Phylogeny of the M superhaplogroup inferred from complete mitochondrial genome sequence of Indian specific lineages

Background  

Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny.     

Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences

The now-emerging mitochondrial DNA (mtDNA) population genomics provides information for reconstructing a well-resolved mtDNA phylogeny and for discerning the phylogenetic status of the subcontinentally specific haplogroups. Although several major East Asian mtDNA haplogroups have been identified in studies elsewhere, some of the most basal haplogroups, as well as numerous minor subhaplogroups, were not yet determined or fully characterized. To fill the lacunae, we selected 48 mtDNAs from >2,000 samples across China for complete sequencing that cover virtually all (sub)haplogroups discernible to date in East Asia. This East Asian mtDNA phylogeny can henceforth serve as a solid basis for phylogeographic analyses of mtDNAs, as well as for studies of mitochondrial diseases in East and Southeast Asia.     

The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes

Many efforts based on complete mitochondrial DNA (mtDNA) genomeshave been made to depict the global mtDNA landscape, but thephylogeny of Indian macrohaplogroup M has not yet been resolvedin detail. To fill this lacuna, we took the same strategy asin our recent analysis of Indian mtDNA macrohaplogroup N andselected 56 mtDNAs from over 1,200 samples across India forcomplete sequencing, with the intention to cover all Indianautochthonous M lineages. As a result, the phylogenetic statusof previously identified haplogroups based on control-regionand/or partial coding-region information, such as M2, M3, M4,M5, M6, M30, and M33, was solidified or redefined here. Moreover,seven novel basal M haplogroups (viz., M34–M40) were identified,and yet another five singular branches of the M phylogeny werediscovered in the present study. The comparison of matrilinealcomponents among India, East Asia, Southeast Asia, and Oceaniaat the deepest level yielded a star-like and nonoverlappingpattern, reflecting a rapid mode of modern human dispersal alongthe Asian coast after the initial "out-of-Africa" event.     

Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology

Subfamily Barnadesioideae (Asteraceae) consists of nine genera and 91 species endemic to South America. They include annual and perennial herbs, arching shrubs and trees up to 30 m tall. Presumed sister to all other Asteraceae, its intergeneric relationships are key to understanding the early evolution of the family. Results of the only molecular study on the subfamily conflict with relationships inferred from morphology. We investigate inter- and intrageneric relationships in Barnadesioideae with novel DNA sequence data and morphological characters using parsimony, likelihood and Bayesian inference. All results verify Barnadesioideae as monophyletic and sister to the rest of the family. A basal split within the subfamily is recognized, with Chuquiraga, Doniophyton and Duseniella in one clade, and Arnaldoa, Barnadesia, Dasyphyllum, Fulcaldea, Huarpea and possibly Schlechtendalia in another. The largest genus, Dasyphyllum, is revealed as biphyletic with the two clades separating along subgeneric and geographic lines. Schlechtendalia, suggested as the earliest diverging lineage of the subfamily by morphological studies and parsimony analyses, is found in a more derived position under model-based inference methods. Competing phylogenetic hypotheses, both previous and present, are evaluated using likelihood-based tests. Evolutionary trends within Barnadesioideae are inferred: hummingbird pollination has developed convergently at least three times. An early vicariance in the subfamily’s distribution is revealed. X = 9 is supported as the ancestral base chromosome number for both Barnadesioideae and the family as a whole.     

Phylogeny and infrageneric classification of Symplocos (Symplocaceae) inferred from DNA sequence data

Symplocos comprises ～300 species of woody flowering plants with a disjunct distribution between the warm-temperate to tropical regions of eastern Asia and the Americas. Phylogenetic analyses of 111 species of Symplocos based on the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast genes rpl16, matK, and trnL-trnF yielded topologies in which only one of the four traditionally recognized subgenera (Epigenia; Neotropics) is monophyletic. Section Cordyloblaste (subgenus Symplocos; eastern Asia) is monophyletic and sister to a group comprising all other samples of Symplocos. Section Palura (subgenus Hopea; eastern Asia) is sister to a group comprising all other samples of Symplocos except those of section Cordyloblaste. Symplocos wikstroemiifolia (eastern Asia) and S. tinctoria (southeastern United States), both of subgenus Hopea, form a clade that groups with S. longipes (tropical North America) and the species of subgenus Epigenia. The remaining samples of subgenus Hopea (eastern Asia) form a clade. Section Neosymplocos (subgenus Microsymplocos; Neotropics) is well nested within a clade otherwise comprising the samples of section Symplocastrum (subgenus Symplocos; Neotropics). Section Urbaniocharis (subgenus Microsymplocos; Antilles) groups as sister to the clade comprising Symplocastrum and Neosymplocos. The data support the independent evolution of deciduousness among section Palura and S. tinctoria. The early initial divergence of sections Cordyloblaste and Palura from the main group warrants their recognition at taxonomic levels higher than those at which they are currently placed. An inferred eastern Asian origin for Symplocos with subsequent dispersal to the Americas is consistent with patterns from other phylogenetic studies of eastern Asian-American disjunct plant groups but contrary to a North American origin inferred from the earliest fossil occurrences of the genus.     

