bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeographical structure of the Dover soleMicrostomus pacificus: the larval retention hypothesis and genetic divergence along the deep continental slope of the northeastern Pacific Ocean
Authors: Stepien C. A. 
Published: March 2003

AbstractPopulation genetic variability and phylogeographical structure of the Dover sole,Microstomus pacificus(Teleostei: Pleuronectidae), were examined along the continental slope of the northeastern Pacific Ocean using sequences of the left domain of the mitochondrial DNA (mtDNA) control region. Six sites were sampled in three primary biogeographical provinces (based on surface water temperatures), ranging from the subarctic to the warm temperate zones. Many haplotypes were discerned, totalling 90 for 110 individuals. Neighbour joining and parsimony analyses of the entire data set showed that some groups of haplotypes of adult Dover sole were widely distributed, suggesting either panmixia or homoplasy and reversals. However, a substantial number of groups of related haplotypes were geographically circumscribed, and there were significant differences among sites in the distribution of restricted haplotypes (based on a reduced number of characters), supporting geographical structure. Geographical differentiation of populations appeared to be consistent with the member‐vagrant hypothesis for retention of the pelagic larvae in currents and recruitment to adult habitats, reducing long‐distance dispersal. Results of this study indicate phylogeographical structure among some populations, despite extended pelagic larval periods, and apparent environmental homogeneity in the adult habitats along the continental slope.
Molecular phylogeography ofDryas integrifolia: glacial refugia and postglacial recolonization
Authors: Tremblay N. O. , Schoen D. J. 
Published: March 2003

AbstractChloroplast DNA variation in the Arctic plant speciesDryas integrifolia(Rosaceae) was analysed in relation to both the present‐day geographical distribution of populations and to Pleistocene fossil records of this species. The phylogeographical structure was weak but the analysis of haplotype diversity revealed several groups of haplotypes having present‐day geographical ranges that overlap locations postulated from geographical and fossil evidence to have been glacial refugia. Based on this information we infer that two important refugial sources of Arctic recolonization by this species were Beringia and the High Arctic. Two other putative refugia, located southeast of the ice sheet and along coastal regions of the eastern Arctic may have served as sources for recolonization of smaller portions of the Arctic. The genetic substructure in the species is mostly due to variation among populations regardless of the ecogeographical region in which they are found. Spatial autocorrelation at the regional scale was also detected. High levels of diversity both within populations and ecogeographical regions are probably indicative of population establishment from several sources possibly combined with recent gene flow.
Phylogeography of a post‐glacial colonizer:Microtus longicaudus(Rodentia: Muridae)
Authors: Conroy C. J. , Cook J. A. 
Published: March 2003

AbstractThe molecular phylogeography ofMicrotus longicauduswas investigated with DNA sequences of the mitochondrial cytochromebgene. We used phylogenetic and pairwise distance methods to reconstruct the history of the species with particular emphasis on the Pacific Northwest. Genetic variation across the species was consistent with vicariant events during the Pleistocene and subsequent northern postglacial expansion following the receding Laurentide and Cordilleran ice sheets. The largest break (> 6% uncorrected sequence divergence) was found to exist between populations found southeast of the Colorado River (eastern Arizona, Colorado, Wyoming and New Mexico) and all other western populations. Other well‐supported subclades were composed of samples from: (i) the islands and north coast of southeast Alaska; (ii) eastern Alaska, British Columbia, Washington and Oregon; and (iii) northern California, Idaho and Montana. Within subclades, divergence was low. Our results suggest that the close relationships among haplotypes within northern subclades are a result of recent colonization, whereas higher among‐subclade divergence is caused by genetic differentiation during prolonged periods of isolation, possibly as a result of mid‐Pleistocene climatic events.
Genetic distinctness of isolated populations of an endangered marsupial, the mountain pygmy‐possum, Burramys parvus
Authors: Osborne M. J. , Norman J. A. , Christidis L. , Murray N. D. 
Published: March 2003

