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Phylogenetic
Kinds of Phylogenetic Terms modified by Phylogenetic Selected AbstractsPHYLOGENETIC AND BIOGEOGRAPHIC AFFINITIES OF THE HALYMENIALES AND RHODYMENIALES (RHODOPHYTA) FROM THE GULF OF MEXICOJOURNAL OF PHYCOLOGY, Issue 2000B. Gavio Generic and species concepts within the red algal assemblages Halymeniales and Rhodymeniales are discussed for taxa inhabiting the western Gulf of Mexico. Two principal biogeographic assemblages occur: an off-shore deep-water group (including Coelarthrum cliftonii, Halymenia spp., Botryocladia spp., Gloiocladia) representing remnants of a Tethyan distribution, and a near-shore intertidal flora (comprising Rhodymenia, Grateloupia and Prionitis) which instead reveals biogeographic affinities with the Carolinian Province. These two distinct marine floras will be contrasted phylogenetically based on DNA sequence analysis inferred from chloroplast-encoded rbcL. The generic descriptions of Grateloupia and Prionitis are in need of taxonomic revision based on a survey of species from Caribbean and Pacific Mexico. [source] A LONG-SNOUTED DYROSAURID (CROCODYLIFORMES, MESOEUCROCODYLIA) FROM THE PALEOCENE OF MOROCCO: PHYLOGENETIC AND PALAEOBIOGEOGRAPHIC IMPLICATIONSPALAEONTOLOGY, Issue 2 2008STEPHANE JOUVE Abstract:, New material of a long-snouted dyrosaurid has been discovered in the Paleocene of Morocco. It consists of a well-preserved skull with embedded mandible and four dorsal vertebrae. The particularly elongate snout, proportionally the longest of all known dyrosaurids, allows precise identification of this material as Atlantosuchus coupateziBuffetaut, 1979a, and presentation of an emended diagnosis for this species previously known only from a mandibular symphysis. A phylogenetic analysis of the dyrosaurids indicates a close relationship between A. coupatezi and Rhabdognathus. It also confirms a previous hypothesis that Congosaurus is distinct from Hyposaurus. It is more closely related to Atlantosuchus than Hyposaurus. The analysis also allows palaeobiogeographic interpretations to be made. Dyrosaurids ranged from North Africa to other areas. They were rare during the Maastrichtian and endemic to each continent at this time. Competition with large marine reptiles, such as mosasaurs, limited their dispersal during the Late Cretaceous. The disappearance of these rivals during the ,K-T crisis' enabled their diversification and widespread dispersal during the Paleocene, with the same genera present on several continents. [source] Phylogenetic and structural analyses of the oxa1 family of protein translocasesFEMS MICROBIOLOGY LETTERS, Issue 2 2001Ming-Ren Yen Abstract Mitochondrial Oxa1p homologs have been shown to function in protein export and membrane insertion in bacteria, mitochondria and chloroplasts, but their mode of action, organismal distribution and evolutionary origins are poorly understood. All sequenced homologs of Oxa1p were retrieved from the databases and multiply aligned. All organisms with a fully sequenced genome possess at least one Oxa1p homolog showing that the family is truly ubiquitous. Most prokaryotes possess just one Oxa1p homolog, but several Gram-positive bacteria and one archaeon possess two, and eukaryotes may have as many as six. Although these proteins vary in length over a 5-fold range, they exhibit a common hydrophobic core region of about 200 residues. Multiple sequence alignments reveal conserved residues and provide the basis for structural and phylogenetic analyses that serve to characterize the Oxa1 family. [source] Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaeaFEMS MICROBIOLOGY REVIEWS, Issue 6 2009Wriddhiman Ghosh Abstract Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta - (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out. [source] Diversification in MHC class II invariant chain-like proteins among fishesJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2004M. Sakai Summary The major histocompatibility complex (MHC) class II invariant chains are important for an efficient and complete presentation of antigens by MHC class II molecules. Invariant chain-like proteins (Iclp) 1 and 2 were identified by expressed sequence tag analysis from cDNA library of common carp head kidney (HK) stimulated with concanavalin A and lipopolysaccharide. The sequences were 1043 and 1016 bp in length encoding 234 and 198 amino acid proteins, respectively. Based on their predicted structure, the genes harboured transmembrane domain (TMD) and Tg (thyroglobulin) type 1 domains. Expression analysis revealed that both genes were expressed in normal tissues of HK, intestine, brain and gill. By database search, similar homologues were found in Atlantic salmon, fugu and catfish. Phylogenetic and alignment analysis indicate diversity among fish Iclps. [source] Surviving climate changes: high genetic diversity and transoceanic gene flow in two arctic,alpine lichens, Flavocetraria cucullata and F. nivalis (Parmeliaceae, Ascomycota)JOURNAL OF BIOGEOGRAPHY, Issue 8 2010József Geml Abstract Aim, We examined genetic structure and long-distance gene flow in two lichenized ascomycetes, Flavocetraria cucullata and Flavocetraria nivalis, which are widespread in arctic and alpine tundra. Location, Circumpolar North. Methods, DNA sequences were obtained for 90 specimens (49 for F. cucullata and 41 for F. nivalis) collected from various locations in Europe, Asia and North America. Sequences of the nuclear internal transcribed spacer (ITS) + 5.8S ribosomal subunit gene region were generated for 89 samples, and supplemented by beta-tubulin (BTUB) and translation elongation factor 1-alpha gene (EF1) sequences for a subset of F. cucullata specimens. Phylogenetic, nonparametric permutation methods and coalescent analyses were used to assess population divergence and to estimate the extent and direction of migration among continents. Results, Both F. cucullata and F. nivalis were monophyletic, supporting their morphology-based