Phylogeny of Cyttaria inferred from nuclear and mitochondrial sequence and morphological data

Cyttaria species (Leotiomycetes, Cyttariales) are obligate, biotrophic associates of Nothofagus (Hamamelididae, Nothofagaceae), the southern beech. As such Cyttaria species are restricted to the southern hemisphere, inhabiting southern South America (Argentina and Chile) and southeastern Australasia (southeastern Australia including Tasmania, and New Zealand). The relationship of Cyttaria to other Leotiomycetes and the relationships among species of Cyttaria were investigated with newly generated sequences of partial nucSSU, nucLSU and mitSSU rRNA, as well as TEF1 sequence data and morphological data. Results found Cyttaria to be defined as a strongly supported clade. There is evidence for a close relationship between Cyttaria and these members of the Helotiales: Cordierites, certain Encoelia spp., Ionomidotis and to a lesser extent Chlorociboria. Order Cyttariales is supported by molecular data, as well as by the unique endostromatic apothecia, lack of chitin and highly specific habit of Cyttaria species. Twelve Cyttaria species are hypothesized, including all 11 currently accepted species plus an undescribed species that accommodates specimens known in New Zealand by the misapplied name C. gunnii, as revealed by molecular data. Thus the name C. gunnii sensu stricto is reserved for specimens occurring on N. cunninghamii in Australia, including Tasmania. Morphological data now support the continued recognition of C. septentrionalis as a species separate from C. gunnii. Three major clades are identified within Cyttaria: one in South America hosted by subgenus Nothofagus, another in South America hosted by subgenera Nothofagus and Lophozonia, and a third in South America and Australasia hosted by subgenus Lophozonia, thus producing a non-monophyletic grade of South American species and a monophyletic clade of Australasian species, including monophyletic Australian and New Zealand clades. Cyttaria species do not sort into clades according to their associations with subgenera Lophozonia and Nothofagus.     

Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India

Indian subcontinent harbours both the human mtDNA macrohaplogroups M and N, of which M is the most prevalent. In this study, we discuss the overall distribution of the various haplogroups and sub-haplogroups of M among the different castes and tribes to understand their diverse pattern with respect to geographical location and linguistic affiliation of the populations. An overview of about 170 studied populations, belonging to four distinct linguistic families and inhabiting different geographic zones, revealed wide diversity of about 22 major haplogroups of M. The tribal populations belonging to the same linguistic family but inhabiting different geographical regions (Dravidian and Austro-Asiatic speakers) exhibited differences in their haplogroup diversity. The northern and southern region castes showed greater diversity than the castes of other regions.     

Phylogeny of wall-less green flagellates inferred from 18SrDNA sequence data

To elucidate the phylogeny of the Dunaliellales sensu Ettl. the taxon often thought to be intermediate between primitive green flagellates such as the prasinophytes and the advanced chlorophycean algae, the sequences of the nuclear-encoded small subunit ribosomal RNA gene (18SrDNA) were determined and analyzed for five green algae, including three dunaliellalean algae. Phylogenetic trees based on 18SrDNA suggest that Oltmannsiellopsis viridis (Margraves et Steele) Chihara et Inouye represents an early divergence in the Ulvophyceae/Trebouxio-phyceae/Chlorophyceae clade and has no close relationship to any other green algae, as also suggested from ultrastructural characters. We propose Oltmannsiellopsidates ord. nov. for this genus. Hafniomonas and Polytomella are included in the clade which is characterized by clockwise basal bodies (CW group). The 18SrDNA trees suggest that multiple losses of the cell wall of the flagellate cell occurred in the CW group, and that the Dunaliellales sensu Ettl has a polyphyletic nature. This study also suggests that Planophita terrestns Groover et Hof-stetter (Chaetopeltidales) and Chaetophora incras-sata (Hudson) Hazen (Chaetophorales) are distinct lineages in the Chlorophyceae.     

