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Major Clades (major + clade)
Selected AbstractsA phylogenetic classification of the land plants to accompany APG IIIBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009MARK W. CHASE A formal classification of the land plants that is compatible with the APG III classification is proposed. Previous classifications inflated taxonomic ranks, particularly of the angiosperms. If the major clades of green algae are recognized as classes, then all land plants, the embryophytes, should be included in a single class, here recognized as Equisitopsida. Accordingly, the 16 major clades of land plants, including the angiosperms, should all be recognized as subclasses, the angiosperms as Magnoliidae. Major clades within the angiosperms are then recognized as superorders. This classification still uses a few informal categories (e.g. eudicots, lamiids, etc.) within the angiosperms because this is convenient. Two new names are established: Amborellanae and Austrobaileyanae. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 122,127. [source] Molecular epidemiology of HIV-1 in Santa Catarina State confirms increases of subtype C in Southern BrazilJOURNAL OF MEDICAL VIROLOGY, Issue 10 2007Dayse Locateli Abstract Recent studies have demonstrated an increased prevalence of human immunodeficiency virus type 1 (HIV-1) subtype C in southern Brazil. Although Santa Catarina State (SC) is located in this area and presents one of the country's highest incidences of HIV/AIDS, knowledge on the molecular epidemiology of HIV-1 in such State is lacking. The aim of this study was to investigate the HIV-1 molecular diversity and epidemiological profile of HIV-1-infected patients from SC. DNA samples were PCR amplified and HIV-1 subtypes were determined using both env and gag genes by direct sequencing. Phylogenetic analyses revealed that 48% were subtype C and 23% were subtype B. Possible recombinant forms were observed for both B/C (23%) and B/F (6%) subtypes. Our results, for the first time, identifies HIV-1 subtype C as a major clade circulating in SC and contributes to the understanding of HIV epidemics in the country by confirming the epidemic spread of the HIV-1 subtype C in southern Brazil. J. Med. Virol. 79:1455,1463, 2007. © Wiley-Liss, Inc. [source] DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and PlanotortrixMOLECULAR ECOLOGY RESOURCES, Issue 3 2009PIA LANGHOFF Abstract Molecular techniques such as DNA barcoding have become popular in assisting species identification especially for cryptic species complexes. We have analysed data from a 468-bp region of the mitochondrial cytochrome oxidase subunit I (COI) gene from 200 specimens of 12 species of endemic New Zealand leafroller moths (Tortricidae) from the genera Planotortrix and Ctenopseustis to assess whether the DNA barcoding region can distinguish these species. Among the 200 sequences analysed, 72 haplotypes were recovered, with each genus forming a separate major clade. Maximum likelihood phylogenetic methods were used to test whether species fell into reciprocally monophyletic clades. The optimal phylogeny showed that four species within the genus Ctenopseustis (C. obliquana, C. herana, C. filicis and C. fraterna) and three within Planotortrix (P. octo, P. excessana and P. avicenniae) are polyphyletic. Shimodaira,Hasegawa tests rejected a null hypothesis of monophyly for the species C. obliquana, C. herana, P. octo and P. excessana. Comparisons of within and between species levels of sequence divergence for the same set of seven species showed cases where maximum levels of within-species divergence were greater than some levels of between-species divergence. DNA barcoding using this region of the COI gene is able to distinguish the two genera and some species within each genus; however, many species cannot be identified using this method. Finally, we discuss the possible reasons for this polyphyly, including incomplete lineage sorting, introgression, horizontal gene transfer and incorrect taxonomy. [source] Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the PleistoceneBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009MARTÍ CORTEY The phylogeography of Atlantic brown trout (Salmo trutta) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 904,917. [source] Comparative floral structure and systematics of Pelagodoxa and Sommieria (Arecaceae)BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2004FRED W. STAUFFER Floral structure is compared in Pelagodoxa and Sommieria (Arecaceae, Arecoideae). Male flowers have three free, imbricate sepals, three basally congenitally united and apically valvate petals, and six stamens. Anthers are dorsifixed and dehiscence introrse. The sterile gynoecium is tricarpellate. Female flowers have three free, imbricate sepals and three free, imbricate petals, which are slightly fused with the sepals at the base. Four to six staminodes are congenitally united at the base and fused with the ovary for a short distance. The gynoecium is syncarpous. Carpels are almost equal in early development; later the gynoecium becomes pseudomonomerous. The three stigmatic branches are equally developed, apical and sessile. The carpels are (syn-)ascidiate up to the level of the placenta and (sym-)plicate above. Each carpel has one ovule, in the sterile carpels it is aborted at anthesis. The fertile ovule is erect up to anthesis and pendant afterwards because of the bulging out of the ovary. Pollen tube transmitting tracts (PTTT) encompass the secretory epidermis of the ventral slits of each carpel. Floral structure in Pelagodoxa and Sommieria supports the sister group relationship between the two genera suggested in recent molecular phylogenies and reflects their close relationships to a major clade of pseudomonomerous arecoid palms from the Indo-Pacific region. © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 146, 27,39. [source] The role of wood anatomy in phylogeny reconstruction of EricalesCLADISTICS, Issue 3 2007Frederic Lens The systematic significance of wood anatomical characters within Ericales is evaluated using