Molecular phylogeny and divergence time of the water penny genus Eubrianax (Coleoptera: Psephenidae) in Japan

The phylogenetic relationships among the Japanese members of the genus Eubrianax (Coleoptera: Psephenidae) were examined using the mitochondrial cytochrome oxidase subunit I (COI) gene and nuclear 28S rRNA gene sequences. Based on the molecular phylogeny as well as morphological features, the species status of Eubrianax brunneicornis Nakane, 1952 was proposed. The phylogenetic analyses recovered monophyly of the previously proposed pellucidus species group with four Japanese species, whereas a single Japanese species of the granicollis group was included in the lineage of the ramicornis group with five Japanese species. The divergence times of the species were estimated by dating the phylogenetic tree against the fossil record and a molecular clock based on the COI gene. The divergence of the Japanese species was inferred to have occurred during the Pliocene epoch.     

Molecular phylogeny of the family Tephritidae (Insecta: Diptera): New insight from combined analysis of the mitochondrial 12S, 16S,and COII genes

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.     

Phylogenetic systematics of Colotis and associated genera (Lepidoptera: Pieridae): evolutionary and taxonomic implications

We investigated the genetic diversity and phylogenetic placement of the butterflies in the genus Colotis and eight related pierid genera using sequence information from two mitochondrial and two nuclear genes. To establish the status of species, we initially barcoded 632 specimens representative of all genera and most species and subspecies in those genera. A subset was then selected for phylogenetic analysis where additional gene regions were sequenced: 16S rRNA (523 bp), EF‐1α (1126 bp) and wg (404 bp). DNA barcode results were largely congruent with the traditional classification of species in the Colotis group, but deep splits or lack of genetic divergence in some cases supported either species‐level differentiation or synonymy. Despite using information from four genes, the deeper nodes in our phylogeny were not strongly supported, and monophyly of the ‘Colotis group’ and the genera Colotis and Eronia could not be established. To preserve the monophyly of Colotis, we revive the genus Teracolus for three outlying species previously in Colotis (i.e. Colotis eris, Colotis subfasciatus and Colotis agoye), as well as the genus Afrodryas for Eronia leda. The position of Calopieris is unresolved although it appears to be well outside the molecular variation in Colotis (s.l.). A dispersal/vicariance analysis suggested that major diversification in Colotis (s.str.) occurred in Africa with subsequent dispersal to India and Madagascar.     

Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini)

We inferred secondary structure models of the internal transcribed spacers (ITS) 1 and 2 of bush crickets using a combined comparative and thermodynamic approach. The inferred secondary structure models were used to account for interdependency of interacting nucleotides in a phylogenetic analysis of the bush cricket genus Poecilimon. Our analysis indicates that the two previously reported conformational structures (i.e., hairpin and ring) of ITS2 are likely to fold in bush crickets as well and that both predicted structures are similar to those proposed for other eukaryotes. Comparing predicted ITS1 secondary structure models proved to be difficult because of substantial variation in their nucleotide sequence length. Our study revealed that the phylogenetic signal of ITS1 and ITS2 is largely congruent with that preserved in the mitochondrial genes 16S rRNA, tRNA‐Val and 12S rRNA. The phylogenetic signal in both the nuclear and the mitochondrial genome question the monophyly of the genus Poecilimon: species of the genera Poecilimonella, Parapoecilimon, Polysarcus and Phonochorion consistently cluster within Poecilimon.     

A molecular phylogenetic analysis of Bulinus (Gastropoda: Planorbidae) with conserved nuclear genes

