Region Sequences (region + sequence)

Distribution by Scientific Domains

Kinds of Region Sequences

  • control region sequence
  • dna control region sequence
  • mitochondrial control region sequence
  • mitochondrial dna control region sequence


  • Selected Abstracts


    POPULATION GENETIC STRUCTURE OF FINLESS PORPOISES, NEOPHOCAENA PHOCAENOIDES, IN CHINESE WATERS, INFERRED FROM MITOCHONDRIAL CONTROL REGION SEQUENCES

    MARINE MAMMAL SCIENCE, Issue 2 2002
    Guang Yang
    Abstract Seven hundred and twenty base pairs (bp) of the mitochondrial control region from 73 finless porpoises, Neophocaena phocaenoides, in Chinese waters were sequenced. Thirteen variable sites were determined and 17 haplotypes were defined. Of these, 5 and 7 were found only in the Yellow Sea population and the South China Sea population, respectively, whereas no specific haplo-type was found in the Yangtze River population. Phylogenetic analyses using NJ and ML algorithm did not divide the haplotypes into monophyletic clades representing recognized geographic populations of finless porpoises in Chinese waters, suggesting the existence of migration and gene flow among populations. Analysis of molecular variance showed the obvious population genetic structure (,st= 0.41, P < 0.05); however, the structure was mainly between either the Yangtze River population or the Yellow Sea population and the South China Sea population. The genetic diversity (nucleotide diversity and haplotypic diversity) of the Yellow Sea population was significantly higher than those of the Yangtze River population and the South China Sea population, suggesting the relatively later divergence of the latter two populations and supporting the Yellow Sea population as the original center of Neophocaena. [source]


    A single nucleotide polymorphism at the splice donor site of the human MYH base excision repair gene results in reduced translation efficiency of its transcripts

    GENES TO CELLS, Issue 5 2002
    Satoru Yamaguchi
    Background: Adenine paired with 8-hydroxyguanine, a major oxidatively damaged DNA lesion, is excised by mutY homologue (MYH) base excision repair protein in human cells. Since genetic polymorphisms of DNA repair genes associated with the activities and the expression levels of their products may modulate cancer susceptibility of individuals, we investigated the effect of a single nucleotide polymorphism (SNP) in the MYH gene on the difference in the expression levels of its products. Results: An aberrant size of the , type nuclear form transcript was detected in a lung cancer cell line, VMRC-LCD, by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. The transcript contained the intron 1 sequence, and it was due to alternative splicing resulting from IVS1+5G/C SNP. The presence of the upstream open reading frame (ORF) on the 5,-side of the native ORF in the , type transcript from the IVS1+5C allele could reduce the translation efficiency of the transcript into the nuclear form protein. Thus, expression vectors bearing the 5,-untranslated region sequence of either the IVS1+5G or 5C allele were constructed. In vitro translation analysis, as well as Western blot and quantitative RT-PCR analyses of the H1299 lung cancer cell line transfected with these vectors, revealed that the translation efficiency of the IVS1+5C transcript into MYH protein was much lower (, 30%) than that of the IVS1+5G transcript. Conclusions: The SNP at the splice donor site of the MYH gene resulted in reduced translation efficiency of its transcripts. This is the fourth case of single nucleotide variations that cause alterations in translation initiation sites and translation efficiencies in human cells. [source]


    Identification and function of Abdominal-A in the silkworm, Bombyx mori

    INSECT MOLECULAR BIOLOGY, Issue 2 2009
    M-H. Pan
    Abstract Abdominal-A (adb-A) is a key gene in the development of insects. To understand its function in the silkworm, we cloned 1193 bp of the abd-A gene of Bombyx mori (Bmabd-A), including the complete coding sequence and part of the 3, untranslated region sequence. Bmabd-A has at least three mRNA splice variants with coding sequences of lengths 1032, 1044 and 1059 bp, encoding 343, 347 and 352 amino acids, respectively. Each splice variant of Bmabd-A has three exons and differs only in second exon size. Bmabd-A was expressed at low levels in unfertilized eggs, but increased gradually in fertilized eggs after laying 22 h. Bmabd-A expression decreased in ant silkworms (newly hatched silkworms). After RNA interference for Bmabd-A, the embryos had two mutant phenotypes, either completely or partially absent abdominal feet from the third to sixth abdominal segments, suggesting that Bmabd-A is responsible for normal development of the third to sixth abdominal segments during embryonic development. [source]


    Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation

    JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2009
    Y.-P. Liu
    Summary The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A,D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows. [source]


    Comparative phylogeography of sympatric sister species, Clevelandia ios and Eucyclogobius newberryi (Teleostei, Gobiidae), across the California Transition Zone