delimitation, and had high and moderately high intraspecific genetic diversity, respectively. Clades within each species contained specimens from both North America and Eurasia. We found only weak genetic differentiation among North American and Eurasian populations, and evidence for moderate to high transoceanic gene flow. Main conclusions, Our results suggest that both F. cucullata and F. nivalis have been able to migrate over large distances in response to climatic fluctuations. The high genetic diversity observed in the Arctic indicates long-term survival at high latitudes, whereas the estimated migration rates and weak geographic population structure suggest a continuing long-distance gene flow between continents that has prevented pronounced genetic differentiation. The mode of long-distance dispersal is unknown, but wind dispersal of conidia and/or ascospores is probably important in the open arctic landscapes. The high genetic diversity and efficient long-distance dispersal capability of F. cucullata and F. nivalis suggest that these species, and perhaps other arctic lichens as well, will be able to track their potential niche in the changing Arctic. [source] Long-standing environmental conditions, geographic isolation and host,symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus SymbiodiniumJOURNAL OF BIOGEOGRAPHY, Issue 5 2010Todd C. LaJeunesse Abstract Aim, This study examines the importance of geographic proximity, host life history and regional and local differences in environment (temperature and water clarity) in driving the ecological and evolutionary processes underpinning the global patterns of diversity and distribution of symbiotic dinoflagellates. By comparing and contrasting coral,algal symbioses from isolated regions with differing environmental conditions, we may assess the potential of coral communities to respond to significant changes in climate. Location, Indian Ocean. Methods, Community assemblages of obligate symbiotic invertebrates were sampled at numerous sites from two regions, the north-eastern Indian Ocean (Andaman Sea, western Thailand) and the western Indian Ocean (Zanzibar, Tanzania). Molecular genetic methods, including denaturing gradient gel electrophoresis analysis of the ribosomal internal transcribed spacers, DNA sequencing and microsatellite genotyping, were used to characterize the ,species' diversity and evolutionary relationships of symbiotic dinoflagellates (genus Symbiodinium). Host,symbiont specificity, geographic isolation and local and regional environmental factors were evaluated in terms of their importance in governing the distribution and prevalence of certain symbiont taxa. Results, Host-generalist symbionts (C3u and D1-4, formerly D1a now designated Symbiodinium trenchi) frequently occurred alone and sometimes together in hosts with horizontal modes of symbiont acquisition. However, the majority of Symbiodinium diversity consisted of apparently host-specific ,species'. Clade C Symbiodinium were diverse and dominated host assemblages from sites sampled in the western Indian Ocean, a pattern analogous to symbiont communities on the Great Barrier Reef with similar environmental conditions. Clade D Symbiodinium were diverse and occurred frequently in hosts from the north-eastern Indian Ocean, especially at inshore locations, where temperatures are warmer, water turbidity is high and large tidal exchanges commonly expose coral populations to aerial desiccation. Main conclusions, Regional and local differences in cnidarian,algal combinations indicate that these symbioses are ecologically and evolutionarily responsive and can thrive under various environmental conditions. The high temperatures and turbid conditions of the north-eastern Indian Ocean partly explain the ecological success of Clade D Symbiodinium relative to Clade C. Phylogenetic, ecological and population genetic data further indicate that Clade D has undergone an adaptive radiation, especially in regions around Southeast Asia, during the Pleistocene. [source] Atlantic reef fish biogeography and evolutionJOURNAL OF BIOGEOGRAPHY, Issue 1 2008S. R. Floeter Abstract Aim, To understand why and when areas of endemism (provinces) of the tropical Atlantic Ocean were formed, how they relate to each other, and what processes have contributed to faunal enrichment. Location, Atlantic Ocean. Methods, The distributions of 2605 species of reef fishes were compiled for 25 areas of the Atlantic and southern Africa. Maximum-parsimony and distance analyses were employed to investigate biogeographical relationships among those areas. A collection of 26 phylogenies of various Atlantic reef fish taxa was used to assess patterns of origin and diversification relative to evolutionary scenarios based on spatio-temporal sequences of species splitting produced by geological and palaeoceanographic events. We present data on faunal (species and genera) richness, endemism patterns, diversity buildup (i.e. speciation processes), and evaluate the operation of the main biogeographical barriers and/or filters. Results, Phylogenetic (proportion of sister species) and distributional (number of shared species) patterns are generally concordant with recognized biogeographical provinces in the Atlantic. The highly uneven distribution of species in certain genera appears to be related to their origin, with highest species richness in areas with the greatest phylogenetic depth. Diversity buildup in Atlantic reef fishes involved (1) diversification within each province, (2) isolation as a result of biogeographical barriers, and (3) stochastic accretion by means of dispersal between provinces. The timing of divergence events is not concordant among taxonomic groups. The three soft (non-terrestrial) inter-regional barriers (mid-Atlantic, Amazon, and Benguela) clearly act as ,filters' by restricting dispersal but at the same time allowing occasional crossings that apparently lead to the establishment of new populations and species. Fluctuations