Jørgensen, A., Madsen, H., Nalugwa, A., Nyakaana, S., Rollinson, D., Stothard, J. R. & Kristensen, T. K. A molecular phylogenetic analysis of Bulinus (Gastropoda: Planorbidae) with conserved nuclear genes. —Zoologica Scripta, 40, 126–136. Mutational saturation of inspected DNA loci and topological incongruence in the phylogenetic inferences have previously confounded attempts to resolve the evolutionary relationships within the freshwater snail genus Bulinus. Traditionally, the 37 species of Bulinus are placed within the four species groups and the evolutionary divergence between groups is substantial. With an intention to shed new light on species group relationships, the present study was designed to investigate the basal divergences in the phylogeny of Bulinus using highly conserved nuclear genes. The resolved phylogeny inferred that the four species groups of Bulinus were monophyletic and Shimodaira‐Hasegawa topology tests found them to be significantly supported. The Bulinus truncatus/tropicus species complex and Bulinus wrighti (Bulinus reticulatus group) formed a well‐supported sister‐group relationship. The Bulinus africanus species group was the sister‐group to the clade (Bulinus truncatus/tropicus + B. wrighti) with the Bulinus forskalii species group as the sister‐group to these taxa. The sister‐group relationship between Indoplanorbis and Bulinus was non‐significant and the basal clade support of Bulinus improved upon exclusion of Indoplanorbis. The finding of basal long branches of Bulinus species originating from Madagascar strongly suggests the presence of additional cryptic species and an evolutionary scenario influenced by this island’s geological vicariance from the African mainland. Speciation by polyploidy was inferred to have evolved within a clade in the Bulinus truncatus/tropicus species complex. Although the monophyletic status of each species group was firmly supported, it was difficult to establish species group concepts equally across the variations and place this precisely in a specific temporal framework.     

Molecular systematics and biodiversity of the Cryptotis mexicanus group (Eulipotyphla: Soricidae): two new species from Honduras supported

Small-eared shrews of the genus Cryptotis (Mammalia: Eulipotyphla: Soricidae) are widespread in the northern Neotropics. Systematic studies of these shrews over the past two decades have revealed previously undocumented morphological and species diversity, resulting in a quadrupling of the number of recognized species. Unfortunately, a small proportion of the species in the genus have been included in molecular phylogenetic studies, and evolutionary relationships within the genus are incompletely known. Traditionally, species have been assigned to four or five morphologically defined ‘species groups’, but tests of the monophyly of some of these groups show weak support and relationships amongst species groups remain somewhat speculative. The largest species group is the C. mexicanus group inhabiting Mexico and northern Central America. We studied sequences from mitochondrial cytochrome-b and 16S genes, as well as nuclear ApoB and BRCA1 genes from 22 species of Cryptotis, including 15 species in the C. mexicanus group. Our combined analysis shows that the C. goldmani subgroup is very weakly supported as monophyletic; however, the C. mexicanus group as a whole is not monophyletic. Our molecular phylogenetic analyses confirm the distinctiveness of two newly described species (C. celaque and C. mccarthyi) from isolated highlands of western Honduras and illustrate their relationship with other species formerly considered part of a widespread C. goodwini.     

African Dacus (Diptera: Tephritidae: Molecular data and host plant associations do not corroborate morphology based classifications

The genus Dacus Fabricius includes economically important pest fruit flies distributed in the Afrotropical and Indo-Australian regions. Two recent revisions based on morphological characters proposed new and partially discordant classifications synonymizing/revalidating several subgeneric names and forming species groups. Regardless these efforts, the phylogenetic relationships among Dacus species remained largely unresolved mainly because of the difficulties in assigning homologous character states. Therefore we investigated the phylogeny of African Dacus by sequencing 71 representatives of 32 species at two mitochondrial (COI, 16S) and one nuclear (period) gene fragments. Phylogenetic relationships were inferred through Bayesian and Maximum Parsimony methods and hypotheses about the monophyly of Dacus subgenera were tested by Shimodaira–Hasegawa tests. The congruence tests and the analyses of the single gene fragments revealed that the nuclear gene supports similar conclusions as the two mitochondrial genes. Levels of intra- and inter-specific differentiation of Dacus species were highly variable and, in some cases, largely overlapping. The analyses of the concatenated dataset resolved two major bootstrap-supported groups as well as a number of well-supported clades and subclades that often comprised representatives of different subgenera. Additionally, specimens of Dacus humeralis from Eastern and Western African localities formed separate clades, suggesting cryptic differentiation within this taxon. The comparisons between the molecular phylogeny and the morphological classification revealed a number of discrepancies and, in the vast majority of cases, the molecular data were not compatible with the monophyly of the currently recognised subgenera. Conversely, the molecular data showed that Apocynaceae feeders are a monophyletic sister group of species feeding on both Cucurbitaceae and Passifloraceae (these latter being also monophyletic). These results show a clear association between the molecular phylogeny of African Dacus and the evolution of host plant choice and provide a basis towards a more congruent taxonomy of this genus.     

