A molecular phylogeny of Equatorial African Lacertidae, with the description of a new genus and species from eastern Democratic Republic of the Congo

Molecular systematics of Middle American harvest mice Reithrodontomys (Muridae), estimated from mitochondrial cytochrome b gene sequences

Taxonomic recommendations for British birds: seventh report

We examined genealogical relationships among six of seven species of crested-tailed mice (Habromys chinanteco, H. delicatulus, H. ixtlani, H. lepturus, H. lophurus, and H. simulatus) using DNA sequence data from the cytochrome-b gene. Gene trees based on maximum likelihood, Bayesian inference and maximum parsimony were largely congruent in that H. lepturus and H. ixtlani were closely related and formed the sister group to H. lophurus. All analyses also arranged H. chinanteco and H. simulatus as sister taxa. These results are concordant with the phenetic groupings of Carleton et al. (2002) based on morphology. Our unweighted maximum parsimony trees did not resolve placement of H. delicatulus relative to other taxa. However, analyses using weighted maximum parsimony, maximum likelihood and Bayesian inference optimality criteria recovered a sister group relationship between H. delicatulus and the clade comprised of ((H. lepturus H. ixtlani)(H. lophurus)). This relationship differs from the overall phenetic similarity of H. delicatulus with H. simulatus and H. chinanteco, influenced by the small size of these three taxa, but is consistent with some derived features of the phallus (Carleton et al., 2002). Based on our sequence data, a specimen from Michoacan, Mexico, recently assigned to Peromyscus sagax likely was inadvertently misidentified (Tiemann-Boege et al., 2000) and actually represents a new locality record for H. delicatulus. Finally, we comment on the conservation status of species of Habromys.

The relationships between Cinara (Cupressobium) aphids inhabiting woody parts and leaves of conifers belonging to Cupressaceae have been studied using a mitochondrial gene (COI) and a nuclear gene (EF1-α). Based on the COI sequences, genetic distances between species ranged from 5.6 % between Cinara (C.) tujafilina (del Guercio) and Cinara (C.) juniperi (De Geer) to 10.5 % between C. (C.) tujafilina and Cinara (C.) mordvilkoi (Pašek). Genetic distances among EF1-α sequences were lower and showed from 0.1 % between C. cupressi and C. juniperi to 2.3 % between C. tujafilina and C. mordvilkoi. Molecular phylogenetic trees were constructed using the Bayesian inference (BI) phylogenetic analysis and maximum parsimony (MP) criterion. Phylogenetic trees obtained based on COI and EF1-α marker genes created two sister clades. Our results indicate that Cinara (Cupressobium) are a monophyletic group of aphids. Phylogenetic relationships amongst Cupressobium aphids do not result from the association with the host plant, but from the feeding site on the host plant or an ability to change the microhabitat on the plant. As closely related species inhabit similar microhabitats on different host plants, it suggests that the host switching is the main mode of speciation in this subgenus.

The phylogeny of Iberian Aphodiini species was reconstructed based on morphology. Wing venation, mouthparts, male and female genitalia, and external morphology provided ninety‐four characters scored for ninety‐three Aphodiini species. Phylogenetic analyses were based on maximum parsimony and Bayesian inference criteria. Maximum parsimony consensus trees recovered Acrossus species as a sister group of the remaining Aphodiini, followed by two other branches, one including Neagolius, Plagiogonus, Ahermodontus and Ammoecius species, and the other including Oxyomus, Nimbus, Heptaulacus and Euheptaulacus species. The remaining studied taxa clustered in an unresolved group. Bayesian inference trees recovered Acrossus as the sister group of the remaining Iberian Aphodiini, followed by Colobopterus erraticus and the rest of the Iberian Aphodiini, but this latter branch was unresolved. The general lack of statistical support for the inferred phylogenetic relationships at terminal nodes using both maximum parsimony and Bayesian inference suggests that variation in morphological characters useful for phylogenetic inference in the present study is small, perhaps as a consequence of a radiation event occurring at the origin of the tribe. A probable evolutionary pattern for Aphodiini is proposed which infers six groups, namely Acrossian, Ammoecian, Oxyomian, Aphodian s.str., Colobopteran and Aphodian s.l. clades.

Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data. In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.