    MOLECULAR ECOLOGY, Issue 6 2002
    M. N Dawson
    Abstract It is paradigmatic in marine species that greater dispersal ability often, but not always, results in greater gene flow and less population structure. Some of the exceptions may be attributable to studies confounded by comparison of species with dissimilar evolutionary histories, i.e. co-occurring species that are not closely related or species that are closely related but allopatric. Investigation of sympatric sister species, in contrast, should allow differences in phylogeographic structure to be attributed reliably to recently derived differences in dispersal ability. Here, using mitochondrial DNA control region sequence, we first confirm that Clevelandia ios and Eucyclogobius newberryi are sympatric sister taxa, then demonstrate considerably shallower phylogeographic structure in C. ios than in E. newberryi. This shallower phylogeographic structure is consistent with the higher dispersal ability of C. ios, which most likely results from the interaction of habitat and life-history differences between the species. We suggest that the paradigm will be investigated most rigorously by similar studies of other sympatric sister species, appended by thorough ecological studies, and by extending this sister-taxon approach to comparative phylogeographic studies of monophyletic clades of sympatric species. [source]


    Phylogeography and genetic structure of northern populations of the yellow warbler (Dendroica petechia)

    MOLECULAR ECOLOGY, Issue 6 2000
    Emmanuel Milot
    Abstract Phylogeographic patterns of intraspecific variation can provide insights into the population-level processes responsible for speciation and yield information useful for conservation purposes. To examine phylogeography and population structure in a migratory passerine bird at both continental and regional geographical scales, we analysed 344 bp of mitochondrial DNA (mtDNA) control region sequence from 155 yellow warblers (Dendroica petechia) collected from seven locations across Canada and from Alaska. There is a major subdivision between eastern (Manitoba to Newfoundland) and western (Alaska and British Columbia) populations which appears to have developed during the recent Pleistocene. Some localities within these two regions also differ significantly in their genetic composition, suggesting further subdivision on a regional geographical scale. Eastern and western birds form distinct phylogeographic entities and the clustering of all western haplotypes with two eastern haplotypes suggests that the western haplotypes may be derived from an eastern lineage. Analyses based on coalescent models support this explanation for the origin of western haplotypes. These results are consistent with important features of Mengel's model of warbler diversification. From a conservation perspective they also suggest that individual populations of migrant birds may form demographically isolated management units on a smaller scale than previously appreciated. [source]


    Testing for endemism, genotypic diversity and species concepts in Antarctic terrestrial microalgae of the Tribonemataceae (Stramenopiles, Xanthophyceae)

    ENVIRONMENTAL MICROBIOLOGY, Issue 3 2009
    Nataliya Rybalka
    Summary The genetic diversity of all available culture strains of the Tribonemataceae (Stramenopiles, Xanthophyceae) from Antarctica was assessed using the chloroplast-encoded psbA /rbcL spacer region sequences, a highly variable molecular marker, to test for endemism when compared with their closest temperate relatives. There was no species endemic for Antarctica, and no phylogenetic clade corresponded to a limited geographical region. However, species of the Tribonemataceae may have Antarctic populations that are distinct from those of other regions because the Antarctic strain spacer sequences were not identical to sequences from temperate regions. Spacer sequences from five new Antarctic isolates were identical to one or more previously available Antarctic strains, indicating that the Tribonemataceae diversity in Antarctic may be rather limited. Direct comparisons of the spacer sequences and phylogenetic analyses of the more conserved rbcL gene revealed that current morphospecies were inadequate to describe the actual biodiversity of the group. For example, the genus Xanthonema, as currently circumscribed, was paraphyletic. Fortunately, the presence of distinctive sequence regions within the psbA/rbcL spacer, together with differences in the rbcL phylogeny, provided significant autoapomorphic criteria to re-define the Tribonemataceae species. [source]


    Characterization of ACC deaminase gene in Pseudomonas entomophila strain PS-PJH isolated from the rhizosphere soil

    JOURNAL OF BASIC MICROBIOLOGY, Issue 2 2010
    Seralathan Kamala-Kannan
    Abstract The enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase cleaves the ethylene precursor ACC into ,-ketobutyrate and ammonia. The decreased level of ethylene allows the plant to be more resistant to a wide environmental stress including plant pathogens. In the present study, we characterized the ACC deaminase activity of a Pseudomonas entomophila strain PS-PJH isolated from the red pepper rhizosphere region of red pepper grown at Jinan, Korea. The isolate produced 23.8 ± 0.4 ,mol of ,-ketobutyrate/mg of protein/h during ACC deamination under in vitro conditions. Polymerase chain reaction for acdS gene showed that the isolated P. entomophila strain PS-PJH carry sequences similar to the known acdS genes. Results of the multiple sequence alignment revealed >99% identity (nucleotide and amino acid) with acdS gene of Pseudomonas putida strains AM15 and UW4. The isolated bacteria promoted 43.3 and 34.1% of growth in Raphanus sativus and Lactuca sativa plants, respectively. Based on the 16S,23S internal transcribed spacer region sequences, the isolate was identified as P. entomophila. To the best of our knowledge this is the first study to report the acdS gene in P. entomophila. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]