A molecular phylogeny of Planorboidea (Gastropoda, Pulmonata): insights from enhanced taxon sampling

Planorbid gastropods are the most diverse group of limnic pulmonates, with both discoidal and highspired taxa. Phylogenetic relationships among these genera are confused and controversial. In particular, the monophyly of the limpet‐like taxa (traditionally Ancylidae) is disputed. Even recent molecular studies have concluded that substantially more work is necessary to solve the remaining issues concerning intergeneric phylogenetic relationships and higher taxa systematics. Planorbid snails are of great significance for humans as several members of this group are intermediate hosts of blood flukes (schistosomes) causing a chronic disease, schistosomiasis. We used the two independent molecular markers COI and 18S (concatenated dataset of 2837 nucleotide bp) to infer phylogenetic relationships of 26 genera (27 species) of Planorboidea, represented mostly by type species from mainly topotypical populations. With the majority of the taxa discussed not having been studied previously, this study attempted to test several hypotheses on planorbid phylogenetic relationships using Bayesian inference techniques. The monophyly of Planorboidea (= ‘Ancyloplanorbidae’) is strongly suggested on the basis of our extensive molecular analysis. Besides a distinct Burnupia clade, two major clades were recovered that correspond to family level taxa (traditional Bulinidae and Planorbidae). Considerable rearrangements of suprageneric taxa are evident from the phylogeny inferred. Therefore, the only clades recognized by current classifications and supported by our analysis are Planorbini and Segmentinini. The present study found that Ancylidae as traditionally understood, i.e. covering most freshwater limpet gastropods, is paraphyletic, as the genera of Burnupia and Protancylus have been shown to lie phylogenetically outside the Ancylini. Chromosome numbers and levels of polyploidy are discussed in the light of the new phylogeny. An earlier theory of shell shape evolution, i.e. that of patelliform taxa being most advanced, was not supported by this study; a limpet‐shaped taxon is most basal within Planorboidea. Although many taxa still remain to be studied, our results will hopefully contribute towards a better understanding of this very important group of freshwater organisms. Some taxonomic implications are discussed.     

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada,Heterotardigrada)

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ornamentation as a phylogenetic character within Echiniscus. To do this, DNA was extracted from single individuals for multiple Echiniscus species, and 18S and 28S rRNA gene fragments were sequenced. Each specimen was photographed, and published in an open database prior to DNA extraction, to make morphological evidence available for future inquiries. An updated phylogeny of the class Heterotardigrada is provided, and conflict between the obtained molecular trees and the distribution of dorsal plates among echiniscid genera is highlighted. The monophyly of Echiniscus was corroborated by the data, with the recent genus Diploechiniscus inferred as its sister group, and Testechiniscus as the sister group of this assemblage. Three groups that closely correspond to specific types of cuticular design in Echiniscus have been found with a parsimony network constructed with 18S rRNA data. © 2013 The Linnean Society of London     

Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re‐examined traditional characters used to define species groups and used multivariate statistics to quantitatively evaluate group structure in morphometric space. Clustering analyses of phenotypic similarity indicate that some (but not all) members of previously defined species groups are phenotypically most similar to other members of the same group. However, when species group membership was mapped on our partitioned Bayesian phylogenetic hypothesis, only one species group corresponds to a clade; all other species group arrangements are strongly rejected by our phylogeny. Our results demonstrate that (1) previously recognized species group relationships were misled by phenotypic convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple lineages have independently invaded the Philippines. Based on this new perspective on the phylogenetic relationships of Philippine Sphenomorphus, we revise the archipelago's diverse assemblage of species at the generic level, and resurrect and/or expand four previously recognized genera, and describe two new genera to accommodate the diversity of Philippine skinks of the Sphenomorphus group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1217–1243.     