A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes)

Molecular systematics of the Middle American genus Hypopachus (Anura: Microhylidae)

Measuring Inconsistency in Phylogenetic Trees

Abstract: The genus Disocactus is native to Mexico and Central America and includes 11 species in four subgenera: D. subg. Ackermannia, D. subg. Aporocactus, D. subg. Disocactus and D. subg. Nopalxochia. Phylogenetic reconstruction was carried out with data from DNA sequences using the maximum parsimony and Bayesian inference criteria to explore the monophyly of the genus, its subgenera and its position within Hylocereeae. Six chloroplast markers (matK, psbA-trnH, rpl16, trnL-F, trnQ-rps16 and ycf1) were sequenced in ten species of Disocactus, 17 representatives from the remaining genera of Hylocereeae and five members of outgroups (Acanthocereus, Lemaireocereus and Pereskia). Our phylogenetic analysis supports neither the monophyly of Disocactus as it is currently defined nor that of the subgenera. The clade Disocactus s.str. was recovered for 13 species, including Epiphyllum anguliger, E. crenatum and E. lepidocarpum. Three subclades were observed within this clade, and three well-supported sister-speci...

Phylogeny reconstructions based on DNA sequences from nuclear ribosomal internal and external transcribed spacers and plastid trnT-trnF regions were used to examine the taxonomy and biogeography of North American Gaillardia (Asteraceae). Phylogenetic analyses based on maximum parsimony, maximum likelihood and Bayesian inference criteria consistently recovered several well-supported clades. Gaillardia comosa, G. gypsophila, and G. suavis, forming sect. Agassizia, were placed sister to the rest of Gaillardia, in which the two major clades correspond to sects. Gaillardia and Hollandia. Section Hollandia consists of the Gulf Coast G. aestivalis complex. Three major, well supported clades were consistently recovered in sect. Gaillardia: (1) G. multiceps and G. turneri were sister to an Intermountain clade of G. parry, G. spathulata, and G. flava; (2) a paraphyletic G. pinnatifida and G. arizonica; and (3) G. pulchella, G. aristata, G. amblyodon, G. coahuilensis, G. mexicana, G. henricksonii, and G. po...

The aim of this paper was to further explore the phylogeny of Siphini by analysing molecular data (two mitochondrial genes and two nuclear markers), together with morphological (29) and ecological (two) characters, for comprehensive analyses concerning the evolution of Siphini, relationships within the tribe, and between Siphini and other Chaitophorinae. Nine Siphini species, which represent all the genera of this tribe, as well as 12 out‐group species (mainly Chaitophorini representatives of the genera Chaitophorus and Periphyllus ), were used in the analyses. Molecular phylogenetic trees were reconstructed by the Bayesian inference (BI) phylogenetic analysis and maximum parsimony (MP) criterion. The cladistic analysis was performed using nona . The monophyly of Siphini was confirmed. Species belonging to subgenera Sipha and Rungsia were clustered together, and this clade was a sister with reference to a clade including the genera Atheroides and Chaetosiphella. Monophyly of Atheroides was confirmed by the molecular data; however, in cladistic analysis Atheroides seemed to be paraphyletic because Atheroides hirtellus was placed as sister to Atheroides serrulatus and Chaetosiphella . The monotypic genera Caricosipha and Laingia formed separate lineages, and Laingia was sister to all other Siphini. Chaitophorini was not retrieved by the molecular and combined data: Periphyllus was sister to a clade containing Chaitophorus and Siphini.

The Australasian region contains a significant proportion of worldwide Poa diversity, but the evolutionary relationships of taxa from this region are incompletely understood. Most Australasian species have been placed in a monophyletic Poa subgenus, Poa supersection Homalopoa section Brizoides clade, but with limited resolution of relationships. In this study, phylogenetic relationships were reconstructed for Australasian Poa, using three plastid (rbcL and matK genes and the rpl32-trnL intergenic spacer) and two nuclear [internal/external transcribed spacer (ITS/ETS)] markers. Seventy-five Poa spp. were represented (including 42 Australian, nine New Guinean, nine New Zealand and three Australian/New Zealand species). Maximum parsimony, maximum likelihood and Bayesian inference criteria were applied for phylogenetic reconstruction. Divergence dates were estimated using Bayesian inference, with a relaxed clock applied and rates sampled from an uncorrelated log-normal distribution. Australasian Poa spp. are placed in three lineages (section Brizoides, section Parodiochloa and the ‘X clade’), each of which is closely related to non-Australasian taxa or clades. Section Brizoides subsection Australopoa is polyphyletic as currently circumscribed. In Australasia, Poa has diversified within the last 4.3 Mya, with divergence dating results broadly congruent with fossil data that record the appearance of vegetation with a prominent grassland understorey or shrubland/grassland mosaic vegetation dating from the mid-Pliocene. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175, 523–552.