    Ecological factors drive differentiation in wolves from British Columbia

    JOURNAL OF BIOGEOGRAPHY, Issue 8 2009
    Violeta Muñoz-Fuentes
    Abstract Aim, Limited population structure is predicted for vagile, generalist species, such as the grey wolf (Canis lupus L.). Our aims were to study how genetic variability of grey wolves was distributed in an area comprising different habitats that lay within the potential dispersal range of an individual and to make inferences about the impact of ecology on population structure. Location, British Columbia, Canada , which is characterized by a continuum of biogeoclimatic zones across which grey wolves are distributed , and adjacent areas in both Canada and Alaska, United States. Methods, We obtained mitochondrial DNA control region sequences from grey wolves from across the province and integrated our genetic results with data on phenotype, behaviour and ecology (distance, habitat and prey composition). We also compared the genetic diversity and differentiation of British Columbia grey wolves with those of other North American wolf populations. Results, We found strong genetic differentiation between adjacent populations of grey wolves from coastal and inland British Columbia. We show that the most likely factor explaining this differentiation is habitat discontinuity between the coastal and interior regions of British Columbia, as opposed to geographic distance or physical barriers to dispersal. We hypothesize that dispersing grey wolves select habitats similar to the one in which they were reared, and that this differentiation is maintained largely through behavioural mechanisms. Main conclusions, The identification of strong genetic structure on a scale within the dispersing capabilities of an individual suggests that ecological factors are driving wolf differentiation in British Columbia. Coastal wolves are highly distinct and representative of a unique ecosystem, whereas inland British Columbia grey wolves are more similar to adjacent populations of wolves located in Alaska, Alberta and Northwest Territories. Given their unique ecological, morphological, behavioural and genetic characteristics, grey wolves of coastal British Columbia should be considered an Evolutionary Significant Unit (ESU) and, consequently, warrant special conservation status. If ecology can drive differentiation in a highly mobile generalist such as the grey wolf, ecology probably drives differentiation in many other species as well. [source]


    Glacial refugia and the phylogeography of Steller's sea lion (Eumatopias jubatus) in the North Pacific

    JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2006
    A. HARLIN-COGNATO
    Abstract Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's sea lions (Eumetopias jubatus) in relation to the presence of Plio-Pleistocene insular refugia. Cytochrome b and control region sequences from 336 Steller's sea lions reveal phylogenetic lineages associated with continental refugia south of the ice sheets in North America and Eurasia. Phylogenetic analysis suggests the genetic structure of E. jubatus is the result of Pleistocene glacial geology, which caused the elimination and subsequent reappearance of suitable rookery habitat during glacial and interglacial periods. The cyclic nature of geological change produced a series of independent population expansions, contractions and isolations that had analogous results on Steller's sea lions and other marine and terrestrial species. Our data show evidence of four glacial refugia in which populations of Steller's sea lions diverged. These events occurred from approximately 60 000 to 180 000 years BP and thus preceded the last glacial maximum. [source]


    Autotransgenic and allotransgenic manipulation of growth traits in fish for aquaculture: a review

    JOURNAL OF FISH BIOLOGY, Issue 1 2008
    Y. K. Nam
    It is noteworthy that the use of transgene elements homologous to both the structural gene and promoter region sequences are more effective than heterologous ones for growth hormone (GH) transgenesis in farmed fish species. The generation of autotransgenic fish carrying the GH-transgene construct (of which elements originate from the same species only) has been given considerable attention as a potential means to produce a desirable fish strain acquiring significantly improved growth phenotype. Currently, several growth-enhanced autotransgenic lines including mud loach, carp and tilapia, have been developed or are ongoing for aquacultural purpose. This review considers the generation, development and prospects of autotransgenic manipulation of fish growth, comparing the growth performance of currently available autotransgenic fish strains with those of relevant fast-growing allotransgenic fishes. [source]


    Enhanced phylogeographic information about Austrian brown trout populations derived from complete mitochondrial control region sequences

    JOURNAL OF FISH BIOLOGY, Issue 2 2003
    N. Duftner
    Complete DNA sequences of the control region revealed a more fine-scale genetic structuring within and among Austrian brown trout Salmo trutta populations providing the opportunity for gene frequency analyses in the phylogeographic context. Ninety-two individuals (75%) were assigned to nine Danubian haplotypes and 31 individuals (25%) comprised seven Atlantic haplotypes of northern European origin. Three of the Atlantic haplotypes were also found in an Austrian hatchery breeding stock. [source]


