A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes

Even though the marsupial order Diprotodontia is one of the most heavily studied groups of Australasian marsupials, phylogenetic relationships within this group remain contentious. The more than 125 living species of Diprotodontia can be divided into two main groups: Vombatiformes (wombats and koalas) and Phalangerida. Phalangerida is composed of the kangaroos (Macropodidae, Potoroidae, and Hypsiprymnodontidae) and possums (Phalangeridae, Burramyidae, Petauridae, Pseudocheiridae, Tarsipedidae, and Acrobatidae). Much of the debate has focused on relationships among the families of possums and whether possums are monophyletic or paraphyletic. A limitation of previous investigations is that no study to date has investigated diprotodontian relationships using all genera. Here, we examine diprotodontian interrelationships using a nuclear multigene molecular data set representing all recognized extant diprotodontian genera. Maximum parsimony, maximum likelihood, and Bayesian methods were used to analyze sequence data obtained from protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF. We also applied a Bayesian relaxed molecular clock method to estimate times of divergence. Diprotodontia was rooted between Vombatiformes and Phalangerida. Within Phalangerida, the model-based methods strongly support possum paraphyly with Phalangeroidea (Burramyidae + Phalangeridae) grouping with the kangaroos (Macropodiformes) to the exclusion of Petauroidea (Tarsipedidae, Acrobatidae, Pseudocheiridae, and Petauridae). Within Petauroidea, Tarsipedidae grouped with both Petauridae and Pseudocheiridae to the exclusion of Acrobatidae. Our analyses also suggest that the diprotodontian genera Pseudochirops and Strigocuscus are paraphyletic and diphyletic, respectively, as currently recognized. Dating analyses suggest Diprotodontia diverged from other australidelphians in the late Paleocene to early Eocene with all interfamilial divergences occurring prior to the early Miocene except for the split between the Potoroidae and Macropodidae, which occurred sometime in the mid-Miocene. Ancestral state reconstructions using a Bayesian method suggest that the patagium evolved independently in the Acrobatidae, Petauridae, and Pseudocheiridae. Ancestral state reconstructions of ecological venue suggest that the ancestor of Diprotodontia was arboreal. Within Diprotodontia, the common ancestor of Macropodidae was reconstructed as terrestrial, suggesting that tree kangaroos (Dendrolagus) are secondarily arboreal.     

A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes

Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.     

A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences

DNA sequences from the first intron of the nuclear gene rhodopsin (RDP1) and from the mitochondrial gene ND2 were used to construct a phylogeny of the avian family Megapodiidae. RDP1 sequences evolved about six times more slowly than ND2 and showed less homoplasy, substitution bias, and rate heterogeneity across sites. Analysis of RDP1 produced a phylogeny that was well resolved at the genus level, but RDP1 did not evolve rapidly enough for intrageneric comparisons. The ND2 phylogeny resolved intrageneric relationships and was congruent with the RDP1 phylogeny except for a single node: this node was the only aspect of tree topology sensitive to weighting in parsimony analyses. Despite differences in sequence evolution, RDP1 and ND2 contained congruent phylogenetic signal and were combined to produce a phylogeny that reflects the resolving power of both genes. This phylogeny shows an early split within the megapodes, leading to two major clades: (1) Macrocephalon and the mound-building genera Talegalla, Leipoa, Aepypodius, and Alectura, and (2) Eulipoa and Megapodius. It differs significantly from previous hypotheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice.     

