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Mol Phylogenet Evol [journal]
- Phylogenetic disassembly of species boundaries in a widespread group of Australian skinks (Scincidae: Ctenotus). [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Apr 11.
Scincid lizards in the genus Ctenotus represent one of Australia's most species-rich vertebrate clades, with more than 100 recognized species. Formal diagnoses of many species have relied on qualitative assessments of adult color pattern, but the validity of many such species has not been tested in a phylogenetic framework. We used mitochondrial and nuclear DNA to perform the first phylogenetic analysis of species in the Ctenotus inornatus group, a complex of at least 11 nominal forms that are distributed widely across the Australian continent. Mitochondrial and nuclear gene phylogenies support the presence of multiple species in the group, but these clades largely fail to match species boundaries as currently defined. Multivariate analyses of color pattern indicate that extreme intraspecific morphological variation in this character has created a significant impediment to understanding taxonomic diversity in the group. Our results suggest that nearly all species in the C. inornatus group require substantial taxonomic revision, and several geographically widespread forms ("C. saxatilis" and "C. robustus") appear to be polyphyletic taxa drawn from phenotypically similar but genetically distinct lineages. We describe one new species and provide redescriptions for three additional species. We synonymize names applied to a number of genetically incoherent or otherwise poorly-defined forms. The results of our study highlight an acute need for population genetic studies of species boundaries in Australian skinks, many of which are recognized by morphological traits that vary greatly within and between populations.
- Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Apr 11.
Myriapods had been considered closely allied to hexapods (insects and relatives). However, analyses of molecular sequence data have consistently placed Myriapoda either as a sister group of Pancrustacea, comprising crustaceans and hexapods, and thereby supporting the monophyly of Mandibulata, or retrieved Myriapoda as a sister group of Chelicerata (spiders, ticks, mites and allies). In addition, the relationships among the four myriapod groups (Pauropoda, Symphyla, Diplopoda, Chilopoda) are unclear. To resolve the phylogeny of myriapods and their relationship to other main arthropod groups, we collected transcriptome data from the symphylan Symphylella vulgaris, the centipedes Lithobius forficatus and Scolopendra dehaani, and the millipedes Polyxenus lagurus, Glomeris pustulata and Polydesmus angustus by 454 sequencing. We concatenated a multiple sequence alignment that contained 1,550 orthologous single copy genes (1,109,847 amino acid positions) from 55 euarthropod and 14 outgroup taxa. The final selected alignment included 181 genes and 37,425 amino acid positions from 55 taxa, with eight myriapods and 33 other euarthropods. Bayesian analyses robustly recovered monophyletic Mandibulata, Pancrustacea and Myriapoda. Most analyses support a sister group relationship of Symphyla in respect to a clade comprising Chilopoda and Diplopoda. Inclusion of additional sequence data from nine myriapod species resulted in an alignment with poor data density, but broader taxon average. With this dataset we inferred Diplopoda + Pauropoda as closest relatives (i.e., Dignatha) and recovered monophyletic Helminthomorpha. Molecular clock calculations suggest an early Cambrian emergence of Myriapoda ∼513 million years ago and a late Cambrian divergence of myriapod classes. This implies a marine origin of the myriapods and independent terrestrialization events during myriapod evolution.
- Evolution of the Viral Hemorrhagic Septicemia Virus: Divergence, Selection and Origin. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Apr 10.
Viral hemorrhagic septicemia virus (VHSV) is an economically significant rhabdovirus that affects an increasing number of freshwater and marine fish species. Extensive studies have been conducted on the molecular epizootiology, genetic diversity, and phylogeny of VHSV. However, there are discrepancies between the reported estimates of the nucleotide substitution rate for the G gene and the divergence times for the genotypes. Herein, Bayesian coalescent analyses were conducted to the time-stamped entire coding sequences of the six VHSV genes. Rate estimates based on the G gene indicated that the marine genotypes/subtypes might not all evolve slower than their major European freshwater counterpart. Age calculations on the six genes revealed that the first bifurcation event of the analyzed isolates might have taken place within the last 300 years, which was much younger than previously thought. Selection analyses suggested that two codons of the G gene might be positively selected. Surveys of codon usage bias showed that the P, M and NV genes exhibited genotype-specific variations. Furthermore, we proposed that VHSV originated from the Pacific Northwest of North America.
- Evolution of the stapeliads (Apocynaceae-Asclepiadoideae) - repeated major radiation across Africa in an Old World group. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Apr 8.