in the effectiveness of the filters, combined with ecological differences among provinces, apparently provide a mechanism for much of the recent diversification of reef fishes in the Atlantic. Main conclusions, Our data set indicates that both historical events (e.g. Tethys closure) and relatively recent dispersal (with or without further speciation) have had a strong influence on Atlantic tropical marine biodiversity and have contributed to the biogeographical patterns we observe today; however, examples of the latter process outnumber those of the former. [source] Morphometric convergence and molecular divergence: the taxonomic status and evolutionary history of Gymnura crebripunctata and Gymnura marmorata in the eastern Pacific OceanJOURNAL OF FISH BIOLOGY, Issue 4 2009W.D. Smith To clarify the taxonomic status of Gymnura crebripunctata and Gymnura marmorata, the extent of morphological and nucleotide variation between these nominal species was examined using multivariate morphological and mitochondrial DNA comparisons of the same characters with congeneric species. Discriminant analysis of 21 morphometric variables from four species (G. crebripunctata, G. marmorata, Gymnura micrura and Gymnura poecilura) successfully distinguished species groupings. Classification success of eastern Pacific species improved further when specimens were grouped by species and sex. Discriminant analysis of size-corrected data generated species assignments that were consistently accurate in separating the two species (100% jackknifed assignment success). Nasal curtain length was identified as the character which contributed the most to discrimination of the two species. Sexual dimorphism was evident in several characters that have previously been relied upon to distinguish G. crebripunctata from G. marmorata. A previously unreported feature, the absence of a tail spine in G. crebripunctata, provides an improved method of field identification between these species. Phylogenetic and genetic distance analyses based on 698 base pairs of the mitochondrial cytochrome b gene indicate that G. crebripunctata and G. marmorata form highly divergent lineages, supporting their validity as distinct species. The closely related batoid Aetoplatea zonura clustered within the Gymnura clade, indicating that it may not represent a valid genus. Strong population structuring (overall ,ST = 0·81,P < 0·01) was evident between G. marmorata from the Pacific coast of the Baja California peninsula and the Gulf of California, supporting the designation of distinct management units in these regions. [source] Comparison of Mitotyper Rules and Phylogenetic-based mtDNA Nomenclature SystemsJOURNAL OF FORENSIC SCIENCES, Issue 5 2010Deborah Polanskey B.S. Abstract:, A consistent nomenclature scheme is necessary to characterize a forensic mitochondrial DNA (mtDNA) haplotype. A standard nomenclature, called the Mitotyper RulesÔ, has been developed that applies typing rules in a hierarchical manner reflecting the forensic practitioner's nomenclature preferences. In this work, an empirical comparison between the revised hierarchical nomenclature rules and the phylogenetic approach to mtDNA type description has been conducted on 5173 samples from the phylogenetically typed European Mitochondrial DNA Population database (EMPOP) to identify the degree and significance of any differences. The comparison of the original EMPOP types and the results of retyping these sequences using the Mitotyper Rules demonstrates a high degree of concordance between the two alignment schemes. Differences in types resulted mainly because the Mitotyper Rules selected an alignment with the fewest number of differences compared with the rCRS. In addition, several identical regions were described in more than one way in the EMPOP dataset, demonstrating a limitation of a solely phylogenetic approach in that it may not consistently type nonhaplogroup-specific sites. Using a rule-based approach, commonly occurring as well as private variants are subjected to the same rules for naming, which is particularly advantageous when typing partial sequence data. [source] Phylogenetic and molecular analysis of HTLV-1 isolates from a medium sized town in Northern of Brazil: Tracing a common origin of the virus from the most endemic city in the country,JOURNAL OF MEDICAL VIROLOGY, Issue 11 2008Themístocles Magalhães Abstract Salvador-Bahia has the highest prevalence of HTLV-1 infection in Brazil; about 2% of the population is infected. In this city, the prevalence of HTLV in pregnant women is 1%. There is no data of the HTLV-1 prevalence in others cities of the Bahia's Recôncavo, where the population has similar social and demography characteristics to those from Salvador. Our aim was to evaluate the seroprevalence of HTLV in pregnant women in Cruz das Almas-Bahia, a medium-sized city from the Bahia's Recôncavo. All individuals were tested for HTLV (ELISA) and the positive samples were confirmed by Western Blot. Phylogenetic analyses of the total LTR region were performed in all positive samples. We tested 408 samples (45.4% of the estimate pregnant women population) between June 1st and October 31, 2005. The prevalence of HTLV-1 infection was 0.98%. In addition, all isolated virus were grouped in the subtype HTLV-1a, in the Latin American group. Our results suggest that the introduction of HTLV-1 occurred after the slave trade into Salvador. In addition, HTLV-1-infection should be screened during the pregnancy in women originating from HTLV-1 endemic areas. J. Med. Virol. 