A phylogeny of Porella (Porellaceae, Jungermanniopsida) based on nuclear and chloroplast DNA sequences

The cosmopolitan family Porellaceae includes about 60 species in two or three genera: the large genus Porella and the monospecific Ascidiota and Macvicaria (alternatively Porella subg. Macvicaria). Maximum parsimony, maximum likelihood and Bayesian inference of phylogeny of a dataset including three markers (rbcL, trnL-trnF region of cp DNA, nrITS region) of 96 accessions resulted in similar topologies supporting the generic status of Ascidiota. Macvicaria is nested in a subclade of Porella. Relationships among species of Porella are in general well resolved and many terminal nodes achieve good statistical support whereas basal relationships are at best moderately supported. Multiple accessions of single species are usually placed in monophyletic lineages. Accessions of P. platyphylla split into a European and a North American clade with one accession from North America embedded within the European samples. The Macaronesian endemic P. inaequalis is closely related to the Asian species P. grandiloba. Porella obtusata and P. canariensis cannot be separated on the basis of the sequence data presented in this study. The molecular topologies indicate a range extension of the Asian P. gracillima subsp. urogea to Eastern North America and of the Neotropical P. swartziana to South Africa. Current supraspecific classifications of Porella are not reflected in the molecular topologies with a correlation between genetic variation and the geographical distribution of the related accessions rather than a correlation between genetic variation and morphology.     

Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences

Phylogenetic relationships of the Poaceae subfamily, Pooideae, were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The entire ITS region of 25 species belonging to 19 genera representing seven tribes was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The published sequence of rice, Oryza saliva, was used as the outgroup. Sequences of these taxa were analyzed with maximum parsimony (PAUP) and the neighbor-joining distance method (NJ). Among the tribes, the Stipeae, Meliceae and Brachypodieae, all with small chromosomes and a basic number more than x=7, diverged in succession. The Poeae, Aveneae, Bromeae and Triticeae, with large chromosomes and a basic number of x=7, form a monophyletic clade. The Poeae and Aveneae are the sister group of the Bromeae and Triticeae. On the ITS tree, the Brachypodieae is distantly related to the Triticeae and Bromeae, which differs from the phylogenies based on restriction-site variation of cpDNA and morphological characters. The phylogenetic relationships of the seven pooid tribes inferred from the ITS sequences are highly concordant with the cytogenetic evidence that the reduction in chromosome number and the increase in chromosome size evolved only once in the pooids and pre-dated the divergence of the Poeae, Aveneae, Bromeae and Triticeae.This paper reports factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitableThis paper is a cooperative investigation of USDA-ARS and the Utah Agricultural Experiment Station. Logan, Utah 84322. Journal Paper No. 4581     

A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences

A phylogeny of the genus Gammarus Fabricius, 1775 was constructed using DNA sequence data from the mitochondrial genes COI and 16S, and the nuclear genes 18S and 28S. Both parsimony and Bayesian analyses were conducted on separate and combined data partitions. The Bayesian phylogeny from the combined analysis was selected as the preferred phylogenetic hypothesis. The hypothesis supports monophyly of the genus Gammarus, paraphyly of the European-North American Gammarus, and monophyly of the Asian Gammarus. The Asian clade was further split into a southeastern group and a northwestern group. The dramatic climate change following the uplift of the Tibetan Plateau was probably the most important factor in triggering the diversification of southeastern and northwestern groups. The genus Sinogammarus is invalid and should be part of the genus Gammarus.     

Molecular phylogeny ofCheirolophus (Asteraceae:Cardueae-Centaureinae) based on ITS sequences of nuclear ribosomal DNA

The genusCheirolophus has an interesting western Mediterranean and Macaronesian distribution. Here we investigate the delimitation of the genus and its exclusion from the large genusCentaurea, the systematic position of the related genusPaleocyanus, the delimitation of some species and the phylogeny of the group. We have carried out a phylogenetic analysis of the PCR-generated sequences of the internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. The results suggest that the genus, includingPaleocyanus crassifolius is monophyletic; thus, a new combination of this species underCheirolophus is proposed. The Macaronesian group of species is also monophyletic, indicating a single colonization of the archipelago. The poor resolution of microspecies in the Macaronesian group reinforces the hypothesis of a very recent differentiation of the group.     