The stapeliads of the Ceropegieae (Apocynaceae-Asclepiadoideae), are approximately 340 species of stem-succulents placed in around 30 genera, found in semi-arid parts of the Old World. Here we sampled 192 species (i.e. nearly two thirds of the total) from across the full geographic range of the group and analysed data from the two nuclear regions (nuclear ribosomal ITS and ncpGS) and five plastid regions (psbA-trnH intergenic spacer, rps16 intron, trnL-trnF intergenic spacer, trnS-trnG intergenic region and the non-coding rpl32-trnL region). We find that the stapeliads radiated first in the northern hemisphere from Africa to southern Europe and Myanmar. This radiation subtends a grade of minor clades in the south-western corner of the African continent. These were followed by a single clade containing major radiation back across Africa from South Africa to tropical Arabia (but no further east than Dhofar, Oman), which includes also a single early spread into Madagascar. We establish the monophyly of many of the genera, such as Echidnopsis Hook.f., Hoodia Hook., Huernia R. Br., Piaranthus R. Br., Rhytidocaulon P.R.O. Bally and Tridentea Haw., but find that Duvalia Haw., Orbea Haw., Stapelia L. and Tromotriche Haw. are polyphyletic. We show that in certain vegetative features, there is broad cohesion across clades. Florally, on the other hand, the stapeliads exhibit considerable plasticity and we are able to show that very differently shaped flowers as well as large and small flowers evolved repeatedly among closely related species.
- Two mitochondrial genomes from the families Bethylidae and Mutillidae: Independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Apr 1.
In animal mitochondrial genomes, gene arrangements are usually conserved across major lineages but might be rearranged within derived groups, and might provide valuable phylogenetic characters. Here, we sequenced the mitochondrial genomes of Cephalonomia gallicola (Chrysidoidea: Bethylidae) and Radoszkowskius oculata (Vespoidea: Mutillidae). In Cephalonomia at least 11 tRNA and 2 protein-coding genes were rearranged, which is the first report of protein-coding gene rearrangements in the Aculeata. In the Hymenoptera, three types of protein-coding gene rearrangement events occur, i.e. reversal, transposition and reverse transposition. Venturia (Ichneumonidae) had the greatest number of common intervals with the ancestral gene arrangement pattern, whereas Philotrypesis (Agaonidae) had the fewest. The most similar rearrangement patterns are shared between Nasonia (Pteromalidae) and Philotrypesis, whereas the most differentiated rearrangements occur between Cotesia (Braconidae) and Philotrypesis. It is clear that protein-coding gene rearrangements in the Hymenoptera are evolutionarily independent across the major lineages but are conserved within groups such as the Chalcidoidea. Phylogenetic analyses supported the sister-group relationship of Orrussoidea and Apocrita, Ichneumonoidea and Aculeata, Vespidae and Apoidea, and the paraphyly of Vespoidea. The Evaniomorpha and phylogenetic relationships within Aculeata remain controversial, with discrepancy between analyses using protein-coding and RNA genes.
- Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Apr 2.
A goal of modern taxonomy is to develop classifications that reflect current phylogenetic relationships and are as stable as possible given the inherent uncertainties in much of the tree of life. Here, we provide an in-depth phylogenetic analysis, based on 14 nuclear loci comprising 10,305 base pairs of aligned sequence data from all but two species of the turtle family Kinosternidae, to determine whether recent proposed changes to the group's classification are justified and necessary. We conclude that those proposed changes were based on (1) mtDNA gene tree anomalies, (2) preliminary analyses that do not fully capture the breadth of geographic variation necessary to motivate taxonomic changes, and (3) changes in rank that are not motivated by non-monophyletic groups. Our recommendation, for this and other similar cases, is that taxonomic changes be made only when phylogenetic results that are statistically well-supported and corroborated by multiple independent lines of genetic evidence indicate that non-monophyletic groups are currently recognized and need to be corrected. We hope that other members of the phylogenetics community will join us in proposing taxonomic changes only when the strongest phylogenetic data demand such changes, and in so doing that we can move toward stable, phylogenetically informed classifications of lasting value.
- Topography as a driver of cryptic speciation in the high-elevation cape sedge Tetraria triangularis (Boeck.) C. B. Clarke (Cyperaceae: Schoeneae). [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Apr 2.