80:2040,2045, 2008. © 2008 Wiley-Liss, Inc. [source] Pleistocene phylogeography and phylogenetic concordance in cold-adapted spring snails (Bythinella spp.)MOLECULAR ECOLOGY, Issue 5 2009M. BENKE Abstract Previous studies on Pleistocene phylogeography of European taxa are biased towards (i) vertebrates, (ii) terrestrial taxa, (iii) single species, and (iv) taxa that survived the Pleistocene in southern refugia. Relatively little is known about whether evolutionary patterns of vertebrate and terrestrial taxa are also applicable to freshwater invertebrates, whether cold-adapted freshwater species could survive in extensive permafrost areas without retreating into refugia, and whether Pleistocene phylogeographical patterns are influenced by phylogeny. Here, the widespread and species-rich European spring snail genus Bythinella Moquin-Tandon, 1856 is utilized in an attempt to mitigate this bias. These strongly cold-adapted freshwater animals mostly occur in springs , highly isolated habitats that are relatively unaffected by anthropogenic influences. Phylogenetic and phylogeographical analyses based on mitochondrial DNA and nuclear DNA sequence data were conducted in 458 specimens from 142 populations occurring throughout Europe. The study provides evidence that most Bythinella spp. survived the Pleistocene in restricted northern glacial refugia that largely correspond to refugia previously recognized for other European biota. However, survival of Bythinella spp. in extensive permafrost areas outside of refugia can likely be rejected. Low dispersal ability and the isolation and fragmentation of spring habitats, as well as the distribution of perennial springs within permafrost regions, may account for this result. Tests involving a total of 29 nominal species showed that phylogenetically closely related Bythinella species did not occupy similar refugia. This lack of phylogenetic concordance could possibly be explained by the stochasticity of survival and dispersal in spring snails. [source] Refugial isolation and secondary contact in the dyeing poison frog Dendrobates tinctoriusMOLECULAR ECOLOGY, Issue 14 2006BRICE P. NOONAN Abstract Recent palaeoclimactic research suggests that fluctuating environmental conditions throughout the Pleistocene of Amazonia occurred with previously unrecognized frequency. This has resulted in a theoretical shift from glacially influenced fluctuations to those driven by precessional rhythms. This theoretical revolution has a profound impact on expectations of biotic diversity within biogeographical regions that have long been based on the idea of large-scale landscape fragmentation associated with increased aridity and glacial cycles. Generally speaking, this shifts phylogeographical expectations from that of (i) large areas of sympatry of closely related (but not sister) species whose origins lie in separate refugia, and current distributions are the results of cyclic connectivity of those two refugia (refuge hypothesis), to that of (ii) fine scale genetic structure, often associated with elevation, and divergence well below expected speciation levels [disturbance,vicariance (DV) hypothesis]. To date there have been few tests of the expectations of the DV hypothesis based on empirical studies of Neotropical floral and faunal communities. Herein we examine phylogeographical structure of Dendrobates tinctorius, an amphibian species endemic to the uplands of the eastern Guiana Shield, based on sampling of 114 individuals from 24 localities. Phylogenetic, nested clade, and dispersal,vicariance (DIVA) analyses of cytochrome b sequence data reveal the presence of two mitochondrial lineages that are associated with previously identified western and eastern uplands of this area. The geographical distribution of mitochondrial haplotypes and the results of DIVA and coalescent analyses suggest that there has been extensive secondary contact between these lineages indicating a complex history of connectivity between these western and eastern highlands, supporting the predictions of the DV hypothesis. [source] Phylogenetic and transcriptional analysis of a strictosidine synthase-like gene family in Arabidopsis thaliana reveals involvement in plant defence responsesPLANT BIOLOGY, Issue 1 2009M. M. Sohani Abstract Protein domains with similarity to plant strictosidine synthase-like (SSL) sequences have been uncovered in the genomes of all multicellular organisms sequenced so far and are known to play a role in animal immune responses. Among several distinct groups of Arabidopsis thaliana SSL sequences, four genes (AtSSL4,AtSSL7) arranged in tandem on chromosome 3 show more similarity to SSL genes from Drosophila melanogaster and Caenorhabditis elegans than to other Arabidopsis SSL genes. To examine whether any of the four AtSSL genes are immune-inducible, we analysed the expression of each of the four AtSSL genes after exposure to microbial pathogens, wounding and plant defence elicitors using real-time quantitative RT-PCR, Northern blot hybridisation and Western blot analysis with antibodies raised against recombinant AtSSL proteins. While the AtSSL4 gene was constitutively expressed and not significantly induced by any treatment, the other three AtSSL genes were induced to various degrees by plant defence signalling compounds, such as salicylic acid, methyl jasmonate and ethylene, as well as by wounding and exposure to the plant pathogens Alternaria brassicicola and cucumber mosaic virus. Our data demonstrate that the four SSL-coding genes are regulated individually, suggesting specific roles in basal (SSL4) and inducible (SSL5-7) plant defence mechanisms. [source] A microsatellite study to disentangle the ambiguity of linguistic, geographic, ethnic and genetic influences on tribes of India to get a better clarity of the antiquity and peopling of South AsiaAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2009S. Krithika Abstract An understanding of the genetic affinity and the past history of the tribal populations of India requires the untangling of the confounding influences of language, ethnicity, and geography on the extant diverse tribes. The present study examines the genetic relationship of linguistically (Dravidian, Austro-Asiatic, and Tibeto-Burman) and ethnically (Australian and East Asian) diverse tribal populations (46) inhabiting different regions of the Indian subcontinent. For the purpose, we have utilized the published data on