    HTLV-1 infection in blood donors from the Western Brazilian Amazon region: Seroprevalence and molecular study of viral isolates

    JOURNAL OF MEDICAL VIROLOGY, Issue 11 2008
    Aline Cristina Mota-Miranda
    Abstract To determine the seroprevalence of HTLV-1 in Brazil, and to review the virus molecular epidemiology in this Amazon population (Rio Branco-Acre), 219 blood donors were screened for HTLV-1. Only one case of infection (0.46% seroprevalence) was detected during July 2004 screening at the Acre Hospital Foundation (FUNDACRE). Neighbor-joining and Maximum Likelihood phylogenetic analyses of two (n,=,2) complete LTR region sequences were performed with the PAUP* software. Since the HTLV-1 envelope surface (gp46) and transmembrane (gp21) glycoproteins are important for virus fitness, three envelope glycoproteins sequences (n,=,3) were analyzed using the Prosite tool to determinate potential protein sites. Phylogenetic analysis demonstrated that the new isolate described in this study, and the unpublished LTR strain described in a previous report belong to the Transcontinental subgroup of the Cosmopolitan subtype, inside the Latin American cluster. A similar result was obtained when submitting, to the Automated Genotyping System, three LTR partial sequences from a previous study of the seroprevalence of HTLV-1 in the same Amazon population. In all analyzed env sequences, the potential protein site was found: two PKC phosphorylation sites at amino acid (aa) positions 310,312 and 342,344, one CK2 phosphorylation site at 194,197aa, three N -glycosylation sites at 222,225aa, 244,247aa and 272,275aa, and a single N -myristylation site at 327,338aa. In conclusion, potential protein sites described in HTLV-1 gp46 and gp21 confirm the presence of conserved sites in the HTLV-1 envelope proteins, likewise phylogenetic analysis suggests a possible recent introduction of the virus into North Brazil. J. Med. Virol. 80:1966,1971, 2008. © 2008 Wiley-Liss, Inc. [source]


    A previously unrecognized sixth genotype of GB virus C revealed by analysis of 5,-untranslated region sequences

    JOURNAL OF MEDICAL VIROLOGY, Issue 1 2006
    A. Scott Muerhoff
    Abstract GB virus C (GBV-C) is a positive-strand RNA virus that infects a large proportion of the world's human population. It has been classified tentatively as a member of the Flaviviridae family and has been shown to exist as a group of five closely related genotypes. Recently, we reported the first full-length genome sequence of a genotype 5 isolate from South Africa [Muerhoff et al. (2005): J Gen Virol 86: 1729,1735]. As part of the analysis of that sequence, a phylogenetic tree was elucidated from the 5,-untranslated region (UTR) that showed excellent congruence to the tree produced by analysis of complete open reading frame sequences. When 5,-UTR analysis was broadened subsequently to include additional isolates from around the globe, a heretofore unrecognized GBV-C genotype was discovered in Indonesia. When first reported in 2000 [Handajani et al. (2000): J Clin Microbiol 38:662,668], these isolates were described as constituting a novel fifth genotype. However, comparison to isolates from the then-known fourth and fifth genotypes (from Myanmar/Vietnam and South Africa, respectively) was not performed. A dataset of 121 GBV-C 5,-UTR sequences was complied and included representatives of the fourth and fifth genotypes as well as the "novel" Indonesian sequences and demonstrated, with strong support via bootstrap analysis, the existence of a sixth GBV-C genotype among infected individuals in Indonesia. The discovery of this sixth genotype emphasizes the diverse nature of GBV-C isolates and may have important implications for the interpretation of studies involving GBV-C/HIV co-infected individuals. J. Med. Virol. 78:105,111, 2006. © 2005 Wiley-Liss, inc. [source]


    RESURRECTION OF MESOPLODON TRAVERSII (GRAY, 1874), SENIOR SYNONYM OF M. BAHAMONDI REYES, VAN WAEREBEEK, CÁRDENAS AND YÁÑEZ, 1995 (CETACEA: ZIPHIIDAE)

    MARINE MAMMAL SCIENCE, Issue 3 2002
    Anton L. van Helden
    Abstract Mesoplodon traversii (Gray, 1874) is shown to be a senior synonym of the recently described beaked whale Mesoplodon hahamondi Reyes et al., 1995 on the basis of a phylogenetic analysis of mitochondrial DNA control region sequences. The mandible and teeth of M. traversii, first reported in 1873 by Hector as Dolichodon layardii. are redescribed. The species can be distinguished by features of the calvaria; including the large jugal, broad rostrum, and small distance between premaxillary foramina. The male teeth, which are large and spade-shaped with a strong terminal denticle, are also diagnostic. M. traversii is known only from Pitt Island and White Island, New Zealand and Robinson Crusoe Island, Juan Fernandez Archipelago, Chile. [source]


    Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris)

    MOLECULAR ECOLOGY, Issue 4 2010
    KIMBERLY R. ANDREWS
    Abstract Spinner dolphins (Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever-changing membership, but in the low carbonate atolls in the NW archipelago they form long-term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci (n = 505). F -statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA ,ST < 0.001, P = 0.357; microsatellite FST = ,0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai'i) has the lowest gene flow (mtDNA 0.042 < ,ST < 0.236, P < 0.05; microsatellite 0.016 < FST < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location (n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < FST < 0.643, P < 0.001; microsatellite 0.058 < FST < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai'i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely-related populations. [source]


    Nuclear and mitochondrial markers reveal distinctiveness of a small population of bottlenose whales (Hyperoodon ampullatus) in the western North Atlantic

    MOLECULAR ECOLOGY, Issue 11 2006
    MEREL L. DALEBOUT
    Abstract Small populations at the edge of a species' distribution can represent evolutionary relics left behind after range contractions due to climate change or human exploitation. The distinctiveness and genetic diversity of a small population of bottlenose whales in the Gully, a submarine canyon off Nova Scotia, was quantified by comparison to other North Atlantic populations using 10 microsatellites and mitrochondrial DNA (mtDNA) control region sequences (434 bp). Both markers confirmed the distinctiveness of the Gully (n = 34) from the next nearest population, off Labrador (n = 127; microsatellites ,FST= 0.0243, P < 0.0001; mtDNA ,,ST = 0.0456, P < 0.05). Maximum likelihood microsatellite estimates suggest that less than two individuals per generation move between these areas, refuting the hypothesis of population links through seasonal migration. Both males and females appear to be philopatric, based on significant differentiation at both genomes and similar levels of structuring among the sexes for microsatellites. mtDNA diversity was very low in all populations (h = 0.51, , = 0.14%), a pattern which may be due to selective sweeps associated with this species' extreme deep-diving ecology. Whaling had a substantial impact on bottlenose whale abundance, with over 65 000 animals killed before the hunt ceased in the early 1970s. Genetic diversity was similar among all populations, however, and no signal for bottlenecks was detected, suggesting that the Gully is not a relic of a historically wider distribution. Instead, this unique ecosystem appears to have long provided a stable year-round habitat for a distinct population of bottlenose whales. [source]


    Recency, range expansion, and unsorted lineages: implications for interpreting neutral genetic variation in the sharp-tailed grouse (Tympanuchus phasianellus)

    MOLECULAR ECOLOGY, Issue 9 2006
    A. W. SPAULDING
    Abstract Both current and historical patterns of variation are relevant to understanding and managing ecological diversity. Recently derived species present a challenge to the reconstruction of historical patterns because neutral molecular data for these taxa are more likely to exhibit effects of recent and ongoing demographic processes. We studied geographical patterns of neutral molecular variation in a species thought to be of relatively recent origin, Tympanuchus phasianellus (sharp-tailed grouse), using mitochondrial control region sequences (CR-I), amplified fragment length polymorphisms (AFLP), and microsatellites. For historical context, we also analysed CR-I in all species of Tympanuchus. Within T. phasianellus, we found evidence for restricted gene flow between eastern and western portions of the species range, generally corresponding with the range boundary of T. p. columbianus and T. p. jamesi. The mismatch distribution and molecular clock estimates from the CR-I data suggested that all Tympanuchus underwent a range expansion prior to sorting of mitotypes among the species, and that sorting may have been delayed as a result of mutation-drift disequilibrium. This study illustrates the challenge of using genetic data to detect historical divergence in groups that are of relatively recent origin, or that have a history dominated by nonequilibrium conditions. We suggest that in such cases, morphological, ecological, and behavioural data may be particularly important adjuncts to molecular data for the recognition of historically or adaptively divergent groups. [source]


    Historical colonization and demography of the Mediterranean damselfish, Chromis chromis