A combined morphological and molecular phylogeny of the genus Chironius Fitzinger, 1826 (Serpentes: Colubridae)

Chironius is one of the most speciose genera of the South American colubrid snakes. Although the genus represents a well‐known radiation of diurnal racers, its monophyly, affinities with other Neotropical colubrid genera, and intrageneric relationships are open questions. Here, we present a phylogenetic analysis of Chironius based on a data matrix that combines one nuclear (c‐mos) and two mitochondrial (12S and 16S rRNA) genes with 37 morphological characters derived from scutellation, skull, and hemipenial features. Phylogenetic relationships were inferred using maximum parsimony (MP) and maximum likelihood (ML). Our combined morphological and molecular analyses strongly support the monophyly of the genus Chironius and its sister‐group relationship with a clade formed by the genera Dendrophidion and Drymobius. Phylogenetic relationships within the genus Chironius is still controversial, although five clades are retrieved with medium to strong support. © 2014 The Linnean Society of London     

Hybrid enrichment of poorly preserved museum specimens refines homology hypotheses in a group of minute litter bugs (Hemiptera: Dipsocoromorpha: Schizopteridae)

Although they are a valuable source of specimens, insect natural history collections continue to be under‐utilized in molecular systematics, mostly due to difficulties in obtaining DNA sequences. Old specimens or specimens stored under suboptimal conditions are intractable for traditional Sanger sequencing. In this study we use an inexpensive hybrid capture with in‐house generated baits to retrieve commonly utilized ribosomal and mitochondrial loci from old museum specimens and combine them with a Sanger‐generated dataset comprising recently collected material. We focus on the Corixidea genus group (Schizopteridae), which comprises rarely collected, small (1–2 mm) and primarily tropical insects of which only c. 10–20% of the species have been described. A molecular phylogeny is needed to resolve relationships and revise the genus‐level classification to correctly place the c. 150 yet to be described species. Applying this approach, we constructed a dataset, containing 101 taxa, 11 of which were preserved in low‐percentage ethanol, 48 are dry and point‐mounted, and 40 are > 20 years old at DNA extraction. The obtained data proved sufficient for reconstructing a well‐supported phylogeny with c. 50% of the predicted diversity, and for the oldest successfully sequenced specimen (95 years) to be unambiguously placed in that phylogeny. We confirmed monophyly of the Corixidea genus group, showed paraphyly of the genus Corixidea, and recovered nine well‐supported clades within the group. Ancestral character states of selected morphological features were inferred and used to re‐examine primary homology hypotheses and inform an upcoming taxonomic revision.     

Molecular phylogeny and systematics of the pseudoxyrhophiine snake genus Liopholidophis (Reptilia, Colubridae): evolution of its exceptional sexual dimorphism and descriptions of new taxa

The pseudoxyrhophiine snake genus Liopholidophis Mocquard, 1904 is endemic to Madagascar and consists of two distinct species groups. We performed molecular phylogenetic analyses using nucleotide sequences of c . 2200 bp from two mitochondrial genes (16S rRNA, cyt b ) and one nuclear gene (c-mos) to test the monophyly of the genus Liopholidophis and to investigate the relationships of the known species and an unidentified Liopholidophis population. Our phylogeny strongly supports the polyphyly of the genus Liopholidophis , confirms the monophyly of both species groups, and reveals that the unidentified population belongs to a new species. We therefore transfer the species of the former L. stumpffi group ( L. epistibes , L. infrasignatus , L. lateralis , L. martae , and L. stumpffi ) to a new genus Bibilava gen. n. and describe Liopholidophis dimorphus sp. n. from the rainforests of Montagne d'Ambre National Park in northern Madagascar. Finally, we compare our phylogeny with previous hypotheses and discuss the evolution of the extreme sexual dimorphism in tail length of Liopholidophis s. str.     

A molecular phylogeny for digger wasps in the tribe Ammophilini (Hymenoptera,Apoidea, Sphecidae)

The evolution of parental care strategies in aculeate (stinging) wasps and bees has been much studied from a functional perspective, but relatively little phylogenetic information is available to place this in a rigorous historical context, especially at the species level. We used mitochondrial cytochrome oxidase I and two nuclear genes, the elongation factor‐1α and LW rhodopsin, to investigate the phylogeny of Sphecidae digger wasps. We focus particularly on the tribe Ammophilini, a clade of nonsocial apoid wasps that exhibit unusually diverse parental care strategies. We analysed a 2232 bp dataset for 40 ammophilines plus nine other taxa from within the remaining Sphecidae. Our Bayesian phylogeny provides strong support for the monophyly of Ammophilini and for the monophyly of all six individual ammophiline genera, except that the position of P. affinis within the genus Podalonia is only weakly supported. The monophyly of some, but not all, previously designated species groups within the genus Ammophila is supported. We discuss the implications of our results for the evolution of morphological traits used previously in ammophiline systematics.     