allele frequency of 15 autosomal STR loci of our study on six Adi sub-tribes of Arunachal Pradesh and compared the same with the reported allele frequency data, for nine common autosomal STR loci, of 40 other tribes. Phylogenetic and principal component analyses exhibit geography based clustering of Tibeto-Burman speakers and separation of the Mundari and Mon-Khmer speaking Austro-Asiatic populations. The combined analyses of all 46 populations show clustering of the groups belonging to same ethnicity and inhabiting contiguous geographic regions, irrespective of their different languages. These results help us to reconstruct and understand three plausible scenarios of the antiquity of Indian tribal populations: the Dravidian and Austro-Asiatic (Mundari) tribes were possibly derived from common early settlers; the Tibeto-Burman tribes possibly belonged to a different ancestry and the Mon-Khmer speaking Austro-Asiatic populations share a common ancestry with some of the Tibeto-Burman speakers. Am J Phys Anthropol, 2009. © 2009 Wiley-Liss, Inc. [source] Phylogenetic and Primary Sequence Characterization of Cathepsin B Cysteine Proteases from the Oxymonad Flagellate MonocercomonoidesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2008JOEL B. DACKS ABSTRACT. Cysteine proteases are crucial for general lysosomal function and for the pathogenic mechanisms of many protistan parasites. Cathepsin B cysteine proteases are currently defined by the presence of the "occluding loop" motif and have been best characterized from humans and their parasites. Though related to a variety of pathogenic excavate flagellates, oxymonads are themselves commensals. While studying this cell biologically aberrant protist lineage, we identified 11 different cathepsin B homologues. These were found to be expressed, at comparable levels to common house-keeping genes, such as elongation factor 1-,, ,-tubulin, ,-tubulin, and glyceraldehyde phosphate dehydrogenase. Primary structure examination of the cathepsin B homologues identified putative signal peptide sequences, and the pre-, pro-, and mature domains of the protein. However, the occluding loop motif was either partially or entirely absent. Comparative genomics, sequence alignment, and phylogenetics of cathepsin sequences from across the diversity of eukaryotes demonstrated that absence of the occluding loop is not a feature exclusive to oxymonads, but is relatively common, suggesting that the "occluding loop" should no longer be used as the defining feature of the cathepsin B subfamily. Overall, this report identifies an abundant protein family in oxymonads, and provides insight both into the evolution and classification of cathepsin B cysteine proteases. [source] Mitochondrial diversity of native pigs in the mainland South and South-east Asian countries and its relationships between local wild boarsANIMAL SCIENCE JOURNAL, Issue 4 2008Kazuaki TANAKA ABSTRACT In this study, we analyzed DNA sequence of mitochondrial DNA (mtDNA) control regions on the 130 native domestic pigs and eight wild boars in the mainland South and South-east Asian countries including Bhutan, Cambodia, Laos, Myanmar, and Vietnam. Forty-four haplotypes were found in the 138 individuals, 41 were in the domestic and four were in wild boars. Only one haplotype was shared by domestic and wild population in Bhutan. In other cases, mtDNA of wild boars did not show close affinity to that of the domestic pigs in the same location, indicating that the native domestic pigs in these countries did not originate in the present habitat. Phylogenetic analyzes of mtDNA haplotypes recapitulated several major clusters identified in other studies, but 11 haplotypes were grouped in a new cluster we named MTSEA. In most cases, more than one lineage group were present in a sampling station, indicating that the present indigenous domestic pigs may have multiple origins. The MTSEA haplotypes were present in relatively high frequencies in domestic pigs in the mountainous area of mainland South-east Asia (Cambodia and Laos), with a few found in Myanmar and Bhutan. The distributions of MTSEA haplotypes are in great conformity with the distribution of present-day Mon-Khmer language and indicated the existence of yet another independent domestication. The D2 haplotypes that distribute high frequency (almost 100%) throughout the Chinese breeds were dominant in Bhutan, Myanmar, and Vietnam. These results suggest an existence of human-mediated dispersal of domestic pigs from north to the south during the historical expansion of Sino-Tibetan and Tai peoples. The D3 haplotypes previously reported in north India were found in sympatric domestic and wild pigs in Bhutan. The D3 haplotype is an important proof of independent domestication event and/or great gene flow between wild and domestic pigs in the foot of Himalaya. [source] Historical biogeography of Hexabathynella , a cosmopolitan genus of groundwater Syncarida (Crustacea, Bathynellacea, Parabathynellidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2003ANA I. CAMACHO Hexabathynella is the only cosmopolitan genus of the order Bathynellacea (Crustacea). The known species number 18, found in Europe (9), Africa (1), South America (2), North America (3) and Australia and New Zealand (3). Phylogenetic analysis suggests that the least derived species are those from South America and the most derived those from the Iberian Peninsula, North America and Australia. The five species with the most plesiomorphic characters occur in salt or brackish water, which supports a marine origin for the genus. Phylogenetic and biogeographical analyses suggest that the distribution of the genus can be explained by dispersion and a double vicariant biogeographical model based on plate tectonics and the evolution of the Tethys during the Mesozoic and Cenozoic. © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 457,466. [source] Phylogeny and biogeography of Crinum L. (Amaryllidaceae) inferred from nuclear and limited plastid