Limb myology and phylogenetic relationships in the superfamily Dipodoidea (birch mice, jumping mice, and jerboas)

Limb muscles were dissected in seven genera, representing all six superfamilies, of dipodoid rodents and myoloic characters were used to construct a phylogenetic hpothesis of relationships within this cfade. Mologic differences among genera suported tie monophyly of the superfamily Dipodoidea reLtive to the outrou taxon and reveaEd thatSicista is the sister group to all other zapodid and dipodid enera. Tkis picement of Sicista differs markedly from its position in previous classifications where it has been regarded merely as a primitive zapodid genus. The phlograrn based on rnyologic characters also indicated that Cardiocranius is not a rimitive dipodid genus; it is the sister group to the subfamily Dipodinae. Although myologic differences among taxa were not sufficient to warrant the continued separation of zaodids and dipodids into two families, a new classification that places Sicista in its own family, ficistidae, and places the remaining zaodids and dipodids in the family Dipodidae, is proposed. Differences in karyology, genitaP morholoy, and postcranial osteological characters among dipodoid rodents are discussed in light or this pjylogeny.     

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

Phylogeny and biogeography of tetralophodont rodents of the tribe Oryzomyini (Cricetidae: Sigmodontinae)

Oryzomyini is the richest tribe among the Sigmodontine rodents, encompassing 32 living and extinct genera and including an increasing number of recently described species and genera. Some Oryzomyini are tetralophodont showing a reduction in the number of molar folds to four, while most taxa in this tribe retain the plesiomorphic pentalophodont state. We applied phylogenetic methods, molecular dating techniques and ancestral area analyses to members of an oryzomyini clade informally named ‘D’ in former studies and included related fossil tetralophodont forms. Based on 98 morphological characters and sequences of five gene fragments, we found that the tetralophodont condition is paraphyletic. Among living taxa, Pseudoryzomys is sister to Holochilus, and Lundomys is derived from a basal divergence. A clade formed by living Holochilus and the fossils Noronhomys and Carletonomys is sister to Holochilus primigenus, making Holochilus paraphyletic. Therefore, we describe a new genus that accommodates the fossil H. primigenus. Because trans‐Andean taxa currently share a common ancestor with taxa of cis‐Adean distribution, the northern Andes uplift may have worked as a postdispersal barrier. The tetralophodont lineages diverged during the Pliocene from a cis‐Andean ancestor, and the Great Plains in South America may have favoured the diversification of tetralophodont forms adapted to open habitats during the Pliocene.     

Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera,Phyllostomidae) with descriptions of two new species

The systematics and taxonomy of the Neotropical genus Micronycteris are not yet resolved; previous studies evidenced paraphyletic relationships, a number of potential undescribed species, and inadequate diagnostic characters. This revision focuses on the pale-bellied members of the genus using phylogenetic and morphometric tools, an increased sample size with all recognized taxa, and an expanded geographic coverage relative to prior studies. For the genetic analyses (n = 166), four molecular markers were concatenated, one mitochondrial (cytb), one nuclear (Fgb-I7), and two Y-chromosomal (DBY5 and DBY7). In the Bayesian and maximum likelihood analyses, the recognized subgenera Schizonycteris, Leuconycteris, Xenoctenes, and Micronycteris were recovered as monophyletic. The pale-bellied subgenera, Schizonycteris and Leuconycteris, were not sister clades; thus, venter coloration was not monophyletic. Leuconycteris was sister to the dark-bellied Micronycteris, and Schizonycteris was sister to the rest of the genus. Micronycteris schmidtorum was genetically defined for the first time, and it was determined all previous phylogenetic studies used a misidentified M. minuta from Bolivia. Our results showed a sister relationship between M. schmidtorum and M. brosseti, which redefines Leuconycteris. The subgenus Schizonycteris was also redefined, and it presented two well-supported clades from Central America and western Ecuador that are described as new species. Results are supported by a multivariate morphometric analyses (n = 114), karyological, and morphological comparisons. The taxonomic implications are discussed and emended diagnoses presented for the pale-bellied subgenera and for M. schmidtorum.     