We provide objective criteria for assessing the taxonomic status of genera, especially those that are monotypic, using the coccid genus Taiwansaissetia Tao, Wong & Chang. This genus contains only the type species, Lecanium formicarii Green [currently Taiwansaissetia formicarii (Green)], known from the Afrotropical and Oriental regions. Here, Taiwansaissetia is synonymised ( syn.nov. ) with Coccus Linnaeus (Hemiptera: Coccidae) on the basis of phylogenetic analyses of DNA sequence data and morphological examination. All analyses (maximum parsimony, neighbour‐joining and Bayesian inference) of four gene regions ( 18S , 28S , COI and EF‐1α ), and a concatenation of these regions, placed the clade including T. formicarii and three unidentified Coccus specimens as sister to the type species of Coccus , C. hesperidum Linnaeus, with high support. Taiwansaissetia formicarii is more closely related to C. hesperidum than C. hesperidum is to C. viridis (Green), which is considered to be a ‘typical’ species of Coccus, and several other current members of Coccus [ C. longulus (Douglas), C. penangensis Morrison and C. pseudomagnoliarum (Kuwana)]. Explicit criteria, including monophyly, diagnosability, sister taxa being of equal rank, and the level of genetic divergence between T. formicarii and C. hesperidum relative to within‐genus divergence of other scale insects, were used to assess the taxonomic status of Taiwansaissetia . The autapomorphic features of Taiwansaissetia that differentiate it from typical species of Coccus might be due to its myrmecophilous habit and adaptation to living inside ant nests – most other species of Coccus live externally on their host plants. Since its description in 1896, T. formicarii has been placed in four different genera: here we transfer it back to Coccus as C. formicarii (Green) stat.rev. We rediagnose the genus Coccus to accommodate the features of C. formicarii . This study also found that Coccus might not be monophyletic, warranting further study of the group.

A phylogenetic analysis of the order Embioptera is presented with a revised classification based on results of the analysis. Eighty‐two species of Embioptera are included from all families except Paedembiidae Ross and Embonychidae Navás. Monophyly of each of the eight remaining currently recognized families is tested except Andesembiidae Ross, for which only a single species was included. Nine outgroup taxa are included from Blattaria, Grylloblattaria, Mantodea, Mantophasmatodea, Orthoptera, Phasmida and Plecoptera. Ninety‐six morphological characters were analysed along with DNA sequence data from the five genes 16S rRNA , 18S rRNA , 28S rRNA , cytochrome c oxidase I and histone III . Data were analysed in combined analyses of all data using parsimony and Bayesian optimality criteria, and combined molecular data were analysed using maximum likelihood. Several major conclusions about Embioptera relationships and classification are based on interpretation of these analyses. Of eight families for which monophyly was tested, four were found to be monophyletic under each optimality criterion: Clothodidae Davis, Anisembiidae Davis, Oligotomidae Enderlein and Teratembiidae Krauss. Australembiidae Ross was not recovered as monophyletic in the likelihood analysis in which one Australembia Ross species was recovered in a position distant from other australembiids. This analysis included only molecular data and the topology was not strongly supported. Given this, and because parsimony and the Bayesian analyses recovered a strongly supported clade including all Australembiidae, we regard this family also as monophyletic. Three other families – Notoligotomidae Davis, Archembiidae Ross and Embiidae Burmeister, as historically delimited – were not found to be monophyletic under any optimality criterion. Notoligotomidae is restricted here to include only the genus Notoligotoma Davis with a new family, Ptilocerembiidae Miller and Edgerly, new family, erected to include the genus Ptilocerembia Friederichs. Archembiidae is restricted here to include only the genera Archembia Ross and Calamoclostes Enderlein. The family group name Scelembiidae Ross is resurrected from synonymy with Archembiidae (new status) to include all other genera recently placed in Archembiidae. Embiidae is not demonstrably monophyletic with species currently placed in the family resolved in three separate clades under each optimality criterion. Because taxon sampling is not extensive within this family in this analysis, no changes are made to Embiidae classification. Relationships between families delimited herein are not strongly supported under any optimality criterion with a few exceptions. Either Clothodidae Davis (parsimony) or Australembiidae Ross (Bayesian) is the sister to the remaining Embioptera taxa. The Bayesian analysis includes Australembiidae as the sister to all other Embioptera except Clothididae, suggesting that each of these taxa is a relatively plesiomorphic representatative of the order. Oligotomidae and Teratembiidae are sister groups, and Archembiidae ( sensu novum ), Ptilocerembiidae, Andesembiidae and Anisembiidae form a monophyletic group under each optimality criterion. Each family is discussed in reference to this analysis, diagnostic combinations and taxon compositions are provided, and a key to families of Embioptera is included.