Unraveling evolutionary lineages in the limbless fossorial skink genus Acontias (Sauria: Scincidae): are subspecies equivalent systematic units?

Subspecies in the limbless, endemic African fossorial skink genus Acontias constitute ill-defined operational taxonomic units, consequently considerable systematic debate has lingered on the systematic diversity within Acontias. In the present study, the systematic affinities among acontine taxa are explored with the utility of partial sequence data from two mitochondrial gene loci (16S rRNA and cytochrome oxidase subunit 1 (COI)) for all taxa, while two additional loci (12S rRNA, cytochrome b) were used to investigate relationships within the Acontias meleagris complex. Phylogenetic results, derived from the combined analysis, revealed two monophyletic clades. Clade 1 is comprised of small-bodied skinks while clade 2 comprised the medium bodied skinks. Within clade 2 none of the traditionally recognized subspecies formed reciprocally monophyletic groups. Furthermore, constraining the topology and enforcing sister taxa relationships between the assumed subspecies, consistently recovered a topology that was statistically significant worse, indicating that the traditionally designated subspecies groupings probably represent invalid taxonomic units, thus clearly reflecting considerable discord with current taxonomy. The burrowing life style of these lizards has probably led to marked convergent evolution and constrained the development of diagnostic morphological characters among these species. Morphological similarities in color as well as scale architecture within Acontias are labile and highly homoplaseous and do not reflect the evolutionary history of the group. Taxonomic implications of these results are discussed.     

Examination of evolutionary relationships in the Cape fossorial skink species complex (Acontinae: Acontias meleagris meleagris) reveals the presence of five cryptic lineages

Variable morphological characters have obscured genealogical relationships in the Cape fossorial skink Acontias meleagris meleagris species complex. Currently the species complex contains four dubious operational taxonomic units (A. meleagris meleagris, A. m. orientalis, A. percivali tasmani and the morph lineicauda) with poorly defined species boundaries. In the present study we examine the evolutionary relationships within the species complex by sampling 24 skink populations from the known geographical distribution in the Western and Eastern Cape provinces of South Africa, representing a total of 119 specimens. We used partial sequence data derived from two mitochondrial DNA genes, 16S rRNA and COI, and one nuclear DNA gene, intron β‐fibrinogen (β‐fibint 7), to examine evolutionary relationships. Phylogenetic relationships were determined using both Maximum Parsimony (MP) and Bayesian inference (BI) from the combined mtDNA, nDNA and the total evidence data. Additionally we employed Maximum likelihood (ML) analyses on the total evidence data that comprised ～1.5 kb. Topologies derived from the combined mtDNA analyses were congruent with the total evidence analyses (mtDNA + nDNA) and retrieved five major clades with strong statistical support inferred from bootstrapping and posterior probabilities. The five clades were genealogically and geographically exclusive, diagnostic at both the mtDNA and nDNA level and characterized by pronounced sequence divergence, with no shared haplotypes between clades. Collectively these results suggest the presence of five putative cryptic operational taxonomic units within the A. meleagris meleagris species complex. Constraining the traditionally recognized taxa always retrieved a statistically worse topology suggesting that considerable taxonomic revision is required. Our results indicate that traditional morphological characters need to be reassessed to define the five novel lineages in the A. meleagris meleagris species complex. The phylogeographic pattern for the fossorial skinks we retrieved was novel compared to phylogeographic studies for codistributed above ground living taxa. These results suggest that the abiotic and biotic factors that impact subterranean taxa may differ from supraterranean taxa.     

Taxonomic subdivisions within the fossorial skink subfamily Acontinae (Squamata: Scincidae) reconsidered: a multilocus perspective