AbstractThe mountain pygmy‐possum, Burramys parvus, exists in isolated and fragmented populations in the Australian alps. To examine the degree of interpopulation divergence, mitochondrial cytochrome b and NADH dehydrogenase subunit 2 (NADH2) sequences were obtained from samples representing all populations of B. parvus. Three divergent mitochondrial DNA (mtDNA) lineages were identified which exhibited strong phylogeographical structure. This indicates the presence of three maternal clades corresponding to populations in the northern, central and southern Australian alps. Molecular clock estimates suggest that the mtDNA lineages diverged from one another 420–680 thousand years ago. On this basis it is argued that B. parvus populations have probably been isolated since the mid‐Pleistocene, and that management should focus on maintaining viable B. parvus populations in each of the three regional localities.
Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among chinook salmon (Oncorhynchus tshawytscha) populations
Authors: Ford Michael J. 
Published: March 2003

AbstractThis paper describes DNA sequence variation within and among four populations of chinook salmon (Oncorhynchus tshawytscha) at the transferrin, somatolactin and p53 genes. Patterns of variation among salmon species at the transferrin gene have been hypothesized to be shaped by positive natural selection for new alleles because the rate of nonsynonymous substitution is significantly greater than the rate of synonymous substitution. The twin goals of this study were to determine if the history of selection among salmon species at the transferrin gene is also reflected in patterns of intraspecific variation in chinook salmon, and to look for evidence of local adaptation at the transferrin gene by comparing patterns of nonsynonymous and synonymous variation among chinook salmon populations. The analyses presented here show that unlike patterns of variation between species, there is no evidence of greater differentiation among chinook salmon populations at nonsynonymous compared to synonymous sites. There is also no evidence of a reduction of within‐species variation due to the hitchhiking effect at the transferrin gene, although in some populations nonsynonymous and synonymous derived mutations are both at higher frequencies than expected under a simple neutral model. Population size weighted selection coefficients (4Ns) that are consistent with both the inter and intraspecific data range from ~10 to ~235, and imply that between 1 and 40% of new nonsynonymous mutations at the transferrin gene have been beneficial.
Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans
Authors: Xu Jianping , Vilgalys Rytas , Mitchell Thomas G. 
Published: March 2003

Abstract Cryptococcus neoformans (= Filobasidiella neoformans) is a significant emerging fungal pathogen of humans. To understand the evolution of this pathogen, 34 strains were obtained from various locations around the world and fragments of four genes were sequenced from each. These strains represented all three varieties and five serotypes. The four sequenced genes are: (i) the mitochondrial large ribosomal subunit RNA; (ii) the internal transcribed spacer region of the nuclear rRNA, including ITS1, 5.8S rRNA subunit and ITS2; (iii) orotidine monophosphate pyrophosphorylase; and (iv) diphenol oxidase. Phylogenetic analyses indicated considerable divergence among lineages, which corresponded to the current classification of C. neoformans into three varieties. However, there is no apparent phylogeographic pattern. Significant incongruences were observed among gene genealogies. The analyses indicated that the major lineages in C. neoformans diverged tens of millions of years ago but have undergone recent dispersion and hybridization.
Dispersal barriers in tropical oceans and speciation in Atlantic and eastern Pacific sea urchins of the genus Echinometra
Authors: Mccartney M. A. , Keller G. , Lessios H. A. 
Published: March 2003