separate and combined parsimony analyses including 23 wood characters and 3945 informative molecular characters. Analyses of wood features alone result in poorly resolved and conflicting topologies. However, when pedomorphic character states are coded as inapplicable, the combined bootstrap topology results in an increase of resolution and support at most deeper nodes compared with the molecular analyses. This suggests that phylogenetic information from the limited number of morphological characters is not completely swamped by an overwhelming amount of molecular data. Based on the morphology of vessels and fibers, and the distribution of axial parenchyma, two major wood types can be distinguished within Ericales: (i) a "primitive" type, nearly identical to the wood structure in the more basal outgroup Cornales, which is likely to have persisted in one major clade, and (ii) a "derived" type that must have evolved in at least two separate evolutionary lines. The occurrence of the first type is strongly correlated with shrubs to small trees growing in cold temperate or tropical montane regions, while the second type is common in tall trees of tropical lowlands. This favors the inclusion of ecologically adaptive features in phylogeny reconstruction. © The Willi Hennig Society 2006. [source] Application of nr-DNA ITS sequence for identification of Fusarium culmorum isolates,EPPO BULLETIN, Issue 3-4 2000P. K. Mishra Variation within the internal transcribed spacers (ITS1 and ITS2) and 5.8S ribosomal DNA region of 60 Fusarium culmorum isolates (section Discolor), representing different hosts and diverse geographical origins was examined by polymerase chain reaction (PCR), coupled with sequencing. Phylogenetic relationships of these F. culmorum isolates were estimated in relation to Fusarium spp. from this and other sections of the form-genus, using sequences available from Genbank. The amplified ITS region was approximately 570 bp long in 56 isolates and approximately 585 bp in four other isolates. The inferred phylogeny distinguished clearly four isolates supplied as F. culmorum. These isolates differed in both morphology and sequence from the remaining F. culmorum material. Sequence analysis revealed that the remaining 56 isolates were divided into three ITS types, within which the divergence was extremely low. ITS sequence comparison among the Fusarium isolates showed two major clades, one comprising sections Discolor, Sporotrichiella and Gibbosum and the other comprising Elegans, Liseola, Martiella and Roseum. These results demonstrate the use of the ITS region to resolve the identification and taxonomic problems of Fusarium spp. especially at sectional level but demonstrate the need to develop some other molecular markers for identification at the level of species or race. [source] Lessons from leeches: a call for DNA barcoding in the labEVOLUTION AND DEVELOPMENT, Issue 6 2006Alexandra E. Bely SUMMARY Many evolution of development labs study organisms that must be periodically collected from the wild. Whenever this is the case, there is the risk that different field collections will recover genetically different strains or cryptic species. Ignoring this potential for genetic variation may introduce an uncontrolled source of experimental variability, leading to confusion or misinterpretation of the results. Leeches in the genus Helobdella have been a workhorse of annelid developmental biology for 30 years. Nearly all early Helobdella research was based on a single isolate, but in recent years isolates from multiple field collections and multiple sites across the country have been used. To assess the genetic distinctness of different isolates, we obtained specimens from most Helobdella laboratory cultures currently or recently in use and from some of their source field sites. From these samples, we sequenced part of the mitochondrial gene cytochrome oxidase I (COI). Sequence divergences and phylogenetic analyses reveal that, collectively, the Helobdella development community has worked on five distinct species from two major clades. Morphologically similar isolates that were thought to represent the same species (H. robusta) actually represent three species, two of which coexist at the same locality. Another isolate represents part of a species complex (the "H. triserialis" complex), and yet another is an invasive species (H. europaea). We caution researchers similarly working on multiple wild-collected isolates to preserve voucher specimens and to obtain from these a molecular "barcode," such as a COI gene sequence, to reveal genetic variation in animals used for research. [source] Generality of vertebrate developmental patterns: evidence for a dermomyotome in fishEVOLUTION AND DEVELOPMENT, Issue 1 2006S. H. Devoto SUMMARY The somitic compartment that gives rise to trunk muscle and dermis in amniotes is an epithelial sheet on the external surface of the somite, and is known as the dermomyotome. However, despite its central role in the development of the trunk and limbs, the evolutionary history of the dermomyotome and its role in nonamniotes is poorly understood. We have tested whether a tissue with the morphological and molecular characteristics of a dermomyotome exists in nonamniotes. We show that representatives of the agnathans and of all major clades of gnathostomes each have a layer of cells on the surface of the somite, external to the embryonic myotome. These external cells do not show any signs of terminal myogenic or dermogenic differentiation. Moreover, in the embryos of bony fishes as diverse as sturgeons (Chondrostei) and zebrafish (Teleostei) this layer of cells expresses the pax3 and pax7 genes that mark myogenic precursors. Some of the pax7- expressing cells also express the differentiation-promoting myogenic regulatory factor Myogenin and appear to enter into the myotome. We therefore suggest that the dermomyotome is an ancient and conserved structure that evolved prior to the last common ancestor of all vertebrates. The identification of a dermomyotome in fish makes it possible to apply the powerful cellular and genetic approaches available