Since some speciation mechanisms are more likely to generate morphological disparity than others, the general failure of vascular plant taxonomists to recognize cryptic diversity may bias perceptions about speciation process in plants. While the exceptional floristic richness of the South African Cape has largely been attributed to adaptive divergence ('ecological' speciation), a combination of climatic dynamism and complex topography has likely provided ample opportunities for 'non-ecological' vicariant speciation, a mechanism which is perhaps more likely to produce cryptic species. We explore the role of topography as a driver of 'non-ecological' speciation in the high-elevation sedge Tetraria triangularis. Within this species, molecular and morphological data reveal five cryptic or semi-cryptic lineages of Miocene-Pliocene age which qualify as evolutionary species. At least three of these maintain their distinctness in sites of sympatry, identifying them as biological species. Negligible range overlap, and the identification of topography as a significant predictor of range turnover, identifies speciation as allopatric and a result of impeded gene flow across low-elevation topographic features. Weak morphological and ecological divergence implies a limited role for adaptive divergence in powering speciation, with character displacement in sympatry possibly arising as a consequence of interspecific competition. Although we cannot exclude a role for disruptive selection in species differentiation, we identify isolation of populations on topographically separated mountains as the principal motor of speciation. We suggest that the importance of topography in the genesis of Cape floristic diversity has been inadequately acknowledged.
- Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Mar 28.:202-210.
The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus Trebouxia, the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus Lasallia pustulata. We further investigated whether putative species of Trebouxia found in L. pustulata are shared with other lichen-forming fungi. We found that L. pustulata is associated with at least five species of Trebouxia and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative Trebouxia species is found exclusively in association with L. pustulata and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus Trebouxia.
- Phylogenetic analysis of mitochondrial genome sequences indicates that the cattle tick, Rhipicephalus (Boophilus) microplus, contains a cryptic species. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Mar 28.
Cattle ticks of the subgenus Rhipicephalus (Boophilus) are major agricultural pests worldwide, causing billions of dollars in losses annually. Rhipicephalus (Boophilus) annulatus and R. microplus are the most well-known and widespread species, and a third species, R. australis, was recently reinstated for 'R. microplus' from Australia and parts of Southeast Asia. We use mitochondrial genome sequences to address the phylogenetic relationships among the species of the subgenus Boophilus. We sequenced the complete or partial mitochondrial genomes of R. annulatus, R. australis, R. kohlsi, R. geigyi, and of three geographically disparate specimens of R. microplus from Brazil, Cambodia and China. Phylogenetic analyses of mitochondrial genomes, as well as cox1 and 16S rRNA sequences, reveals a species complex of R. annulatus, R. australis, and two clades of R. microplus, which we call the R. microplus complex. We show that cattle ticks morphologically identified as R. microplus from Southern China and Northern India (R. microplus clade B) are more closely related to R. annulatus than other specimens of R. microplus s.s. from Asia, South America and Africa (R. microplus clade A). Our analysis suggests that ticks reported as R. microplus from Southern China and Northern India are a cryptic species. This highlights the need for further molecular, morphological and crossbreeding studies of the R. microplus complex, with emphasis on specimens from China and India. We found that cox1 and, to a lesser extent, 16S rRNA were far more successful in resolving the phylogenetic relationships within the R. microplus complex than 12S rRNA or the nuclear marker ITS2. We suggest that future molecular studies of the R. microplus complex should focus on cox1, supplemented by 16S rRNA, and develop nuclear markers alternative to ITS2 to complement the mitochondrial data.
- Multilocus approach to clarify species status and the divergence history of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex. [JOURNAL ARTICLE]
- Mol Phylogenet Evol 2014 Mar 29.:172-180.
The sweet potato whitefly, Bemisia tabaci, is a highly differentiated species complex. Despite consisting of several morphologically indistinguishable entities and frequent invasions on all continents with important associated economic losses, the phylogenetic relationships, species status, and evolutionary history of this species complex is still debated. We sequenced and analyzed one mitochondrial and three single-copy nuclear genes from 9 of the 12 genetic groups of B. tabaci and 5 closely related species. Bayesian species delimitation was applied to investigate the speciation events of B. tabaci. The species statuses of the different genetic groups were strongly supported under different prior settings and phylogenetic scenarios. Divergence histories were estimated by a multispecies coalescence approach implemented in (*)BEAST. Based on mitochondrial locus, B. tabaci was originated 6.47 million years ago (MYA). Nevertheless, the time was 1.25MYA based on nuclear loci. According to the method of approximate Bayesian computation, this difference is probably due to different degrees of migration among loci; i.e., although the mitochondrial locus had differentiated, gene flow at nuclear loci was still possible, a scenario similar to parapatric mode of speciation. This is the first study in whiteflies using multilocus data and incorporating Bayesian coalescence approaches, both of which provide a more biologically realistic framework for delimiting species status and delineating the divergence history of B. tabaci. Our study illustrates that gene flow during species divergence should not be overlooked and has a great impact on divergence time estimation.