Evolution of the Neotropical ant genus Linepithema

Abstract A comprehensive species‐level phylogeny of the ant genus Linepithema Mayr, a Neotropical group best known for the invasive Argentine ant L. humile (Mayr), is inferred for the first time using fragments from three nuclear loci [wingless (WG), long‐wavelength rhodopsin (LWR) and internal transcribed spacer (ITS‐2)] and the mitochondrial cytochrome oxidase subunit I (COI) gene. Monophyly of the genus is strongly supported in parsimony, likelihood and Bayesian analyses of the concatenated data, as is the monophyly of four species groups defined previously on the basis of morphology. An Andean species, L. oblongum (Santschi), is the sister taxon of the Argentine ant. Eight of the 11 species whose monophyly was testable in the analysis were inferred to be monophyletic. Several instances of species paraphyly and one case of mitochondrial introgression suggest that complex population genetic processes underpin the patterns of diversity in Linepithema, and that simple genetic approaches to taxonomy such as DNA barcoding should be treated with caution. A maximum likelihood reconstruction of ancestral distributions suggests that Linepithema is of southern South American origin and that populations in the Greater Antilles are the result of four independent colonization events.     

Phylogeny of the Heterodoxus octoseriatus group (Phthiraptera: Boopiidae) from rock-wallabies (Marsupialia: Petrogale)

The phylogenetic position of the Heterodoxus octoseriatus group is inferred from morphological characters. Two character states support monophyly of this group. Another indicates that its sister-group is a group of 11 other Heterodoxus species (here called the H. calabyi group), that infest at least seven other genera of macropodid marsupials. Fourteen potential apomorphies, associated with the male and female genitalia, are identified. Evident rapid and divergent evolution of the genitalia, however, precludes determination of their polarity by comparison with an out-group (the sister-group). Consequently, phylogeny in the H. octoseriatus group is inferred from the close similarity of morphological characters. In light of the phylogenetic analysis and a phenogram, speciation and the evolution of morphological characters in the H. octoseriatus group is discussed.     

PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA,ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES1

The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast‐encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family‐level classification. The genus Cymopolia Lamouroux was inferred to be the basal‐most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier‐Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition‐to‐transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g₁ values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies.     

Molecular phylogeny of the South American land slug Phyllocaulis (Mollusca,Soleolifera, Veronicellidae)

Gomes, S. R., Britto da Silva, F., Mendes, I. L. V., Thomé, J. W. & Bonatto, S. L. (2009). Molecular phylogeny of the South American land slug Phyllocaulis (Mollusca, Soleolifera, Veronicellidae). —Zoologica Scripta, 39, 177–186. Our main objectives were investigate the phylogenetic relationships between the species of the land slug Phyllocaulis and the monophyly of the genus based on mitochondrial (16S and COI) and nuclear (ITS2) DNA sequences from multiple individuals from each species. Evolutionary trees were constructed using Bayesian inference, maximum likelihood, maximum parsimony and neighbor‐joining methods. All species accepted in the current taxonomy based on penial characteristics and radular measurements were reciprocally monophyletic. Five species out of six formed a clade with the following highly supported relationship: Phyllocaulis gayi, Phyllocaulis soleiformis, Phyllocaulis renschi, Phyllocaulis variegatus, Phyllocaulis boraceiensis. The position of Vaginulus taunaisii changed according to the analysis, appearing as sister‐group of Phyllocaulis or as sister‐group of Phyllocaulis tuberculosus. Divergence times estimated from the 16S tree indicated that the extant species of Phyllocaulis shared a common ancestor around 1.3 Ma and that most species originated between 0.8 and 0.6 Ma.