in zebrafish to the understanding of this key developmental structure. [source] High vertical and low horizontal diversity of Prochlorococcus ecotypes in the Mediterranean Sea in summerFEMS MICROBIOLOGY ECOLOGY, Issue 2 2007Laurence Garczarek Abstract Natural populations of the marine cyanobacterium Prochlorococcus exist as two main ecotypes, inhabiting different layers of the ocean's photic zone. These so-called high light- (HL-) and low light (LL-) adapted ecotypes are both physiologically and genetically distinct. HL strains can be separated into two major clades (HLI and HLII), whereas LL strains are more diverse. Here, we used several molecular techniques to study the genetic diversity of natural Prochlorococcus populations during the Prosope cruise in the Mediterranean Sea in the summer of 1999. Using a dot blot hybridization technique, we found that HLI was the dominant HL group and was confined to the upper mixed layer. In contrast, LL ecotypes were only found below the thermocline. Secondly, a restriction fragment length polymorphism analysis of PCR-amplified pcb genes (encoding the major light-harvesting proteins of Prochlorococcus) suggested that there were at least four genetically different ecotypes, occupying distinct but overlapping light niches in the photic zone. At comparable depths, similar banding patterns were observed throughout the sampled area, suggesting a horizontal homogenization of ecotypes. Nevertheless, environmental pcb gene sequences retrieved from different depths at two stations proved all different at the nucleotide level, suggesting a large genetic microdiversity within those ecotypes. [source] Genetic population structure of the net-winged midge, Elporia barnardi (Diptera: Blephariceridae) in streams of the south-western Cape, South Africa: implications for dispersalFRESHWATER BIOLOGY, Issue 1 2003M. J. Wishart SUMMARY 1.,The net-winged midges (Diptera: Blephariceridae), with highly specific habitat requirements and specialised morphological adaptations, exhibit high habitat fidelity and a limited potential for dispersal. Given the longitudinal and hierarchical nature of lotic systems, along with the geological structure of catchment units, we hypothesise that populations of net-winged midge should exhibit a high degree of population sub-structuring. 2.,Sequence variation in the cytochrome c oxidase subunit I (COI) region of the mitochondrial DNA (mtDNA) was examined to determine patterns of genetic variation and infer historical and contemporary processes important in the genetic structuring of populations of Elporia barnardi. The DNA variation was examined at sites within streams, between streams in the same range, and between mountain ranges in the south-western Cape of South Africa. 3.,Twenty-five haplotypes, 641 bp in length, were identified from the 93 individuals sampled. A neighbour-joining tree revealed two highly divergent clades (,5%) corresponding to populations from the two mountain ranges. A number of monophyletic groups were identified within each clade, associated with individual catchment units. 4.,The distribution of genetic variation was examined using analysis of molecular variance (amova). This showed most of the variation to be distributed among the two ranges (,80%), with a small percentage (,15%) distributed among streams within each range. Similarly, variation among streams on Table Mountain was primarily distributed among catchment units (86%). A Mantel's test revealed a significant relationship between genetic differentiation and geographical distance, suggesting isolation by distance (P < 0.001). 5.,Levels of sequence divergence between the two major clades, representing the two mountain ranges, are comparable with those of some intra-generic species comparisons. Vicariant events, such as the isolation of the Peninsula mountain chain and Table Mountain, may have been important in the evolution of what is now a highly endemic fauna. 6.,The monophyletic nature of the catchment units suggests that dispersal is confined to the stream environment and that mountain ridges provide effective physical barriers to dispersal of E. barnardi. [source] Molecular systematics of the speciose Indo-Pacific soft coral genus, Sinularia (Anthozoa: Octocorallia)INVERTEBRATE BIOLOGY, Issue 4 2009Catherine S. McFadden Abstract. The speciose tropical soft coral genus Sinularia traditionally has been divided into five intrageneric taxonomic groups based on variation in a single morphological character: the shape of the club sclerites (calcite skeletal elements) embedded in the surface tissues of the colony. To test the phylogenetic utility of this system of classification, we used a 735-bp fragment of the octocoral-specific mitochondrial msh1 gene to construct a molecular phylogeny that included 80 of the ,150 recognized morphospecies of Sinularia. The msh1 phylogeny recovered five well-supported clades, but they were not congruent with the traditional intrageneric taxonomic groups. Mapping of characters onto the tree suggested that the five major clades plus several additional sub-clades of Sinularia can be distinguished based on a suite of four morphological characters; these include the presence of sclerites in the tentacle, collaret, and point regions of the polyps, in addition to the shape of the club sclerites in the surface tissues. The overall growth form of the colony also distinguishes some clades. Polyp sclerites have for the most part been overlooked taxonomically in Sinularia, and as a result information on these characters is lacking or is incorrect in many species descriptions. As has been the case in other recent studies of lower metazoan groups, construction of a molecular phylogeny has led us to recognize the phylogenetic and taxonomic importance of previously overlooked morphological characters. A revised taxonomic key that includes these characters is already improving our ability to discriminate species boundaries, and facilitating description of new Sinularia species. [source] Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler Pomatostomus halliJOURNAL OF AVIAN BIOLOGY, Issue 2 2001Grant