non-coding DNA sequencesBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2003ALAN W. MEEROW The genus Crinum L. is the only pantropical genus of the Amaryllidaceae. Phylogenetic and biogeographical analyses of nrDNA ITS and plastid trnL-F sequences for all continental groups of the genus Crinum and related African genera are presented, with the genus Amaryllis used as outgroup. ITS indicates that C. baumii is more closely related to Ammocharis and Cybistetes than to Crinum sensu stricto. Three clades are resolved in Crinum s.s. One unites a monophyletic American group with tropical and North African species. The second includes all southern African species and the Australian endemic C. flaccidum. The third includes monophyletic Madagascar, Australasian and Sino-Himalayan clades, with southern African species. The trnL-F phylogeny resolves an American and an Asian/Madagscar clade, and confirms the relationship of C. flaccidum with species endemic to southern Africa. The salverform, actinomorphic perianths of subg. Crinum appear to have evolved several times in the genus from ancestors with zygomorphic perianths (subg. Codonocrinum), thus neither subgenus is monophyletic. Biogeographical analyses place the origin of Crinum in southern Africa, as the region is optimized at all ancestral nodes in the tree topology, and in basal interior nodes of all but one of the major clades. The genus underwent three major waves of radiation corresponding to the three main clades resolved in our trees. Two entries into Australia for the genus are indicated, as are separate Sino-Himalayan and Australasian dispersal events. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 141, 349,363. [source] The cortex in multidimensional space: where do cortical areas come from?DEVELOPMENTAL SCIENCE, Issue 2 2001Marcy A. Kingsbury The concept of a cortical ,area' as a discrete phylogenetic, developmental and computational unit is evaluated. Evidence including the comparative organization of the forebrain in vertebrates, the organization of cortex in different mammals, the scaling of the areas of the isocortex in mammals, and the early molecular differentiation of the cortex all suggest a special status for the primary sensory cortical areas, particularly the visual cortex. Furthermore, the overlapping gradients of early molecular expression and the patterning of cortical structure and connectivity by thalamic input suggest a new view of cortical organization that is different from the traditional view of a developmentally mosaic cortex; this view proposes that distinct cortical areas arise combinatorily from the multiple overlapping processes imposed upon the developing cortex. [source] Comparative morphology and evolutionary pathways of the mouthparts in spore-feeding Staphylinoidea (Coleoptera)ACTA ZOOLOGICA, Issue 3 2003Oliver Betz Abstract This study surveys the external morphology of the mouthparts in the guild of spore-feeders among the coleopterous superfamily Staphylinoidea, evaluating the influence of different phylogenetic and ecological starting points on the formation of their mouthparts. Our emphasis is on a scanning electron microscope analysis (SEM) of the involved trophic structures in spore-feeding larvae and adults of the Ptiliidae, Leiodidae and Staphylinidae, describing the fine structure of their main functional elements. Functionally, mouthpart structures resemble brushes, brooms, combs, rakes, rasps, excavators, knives, thorns, cram-brushes, bristle troughs, blocks and differently structured grinding surfaces. Their different involvement in the various aspects of the feeding process (i.e. food gathering, transporting, channelling and grinding) is deduced from our SEM analyses plus direct video observations. We infer five different patterns of food transport and processing, discriminating adults of ptiliids, leiodids plus staphylinids (excluding some aleocharines), several aleocharine staphylinids, and the larvae of leiodids and staphylinids. The structural diversity of the mouthparts increases in the order from (1) Ptiliidae, (2) Leiodidae towards (3) Staphylinidae, reflecting the increasing systematic and ecological diversity of these groups. Comparisons with non-spore-feeders show that among major lineages of staphylinoids, shifts from general microphagy to sporophagy are not necessarily constrained by, nor strongly reflected in, mouthpart morphology. Nevertheless, in several of these lineages the organs of food intake and grinding have experienced particular fine-structural modifications, which have undergone convergent evolution, probably in response to specialized mycophagy such as spore-feeding. These modifications involve advanced galeal rakes, galeal or lacinial ,spore brushes' with arrays of stout bristles, reinforced obliquely ventrad orientated prosthecal lobes and the differentiations of the molar grinding surfaces into stout teeth or tubercles. In addition, several staphylinids of the tachyporine and oxyteline groups with reduced mandibular molae have evolved secondary trituration surfaces, which in some aleocharines are paralleled by considerable re-constructions of the labium,hypopharynx. [source] Fine structure of unusual spermatozoa and spermiogenesis of the mite Megisthanus floridanus Banks, 1904 (Acari: Gamasida: Antennophorina)ACTA ZOOLOGICA, Issue 4 2002Gerd Alberti Abstract The aflagellate spermatozoa of the gamasid mite Megisthanus floridanus are characterized by a large vacuole which contains a cytoplasmic column protruding into the vacuole from the region defined as the posterior part of the cell. The membrane of the column and the inner membrane of the posterior part of the cytoplasmic mantle (outer sheath) surrounding the vacuole bear numerous so-called cellular processes. However, most of the outer sheath is reduced and represented solely by a very thin membrane-like envelope. The posterior part of the cell bears extensive folds. The cell, or, more precisely, the column, shows a deep posterior