A molecular phylogeny of Arceuthobium (Viscaceae) based on nuclear ribosomal DNA internal transcribed spacer sequences

Ribosomal DNA (rDNA) internal transcribed spacer (ITS) and 5.8S rDNA sequences were obtained from 22 species of dwarf mistletoes (Arceuthobium — Viscaceae) to test phylogenetic relationships. Interspecific distances ranged from 0 to 21.4% between New World species, values two to five times higher than those measures for the ITS region in other plants. One Old World species (A. oxycedri) and one New World species (A. abietis-religiosae) were remarkably similar to each other but exhibited up to 41% sequence divergence from the remaining species. Minimum length trees support the concept of a verticillately branched subgenus Arceuthobium; however, interspecific distances indicate this group is extremely heterogeneous. Subgenus Vaginata, Section Vaginata, is centered in Mexico and encompasses all the taxa previously placed in this group but is expanded to include several species previously classified in Section Campylopoda (e.g., A. divaricatum, A. rubrum, and A. strictum). The sister group relationship between A. divaricatum and A. douglasii, first seen following isozyme analysis, is supported by ITS sequence data. Section Campylopoda s. s. is now composed of 13 mainly U.S. species that show a high degree of morphological and genetic similarity. The eastern dwarf mistletoe, A. pusillum, is not closely related to A. douglasii but rather with A. bicarinatum from Hispaniola, which suggests that these taxa represent highly modified relicts that shared an ancestor in the early Tertiary. Two endemic species from Mexico and Central America (A. guatemalense and A. pendens) formed a sister group and have been placed in a new Section (Penda). Rapid molecular evolution in Arceuthobium may be associated with the adaptive radiation of this genus on numerous conifer hosts.     

Green lacewing phylogeny, based on three nuclear genes (Chrysopidae, Neuroptera)

Abstract.  Systematic relationships among higher taxa within Chrysopidae, a large and agriculturally significant neuropteran family, are poorly understood. A molecular phylogenetic survey of Chrysopidae was performed with three nuclear genes, namely wingless (546 bp), phosphoenolpyruvate carboxykinase (483 bp), and sodium/potassium ATPase alpha subunit (410 bp). We examined 83 species in 24 genera, mainly from Japan, Eurasia and Africa. Parsimony and Bayesian analyses of combined datasets of a total of 1439 bp demonstrated that (1) monophyly of the subfamily Chrysopinae was supported but the relationship between Nothochrysinae and Apochrysinae was unclear, although the two subfamilies together may constitute the sister taxon of Chrysopinae; (2) of the three tribes examined within Chrysopinae (Ankylopterygini, Belonopterygini and Chrysopini), monophyly of Ankylopterygini and Belonopterygini was supported, but the relationships among the three remain unclear; (3) seven sub-clades in Chrysopini were indicated, namely (i) Brinckochrysa , (ii) Chrysemosa  +  Suarius , (iii) Chrysotropia  +  Nineta , (iv) Mallada  +  Chrysoperla  +  Peyerimhoffina , (v) Cunctochrysa  +  Meleoma  +  Nipponochrysa  +  Apertochrysa albolineatoides , (vi) Chrysopa  +  Plesiochrysa , and (vii) Dichochrysa  +  Apertochrysa eurydera ; and (4) most genera were monophyletic, except for Apertochrysa and Cunctochrysa , each of which was shown to have two distinct origins. Our molecular analysis allowed the assignment of several species of uncertain affinities to known genera. There was some disagreement between the molecular and previously published morphological phylogenies, but in general our results confirmed existing morphological hypotheses of evolution within the family.     

Molecular phylogeny of Lysimachia (Myrsinaceae) based on chloroplast trnL-F and nuclear ribosomal ITS sequences