Despite recent molecular systematic studies on the fossorial southern African skink subfamily Acontinae, evolutionary relationships among the three genera remain unresolved and disputed. Among these, the most recent study suggests that both Typhlosaurus and Acontias are paraphyletic, contrasting earlier results that suggest the presence of two divergent clades within Acontias. Here we further investigate the evolutionary relationships in the limbless fossorial southern African subfamily Acontinae with partial sequenced data derived from four mitochondrial loci (16S rRNA, 12S rRNA, cytochrome oxidase I and cytochrome b), as well as two nuclear protein coding loci (c‐mos and RAG‐1), in an attempt to clarify evolutionary relationships. Phylogenetic results derived from combined data analyses (comprising all six loci and totalling ～3.1 kb) using maximum parsimony, maximum likelihood and Bayesian inferences converged on the same topology. The resulting phylogeny showed Typhlosaurus as monophyletic, while the monotypic genus Acontophiops was nested intermediate to two reciprocally monophyletic Acontias clades. These two Acontias clades can be distinguished on the basis of a number of morphological, morphometric and biogeographical characters, underscoring the presence of two distinct groups. In the present study, we propose the following taxonomic changes based on the multilocus phylogeny. We retain the genus name Acontias for the medium‐ and large‐bodied skinks in clade 2 comprising all taxa in the Acontias meleagris complex as well as Acontias plumbeus, Acontias gracilicauda gracilicauda, Acontias breviceps, Acontias percivali percivali and Acontias percivali occidentalis. We designate a new genus Microacontias gen. nov. for the reciprocally monophyletic taxa in clade 1 comprised of all the small‐bodied taxa that include Microacontias litoralis, Microacontias lineatus lineatus, Microacontias lineatus grayi and Microacontias lineatus tristis. We examine the evolution of characters used in the taxonomy of the Acontinae and suggest that symplesiomorphic morphological characters among fossorial taxa have been an impediment to understanding the evolution of this subfamily. This study underscores the importance of the application of multiple molecular markers (both nuclear and mitochondrial) in determining the taxonomic diversity among fossorial skinks and emphasizes the application of phylogenetics in defining synapomorphic (shared derived) features.     

Contributions to molecular systematics of water scavenger beetles (Hydrophilidae,Coleoptera)

Phylogenetic relationships within Hydrophilidae were examined by analyses of separate and combined nuclear and mitochondrial markers (28S rRNA, 18S rRNA, 16S rRNA, 12S rRNA, COI and COII genes). The preferred (Bayesian) tree topology suggests a sister group relationship between Spercheidae and Hydrophilidae, supporting the ‘hydrophilid lineage’; Epimetopidae are placed on the base of the ‘helophorid branch’, the monophyly of Sphaeridiinae is highly supported, nested deeply within Hydrophilidae closest to Enochrus, making Hydrophilinae and Acidocerini paraphyletic; Hydrobius appears as sister taxon to (Hydrochara + Hydrophilus) without a closer relationship to Acidocerini; the hydrophiloid–histeroid sister group relationship is confirmed. The topology of several taxa remains contradictory, and requires further investigations with a larger taxon sampling and additional molecular markers.     

The skull and the jaw adductor musculature in some burrowing scincomorph lizards of the genera Acontias, Typhlosaurus and Feylinia

The skull and the jaw adductor musculature are analysed in a number of representatives of the Ethiopian scincomorph lizard genera Acontias, Typhlosaurus and Feylinia. Acontias and Typhlosaurus are closely related and are to be included in a single taxon, the Acontinae, provisionally classified as a subfamily of the Scincidae. The family Feyliniidae (including the genera Feylinia and Chabanaudia) is revalidated and an amended diagnosis is given, The Feyliniidae are a scincomorph family, possibly with gekkotan affinities.     

Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)

Phylogenetic relationships within the Pentatomoidea are investigated through the coding and analysis of character data derived from morphology and DNA sequences. In total, 135 terminal taxa were investigated, representing most of the major family groups; 84 ingroup taxa are coded for 57 characters in a morphological matrix. As many as 3500 bp of DNA data are adduced for each of 52 terminal taxa, including 44 ingroup taxa, comprising the 18S rRNA, 16S rRNA, 28S rRNA, and COI gene regions. Character data are analysed separately and in the form of a total evidence analysis. Major conclusions of the phylogenetic analysis include: the concept of Urostylididae is restricted to that of earlier authors; the Saileriolinae is raised to family rank and treated as the sister group of all Pentatomoidea exclusive of Urostylididae sensu stricto; a broadly conceived Cydnidae, as recognized by Dolling, 1981 , is not supported; the placement of Thaumastellidae within the Pentatomoidea is affirmed and the taxon is recognized at family rank rather than as a subfamily of Cydnidae, although its exact phylogenetic position within the Pentatomoidea remains equivocal; the Parastrachiinae is treated as also including Dismegistus Amyot & Serville and placed within a broadly conceived Corimelaenidae, the latter group being treated at family rank; the family‐group taxa Dinidoridae and Tessaratomidae probably represent a monophyletic group, but the recognition of monophyletic subgroups will benefit from additional representation in the sequence data set; and the Lestoniidae is treated as the sister group of the Acanthosomatidae. The Acanthosomatidae and Scutelleridae are consistently recovered as monophyletic. The monophyly of the Pentatomidae appears unequivocal, inclusive of the Aphylinae and Cyrtocorinae, on the basis of morphology, the latter two taxa not being represented in the molecular data set. © The Willi Hennig Society 2008.     