invagination. This invagination contains extracellular material composed of thin filaments or strands. Peripheral folds emerging from the posterior rim of the cell form a thin-walled tube that contains the same material as the invagination. The elongated nucleus is attached to a peculiar acrosomal complex consisting of a flat acrosomal cisterna that parallels most of the cell membrane, an attachment cone, and a short acrosomal filament which is embedded in a narrow canal within the nucleus. The spermatozoa of M. floridanus represent a peculiar version of the vacuolated type of sperm known to be plesiomorphic within the anactinotrichid Acari. Some details of spermiogenesis are described and consequences for phylogenetic and systematic considerations are discussed. [source] Biodiverse, a tool for the spatial analysis of biological and related diversityECOGRAPHY, Issue 4 2010Shawn W. Laffan Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix (e.g. genetic dissimilarity) relationships. The explosion in georeferenced biological specimen and survey data means there is an increasing need for such tools. Biodiverse supports four processes: 1) linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces; 2) spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity; 3) spatially constrained agglomerative cluster analyses; and 4) randomisations for hypothesis testing. Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface and scripts. Biodiverse can be downloaded from Geographic body size gradients in tropical regions: water deficit and anuran body size in the Brazilian CerradoECOGRAPHY, Issue 4 2009Miguel Á. Olalla-Tárraga A recent interspecific study found Bergmann's size clines for Holarctic anurans and proposed an explanation based on heat balance to account for the pattern. However, this analysis was limited to cold temperate regions, and exploring the patterns in warmer tropical climates may reveal other factors that also influence anuran body size variation. We address this using a Cerrado anuran database. We examine the relationship between mean body size in a grid of 1° cells and environmental predictors and test the relative support for four hypotheses using an AIC-based model selection approach. Also, we considered three different amphibian phylogenies to partition the phylogenetic and specific components of the interspecific variation in body size using a method analogous to phylogenetic eigen vector regression (PVR). To consider the potential effects of spatial autocorrelation we use eigenvector-based spatial filters. We found the largest species inhabiting high water deficit areas in the northeast and the smallest in the wet southwest. Our results are consistent with the water availability hypothesis which, coupled with previous findings, suggests that the major determinant of interspecific body size variation in anurans switches from energy to water towards the equator. We propose that anuran body size gradients reflect effects of reduced surface to volume ratios in larger species to control both heat and water balance. [source] The implications of different species concepts for describing biodiversity patterns and assessing conservation needs for African birdsECOGRAPHY, Issue 5 2005Shaun Dillon It has been suggested that switching from the widely used Biological Species Concept to a Phylogenetic Species Concept, would result in the appearance of hitherto neglected patterns of endemism. The problem has mainly been analyzed with respect to endemic taxa and for rather limited geographical regions, but will here be analysed for the entire resident avifauna of sub-Saharan Africa. A database of African bird distributions was re-edited to create two new datasets representing 1572 biological species and 2098 phylogenetic species. Species richness patterns were virtually identical with the two taxonomies, and only subtle changes were found in the geographical variation in range-size rarity sum. However, there were some differences in the most range-restricted species, with increased complexity of long-recognized centres of endemism. Overall, then, the large-scale biogeographic patterns are robust to changes in species concepts. This reflects the aggregated nature of endemism, with certain areas acting as "species pumps" and large intervening areas being characterised by a predominance of widespread species which distribute themselves in accordance with contemporary environmental conditions. The percentages of phylogenetic and threatened species captured in a BSC near-minimum set of 64 grid-cells and a PSC near-maximum set, with the same number of grid-cells, are very similar. [source] Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analysesENVIRONMENTAL MICROBIOLOGY, Issue 9 2007Rodrigo Costa Summary The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas -specific gacA gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene-based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured Pseudomonas in bulk and rhizosphere soils. Pseudomonas -specific gacA fingerprints of total-community (TC) rhizosphere DNA were surprisingly diverse, plant-specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture-dependent and independent surveys, a group of Pseudomonas isolates antagonistic towards V. dahliae was shown to be genotypically conserved, to carry the phlD biosynthetic locus (involved in the biosynthesis of 2,4-diacetylphloroglucinol , 2,4-DAPG), and to correspond to a dominant and highly frequent Pseudomonas population in the rhizosphere of field-grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the Pseudomonas fluorescens phylogenetic lineage and showed closest relatedness to P. fluorescens strain F113 (97% gacA gene sequence identity in 492-bp sequences), a biocontrol agent and 2,4-DAPG producer. Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis. [source] Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCRENVIRONMENTAL MICROBIOLOGY, Issue 7 2006Axel Schippers Summary Deeply buried marine sediments harbour a large fraction of all prokaryotes on Earth but it is still unknown which phylogenetic and physiological microbial groups dominate the deep biosphere. In this study real-time PCR allowed a comparative quantitative microbial community analysis in near-surface and deeply buried marine sediments from the Peru continental margin. The 16S rRNA gene copy numbers of prokaryotes and Bacteria were almost identical with a maximum of 108,1010 copies cm,3 in the near-surface sediments. Archaea exhibited one to three orders of magnitude lower 16S rRNA gene copy numbers. The 18S rRNA gene of Eukarya was always at least three orders of magnitude less abundant than the 16S rRNA gene of prokaryotes. The 16S rRNA gene of the Fe(III)- and Mn(IV)-reducing bacterial family Geobacteraceae and the dissimilatory (bi)sulfite reductase gene (dsrA) of sulfate-reducing prokaryotes were abundant with 106,108 copies cm,3 in near-surface sediments but showed lower numbers and an irregular distribution in the deep sediments. The copy numbers of all genes decreased with sediment depth exponentially. The depth gradients were steeper for the gene copy numbers than for numbers of total prokaryotes (acridine orange direct counts), which reflects the ongoing degradation of the high-molecular-weight DNA with sediment age and depth. The occurrence of eukaryotic DNA also suggests DNA preservation in the deeply buried sediments. [source] CLINES IN CUTICULAR HYDROCARBONS IN TWO DROSOPHILA SPECIES WITH INDEPENDENT POPULATION HISTORIESEVOLUTION, Issue 6 2010Francesca D. Frentiu We took a comparative approach utilizing clines to investigate the extent to which natural selection may have shaped population divergence in cuticular hydrocarbons (CHCs) that are also under sexual selection in Drosophila. We detected the presence of CHC clines along a latitudinal gradient on the east coast of Australia in two fly species with independent phylogenetic and population histories, suggesting adaptation to shared abiotic factors. For both species, significant associations were detected between clinal variation in CHCs and temperature variation along the gradient, suggesting temperature maxima as a candidate abiotic factor shaping CHC variation among populations. However, rainfall and humidity correlated with CHC variation to differing extents in the two species, suggesting that response to these abiotic factors may vary in a species-specific manner. Our results suggest that natural selection, in addition to sexual selection, plays a significant role in structuring among-population variation in sexually selected traits in Drosophila. [source] THE COMBINED EFFECTS OF RIVERS AND REFUGIA GENERATE EXTREME CRYPTIC FRAGMENTATION WITHIN THE COMMON GROUND SKINK (SCINCELLA LATERALIS)EVOLUTION, Issue 2 2010Nathan D. Jackson Rivers can act as both islands of mesic refugia for terrestrial organisms during times of aridification and barriers to gene flow, though evidence for long-term isolation by rivers is mixed. Understanding the extent to which riverine barrier effects can be heightened for populations trapped in mesic refugia can help explain maintenance and generation of diversity in the face of Pleistocene climate change. Herein, we implement phylogenetic and population genetic approaches to investigate the phylogeographic structure and history of the ground skink, Scincella lateralis, using mtDNA and eight nuclear loci. We then test several predictions of a river,refugia model of diversification. We recover 14 well-resolved mtDNA lineages distributed east,west along the Gulf Coast with a subset of lineages extending northward. In contrast, ncDNA exhibits limited phylogenetic structure or congruence among loci. However, multilocus population structure is broadly congruent with mtDNA patterns and suggests that deep coalescence rather than differential gene flow is responsible for mtDNA,ncDNA discordance. The observed patterns suggest that most lineages originated from population vicariance due to riverine barriers strengthened during the Plio,Pleistocene by a climate-induced coastal distribution. Diversification due to rivers is likely a special case, contingent upon other environmental or biological factors that reinforce riverine barrier effects. [source] HOW BRIGHT AND HOW NASTY: EXPLAINING DIVERSITY IN WARNING SIGNAL STRENGTHEVOLUTION, Issue 3 2007Michael P. Speed The conspicuous displays that warn predators of defenses carried by potential prey have been of interest to evolutionary biologists from the time of Wallace and Darwin to the present day. Although most studies implicitly assume that these "aposematic" warning signals simply indicate the presence of some repellent defense such as a toxin, it has been speculated that the intensity of the signal might reliably indicate the strength of defense so that, for example, the nastiest prey might "shout loudest" about their unprofitability. Recent phylogenetic and empirical studies of Dendrobatid frogs provide contradictory views, in one instance showing a positive correlation between toxin levels and conspicuousness, in another showing a breakdown of this relationship. In this paper we present an optimization model, which can potentially account for these divergent results. Our model locates the optimal values of defensive traits that are influenced by a range of costs and benefits. We show that optimal aposematic conspicuousness can be positively correlated with optimal prey toxicity, especially where population sizes and season lengths vary between species. In other cases, optimal aposematic conspicuousness may be negatively correlated with toxicity; this is especially the case when the marginal costs of aposematic displays vary between members of different populations. Finally, when displays incur no allocation costs there may be no single optimum value for aposematic conspicuousness, rather a large array of alternative forms of a display may have equal fitness. [source]
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