I. Miura Sequence variation was examined in domain I of the mitochondrial control region in three Queensland populations of Hall's Babbler Pomatostomus halli, a geographically restricted, monotypic songbird in eastern Australia. Surprisingly, we found that domain I sequences were strongly differentiated into two major clades differing by 3.29%. These two clades exhibited nearly complete geographic concordance with northern and southern populations, except for two haplotypes which were sampled in the north of the range but were phylogenetically allied to the southern clade. We also found a seven-fold higher level of genetic diversity in the northern than in the southern populations. Neutrality and molecular clock tests suggested that selection or differences in substitution rates were not responsible for this difference in diversity. However, a maximum likelihood analysis of gene flow between the north and south suggested that the difference in diversity could be due to both greater population size in the north and asymmetric gene flow dominated by south to north dispersal events. A likelihood ratio test rejected a model in which population sizes were equal and rates of gene flow symmetric, and came close to rejecting a model in which only population sizes were constrained to be equal. These results suggest that different population sizes and asymmetric gene flow could be a major source of differences in genetic variation between populations of Hall's Babbler, although ecological and biogeographic causes for these differences are obscure. [source] Out of the Palaeotropics?JOURNAL OF BIOGEOGRAPHY, Issue 4 2009Historical biogeography, diversification of the cosmopolitan ectomycorrhizal mushroom family Inocybaceae Abstract Aim, The ectomycorrhizal (ECM) mushroom family Inocybaceae is widespread in north temperate regions, but more than 150 species are encountered in the tropics and the Southern Hemisphere. The relative roles of recent and ancient biogeographical processes, relationships with plant hosts, and the timing of divergences that have shaped the current geographic distribution of the family are investigated. Location, Africa, Australia, Neotropics, New Zealand, north temperate zone, Palaeotropics, Southeast Asia, South America, south temperate zone. Methods, We reconstruct a phylogeny of the Inocybaceae with a geological timeline using a relaxed molecular clock. Divergence dates of lineages are estimated statistically to test vicariance-based hypotheses concerning relatedness of disjunct ECM taxa. A series of internal maximum time constraints is used to evaluate two different calibrations. Ancestral state reconstruction is used to infer ancestral areas and ancestral plant partners of the family. Results, The Palaeotropics are unique in containing representatives of all major clades of Inocybaceae. Six of the seven major clades diversified initially during the Cretaceous, with subsequent radiations probably during the early Palaeogene. Vicariance patterns cannot be rejected that involve area relationships for Africa,Australia, Africa,India and southern South America,Australia. Northern and southern South America, Australia and New Zealand are primarily the recipients of immigrant taxa during the Palaeogene or later. Angiosperms were the earliest hosts of Inocybaceae. Transitions to conifers probably occurred no earlier than 65 Ma. Main conclusions, The Inocybaceae initially diversified no later than the Cretaceous in Palaeotropical settings, in association with angiosperms. Diversification within major clades of the family accelerated during the Palaeogene in north and south temperate regions, whereas several relictual lineages persisted in the tropics. Both vicariance and dispersal patterns are detected. Species from Neotropical and south temperate regions are largely derived from immigrant ancestors from north temperate or Palaeotropical regions. Transitions to conifer hosts occurred later, probably during the Palaeogene. [source] Surviving glacial ages within the Biotic Gap: phylogeography of the New Zealand cicada Maoricicada campbelliJOURNAL OF BIOGEOGRAPHY, Issue 4 2009Kathy B. R. Hill Abstract Aim, New Zealand is an ideal location in which to investigate the roles of landscape and climate change on speciation and biogeography. An earlier study of the widespread endemic cicada Maoricicada campbelli (Myers) found two phylogeographically distinguishable major clades , northern South Island plus North Island (northern-SI + NI) and Otago. These two clades appeared to have diverged on either side of an area of the South Island known as the Biotic Gap. We sampled more intensively to test competing theories for this divergence. We aimed to discover if M. campbelli had survived within the Biotic Gap during recent glacial maxima, and if predicted areas of secondary contact between the two major clades existed. Location, New Zealand. Methods, We analysed mitochondrial DNA sequences (1520 bp; 212 individuals; 91 populations) using phylogenetic (maximum likelihood, Bayesian), population genetic (analysis of molecular variance) and molecular dating methods (Bayesian relaxed clock with improved priors). Results, We found strong geographical structuring of genetic variation. Our dating analyses suggest that M. campbelli originated 1.83,2.58 Ma, and split into the two major clades 1.45,2.09 Ma. The main subclades in the northern-SI + NI clade arose almost simultaneously at 0.69,1.03 Ma. Most subclades are supported by long internal branches and began to diversify 0.40,0.78 Ma. We found four narrow areas of secondary contact between the two major clades. We also found a difference between calling songs of the Otago vs. northern-SI + NI clades. Main conclusions, Phylogeographical patterns within M. campbelli indicate an early Pleistocene split into two major clades, followed by late Pleistocene range expansion and in situ population differentiation of subclades. The northern-SI + NI clade diversified so rapidly that the main subclade relationships cannot be resolved, and we now have little evidence for a disjunction across the Biotic Gap. Structure within