The genus Gymnospermium (Berberidaceae) in Italy: identity and relationships of the populations at the western limit of the genus range

Abstract

Gymnospermium is a small genus of 7–12 taxa subject to diverging taxonomic treatments and distributed from east China to the Balkans. The recent discovery of Gymnospermium in the S-Apennines posed questions about origin and identity. Accordingly, we performed a systematic investigation by means of morphological, karyological and molecular tools. All populations were diploid with 2n = 14 as for the Balkan G. scipetarum (incl. G. maloi), and also morphology suggested a close affinity to the latter. However, the Italian populations differed from typical G. scipetarum by the lower stamen:petal length and style:carpel length. By including all European and most Asian taxa in a phylogenetic analysis, we shed new light into the species-level relationships in this genus. In the combined ITS-trnL-F phylogeny, two major clades were retrieved. One included the central Asian and eastern European taxa plus the Greek endemic G. peloponnesiacum sister to G. odessanum, and one the Balkan and Apennine populations. Such findings further corroborated that the Apennine plant belong to G. scipetarum. The native status of the Italian population is supported by exclusive SNPs in both ITS1 and trnL-F sequences. Along with morphological evidence, this allows to refer it to the new subspecies G. scipetarum subsp. eddae.     

Molecular phylogeny of flat‐footed flies (Diptera: Platypezidae): main clades supported by new morphological evidence

The molecular phylogeny of flat‐footed flies is inferred from analysis of DNA sequence data from the five mitochondrial genes 12S, 16S, COI, COII and CytB, and the nuclear gene 28S and discussed with the recent systematics based on morphological features. The Bayesian inference, maximum likelihood and maximum parsimony analyses included 42 species of 18 genera, representing all four extant subfamilies (Microsaniinae, Melanderomyiinae, Callomyiinae and Platypezinae) and all known genera except one (Metaclythia). Representatives of the brachycerous taxa Lonchopteridae, Phoridae, Sciadocerinae (Phoridae) and Opetiidae are used as outgroups, and Lonchoptera was used to root the trees. Our results show Platypezidae consisting of two well‐supported clades, the first with the subfamilies Melanderomyiinae + Callomyiinae and the second formed by subfamily Platypezinae. Genus Microsania was resolved as a separate lineage distant from Platypezidae which clustered with Opetiidae as its sister group, both together forming a sister group to Platypezidae. At the generic level, the genus Agathomyia proved not to be monophyletic in any of the analyses. The species Chydaeopeza tibialis is sister to Agathomyia sexmaculata, and consequently, the genus Chydaeopeza Shatalkin, 1992 is a new junior synonym of Agathomyia Verrall, 1901. Bifurcated setae on legs of adult Platypezidae are documented as a new synapomorphy of the family, exclusive of Microsania. Outstretched wings and only a small overlap of their surfaces at resting position are considered a new synapomorphy for the subfamily Platypezinae. Other phylogenetically important characters defining main clades are documented, and their relevance/validity in phylogenetic studies is discussed. The current systematic concept of Platypezidae is discussed, and new phylogenetic hypotheses are proposed.     

Phylogenetic relationships in the skin-inhabiting Sarcoptoidea (Acari: Astigmata)

A phylogenetic analysis of relationships is carried out among the skin-inhabiting mites presently included in the families Rhyncoptidae, Audycoptidae and Sarcoptidae. The analysis included eight taxa (five genera of follicle associates and three subfamilies of skin-burrowing sarcoptids) and 41 characters, and generated a single most parsimonious tree of length 60 with a consistency index of 0.745. The genus Caenolestocoptes (Sarcoptidae, Caenolestocoptinae) is the sister group of the assemblage of Ursicoptes, Saimirioptes, Audycoptes (all Audycoptidae) and Rhyncoptes (Rhyncoptidae). Within the latter grouping Audycoptes is the sister group of Rhyncoptes. Based on these results the Caenolestocoptinae Fain & Lukoschus, 1976 and Audycoptidae Lavoipierre, 1964 are synonymised with the Rhyncoptidae Lawrence, 1956. The Rhyncoptidae (sensu nov.) appears to be the sister group of the Sarcoptidae (sensu stricto).The distribution pattern of follicle inhabitation and skin-burrowing in the Sarcoptoidea can be explained by one adaptation to follicle inhabitation (Rhyncoptidae), another to skin-burrowing (Sarcoptidae) and possibly a third in their common ancestor from living on the hairs or on the skin to living in the skin (follicles, burrows or both).New host and locality data for various taxa in the Rhyncoptidae (sensu nov.) are provided. The larva of Audycoptes lawrencei Lavoipierre, 1964, is described and the female redescribed.     

The higher‐level phylogenetic relationships of the Eumeninae (Insecta,Hymenoptera, Vespidae), with emphasis on Eumenes sensu lato

Cladistic analyses were carried out to infer the phylogenetic relationships among taxa that were originally part of the large genus Eumenes. Terminals belonging to other eumenine lineages were also included, as well as terminals from other vespid subfamilies. Analyses under equal weights and implied weights were carried out, and better results were obtained with the latter. The results corroborated the monophyly of Eumeninae, and recovered Zethini sensu lato as the sister‐lineage to the remaining eumenines. Eumenes sensu lato as originally recognized is paraphyletic relative to Odynerus sensu lato. A natural classification at the tribal level congruent with the phylogenetic results may be proposed, and the names Zethini, Odynerini, and Eumenini are already available. This is the most comprehensive phylogeny of the Eumeninae to date. A new generic synonymy is Alfieria Giordani Soika, 1934 = Delta de Saussure, 1855.     