Molecules,morphology and minute hooded beetles: a phylogenetic study with implications for the evolution and classification of Corylophidae (Coleoptera: Cucujoidea)

Eight genes (nuclear: 18S, 28S, H3, CAD; mitochondrial: 12S, 16S, COI, COII) and morphology were used to infer the evolutionary history of Corylophidae, some of the smallest free‐living insects. The study included 36 corylophid exemplars, representing approximately 60% of the known generic diversity of the family and 16 cucujoid outgroup taxa. Multiple partitioning strategies, molecular datasets, combined datasets and different taxon sampling regimes using maximum likelihood and mixed‐model Bayesian inference were utilized to analyse these data. Most results were highly concordant across analyses. There was strong agreement across (i) partitioning strategies, (ii) maximum likelihood and Bayesian inference analyses of the molecular data, and (iii) Bayesian inference of the molecular data alone and Bayesian inference of the combined morphological and molecular data when all terminal taxa were included. When a strict taxon sampling protocol was employed so that only single generic exemplars were included, deep relationships were affected in the resulting phylogenetic hypotheses. Under such narrow sampling strategies, deep phylogenetic relationships were also sensitive to the choice of generic exemplars. Although it is often challenging to obtain single representatives for many taxa in higher‐level phylogenetic analyses, these results indicate the importance of using denser taxon sampling approaches even at the specific level for genera included in such studies. Molecular data alone support Anamorphinae (Endomychidae) strongly as the sister group of Corylophidae. In combined data analyses, Coccinellidae is recovered as the sister group to Corylophidae. In all analyses, Corylophidae and the subfamily Corylophinae are recovered as monophyletic. The monophyly of Periptyctinae was untested, as only a single species was included. All included corylophine tribes were recovered as monophyletic with the exception of Aenigmaticini; Aenigmaticum Matthews forms the sister group to Orthoperus Stephens and Stanus?lipiński et al. is recovered as the sister group of Sericoderus Stephens. Stanus tasmanicus?lipiński et al. is transferred to a new genus, Pseudostanus Robertson, ?lipiński & McHugh gen.n. incertae sedis. We propose a new tribe, Stanini Robertson, ?lipiński & McHugh trib.n. for Stanus bowesteadi?lipiński et al. and a new concept of Aenigmaticini sensu.n. to include only the nominate genus. Anatomical transitions associated with corylophid miniaturization are highlighted. Key phenotypic modifications and elevated rates of substitution in nuclear rRNA genes are evident in a subgroup of Corylophinae that includes the most diminutive species. Other taxonomic and evolutionary implications are discussed in light of the results.     

Systematic position of the pelagic Thecosomata and Gymnosomata within Opisthobranchia (Mollusca, Gastropoda) – revival of the Pteropoda

The complete 18S (SSU) rRNA as well partial 28S (LSU) rRNA and partial mitochondrial COI sequences have been used to reconstruct the phylogenetic relationships within Opisthobranchia with special focus on the pelagic orders Thecosomata and Gymnosomata. Maximum parsimony, maximum likelihood, distance as well as Bayesian analysis of a combined dataset of the three genes reveals that Thecosomata and Gymnosomata are sister groups and together are closely related to Anaspidea. Possible sister taxon to Thecosomata, Gymnosomata and Anaspidea is Cephalaspidea s. str . Analysis of a taxon-extended dataset of partial 28S sequences supported a basal position of Limacina within Euthecosomata. Within Cavolinidae, Creseis is basal to the other taxa. Other phylogenetic implications from the present results are also discussed. Investigation of the morphology and histology of Thecosomata and Gymnosomata as well as several other opisthobranch taxa helped to identify autapomorphies for Thecosomata and Gymnosomata as well as apomorphies for the clades including these taxa.     

Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards

Partitioned Bayesian analyses of approximately 2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean -lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2 ln Bayes factor > 10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.     

A phylogeny of the Australian Sphenomorphus group (Scincidae: Squamata) and the phylogenetic placement of the crocodile skinks (Tribolonotus): Bayesian approaches to assessing congruence and obtaining confidence in maximum likelihood inferred relationships

Australian scincid lizards are a diverse squamate assemblage ( approximately 385 species), divided among three major clades (Egernia, Eugongylus, and Sphenomorphus groups). The Sphenomorphus group is the largest, comprising 61% of the Australian scincid fauna. Phylogenetic relationships within the Australian Sphenomorphus group and the phylogenetic placement of Tribolonotus are inferred using mtDNA (12S and 16S rRNA genes, ND4 protein-coding gene, and associated tRNA genes; 2185bp total). These data were analyzed separately (structural RNA vs protein-coding partitions) and combined using maximum likelihood. Confidence in inferred clades was assessed using non-parametric bootstrapping and Bayesian analysis. Analysis of the combined data strongly supports Sphenomorphus group (as well as the Australian subgroup) monophyly. Notoscincus is strongly placed as the sister taxon of the remaining Australian Sphenomorphus group taxa, with this more exclusive clade being divided into two major groups (one restricted to mesic eastern Australia and the other continent wide). The speciose Australian "Eulamprus" and "Glaphyromorphus" are both polyphyletic. All remaining non-Sphenomorphus group lygosomine skinks strongly form a clade, with Tribolonotus placed as the sister taxon of the Australian Egernia group.     