the main subclades indicates rapid divergence after a common bottlenecking event, perhaps attributable to an extremely cold glacial maximum at c. 0.43 Ma. Clade structure and dating analyses indicate that M. campbelli survived in many refugia during recent glacial maxima, including within the Biotic Gap. The narrow overlap between the two major clades is attributed to recent contact during the current interglacial and slow gene diffusion. The two major clades appear to be in the early stages of speciation based on genetic and behavioural differences. [source] Speciation chronology of rockhopper penguins inferred from molecular, geological and palaeoceanographic dataJOURNAL OF BIOGEOGRAPHY, Issue 4 2009Marc De Dinechin Abstract Aim, The Southern Ocean is split into several biogeographical provinces between convergence zones that separate watermasses of different temperatures. Recent molecular phylogenies have uncovered a strong phylogeographic structure among rockhopper penguin populations, Eudyptes chrysocome sensu lato, from different biogeographical provinces. These studies suggested a reclassification as three species in two major clades, corresponding, respectively, to warm, subtropical and cold sub-Antarctic watermasses rather than to geographic proximity. Such a phylogeographic pattern, also observed in plants, invertebrates and fishes of the Southern Ocean, suggests that past changes in the positions of watermasses may have affected the evolutionary history of penguins. We calculated divergence times among various rockhopper penguin clades and calibrated these data with palaeomagmatic and palaeoceanographic events to generate a speciation chronology in rockhopper penguins. Location, Southern Ocean. Methods, Divergence times between populations were calculated using five distinct mitochondrial DNA loci, and assuming a molecular clock model as implemented in mdiv. The molecular evolution rate of rockhopper penguins was calibrated using the radiochronological age of St Paul Island and Amsterdam Island in the southern Indian Ocean. Separations within other clades were correlated with palaeoceanographic data using this calibrated rate. Results, The split between the Atlantic and Indian populations of rockhopper penguins was dated as 0.25 Ma, using the date of emergence of St Paul and Amsterdam islands, and the divergence between sub-Antarctic and subtropical rockhopper penguins was dated as c. 0.9 Ma (i.e. during the mid-Pleistocene transition, a major change in the Earth's climate cycles). Main conclusions, The mid-Pleistocene transition is known to have caused a major southward shift in watermasses in the Southern Ocean, thus changing the environment around the northernmost rockhopper penguin breeding sites. This ecological isolation of northernmost populations may have caused vicariant speciation, splitting the species into two major clades. After the emergence of St Paul and Amsterdam islands in the subtropical Indian Ocean 0.25 Ma, these islands were colonized by penguins from the subtropical Atlantic, 6000 km away, rather than by penguins from the sub-Antarctic Indian Ocean, 5000 km closer. [source] Phylogeographic structuring and volant mammals: the case of the pallid bat (Antrozous pallidus)JOURNAL OF BIOGEOGRAPHY, Issue 7 2007Sarah E. Weyandt Abstract Aim, To examine the phylogeographic pattern of a volant mammal at the continental scale. The pallid bat (Antrozous pallidus) was chosen because it ranges across a zone of well-studied biotic assemblages, namely the warm deserts of North America. Location, The western half of North America, with sites in Mexico, the United States, and Canada. Methods, PCR amplification and sequencing of the mitochondrial control region was performed on 194 pallid bats from 36 localities. Additional sequences at the cytochrome- b locus were generated for representatives of each control-region haplotype. modeltest was used to determine the best set of parameters to describe each data set, which were incorporated into analyses using paup*. Statistical parsimony and measurements of population differentiation (amova, FST) were also used to examine patterns of genetic diversity in pallid bats. Results, We detected three major lineages in the mitochondrial DNA of pallid bats collected across the species range. These three major clades have completely non-overlapping geographic ranges. Only 6 of 80 control-region haplotypes were found at more than a single locality, and sequences at the more conserved cytochrome- b locus revealed 37 haplotypes. Statistical parsimony generated three unlinked networks that correspond exactly to clades defined by the distance-based analysis. On average there was c. 2% divergence for the combined mitochondrial sequences within each of the three major clades and c. 7% divergence between each pair of clades. Molecular clocks date divergence between the major clades at more than one million years, on average, using the faster rates, and at more than three million years using more conservative rates of evolution. Main conclusions, Divergent haplotypic lineages with allopatric distributions suggest that the pallid bat has responded to evolutionary pressures in a manner consistent with other taxa of the American southwest. These results extend the conclusions of earlier studies that found the genetic structuring of populations of some bat species to show that a widespread volant species may comprise a set of geographically replacing monophyletic lineages. Haplotypes were usually restricted to single localities, and the clade showing geographic affinities to the Sonoran Desert contained greater diversity than did clades to the east and west. While faster molecular clocks would allow for glacial cycles of the Pleistocene as plausible agents of diversification of pallid bats, evidence from co-distributed taxa suggests support for older events being responsible for the initial divergence among clades. [source] Australian biogeographical connections and the phylogeny of large genera in the plant family MyrtaceaeJOURNAL OF BIOGEOGRAPHY, Issue 7 2003Pauline Y. Ladiges Abstract Aim To compare the phylogeny