Abstract Echinometra is a pantropical sea urchin made famous through studies of phylogeny, speciation, and genetic structure of the Indo‐West Pacific (IWP) species. We sequenced 630 bp of the cytochrome oxidase I (COI) mitochondrial gene to provide comparable information on the eastern Pacific and Atlantic species, using divergence between those separated by closure of the Isthmus of Panama 3.1 million years ago (Ma) to estimate dates for cladogenic events. Most recently (1.27–1.62 Ma), the Atlantic species E. lucunter and E. viridis diverged from each other, at a time in the Pleistocene that sea levels fell and Caribbean coral speciation and extinction rates were high. An earlier split, assumed to have been coincident with the completion of the Isthmus of Panama, separated the eastern Pacific E. vanbrunti from the Atlantic common ancestor. Transisthmian COI divergence similar to that in the sea urchin genus Eucidaris supports this assumption. The most ancient split in Echinometra occurred between the IWP and the neotropical clades, due to cessation of larval exchange around South Africa or across the Eastern Pacific Barrier. Gene flow within species is generally high; however, there are restrictions to genetic exchange between E. lucunter populations from the Caribbean and those from the rest of the Atlantic. Correlation between cladogenic and vicariant events supports E. Mayr’s contention that marine species, despite their high dispersal potential, form by means of geographical separation. That sympatric, nonhybridizing E. lucunter and E. viridis were split so recently suggests, however, that perfection of reproductive barriers between marine species with large populations can occur in less than 1.6 million years (Myr).
Evidence for predominant clones in a cyclically parthenogenetic organism provided by combined demographic and genetic analyses
Authors: Haack L. , Simon J.‐C. , Gauthier J.‐P. , Plantegenest M. , Dedryver C.‐A. 
Published: March 2003

AbstractAphids are particularly interesting models in the study of genetic and demographic components of plant adaptation because of their breeding system which combines parthenogenesis and sexual reproduction (i.e. cyclical parthenogenesis), and the frequent emergence of host‐adapted races reported in this group. In this paper, patterns of host adaptation were assessed on local populations of the aphid Sitobion avenae by following their demographic and genetic structure in a maize field for two consecutive years. The existence of putative generalist (polyphagous) or specialized (host‐adapted) genotypes was also investigated by comparing the genotypic distribution of this aphid on maize and other cultivated host plants, using five microsatellite loci. Although population dynamics revealed strong variation in aphid abundance during the colonization period on maize, two genotypes identified at seven additional microsatellite loci were predominant and exhibited stable frequencies over cropping season and between years. Based on present and earlier studies, these two prevalent genotypes were shown to survive on different host plants other than maize, to colonize large geographical zones and to persist parthenogenetically for several years. All these data strongly suggest that these two genotypes are asexual generalist clones that could have been favoured by agricultural practices encountered in western Europe. Besides these two clones, a continual replacement of rare genotypes was observed on maize in both years. Hypotheses involving selection via aphid–plant interactions and natural enemies were proposed for explaining the disappearance of these genotypes on maize.
Temporal and spatial genetic variation in spawning grounds of European hake (Merluccius merluccius) in the Bay of Biscay
Authors: Lundy Caroline J. , Rico Ciro , Hewitt Godfrey M. 
Published: March 2003

AbstractPolymorphism at five microsatellite loci were screened to determine the genetic variability and the temporal stability of population structure in natural populations of European hake (Merluccius merluccius, L.) within the Bay of Biscay. In addition, the control region (900 bp) and two protein coding genes (ATPase, subunits 6 and 8, 842 bp and a partial sequence of the ND1, 800 bp) of the mitochondrial DNA (mtDNA) were sequenced from geographically distant populations from the extremes of the species range. One hundred individuals from either side of a supposed stock boundary within the bay were collected in autumn 1997. This sampling strategy was repeated during hake spawning seasons in late spring of 1998 and 1999. Low levels of population subdivision were found between putative populations within years. Similarly, low levels of differentiation were found between autumn 1997 northern samples and spring 1998 southern samples which were collected 7 months later on spawning grounds. These results are discussed in relation to ecological, behavioural and oceanographic information. Sampling effects, which may influence these results, are also discussed. Theta (θ) estimates were significantly different from zero in every other pairwise comparison between geographical areas (north and south of the Bay of Biscay) and between years within the same area (P < 0.05). Hierarchical analysis of molecular variance (amova) does not confirm the temporal persistence of population structure. These results are discussed in relation to variance in reproductive success, and temporal spawning patterns, which may exist within the bay. mtDNA variability was very low between geographically distant samples from Norway and the Mediterranean Sea with only 10 variable sites found in a total of 2542 bp of mtDNA, these differences being exclusively in the d‐loop.
Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae)
Authors: Eizirik Eduardo , Kim Jae‐Heup , Menotti‐Raymond Marilyn , Crawshaw JR. Peter G. , O’Brien Stephen J. , Johnson Warren E. 
Published: March 2003