The systematics of right whales (Mysticeti: Balaenidae)

Balaenidae (right whales) are large, critically endangered baleen whales represented by four living species. The evolutionary relationships of balaenids are poorly known, with the number of genera, relationships to fossil taxa, and position within Mysticeti in contention. This study employs a comprehensive set of morphological characters to address aspects of balaenid phylogeny. A sister‐group relationship between neobalaenids and balaenids is strongly supported, although this conflicts with molecular evidence, which may be an artifact of long‐branch attraction (LBA). Monophyly of Balaenidae is supported, and three major clades are recognized: (1) extinct genus Balaenula, (2) extant and extinct species of the genus Eubalaena, and (3) extant and extinct species of the genus Balaena plus the extinct taxon, Balaenella. The relationships of these clades to one another, as well as to the early Miocene stem balaenid, Morenocetus parvus, remain unresolved. Pliocene taxa, Balaenula astensis and Balaenula balaenopsis, form a clade that is the sister group to the Japanese Pliocene Balaenula sp. Eubalaena glacialis and Pliocene Eubalaena belgica, are in an unresolved polytomy with a clade including E. japonica and E. australis. Extant and fossil species of Balaena form a monophyletic group that is sister group to the Dutch Pliocene Balaenella, although phylogenetic relationships within Balaena remain unresolved.     

An integrative approach to species delimitation in Echinodorus (Alismataceae) and the description of two new species

Summary  Taxonomy of the genus Echinodorus is partially revisited in the light of current understanding of the phylogenetic relationships of the genus. As a result of new taxonomy, the species status of some previously synonymised taxa are restored, other names are synonymised, and some nomenclatural problems unnoticed by previous authors are resolved. Two new species, Echinodorus reptilis and E. emersus are described. The subgeneric divisions of the genus are not accepted, and all subspecific taxa are either rejected or established as species. As a result, 28 species based on a phylogenetic species concept are now recognised in Echinodorus and an identification key to these species is provided.     

Molecular phylogeny,biogeography and chromosome evolution of Malagasy dwarf geckos of the genus Lygodactylus (Squamata,Gekkonidae)

We performed a phylogenetic analysis using nuclear (RAG‐1, RAG‐2) and mitochondrial (16S) markers, a statistical Bayesian reconstruction of ancestral distribution areas and a karyological analysis on most Malagasy species of the gekkonid genus Lygodactylus. The phylogenetic analysis largely confirms major basal branching pattern of previous molecular studies, but highlights significant differences concerning both the relationships between different species groups as well as those within groups. The biogeographic analysis supports a Malagasy origin of Lygodactylus, an oversea dispersal to continental Africa and a return to Madagascar. The L. madagascariensis group (also including a new candidate species identified herein) is the most basal clade in Lygodactylus, and the sister group of a clade with all the remaining species. The second most basal clade is the L. verticillatus group, placed as the sister group of a clade comprising African and Malagasy species. The sister lineage of the L. verticillatus group originated the African radiation through an oversea dispersal out of Madagascar. Eventually, the sister lineage of the L. capensis group originated secondary dispersals from Africa to Madagascar. In Madagascar, lineage diversification in different species groups mainly occurred from southern to northern and eastern regions. Dispersal, vicariance and paleoclimatic refugia probably played a relevant role in the evolutionary history of closely related taxa and in speciation mechanisms. The cytogenetic analysis evidenced a high karyotypic variability in Lygodactylus (from 2n = 34 to 2n = 40), which is at least partly consistent with the phylogenetic relationships and the composition of the various species group. Chromosome evolution occurred independently in different lineages, mainly through a reduction in the chromosome number and starting from a putative primitive karyotype of 2n = 40 with all telocentric elements.     