of the eucalypt and melaleuca groups with geological events and ages of fossils to discover the time frame of clade divergences. Location Australia, New Caledonia, New Guinea, Indonesian Archipelago. Methods We compare published molecular phylogenies of the eucalypt and melaleuca groups of the plant family Myrtaceae with geological history and known fossil records from the Cretaceous and Cenozoic. Results The Australasian eucalypt group includes seven genera, of which some are relictual rain forest taxa of restricted distribution and others are species-rich and widespread in drier environments. Based on molecular and morphological data, phylogenetic analyses of the eucalypt group have identified two major clades. The monotypic Arillastrum endemic to New Caledonia is related in one clade to the more species-rich Angophora, Corymbia and Eucalyptus that dominate the sclerophyll vegetation of Australia. Based on the time of rifting of New Caledonia from eastern Gondwana and the age of fossil eucalypt pollen, we argue that this clade extends back to the Late Cretaceous. The second clade includes three relictual rain forest taxa, with Allosyncarpia from Arnhem Land the sister taxon to Eucalyptopsis of New Guinea and the eastern Indonesian archipelago, and Stockwellia from the Atherton Tableland in north-east Queensland. As monsoonal, drier conditions evolved in northern Australia, Arnhem Land was isolated from the wet tropics to the east and north during the Oligocene, segregating ancestral rain forest biota. It is argued also that the distribution of species in Eucalyptopsis and Eucalyptus subgenus Symphyomyrtus endemic in areas north of the stable edge of the Australian continent, as far as Sulawesi and the southern Philippines, is related to the geological history of south-east Asia-Australasia. Colonization (dispersal) may have been aided by rafting on micro-continental fragments, by accretion of arc terranes onto New Guinea and by land brought into closer proximity during periods of low sea-level, from the Late Miocene and Pliocene. The phylogenetic position of the few northern, non-Australian species of Eucalyptus subgenus Symphyomyrtus suggests rapid radiation in the large Australian sister group(s) during this time frame. A similar pattern, connecting Australia and New Caledonia, is emerging from phylogenetic analysis of the Melaleuca group (Beaufortia suballiance) within Myrtaceae, with Melaleuca being polyphyletic. Main conclusion The eucalypt group is an old lineage extending back to the Late Cretaceous. Differentiation of clades is related to major geological and climatic events, including rifting of New Caledonia from eastern Gondwana, development of monsoonal and drier climates, collision of the northern edge of the Australian craton with island arcs and periods of low sea level. Vicariance events involve dispersal of biota. [source] Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolutionJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2009R. J. BUTLER Abstract Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to poor sampling in the Turonian,Santonian interval. Stegosauria shows a significant negative correlation with flowering plants and a significant positive correlation with the nonflowering cycadophytes (cycads, Bennettitales). This interesting pattern is worthy of further investigation, and it reflects the decline of both stegosaurs and cycadophytes during the Early Cretaceous. [source] Cope's rule in cryptodiran turtles: do the body sizes of extant species reflect a trend of phyletic size increase?JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2006D. S. MOEN Abstract Cope's rule of phyletic size increase is questioned as a general pattern of body size evolution. Most studies of Cope's rule have examined trends in the paleontological record. However, neontological approaches are now possible due to the development of model-based comparative methods, as well as the availability of an abundance of phylogenetic data. I examined whether the phylogenetic distribution of body sizes in extant cryptodiran turtles is consistent with Cope's rule. To do this, I examined body size evolution in each of six major clades of cryptodiran turtles and also across the whole tree of cryptodirans (n = 201 taxa). Extant cryptodiran turtles do not appear to follow Cope's rule, as no clade showed a significant phyletic body size trend. Previous analyses in other extant vertebrates have also found no evidence for phyletic size increase, which is in contrast to the paleontological data that support the rule in a number of extinct vertebrate taxa. [source] The lissamphibian humerus and elbow joint, and the origins of modern amphibiansJOURNAL OF MORPHOLOGY, Issue 12 2009Trond Sigurdsen Abstract The origins and evolution of the three major clades of modern amphibians are still a source of controversy, and no general consensus exists as to their relationship to the various known Paleozoic taxa. This may indicate that additional character complexes should be studied to resolve their phylogenetic relationship. The salamander elbow joint has been fundamentally misinterpreted in previous morphological descriptions. In caudates and anurans, both the radius and ulna (fused in anurans) articulate with the characteristically large capitulum (radial condyle), although part of the ulnar articulating surface fits into to the smooth trochlear region. The salamander "ulnar condyle" of previous descriptions is in fact the entepicondyle. The condition seen in batrachians (i.e., salamanders and frogs) may be a lissamphibian synapomorphy because the elbow region of the primitive fossil caecilian Eocaecilia resembles those of frogs and salamanders. In addition to the large and bulbous capitulum, all lissamphibian humeri lack an entepicondylar foramen, and possess a distally pointing entepicondyle, a low and rounded ectepicondyle, and an elongated shaft. These characters are identified in key fossil forms to assess the support for the different hypotheses proposed for the evolutionary origins of lissamphibians. Temnospondyli is the only group of early tetrapods