of specific model setups with the inherent pattern of covariation in rRNA stems and substitution rate variation among loop regions.</p> <p>Results</p> <p>We found an explicit impact of RNA substitution models on tree reconstruction analyses. The application of specific RNA models in tree reconstructions is hampered by interaction between the appropriate modelling of covarying sites in stem regions, and excessive homoplasy in some loop regions. RNA models often failed to recover reasonable trees when single-stranded regions are excessively homoplastic, because these regions contribute a greater proportion of the data when covarying sites are essentially downweighted. In this context, the RNA6A model outperformed all other models, including the more parametrized RNA7 and RNA16 models.</p> <p>Conclusions</p> <p>Our results depict a trade-off between increased accuracy in estimation of interdependencies in helical regions with the risk of magnifying positions lacking phylogenetic signal. We can therefore conclude that caution is warranted when applying rRNA covariation models, and suggest that loop regions be independently screened for phylogenetic signal, and eliminated when they are indistinguishable from random noise. In addition to covariation and homoplasy, other factors, like non-stationarity of substitution rates and base compositional heterogeneity, can disrupt the signal of ribosomal RNA data. All these factors dictate sophisticated estimation of evolutionary pattern in rRNA data, just as other molecular data require similarly complicated (but different) corrections.</p

The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life’s species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’