Both nuclear ribosomal ITS and chloroplast trnL-F sequences were acquired for 57 species (accessions) of Lysimachia and its close relatives, and were analyzed together with sequences retrieved from databases. The results of phylogenetic analyses based on these data (separately or combined) show that Lysimachia is paraphyletic, with the monotypic genus Glaux nested deeply inside. Previous suggestions that Anagallis and Trientalis could be ingroups of Lysimachia were not corroborated by our results. The molecular phylogenies do not support the current infrageneric divisions of Lysimachia. Subgenus Lysimachia contains at least five independent lineages. The Hawaii endemic subgenus Lysimachiopsis was shown to group with subgenera Palladia and Heterostylandra, instead of subgenus Idiophyton as previously suggested. The two North American representatives of Lysimachia, subgenus Seleucia and section Verticillatae of subgenus Lysimachia are group together as the most basal clade of the genus. Parallel and independent evolutions were inferred for morphological characters that were previously used as diagnostic criteria. Molecular phylogenies do not offer clear inferences on the overall historical biogeography of Lysimachia, but Southeast Asia origins of several clades, including the Hawaiian endemic clade and the Iberian Lysimachia ephemerum are strongly supported.     

Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.     

Phylogenetic relationships of living and recently extinct bandicoots based on nuclear and mitochondrial DNA sequences

Bandicoots (Peramelemorphia) are a major order of australidelphian marsupials, which despite a fossil record spanning at least the past 25 million years and a pandemic Australasian range, remain poorly understood in terms of their evolutionary relationships. Many living peramelemorphians are critically endangered, making this group an important focus for biological and conservation research. To establish a phylogenetic framework for the group, we compiled a concatenated alignment of nuclear and mitochondrial DNA sequences, comprising representatives of most living and recently extinct species. Our analysis confirmed the currently recognised deep split between Macrotis (Thylacomyidae), Chaeropus (Chaeropodidae) and all other living bandicoots (Peramelidae). The mainly New Guinean rainforest peramelids were returned as the sister clade of Australian dry-country species. The wholly New Guinean Peroryctinae was sister to Echymiperinae. The poorly known and perhaps recently extinct Seram Bandicoot (Rhynchomeles) is sister to Echymipera. Estimates of divergence times from relaxed-clock Bayesian methods suggest that living bandicoots originated in the late Oligocene or early Miocene, much earlier than currently thought based on fossils. Subsequent radiations within Peramelemorphia probably took place on the Australian mainland during the Miocene, with diversification of rainforest taxa on the newly emergent New Guinean landmasses through the middle-late Miocene and complete establishment of modern lineages by the early Pliocene.     

A preliminary phylogeny of the Pentatomomorpha (Hemiptera: Heteroptera) based on nuclear 18S rDNA and mitochondrial DNA sequences

Pentatomomorpha is the second suborder in size only to Cimicomorpha in Heteroptera. However, the phylogenetic relationships among members of the suborder are not well established. Sequences from partial nuclear ribosomal 18S gene and mitochondrial COX1 gene were analyzed separately and in combination to generate a preliminary molecular phylogeny of Pentatomomorpha based on 40 species representing 17 putative families. Analyses of the combined sequence data provided a better-resolved and more robust hypothesis of Pentatomomorpha phylogeny than did separate analyses of the individual genes. The phylogenies were mostly congruent with morphological studies. Results strongly supported the monophyly of the infraorder Pentatomomorpha, and the placement of Aradoidea as sister to Trichophora. The monophyletic Trichophora was grouped into two major lineages, one being the superfamily Pentatomoidea, and the other comprising Lygaeoidea, Coreoidea, and Pyrrhocoroidea. The analysis of the ML and ME trees of combined dataset supported the monophyletic Pentatomoidea. In all analysis the Pyrrhocoroidea was polyphyletic; the monophyletic Lygaeoidea was supported only in the analysis of ME tree, and Coreoidea was polyphyletic except in the MP tree of combined dataset. The molecular and morphylogical data both indicated that the family Coreoidae should be revised subsequently. Our phylogenetic results suggested that the COX1 segment alone might not be an optimal molecular marker for the phylogeny of Pentatomomorpha.     