that shows a progressive evolution of lissamphibian traits in the humerus and elbow joint. Furthermore, among Paleozoic taxa, the dissorophoid temnospondyl Doleserpeton annectens is the only taxon that has the full set of humeral features shared by all lissamphibians. These results add support for the theory of a monophyletic origin of lissamphibians from dissorophoidtemnospondyls. J. Morphol., 2009. © 2009 Wiley-Liss, Inc. [source] PHYLOGENY OF THE EUGLENALES INFERRED FROM PLASTID LSU rDNA SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 4 2008Jong Im Kim To gain insights into the phylogeny of the Euglenales, we analyzed the plastid LSU rDNA sequences from 101 strains of the photosynthetic euglenoids belonging to nine ingroup genera (Euglena, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium, Discoplastis, Phacus, and Lepocinclis) and two outgroup genera (Eutreptia and Eutreptiella). Bayesian and maximum-likelihood (ML) analyses resulted in trees of similar topologies and four major clades: a Phacus and Lepocinclis clade; a Colacium clade; a Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade; and a Euglena clade. The Phacus and Lepocinclis clade was the sister group of all other euglenalian genera, followed by Discoplastis spathirhyncha (Skuja) Triemer and the Colacium clade, respectively, which was inconsistent with their placement based on nuclear rDNA genes. The Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade was sister to the Euglena clade. The loricate genera, Trachelomonas and Strombomonas, were closely related to each other, while Monomorphina and Cryptoglena also grouped together. The Euglena clade formed a monophyletic lineage comprising most species from taxa formerly allocated to the subgenera Calliglena and Euglena. However, within this genus, none of the subgenera was monophyletic. [source] PHYLOGENY OF THE EUGLENALES BASED UPON COMBINED SSU AND LSU RDNA SEQUENCE COMPARISONS AND DESCRIPTION OF DISCOPLASTIS GEN.JOURNAL OF PHYCOLOGY, Issue 3 2006NOV. (EUGLENOPHYTA) A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid-containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well-supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well-supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well-supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well-supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage. [source] INTER- AND INTRASPECIFIC VARIATION OF THE PSEUDO-NITZSCHIA DELICATISSIMA COMPLEX (BACILLARIOPHYCEAE) ILLUSTRATED BY RRNA PROBES, MORPHOLOGICAL DATA AND PHYLOGENETIC ANALYSES,JOURNAL OF PHYCOLOGY, Issue 2 2006Nina Lundholm A study of 25 cultures tentatively identified as Pseudo-nitzschia delicatissima (Cleve) Heiden, and originating from geographically widely distributed locations, showed both morphological and genetic variation among strains. Use of rRNA-targeted DNA probes on 17 different strains showed large variation in the hybridization patterns. Detailed morphological studies placed the isolates into three groups. The sample on which the neotype of P. delicatissima is based was also examined, and used to establish the morphological identity of P. delicatissima. Phylogenetic analyses of 16 strains, based on sequences of internal transcriber spacer 1 (ITS1), 5.8S and ITS2 of the nuclear-encoded rDNA, supported the morphological observations and the hybridization studies, and revealed large genetic variation among strains. A combination of the morphological and molecular findings resulted in the description of two new species, P. decipiens sp. nov. and P. dolorosa sp. nov. P. dolorosa has a mixture of one or two rows of poroids in the striae whereas P. delicatissima always has two rows. In addition, P. dolorosa has wider valves and a lower density of poroids. P. decipiens differs from P. delicatissima by a higher density of striae on the valve face as well as a higher density of poroids on the girdle bands. Among the strains referred to P. delicatissima, an epitype was selected. Large genetic variation was found among the P. delicatissima strains and a subdivision into two major clades represent cryptic species. [source] DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA),JOURNAL OF PHYCOLOGY, Issue 2 2006Hwan Su Yoon Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well-supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1,3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter-clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella, and Erythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, and Rufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera). [source] PHYLOGENY OF AULACOSEIRA (BACILLARIOPHYTA) BASED ON MOLECULES AND MORPHOLOGY,JOURNAL OF PHYCOLOGY, Issue 4 2004Stacy M. Edgar The phylogeny of 67 populations representing 45 species of Aulacoseira Thwaites was estimated by maximum parsimony methods using a combination of nucleotide sequence data and qualitative and quantitative morphological characteristics of the silica cell wall gathered primarily from original observation by LM and SEM. A new type of character using continuous quantitative variables that describe the ontogenetic-allometric trajectories of cell wall characteristics over the life cycle (size range) of diatoms is introduced. In addition to the 45 Aulacoseira species, the phylogeny also incorporated one Miosira Krammer, Lange-Bertalot, and Schiller species and two outgroup species (Melosira varians Agardh and Stephanopyxis nipponica Gran & Yendo). Fifteen species, represented by 24 populations, also contained molecular data from the nuclear genome (18S rDNA), and 11 of these species (18 populations) contained data from the chloroplast genome (rbcL) as well, which were sequenced or downloaded from GenBank. The phylogeny of Aulacoseira is composed of five major clades: 1) an A. crenulata (Ehrenburg) Thwaites and A. italica (Ehrenburg) Simonsen clade, which is the most basal; 2) an A. granulata (Ehrenburg) Simonsen complex clade; 3) an A. ambigua (Grunow) Simonsen clade; 4) an A. subarctica (O. Müller) Haworth and A. distans (Ehrenburg) Simonsen clade; and 5) an A. islandica (O. Müller) Simonsen