Phylogeny of calcareous dinoflagellates as inferred from ITS and ribosomal sequence data

The phylogenetic relationships of calcareous dinoflagellates (i.e., Calciodinellaceae and Thoracosphaera) are investigated. Molecular data from the ribosomal 5.8S rRNA and highly conserved motifs of the ITS1 show Calciodinellaceae s.l. to be monophyletic when few non-calcareous taxa are included. They segregate into three monophyletic assemblages in a molecular analysis that considers the 5.8S rRNA and both the Internal Transcribed Spacer regions ITS1 and ITS2: a clade comprising species of Ensiculifera and Pentapharsodinium (E/P-clade), Scrippsiella s.l. (including fossil-based taxa such as Calciodinellum and Calcigonellum), and a heterogeneous group (T/P-clade) of calcareous (e.g., Thoracosphaera) and non-calcareous taxa (e.g., the highly toxic Pfiesteria). The potential to produce calcareous structures is considered as apomorphic within alveolates, and non-calcareous taxa nesting with calcareous dinoflagellates may have reduced calcification secondarily. Molecular results do not contradict general evolutionary scenarios provided by previous morphological (mainly paleontological) investigations.     

Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology

Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This region of phytochrome B was most useful for examining relationships among closely related genera. Fifty-one species from 38 genera of Celastraceae were sampled. The Celastraceae sensu lato (including Hippocrateaceae) were resolved as a monophyletic group. Loesener's subfamilies and tribes of Celastraceae were not supported. The Hippocrateaceae were resolved as a monophyletic group nested within a paraphyletic Celastraceae sensu stricto. Goupia was resolved as more closely related to Euphorbiaceae, Corynocarpaceae, and Linaceae than to Celastraceae. Plagiopteron (Flacourtiaceae) was resolved as the sister group of Hippocrateoideae. Brexia (Brexiaceae) was resolved as closely related to Elaeodendron and Pleurostylia. Canotia was resolved as the sister group of Acanthothamnus within Celastraceae. Perrottetia and Mortonia were resolved as the sister group of the rest of the Celastraceae. Siphonodon was resolved as a derived member of Celastraceae. Maytenus was resolved as three disparate groups, suggesting that this large genus needs to be recircumscribed.     

Phylogeny ofRubiaceae-Rubieae inferred from the sequence of a cpDNA intergene region

A phylogenetic analysis of 25 species, representing eight genera of theRubieae tribe (Rubiaceae), has been made using the DNA sequence of the chloroplastatp B-rbc L intergene region. Six tropical genera from other tribes ofRubiaceae have been used as outgroups. Whatever the method of analysis (distance, parsimony or maximum likelihood), five groups are clearly separated and described as informal clades. Their relative relationships are not clearly resolved by the parsimony analysis, resulting in eight equally parsimonious trees, 327 steps long, with a consistency index (CI) of 0.749 (excluding uninformative sites). TheRubieae tribe appears monophyletic from the data available. Some new and partly unexpected phylogenetic relationships are suggested. The genusRubia forms a separate clade and appears to be the relatively advanced sister group of the remaining taxa. TheSherardia clade also includes the generaCrucianella andPhuopsis. Galium sect.Aparinoides appears closely attached to theAsperula sect.Glabella clade. The remaining taxa ofGalium are paraphyletic:Galium sect.Platygalium (in theCruciata clade) is linked to the advanced generaCruciata andValantia; the more apomorphic groups ofGalium form theGalium sect.Galium clade, including the perennial sectionsGalium, Leiogalium, andLeptogalium as well as the annual (and possibly polyphyletic) sect.Kolgyda.     

Phylogeny of "Oxycanus" lineages of hepialid moths from New Zealand inferred from sequence variation in the mtDNA COI and II gene regions

The phylogeny of the New Zealand hepialid moths was estimated from a 527-bp nucleotide sequence from the mitochondrial DNA cytochrome oxidase subunit I and II gene regions. New haplotypes were identified for Wiseana cervinata, W. copularis, and W. signata. Phylogenetic reconstructions using maximum parsimony and maximum likelihood methods indicated that the four hepialid lineages Aenetus, Aoraia, "Oxycanus" Cladoxycanus, and "Oxycanus" s. str. hypothesized by Dugdale (1994) based on a morphological taxonomic revision were monophyletic within New Zealand. Addition of exemplars from the Australian genera Fraus, Jeana, Oxycanus, and Trictena to the data set tentatively support the monophyly of the New Zealand "Oxycanus" lineages. Estimated times of divergence for the genus Wiseana taxa fitted well with known geological events and suggest that the genus may have diverged 1-1.5 mya.     

Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen for complete sequencing from a collection of >800 control-region sequences sampled across India. We identified five new autochthonous haplogroups (R7, R8, R30, R31, and N5) and fully characterized the autochthonous haplogroups (R5, R6, N1d, U2a, U2b, and U2c) that were previously described only by first hypervariable segment (HVS-I) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings demonstrate that the Indian mtDNA pool, even when restricted to macrohaplogroup N, harbors at least as many deepest-branching lineages as the western Eurasian mtDNA pool. Moreover, the distribution of the earliest branches within haplogroups M, N, and R across Eurasia and Oceania provides additional evidence for a three-founder-mtDNA scenario and a single migration route out of Africa.     

Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS sequence data

Parsimony analysis based on ITS sequence data was carried out to investigate the Hypochnicium punctulatum complex (Basidiomycota). The study gives full support to earlier, crossing test-based species delimitations. Altogether, 18 specimens were sequenced and their spore sizes plotted together with measurements from the corresponding type specimens. Spore sizes were found to cluster readily into four groups, all of which were supported by the phylogenetic analysis. However, in the case of H. punctulatum and H. albostramineum, the morphological delimitation is unsatisfactory and a zone of potential spore size overlap is shown to exist. The new combination Hypochnicium cremicolor is proposed for a species previously known as a small-spored taxon in the H. punctulatum complex, and H. caucasicum is shown to be a younger synonym to H. wakefieldiae. A key to the species is provided.     

人类线粒体DNA世系的系统发育关系研究

本文以人类线粒体DNA为例,回顾了其系统发育关系的重建的研究历史,进而总结介绍了该分析方法在人类进化历史研究、线粒体DNA数据质量评估以及疾病相关线粒体DNA突变的甄别等方面的应用,以期对该方法在国内的推广应用有所裨益。     

Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data

Phylogenetic relationships among major groups of passeriform birds were studied by analyses of nucleotide sequence data from two nuclear genes, c- myc and RAG-1. The results corroborated both the monophyly of the order Passeriformes, and the major dichotomy into oscine and suboscine passerines previously suggested based on syringeal morphology and DNA-DNA hybridizations. The representatives of the Old World suboscines (families Eurylaimidae, Philepittidae and Pittidae) formed a monophyletic clade. The New World suboscines clustered into two clades. The first contained Conopophaga (Conopophagidae), Furnarius (Furnariidae), Lepidocolaptes (Dendrocolaptidae), Thamnophilus (Formicariidae), and Rhinocrypta (Rhinocryptidae). Previously, the monophyly of this group has been inferred from their possession of a unique, "tracheophone" syrinx, and from DNA-DNA hybridisation data. The second clade of New World suboscines includes Gubernetes and Muscivora (Tyrannidae), Phytotoma (Phytotomidae), Tityra (Cotingidae) and Pipra (Pipridae). This group of families have been considered monophyletic based on morphology (although ambiguously) and DNA-DNA hybridisation. The sister group relationship of Tityra and Phytotoma supports the previously supposed cotingid affinity of Phytotoma . Nuclear DNA data also unambiguously group the lyrebirds Menura with the oscines.
The presented results from the analysis of nuclear DNA agree well with morphology and DNA-DNA hybridisation data. The precise age of the divergences studied herein are unknown but based on interpretations of the fossil record of passerine birds many of them might date back to the early Tertiary. The agreement between data from the nuclear DNA and other sources, along with the fact that neither of the studied genes showed sign of saturation, indicate the great potential of these two nuclear genes to resolve very old divergences in birds.     

Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

Trogidae constitute a monophyletic and biologically unique family within Scarabaeoidea, being the only keratinophagous group in the superfamily. Traditionally, the family has been divided into three distinctive genera, Polynoncus Burmeister, Omorgus Erichson and Trox Fabricius. Although the taxonomy of the group is relatively well studied, changes to the existing classification have recently been proposed and the family as currently constituted has not been subjected to phylogenetic analyses. Here we present a molecular phylogeny for this cosmopolitan family based on three partially sequenced gene regions: 16S rRNA, 18S rRNA and 28S rRNA (domain 2). Included in the analyses are representatives belonging to four of the five extant genera (and three of the four subgenera) from all major zoogeographic regions, representing about 20% of the known trogid species diversity in the family. Phylogenetic analyses performed included parsimony and Bayesian inference. We deduce their historical biogeography by using trogid fossils as calibration points for divergence estimates. Our analyses resolved relationships between and within genera and subgenera that are largely congruent with existing phylogeny hypotheses based on morphological data. We recovered four well‐supported radiations: Polynoncus, Omorgus, Holarctic Trox and African Phoberus MacLeay. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. The subgenera Trox and Phoberus should be elevated to genera to include the Holarctic and all the Afrotropical species, respectively, and Afromorgus returned to subgeneric rank. Estimates of divergence time are consistent with a Pangaean origin of the family in the Early Jurassic. The subsequent diversification of the major lineages is largely attributed to the break‐up of Pangaea and Gondwana in the Middle Jurassic and early Late Cretaceous, respectively.