AbstractThe jaguar (Panthera onca), the largest felid in the American Continent, is currently threatened by habitat loss, fragmentation and human persecution. We have investigated the genetic diversity, population structure and demographic history of jaguars across their geographical range by analysing 715 base pairs of the mitochondrial DNA (mtDNA) control region and 29 microsatellite loci in ≈40 individuals sampled from Mexico to southern Brazil. Jaguars display low to moderate levels of mtDNA diversity and medium to high levels of microsatellite size variation, and show evidence of a recent demographic expansion. We estimate that extant jaguar mtDNA lineages arose 280 000–510 000 years ago (95% CI 137 000–830 000 years ago), a younger date than suggested by available fossil data. No strong geographical structure was observed, in contrast to previously proposed subspecific partitions. However, major geographical barriers such as the Amazon river and the Darien straits between northern South America and Central America appear to have restricted historical gene flow in this species, producing measurable genetic differentiation. Jaguars could be divided into four incompletely isolated phylogeographic groups, and further sampling may reveal a finer pattern of subdivision or isolation by distance on a regional level. Operational conservation units for this species can be defined on a biome or ecosystem scale, but should take into account the historical barriers to dispersal identified here. Conservation strategies for jaguars should aim to maintain high levels of gene flow over broad geographical areas, possibly through active management of disconnected populations on a regional scale.
Mating asymmetry and the direction of evolution in the Hawaiian cricket genus Laupala
Authors: Shaw Kerry L. , Lugo Ezequiel 
Published: March 2003

AbstractBased on studies from native Hawaiian Drosophila, a model was proposed to explain sexual isolation and mating asymmetry, from which one could potentially infer the ‘direction of evolution’. We examined sexual isolation between allopatric cricket species of the genus Laupala, another endemic Hawaiian insect with an elaborate mating system, to begin to explore the nature of sexual isolation and mating asymmetry in closely related Hawaiian organisms. We studied sexual isolation and mating asymmetry in two contrasts. First, an inter‐island comparison, including L. makaio from the older island of Maui and L. paranigra from the younger island of Hawaii, and second, an intra‐island (Hawaii) comparison, including L. nigra from the older volcano of Mauna Kea and L. paranigra with a primary distribution on the younger volcanoes of Mauna Loa and Kilauea. We used a ‘no‐choice’ experimental design, pairing individual males and females in homospecific or heterospecific combinations. Several behavioural aspects of courtship (proportion of male singing, latency to male singing, production of spermatophores and courtship initiation speed) were quantified as well as the success or failure of matings. We demonstrate asymmetry in sexual isolation between reciprocal combinations of L. makaio and L. paranigra. This result is examined in light of the differences in courtship behaviour manifest in the experiments with these two species. We did not find evidence of asymmetry in sexual isolation between L. nigra and L. paranigra, although differences in courtship initiation speed were evident between reciprocal combinations of these two species. In addition to the geological argument that species on older islands and older volcanoes give rise to species on younger islands and younger volcanoes, we discuss phylogenetic evidence consistent with these biogeographic hypotheses of relationships among the focal taxa. The patterns of asymmetrical sexual isolation and mating asymmetry are consistent with those found in the native Hawaiian Drosophila.
The evolution of geographic parthenogenesis in Timema walking‐sticks
Authors: Law Jennifer H. , Crespi Bernard J. 
Published: March 2003