clade that also contained endemic species from Lake Baikal, Siberia and many extinct Aulacoseira taxa. Monophyly of Aulacoseira can only be achieved if Miosira is no longer given separate generic status. [source] PHYLOGENY OF THE EUGLENOPHYTES INFERRED FROM SSU AND LSU rDNAJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Zimmermann, S. & Triemer, R. E. Department of Life Sciences, Rutgers University, Piscataway, NJ 08854 USA The phylogeny of the Euglenophytes has previously been examined using the SSU rDNA. Results from these analyses indicated that the phototrophic genera are not monophyletic. To test this hypothesis, a second gene was sequenced, the LSU rDNA. The taxa used in this study were selected from clades represented in the SSU analyses so that comparisons could be made between gene phylogenies and a combined dataset could be created. Conserved areas of the aligned sequences for both the LSU and SSU were used to generate parsimony, maximum likelihood, and distance trees. Topology of the SSU and LSU trees was similar. The SSU and LSU data consistently generated the same four highly supported terminal clades and varied only in the placement of Euglena stellata and Euglena viridis. The internal nodes of the SSU trees were weakly supported, whereas the LSU provided higher support for these nodes. A combined LSU and SSU dataset was then created. Analysis of the combined dataset yielded trees with identical topologies to those found in the individual datasets and demonstrated strong support for the four terminal clades. These results show that phylogeny of the Euglenophytes as inferred previously from SSU data is confirmed by the LSU data and that the LSU rDNA gene may be useful in elucidating relationships among the major clades. [source] Chloroplast evidence for geographic stasis of the Australian bird-dispersed shrub Tasmannia lanceolata (Winteraceae)MOLECULAR ECOLOGY, Issue 14 2010J. R. P. WORTH Abstract Few chloroplast-based genetic studies have been undertaken for plants of mesic temperate forests in the southern hemisphere and fossil-based models have provided evidence of vegetation history only at the broadest scales in this region. This study investigates the chloroplast DNA phylogeography of Tasmannia lanceolata (Winteraceae), a fleshy-fruited, bird-dispersed shrub that is widespread in the mountains of southeastern Australia and Tasmania. Thirty haplotypes were identified after sequencing 3206 bp of chloroplast DNA in each of 244 individuals collected across the species' range. These haplotypes showed unexpectedly strong phylogeographic structuring, including a phylogeographic break within a continuous part of the species' range, with the distribution of four major clades mostly not overlapping, and geographic structuring of haplotypes within these clades. This strong geographic patterning of chloroplast DNA provided evidence for the survival of T. lanceolata in multiple putative wet forest refugia as well as evidence for additional wet forest species refugia in southeastern Australia. In western Tasmania lower haplotype diversity below the LGM tree line compared to above the LGM tree line suggests that glacial refugia at high altitudes may have been important for T. lanceolata. The level of geographic structuring in T. lanceolata is similar to gravity dispersed southern hemisphere plants such as Nothofagus and Eucalyptus. Behavioural traits of the birds transporting seed may have had a strong bearing on the limited transport of T. lanceolata seed, although factors limiting establishment, possibly including selection, may also have been important. [source] Mitochondrial phylogeography of the European sprat (Sprattus sprattus L., Clupeidae) reveals isolated climatically vulnerable populations in the Mediterranean Sea and range expansion in the northeast AtlanticMOLECULAR ECOLOGY, Issue 17 2008P. V. DEBES Abstract We examined the genetic structure of the European sprat (Sprattus sprattus) by means of a 530-bp sequence of the mitochondrial control region from 210 fish originating from seven sampling localities of its distributional range. Phylogeographical analysis of 128 haplotypes showed a phylogenetic separation into two major clades with the Strait of Sicily acting as a barrier to gene flow between them. While no population differentiation was observed based on analysis of molecular variance and net nucleotide differences between samples of the Baltic Sea, the North Sea and the Bay of Biscay nor between the Black Sea and the Bosporus, a strong population differentiation between these samples and two samples from the Mediterranean Sea was found. Further, the biggest genetic distance was observed within the Mediterranean Sea between the populations of the Gulf of Lyon and the Adriatic Sea, indicating genetic isolation of these regions. Low genetic diversities and star-like haplotype networks of both Mediterranean Sea populations point towards recent demographic expansion scenarios after low population size, which is further supported by negative FS values and unimodal mismatch distributions with a low mean. Along the northeast Atlantic coast, a northwards range expansion of a large and stable population can be assumed. The history of a diverse but differentiated Black Sea population remains unknown due to uncertainties in the palaeo-oceanography of this sea. Our genetic data did not confirm the presently used classification into subspecies but are only preliminary in the absence of nuclear genetic analyses. [source] Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotasMOLECULAR ECOLOGY, Issue 10 2005JEF R. JAEGER Abstract We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid-dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species' range. Parsimony-based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene,Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert,Colorado Plateau) and Western (Mojave,Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene,early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post-Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene. [source] | ||||||||||||||||||||||||||||