    MOLECULAR ECOLOGY, Issue 13 2005
    VERA S. DOMINGUES
    Abstract The desiccation of the Mediterranean Sea during the Messinian Salinity Crisis 6.0,5.3 million years ago (Ma), caused a major extinction of the marine ichthyofauna of the Mediterranean. This was followed by an abrupt replenishment of the Mediterranean from the Atlantic after the opening of the Strait of Gibraltar. In this study, we combined demographic and phylogeographic approaches using mitochondrial and nuclear DNA markers to test the alternative hypotheses of where (Atlantic or Mediterranean) and when (before or after the Messinian Salinity Crisis) speciation occurred in the Mediterranean damselfish, Chromis chromis. The closely related geminate transisthmian pair Chromis multilineata and Chromis atrilobata was used as a way of obtaining an internally calibrated molecular clock. We estimated C. chromis speciation timing both by determining the time of divergence between C. chromis and its Atlantic sister species Chromis limbata (0.93,3.26 Ma depending on the molecular marker used, e.g. 1.23,1.39 Ma for the control region), and by determining the time of coalescence for C. chromis based on mitochondrial control region sequences (0.14,0.21 Ma). The time of speciation of C. chromis was always posterior to the replenishment of the Mediterranean basin, after the Messinian Salinity Crisis. Within the Mediterranean, C. chromis population structure and demographic characteristics revealed a genetic break at the Peloponnese, Greece, with directional and eastbound gene flow between western and eastern groups. The eastern group was found to be more recent and with a faster growing population (coalescent time = 0.09,0.13 Ma, growth = 485.3) than the western group (coalescent time = 0.13,0.20 Ma, growth = 325.6). Our data thus suggested a western origin of C. chromis, most likely within the Mediterranean. Low sea water levels during the glacial periods, the hydrographic regime of the Mediterranean and dispersal restriction during the short pelagic larval phase of C. chromis (18,19 days) have probably played an important role in C. chromis historical colonization. [source]


    Natal homing in juvenile loggerhead turtles (Caretta caretta)

    MOLECULAR ECOLOGY, Issue 12 2004
    BRIAN W. BOWEN
    Abstract Juvenile loggerhead turtles (Caretta caretta) from West Atlantic nesting beaches occupy oceanic (pelagic) habitats in the eastern Atlantic and Mediterranean, whereas larger juvenile turtles occupy shallow (neritic) habitats along the continental coastline of North America. Hence the switch from oceanic to neritic stage can involve a trans-oceanic migration. Several researchers have suggested that at the end of the oceanic phase, juveniles are homing to feeding habitats in the vicinity of their natal rookery. To test the hypothesis of juvenile homing behaviour, we surveyed 10 juvenile feeding zones across the eastern USA with mitochondrial DNA control region sequences (N = 1437) and compared these samples to potential source (nesting) populations in the Atlantic Ocean and Mediterranean Sea (N = 465). The results indicated a shallow, but significant, population structure of neritic juveniles (,ST = 0.0088, P = 0.016), and haplotype frequency differences were significantly correlated between coastal feeding populations and adjacent nesting populations (Mantel test R2 = 0.52, P = 0.001). Mixed stock analyses (using a Bayesian algorithm) indicated that juveniles occurred at elevated frequency in the vicinity of their natal rookery. Hence, all lines of evidence supported the hypothesis of juvenile homing in loggerhead turtles. While not as precise as the homing of breeding adults, this behaviour nonetheless places juvenile turtles in the vicinity of their natal nesting colonies. Some of the coastal hazards that affect declining nesting populations may also affect the next generation of turtles feeding in nearby habitats. [source]


    Population structure of loggerhead shrikes in the California Channel Islands

    MOLECULAR ECOLOGY, Issue 8 2004
    LORI S. EGGERT
    Abstract The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity. [source]


    Genetic evaluation of a proposed introduction: the case of the greater prairie chicken and the extinct heath hen

    MOLECULAR ECOLOGY, Issue 7 2004
    Eric P. Palkovacs
    Abstract Population introduction is an important tool for ecosystem restoration. However, before introductions should be conducted, it is important to evaluate the genetic, phenotypic and ecological suitability of possible replacement populations. Careful genetic analysis is particularly important if it is suspected that the extirpated population was unique or genetically divergent. On the island of Martha's Vineyard, Massachusetts, the introduction of greater prairie chickens (Tympanuchus cupido pinnatus) to replace the extinct heath hen (T. cupido cupido) is being considered as part of an ecosystem restoration project. Martha's Vineyard was home to the last remaining heath hen population until its extinction in 1932. We conducted this study to aid in determining the suitability of greater prairie chickens as a possible replacement for the heath hen. We examined mitochondrial control region sequences from extant populations of all prairie grouse species (Tympanuchus) and from museum skin heath hen specimens. Our data suggest that the Martha's Vineyard heath hen population represents a divergent mitochondrial lineage. This result is attributable either to a long period of geographical isolation from other prairie grouse populations or to a population bottleneck resulting from human disturbance. The mtDNA diagnosability of the heath hen contrasts with the network of mtDNA haplotypes of other prairie grouse (T. cupido attwateri, T. pallidicinctus and T. phasianellus), which do not form distinguishable mtDNA groupings. Our findings suggest that the Martha's Vineyard heath hen was more genetically isolated than are current populations of prairie grouse and place the emphasis for future research on examining prairie grouse adaptations to different habitat types to assess ecological exchangeability between heath hens and greater prairie chickens. [source]