Diversity of North American map and sawback turtles (Testudines: Emydidae: Graptemys)

Map turtles of the genus Graptemys are native to North America, where a high degree of drainage endemism is believed to have shaped current diversity. With 14 species and one additional subspecies, Graptemys represents the most diverse genus in the family Emydidae. While some Graptemys species are characterized by pronounced morphological differences, previous phylogenetic analyses have failed yet to confirm significant levels of genetic divergence for many taxa. As a consequence, it has been debated whether Graptemys is taxonomically inflated or whether the low genetic divergence observed reflects recent radiations or ancient hybridization. In this study, we analysed three mtDNA blocks (3228 bp) as well as 12 nuclear loci (7844 bp) of 89 specimens covering all species and subspecies of Graptemys. Our analyses of the concatenated mtDNA sequences reveal that the widespread G. geographica constitutes the sister taxon of all other Graptemys species. These correspond to two clades, one comprised of all broad‐headed Graptemys species and another clade containing the narrow‐headed species. Most species of the broad‐headed clade are reciprocally monophyletic, except for G. gibbonsi and G. pearlensis, which are not differentiated. By contrast, in the narrow‐headed clade, many currently recognized species are not monophyletic and divergence is significantly less pronounced. Haplotype networks of phased nuclear loci show low genetic divergence among taxa and many shared haplotypes. Principal component analyses using coded phased nuclear DNA sequences revealed eight distinct clusters within Graptemys that partially conflict with the terminal mtDNA clades. This might be explained by male‐mediated gene flow across drainage basins and female philopatry within drainage basins. Our results support that Graptemys is taxonomically oversplit and needs to be revised.     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

New data on the phylogeny of Ariantinae (Pulmonata,Helicidae) and the systematic position of Cylindrus obtusus based on nuclear and mitochondrial DNA marker sequences

The phylogenetic relationships among genera of the subfamily Ariantinae (Pulmonata, Helicidae), especially the sister‐group relationship of Cylindrus obtusus, were investigated with three mitochondrial (12S rRNA, 16S rRNA, Cytochrome c oxidase subunit I) and two nuclear marker genes (Histone H4 and H3). Within Ariantinae, C. obtusus stands out because of its aberrant cylindrical shell shape. Here, we present phylogenetic trees based on these five marker sequences and discuss the position of C. obtusus and phylogeographical scenarios in comparison with previously published results. Our results provide strong support for the sister‐group relationship between Cylindrus and Arianta confirming previous studies and imply that the split between the two genera is quite old. The tree reveals a phylogeographical pattern of Ariantinae with a well‐supported clade comprising the Balkan taxa which is the sister group to a clade with individuals from Alpine localities. Additional lineages representing samples from southern Alpine localities as well as from Slovakia split from more basal nodes, but their relationships are not clearly resolved. To achieve more definitive conclusions concerning the geographical origin of Ariantinae, still more sequence data are needed to obtain a tree with better resolution of basal nodes. The genetic data also provided new insights concerning the genus Cepaea, which was used as one of the outgroup taxa. Cepaea vindobonensis is only distantly related to Cepaea nemoralis and Cepaea hortensis, the latter two being more closely related to Eobania vermiculata. Thus, in our tree, the genus Cepaea is paraphyletic.     

The phylogeny of Anophelinae revisited: inferences about the origin and classification of Anopheles (Diptera: Culicidae)

The evolution of anopheline mosquitoes (Culicidae: Anophelinae) has been the subject of speculation and study for decades, but a comprehensive phylogeny of these insects is far from complete. The results of phylogenetic studies based on morphological and molecular data sets are conspicuously ambiguous. Here, we revisit the phylogenetic relationships of anopheline mosquitoes using state‐of‐the‐art software and cladistic methods to analyse the data set of Harbach & Kitching (2005). We present a refined interpretation of relationships based on analyses of a revised data set that includes an additional species. Implied weighting analyses were conducted with TNT with the concavity constant K ranging from 1 to 33. We determined the optimal K value by summing the GC supports for each MPC and selected the tree with the highest support, K = 30, as the preferred cladogram. We then collapsed the branches with GC support < 1 to obtain the ‘best’ topography of relationships. Genus Chagasia is the basalmost taxon of Anophelinae, and genus Anopheles is recovered as monophyletic but only if Anopheles implexus is excluded and genus Bironella is subordinated within it. The Afrotropical An. implexus is recovered as the sister to all other anophelines, and Christya Theobald, stat. nov., is elevated from synonymy with Anopheles Meigen as a subgenus to accommodate it. The other anophelines comprise two large clades. The first includes the reciprocally monophyletic subgenera Kerteszia + Nyssorhynchus; the second consists of subgenus Cellia as the sister to a heterogeneous clade that includes genus Bironella and subgenera Anopheles, Baimaia, Lophopodomyia and Stethomyia of genus Anopheles. The sister relationship of Cellia and the heterogeneous clade is lost when the branches with GC <1 are collapsed. The monophyly and non‐monophyly of the informal subordinate taxa of subgenera Nyssorhynchus, Cellia and Anopheles, and also evolutionary scenarios, are discussed in relation to previous studies.