AbstractPhylogenetic studies of asexual lineages and their sexual progenitors are useful for inferring the causes of geographical parthenogenesis and testing hypotheses regarding the evolution of sex. With five known parthenogens and well‐studied ecology, Timema walking‐sticks are a useful system for studying these questions. Timema are mainly endemic to California and they exhibit the common pattern of geographical parthenogenesis, with asexuals exhibiting more‐northerly distributions. Neighbour‐joining and maximum‐parsimony analyses of 416 bp of mitochondrial cytochrome oxidase I (COI) from 168 individuals were used to infer general phylogenetic relationships, resulting in three major phylogeographical subdivisions: a Northern clade; a Santa Barbara clade; and a Southern clade. A nested cladistic analysis, comparing intra‐ and interspecific haplotypic variation on a geographical scale, revealed that the overall pattern of geographical parthenogenesis in Timema could be attributed to historical range expansion. These results suggest that geographical parthenogenesis is the result of more‐extensive northerly dispersal of asexuals than sexuals.
Selection and gene flow between microenvironments: the case of Drosophila at Lower Nahal Oren, Mount Carmel, Israel
Authors: Colson I. 
Published: March 2003

Abstract Drosophila melanogaster and D. simulans from contrasted microenvironments (south‐ and north‐facing slopes of Lower Nahal Oren Canyon in Israel) were tested for genetic differentiation at microsatellite loci, which might be linked to differential adaptation to local ecological factors. No overall genetic differentiation was observed in either species. This indicates that the contrasted selective pressures on the two sides of the valley are not strong enough to cause population subdivision in highly mobile species such as Drosophila. Significant differences in allele frequencies were observed at two microsatellite loci, but on the whole the level of divergence we observed is far lower than has been reported previously.
The incidence and diversity ofWolbachiain gallwasps (Hymenoptera; Cynipidae) on oak
Authors: Rokas A. , Atkinson R. J. , Nieves‐Aldrey J.‐L. , West S. A. , Stone G. N. 
Published: March 2003

AbstractWolbachiabacteria infect ≈ 20% of all insect species, and cause a range of alterations to host reproduction, including imposition of thelytoky. The incidence and phenotypic impact ofWolbachiaremains to be established in many insect taxa, and considerable research effort is currently focused on its association with particular reproductive modes and the relative importance of the various pathways via which infection occurs. Gallwasps represent an attractive system for addressing these issues for two reasons. First, they show a diversity of reproductive modes (including arrhenotoky, thelytoky and cyclical parthenogenesis) in which the impact ofWolbachiainfection can be examined. Second, they occupy two intimately linked trophic niches (gall‐inducers and inquilines) between which there is potential for the horizontal exchange ofWolbachiainfection. In the arrhenotokous gallwasp lineages screened to date (the herb‐galling ‘Aylacini’ and the rose‐galling Diplolepidini),Wolbachiainfection always induces thelytoky. The impact ofWolbachiain other arrhenotokous clades, and in the cyclically parthenogenetic clades remains unknown. Here we use polymerase chain reaction (PCR) screening and sequence data for twoWolbachiagenes (wspandftsZ) to examine the prevalence and incidence ofWolbachiainfection in 64 species (a total of 609 individuals) in two further tribes: the arrhenotokous inquilines (tribe Synergini), and the cyclically parthenogenetic oak gallwasps (tribe Cynipini). We ask: (i) whetherWolbachiainfection has any apparent impact on host reproduction in the two tribes and (ii) whether there is any correlation betweenWolbachiainfection and the apparent lack of an arrhenotokous generation in many oak gallwasp life cycles. We show: (i) thatWolbachiainfection is rare in the Cynipini. Infected species show no deviation from cyclical parthenogenesis, and infection is no more common in species known only from a thelytokous generation; (ii) that there is a higher incidence of infection within the arrhenotokous inquilines, and generally in gallwasp tribes without cyclical parthenogensis; (iii) allWolbachia‐positive inquiline species are known to possess males, implying either thatWolbachiainfection does not result in loss of sex in this tribe or, more probably, that (as for some rose gallwasps)Wolbachiainfection leads to loss of sex in specific populations; and (iv) although we find some inquilines and gall inducers to be infected withWolbachiahaving the samewspsequence, these hosts are not members of the same gall communities, arguing against frequent horizontal transmission between these two trophic groups. We suggest that exchange may be mediated by the generalist parasitoids common in oak galls.