    Population genetics of the endangered Knysna seahorse, Hippocampus capensis

    MOLECULAR ECOLOGY, Issue 7 2003
    P. R. Teske
    Abstract The evolutionary history of the endangered Knysna seahorse, Hippocampus capensis, and the extent of gene flow among its three known populations, were investigated using 138 mitochondrial DNA control region sequences. Similarly high levels of genetic diversity were found in two of the populations (Knysna and Keurbooms Estuaries), whereas diversity in the third population (Swartvlei Estuary) was lower. Although most haplotypes are shared between at least two populations, based on the haplotype frequency distributions the three assemblages constitute distinct management units. The extant population structure of H. capensis suggests that the Knysna seahorse originated in the large Knysna Estuary. The presence of seahorses in the two smaller estuaries is either the result of a vicariance event at the beginning of the present interglacial period, colonization of the estuaries via the sea, or a combination of the two. [source]


    Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences

    MOLECULAR ECOLOGY, Issue 10 2002
    C. Grunwald
    Abstract Shortnose sturgeon is an anadromous North American acipenserid that since 1973 has been designated as federally endangered in US waters. Historically, shortnose sturgeon occurred in as many as 19 rivers from the St. John River, NB, to the St. Johns River, FL, and these populations ranged in census size from 101 to 104, but little is known of their population structure or levels of gene flow. We used the polymerase chain reaction (PCR) and direct sequence analysis of a 440 bp portion of the mitochondrial DNA (mtDNA) control region to address these issues and to compare haplotype diversity with population size. Twenty-nine mtDNA nucleotide-substitution haplotypes were revealed among 275 specimens from 11 rivers and estuaries. Additionally, mtDNA length variation (6 haplotypes) and heteroplasmy (2,5 haplotypes for some individuals) were found. Significant genetic differentiation (P < 0.05) of mtDNA nucleotide-substitution haplotypes and length-variant haplotypes was observed among populations from all rivers and estuaries surveyed with the exception of the Delaware River and Chesapeake Bay collections. Significant haplotype differentiation was even observed between samples from two rivers (Kennebec and Androscoggin) within the Kennebec River drainage. The absence of haplotype frequency differences between samples from the Delaware River and Chesapeake Bay reflects a probable current absence of spawning within the Chesapeake Bay system and immigration of fish from the adjoining Delaware River. Haplotypic diversity indices ranged between 0.817 and 0.641; no relationship (P > 0.05) was found between haplotype diversity and census size. Gene flow estimates among populations were often low (< 2.0), but were generally higher at the latitudinal extremes of their distribution. A moderate level of haplotype diversity and a high percentage (37.9%) of haplotypes unique to the northern, once-glaciated region suggests that northern populations survived the Pleistocene in a northern refugium. Analysis of molecular variance best supported a five-region hierarchical grouping of populations, but our results indicate that in almost all cases populations of shortnose sturgeon should be managed as separate units. [source]


    Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus)

    MOLECULAR ECOLOGY, Issue 7 2001
    D. J. Girman
    Abstract African wild dogs are large, highly mobile carnivores that are known to disperse over considerable distances and are rare throughout much of their geographical range. Consequently, genetic variation within and differentiation between geographically separated populations is predicted to be minimal. We determined the genetic diversity of mitochondrial DNA (mtDNA) control region sequences and microsatellite loci in seven populations of African wild dogs. Analysis of mtDNA nucleotide diversity suggests that, historically, wild dog populations have been small relative to other large carnivores. However, population declines due to recent habitat loss have not caused a dramatic reduction in genetic diversity. We found one historical and eight recent mtDNA genotypes in 280 individuals that defined two highly divergent clades. In contrast to a previous, more limited, mtDNA analysis, sequences from these clades are not geographically restricted to eastern or southern African populations. Rather, we found a large admixture zone spanning populations from Botswana, Zimbabwe and south-eastern Tanzania. Mitochondrial and microsatellite differentiation between populations was significant and unique mtDNA genotypes and alleles characterized the populations. However, gene flow estimates (Nm) based on microsatellite data were generally greater than one migrant per generation. In contrast, gene flow estimates based on the mtDNA control region were lower than expected given differences in the mode of inheritance of mitochondrial and nuclear markers which suggests a male bias in long-distance dispersal. [source]


    Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density

    MOLECULAR ECOLOGY, Issue 2 2001
    D. Ehrich
    Abstract The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks. [source]


    World-wide genetic differentiation of Eubalaena: questioning the number of right whale species

    MOLECULAR ECOLOGY, Issue 11 2000
    H. C. Rosenbaum
    Abstract Few studies have examined systematic relationships of right whales (Eubalaena spp.) since the original species descriptions, even though they are one of the most endangered large whales. Little morphological evidence exists to support the current species designations for Eubalaena glacialis in the northern hemisphere and E. australis in the southern hemisphere. Differences in migratory behaviour or antitropical distribution between right whales in each hemisphere are considered a barrier to gene flow and maintain the current species distinctions and geographical populations. However, these distinctions between populations have remained controversial and no study has included an analysis of all right whales from the three major ocean basins. To address issues of genetic differentiation and relationships among right whales, we have compiled a database of mitochondrial DNA control region sequences from right whales representing populations in all three ocean basins that consist of: western North Atlantic E. glacialis, multiple geographically distributed populations of E. australis and the first molecular analysis of historical and recent samples of E. glacialis from the western and eastern North Pacific Ocean. Diagnostic characters, as well as phylogenetic and phylogeographic analyses, support the possibility that three distinct maternal lineages exist in right whales, with North Pacific E. glacialis being more closely related to E. australis than to North Atlantic E. glacialis. Our genetic results provide unequivocal character support for the two usually recognized species and a third distinct genetic lineage in the North Pacific under the Phylogenetic Species Concept, as well as levels of genetic diversity among right whales world-wide. [source]


    Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis

    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2010
    Lars Fehren-Schmitz
    Abstract Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021,16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups. Am J Phys Anthropol 2010. © 2009 Wiley-Liss, Inc. [source]


    A molecular diagnostic for identifying central African forest artiodactyls from faecal pellets

    ANIMAL CONSERVATION, Issue 1 2010
    S. Ntie
    Abstract Small to medium-sized central African forest artiodactyls constitute a diverse yet heavily hunted group composed primarily of species within the genera Cephalophus, Neotragus, Tragelaphus and Hyemoschus. Of these genera, Cephalophus is the richest with as many as seven sympatric species known to occur in central African forests. However, differentiating species from their faeces or from tissue where the whole carcass is unavailable is very difficult. In order to develop a robust molecular diagnostic for species identification, a database of mitochondrial cytochrome b (553 bp) and control region (,675 bp) sequences was compiled from all forest Cephalophus species and other similarly sized, sympatric Tragelaphus, Neotragus and Hyemoschus species. Reference phylogenies from each marker were then used to recover the identity of sequences obtained from unknown faecal samples collected in the field. Results were then compared to determine which region best recovered species identity with the highest statistical support. Restriction fragment length polymorphisms (RFLPs) were also assessed as an alternative method for rapid species identification. Of the methods examined, tree-based analyses built on a geographically comprehensive database of control region sequences was the best means of reliably recovering species identity from central African duikers. However, three sister taxa appear indistinguishable (Cephalophus callipygus, Cephalophus ogilbyi and Cephalophus weynsi) and not all species were monophyletic. This lack of monophyly may be due to incomplete lineage sorting commonly observed in recently derived taxa, hybridization or the presence of nuclear translocated copies of mitochondrial DNA. The high level of intra-specific variation and lack of robust species-specific diagnostic sites made an RFLP-based approach to duiker species identification difficult to implement. The tree-based control region diagnostic presented here has many important applications including fine-scale mapping of species distributions, identification of confiscated tissue and environmental impact assessments. [source]


    Farmed arctic foxes on the Fennoscandian mountain tundra: implications for conservation

    ANIMAL CONSERVATION, Issue 5 2009
    K. Norén
    Abstract Hybridization between wild and captive-bred individuals is a serious conservation issue that requires measures to prevent negative effects. Such measures are, however, often considered controversial by the public, especially when concerning charismatic species. One of the threats to the critically endangered Fennoscandian arctic fox Alopex lagopus is hybridization with escaped farm foxes, conveying a risk of outbreeding depression through loss of local adaptations to the lemming cycle. In this study, we investigate the existence of escaped farm foxes among wild arctic foxes and whether hybridization has occurred in the wild. We analysed mitochondrial control region sequences and 10 microsatellite loci in samples from free-ranging foxes and compared them with reference samples of known farm foxes and true Fennoscandian arctic foxes. We identified the farm fox specific mitochondrial haplotype H9 in 25 out of 182 samples, 21 of which had been collected within or nearby the wild subpopulation on Hardangervidda in south-western Norway. Genetic analyses of museum specimens collected on Hardangervidda (1897,1975) suggested that farm fox genotypes have recently been introduced to the area. Principal component analysis as well as both model- and frequency-based analyses of microsatellite data imply that the free-ranging H9s were farm foxes rather than wild arctic foxes and that the entire Hardangervidda population consisted of farm foxes or putative hybrids. We strongly recommend removal of farm foxes and hybrids in the wild to prevent genetic pollution of the remaining wild subpopulations of threatened arctic foxes. [source]