Aligned 18S and insect phylogeny

The nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

Molecular systematics of cytochrome oxidase I and 16S from Neochlamisus leaf beetles and the importance of sampling.

If a gene tree is to be judiciously used for inferring the histories of closely related taxa, (1) its topology must be sufficiently resolved and robust that noteworthy phylogenetic patterns can be confidently documented, and (2) sampling of species, populations, and pertinent biological variation must be sufficiently broad that otherwise misleading sources of genetic variation can be detected. These principles are illustrated by the complex gene tree of Neochlamisus leaf beetles that I reconstructed using 90,000 bp of cytochrome oxidase I (COI) and 16S mitochondrial DNA (mtDNA) sequences from over 100 specimens. Cytochrome oxidase I haplotypes varied up to 25.1% within Neochlamisus and up to 11.1% within the gibbosus species group, while exhibiting very low A + T bias for insect mtDNA (63%), low transition saturation, and conservative patterns of amino acid variation. 16S exhibited lower sequence divergences and greater A + T bias and transition saturation than COI, and substitutions were more constrained in stems than in loops. Comparisons with an earlier study of Ophraella leaf beetles highlighted conservative and labile elements of molecular evolution across genes and taxa. Cytochrome oxidase I parsimony and neighbor-joining analyses strongly supported a robust mtDNA genealogy that revealed the monophyly of Neochlamisus and of the gibbosus species group. Phylogeographic relationships suggested that the eastern U.S. gibbosus group derives from southwestern velutinus group ancestors. Haplotypes from individual velutinus group species clustered monophyletically, as expected. However, haplotypes from each of several gibbosus group taxa were polyphyletically distributed, appearing in divergent parts of the tree. 16S provided a less-resolved gibbosus group topology that was congruent with the COI tree and corroborated patterns of mitochondrial polyphyly. By subsampling haplotypes corresponding to particular species, populations, and ecological variants of gibbosus group taxa, I demonstrate that recovered topologies and genetic distances vary egregiously according to sampling regime. This study thus documents the potentially dire consequences of inadequate sampling when inferring the evolutionary history of closely related and mitochondrially polyphyletic taxa.     

COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae)

The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, are often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers, thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.     

Systematic position of Lythriini revised: transferred from Larentiinae to Sterrhinae (Lepidoptera, Geometridae)

The tribe Lythriini is a small group of diurnally active geometrid moths consisting of a single Palaearctic genus Lythria with five species. The systematic placement of Lythriini has remained controversial: though traditionally it has been placed into the subfamily Larentiinae, a number of morphological characters link this tribe with the subfamily Sterrhinae. A molecular phylogenetic study was conducted to verify the systematic position of Lythriini, using sequences of both mitochondrial and nuclear genes: elongation factor 1α ( EF-1α ), wingless ( wgl ), 28S rRNA expansion segment D2 ( 28S D2 ), cytochrome oxidase subunit 1 ( COI ) and NADH dehydrogenase subunit 1 ( ND1 ) (a total of 3784 bp). Phylogenetic analysis reliably demonstrated that Lythriini belong to the subfamily Sterrhinae. Therefore, we propose to remove tribe Lythriini from Larentiinae and unite it with Sterrhinae. Moreover, our analysis supports the monophyly of both Sterrhinae and Larentiinae. However, although both morphological data and interspecific genetic distances insinuated that Lythria cruentaria and L. sanguinaria are sister species, the latter formed a clade of sister taxa together with L. purpuraria .     

Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning

The phylogenetic relationships among the southern African freshwater crab species were examined using partial sequence data from three mitochondrial genes (12S rRNA, 16S rRNA, and mtDNA COI) 26 morphological characters and 14 allozyme loci. The aims of the present study were firstly to determine whether freshwater crab species that live in the same geographic region share a close phylogenetic relationship. Secondly, to investigate whether hybridizing species are genetically closely related and thirdly, to test for the validity of subgenera based on the genetic data sets. Phylogenetic analysis based on sequence data revealed largely congruent tree topologies and some associations had consistently high bootstrap support, and these data did not support Bott's subgeneric divisions. The morphological data were less informative for phylogenetic reconstruction while the allozyme data generally supported patterns recovered by the sequence data. A combined analysis of all the data recovered two monophyletic clades, one comprised of small-bodied mountain stream species and the other clade consisting of large-bodied riverine species. The combined analyses reflected clear biogeographic patterning for these river crabs. In addition, there was a clear correlation between genetic distance values and the ability of sympatric species to hybridize.     

Multigene Barcoding and Phylogeny of Geographically Widespread Muricids (Gastropoda: Neogastropoda) Along the Coast of China

The identification and phylogeny of muricids have been in a state of confusion for a long time due to the morphological convergence and plasticity. DNA-based identification and phylogeny methods often offer an analytically powerful addition or even an alternative. In this study, we employ a DNA barcoding method to identify 17 known and easily confused muricid species (120 individuals) from the whole China coast based on mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA sequences, and nuclear ITS-1 and 28S rRNA sequences. The phylogeny of muricid subfamilies is also analysed based on all mitochondrial and nuclear sequences. The universal COI and 16S rRNA primers did not work broadly across the study group, necessitating the redesign of muricid specific COI and 16S rRNA primers in this paper. Our study demonstrates that COI gene is a suitable marker for barcoding muricids, which can distinguish all muricid species studied. Phylogenetic analysis of 16S rRNA, ITS-1 and 28S rRNA data also provide good support for the species resolution observed in COI data. The relationships of muricid subfamilies are resolved based on the separate and combined gene data that showed the monophyly of each the subfamilies Ergalataxinae, Rapaninae, Ocenebrinae and Muricinae, especially that Ergalataxinae did not fall within Rapaninae.     

Molecular phylogeny of lugworms (Annelida, Arenicolidae) inferred from three genes

Arenicolids comprise a group of four genera in which about 30 nominal species are described. Whereas the biology of many arenicolids is well known, the phylogenetic relationships of these worms are inadequately studied. A close relationship of Arenicolidae and Maldanidae is generally accepted. The phylogenetic relationships of arenicolid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA gene, the nuclear 18S rRNA gene, and a small fraction of the nuclear 28S rRNA gene. Members of all described arenicolid genera are included in the data set. Phylogenetic analyses were conducted using Maximum Likelihood, Bayesian inference, and Maximum Parsimony. The monophyly of the Maldanidae, as well as of the Arenicolidae is supported by all conducted analyses. Two well supported major clades are highest ranked sister taxa in the Arenicolidae: one containing all Abarenicola species and one containing Arenicola, Arenicolides, and Branchiomaldane. Evidence is given for a closer relationship between the two investigated Branchiomaldane species and Arenicolides ecaudata in the combined analysis. In the light of the molecular data the best explanation for structural and morphological observations is that Branchiomaldane evolved by progenesis.     

Phylogeny of North American amblemines (Bivalvia, Unionoida): prodigious polyphyly proves pervasive across genera

Abstract. The subfamily Ambleminae is the most diverse subfamily of fresh‐water mussels (order Unionoida), a globally diverse and ecologically prominent group of bivalves. About 250 amblemine species occur in North America; however, this diversity is highly imperiled, with the majority of species at risk. Assessing and protecting this diversity has been hampered by the uncertain systematics of this group. This study sought to provide an improved phylogenetic framework for the Ambleminae. Currently, 37 North American genera are recognized in Ambleminae. Previous phylogenetic studies of amblemines highlighted the need for more extensive sampling due to the uncertainties arising from polyphyly of many currently recognized taxa. The present study incorporated all amblemine genera occurring in North America north of the Rio Grande, with multiple species of most genera, including the type species for all but seven genera. A total of 192 new DNA sequences were obtained for three mitochondrial gene regions: COI, 16S, and ND1. In combination with published data, this produced a data matrix incorporating 357 gene sequences for 143 operational taxonomic units, representing 107 currently recognized species. Inclusion of published data provides additional taxa and a summary of present molecular evidence on amblemine phylogeny, if at the cost of increasing the amount of missing data. Parsimony and Bayesian analyses suggest that most amblemine genera, as currently defined, are polyphyletic. At higher taxonomic levels, the tribes Quadrulini, Lampsilini, and Pleurobemini were supported; the extent of Amblemini and the relationships of some genera previously assigned to that tribe remain unclear. The eastern North American amblemines appear monophyletic. Gonidea and some Eurasian taxa place as probable sister taxa for the eastern North American Ambleminae. The results also highlight problematic taxa of particular interest for further work.