Molecular phylogeny and a chronology of diversification for "phractocephaline" catfishes (Siluriformes: Pimelodidae) based on mitochondrial DNA and nuclear recombination activating gene 2 sequences

The Maracaibo basin in northwestern Venezuela is home to over 108 species of freshwater fishes, over half of which occur nowhere else. The rise of the Mérida Andes between 8 and 10 million years ago is believed to have divided a preexisting biota and facilitated allopatric speciation. The distinctive "phractocephaline" clade of pimelodid catfishes has a distribution that includes the Maracaibo historically and today is represented by Perrunichthys (Maracaibo endemic), Leiarius, Phractocephalus, and Steindachneridion. A resolved and well-supported phylogeny was obtained from the phylogenetic analysis of over 3.4kb (including cytochrome b, NADH dehydrogenase subunit 1, recombination activating gene subunit 2). Rates of divergence among "phractocephalines" were calibrated with fossil material and the Mérida uplift. These independent calibrators provided different node-age estimates when the rates were applied separately to the gene partitions (mtDNA and rag2). Node-age discrepancies were particularly evident at older nodes. This is due to two factors: (1) multiple substitution of mtDNA underestimates the amount of change and therefore time since cladogenesis, whereas (2) calibration of an ancient node with fossils produces an artificially slow rate (due to the masking of divergence through multiple substitution) that overestimates time when applied to younger nodes. Node-age estimates provided by the more slowly evolving rag2 sequences were more consistent with other sources of historical inference, e.g., paleogeography and the fossil record. Given these points, we provide a synthetic chronology of diversification and discuss the reasons for its preference. The phylogeny and synthetic chronology suggest Perrunichthys perruno (Maracaibo endemic) and Leiarius pictus (Orinoco and Guianas) to be a vicariant species pair that last shared a common ancestor during the period of Mérida uplift.     

Molecular phylogeny and systematics of the Lilium carniolicum group (Liliaceae) based on nuclear ITS sequences

The Lilium carniolicum group consists of several taxonomically dubious taxa endemic to the European flora. Internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nrDNA) were used to clarify both the delineation of, and relationships among, taxa in the group as well as to provide insight on the phylogenetic position of the group within the genus. Maximum parsimony, maximum likelihood and Bayesian analyses were in general agreement, with all taxa in the group being very closely related, and the entire group being monophyletic. L. pyrenaicum and L. pomponium are placed at the basal position in the group, while L. chalcedonicum is shown to be more closely related to L. carniolicum than previously thought. Our analyses suggested that L. albanicum and L. jankae are distinct from L. carniolicum, while no evidence was found to support the same separation for L. bosniacum.     

Towards a phylogeny for Astragalus section Caprini (Fabaceae) and its allies based on nuclear and plastid DNA sequences

We conducted phylogenetic analyses of the sect. Caprini and its closely related sections within Astragalus. Analyses of a combined dataset including nrDNA ETS and three cpDNA markers using maximum parsimony and Bayesian inference from 44 species of sect. Caprini and its allied taxa yielded congruent relationships among several major lineages. These results largely disagree with previously recognized taxonomic groups, most notably in the following ways: (1) subsects. Caprini and Purpurascentes of sect. Caprini are not natural groups; (2) sects. Alopecuroidei and Laxiflori are nested within sect. Astragalus; and (3) subsect. Chronopus constitutes a separate phylogenetic lineage. Representatives of sects. Astragalus, Alopecuroidei, and Laxiflori share a common ancestor with that of sect. Caprini. Our studies indicate that Astragalus annularis is an outlier species for the genus Astragalus and sect. Caraganella is the first-diverging clade within the genus Astragalus. Results of these analyses are supported by morphology and suggest the need for new taxonomic delimitations, which are forthcoming. Key morphological characters were mapped onto the phylogenetic tree and discussed.     

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families. It is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates. Here, we have analyzed and compared the performance of three nuclear genes (von Willebrand Factor, interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic receptor) for a large taxonomic sampling, covering the whole rodent and placental diversity. The phylogenetic results significantly support rodent monophyly, the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade. The resolution of relationships among rodents is also greatly improved. The currently recognized families are divided here into seven well-defined clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae, Myodonta, and Sciuroidea) that can be grouped into three major clades: Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular datings based on these three genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene. The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights.