bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial phylogeography and population history of pine martens Martes martes compared with polecats Mustela putorius
Authors: Davison Angus , Birks Johnny D. S. , Brookes Rachael C. , Messenger John E. , Griffiths Huw I. 
Published: March 2003

AbstractThe flora and fauna of Europe are linked by a common biogeographic history, most recently the Pleistocene glaciations that restricted the range of most species to southern refugial populations. Changes in population size and migration, as well as selection, have all left a signature on the genetic differentiation. Thus, three paradigms of postglacial recolonization have been described, inferred from the patterns of DNA differentiation. Yet some species, especially wide‐ranging carnivores, exhibit little population structuring between the proposed refugia, although relatively few have been studied due to the difficulty of obtaining samples. Therefore, we investigated mitochondrial variation in pine martens, Martes martes, in order to understand the extent to which they were affected by glacial cycles, and compared the results with an analysis of sequences from polecats, Mustela putorius. A general lack of ancient lineages, and a mismatch distribution that is consistent with an expanding population, is evidence that the present‐day M. martes and Mu. putorius in central and northern Europe colonized from a single European refugium following a recent glaciation. There has also been interspecific mitochondrial introgression between M. martes and the sable M. zibellina in Fennoscandia.
Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar)
Authors: Landry Christian , Bernatchez Louis 
Published: March 2003

AbstractEvidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.
Population structure of an endangered species living in contrasted habitats: Parnassia palustris (Saxifragaceae)
Authors: Bonnin Isabelle , Colas Bruno , Bacles Cécile , Holl Anne‐Catherine , Hendoux Frédéric , Destiné Benoit , Viard Frédérique 
Published: March 2003

AbstractIn endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within‐population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.
Evaluating the effect of stage‐specific survivorship on the Ne/N ratio
Authors: Waples Robin S. 
Published: March 2003

AbstractEvaluating effective population size (Ne) and the effective size to census size ratio (Ne/N) in species with Type III survivorship curves is complicated when key demographic parameters [mean (&#x006b;̄) and variance (Vk) of family size] are measured during early life stages. The method of Crow & Morton (1955) for scaling demographic data collected at a juvenile stage to expected values at adulthood is extended to consider sequential episodes of random and family correlated survival. Results show the following: (i) The order in which the episodes of random and family‐correlated survival occur does not affect Ne or Ne/N; (ii) If a population experiences an episode of family‐correlated survival, Ne/N scaled to its expected value in a population of constant size (&#x006b;̄ = 2) is simply the survival rate during the family‐correlated stage. If multiple such stages occur, scaled Ne/N is the product of the survivals during all family‐correlated life stages; (iii) Under the assumption of random post‐enumeration survival, adjusting the variance effective size to its expected value at &#x006b;̄ = 2 is equivalent to computing the inbreeding effective size at the earlier life stage. Application to experimental data for hatchery populations of Pacific salmon (Oncorhynchus spp.) indicates that nonrandom survival during the marine phase led to estimated reductions in effective size of 0–62% (mean 19%) in 12 different cohorts. This approach can provide insights into Ne/N in highly fecund species, including some marine species in which Ne has been estimated to be several orders of magnitude less than N.
Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process
Authors: Emerson B. C. 
Published: March 2003

AbstractBy their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands.
The highly cross‐fertile coral species,Acropora hyacinthusandAcropora cytherea, constitute statistically distinguishable lineages
Authors: Márquez L. M. , Van Oppen M. J. H. , Willis B. L. , Reyes A. , Miller D. J. 
Published: March 2003

AbstractA major challenge for understanding the evolutionary genetics of mass‐spawning corals is to explain the maintenance of discrete morphospecies in view of high rates of interspecific fertilizationin vitroand nonmonophyletic patterns in molecular phylogenies. In this study, we focused onAcropora cythereaandA. hyacinthus, which have one of the highest potentials for interspecific fertilization. Using sequences of a nuclear intron, we performed phylogenetic and nested clade analyses (NCA). Both species were polyphyletic in molecular phylogenies, but the NCA indicated that they constitute statistically distinguishable lineages. Phylogenetic analysis using an intergenic region of the mitochondrial DNA (mtDNA), was inconclusive because of low levels of variability in this marker. The position of these two species differed between the nuclear DNA (nDNA) and mtDNA phylogenies and was also at odds with a cladistic analysis based on morphology. We conclude that despite the potential for high levels of hybridization and introgression,A. cythereaandA. hyacinthusconstitute statistically distinguishable lineages and their taxonomic status is consistent with the cohesion species concept.
Gender and viability selection on morphology in fledgling pied flycatchers
Authors: Potti J. , Dávila J. A. , Tella J. L. , Frías Ó. , Villar S. 
Published: March 2003

AbstractUntil recently, analyses of gender‐dependent differences in viability selection and the ontogeny of sexual size dimorphism have been plagued by difficulties in determining the sex of nestling birds on the basis of morphology. Recently, this problem was overcome using molecular sex identification to report for the first time body‐size‐mediated antagonistic selection on the viability of male and female collared flycatchers. We used molecular sex identification to analyse natural selection on fledgling viability, sexual size dimorphism and effects of parasites in relation to gender in a Mediterranean population of the related pied flycatcherFicedula hypoleuca. There was directional positive selection on fledgling weight but no selection on tarsus length. Fledgling weight was the most important determinant of fledgling survival, with heavier fledglings having increased viability. Although selective trends were of the same sign for both sexes, only among female fledglings were selection differentials and gradients statistically significant. Therefore, similar trends in selection were revealed in analyses of a data set where sex was ignored and in separate analyses using same‐sex sibship trait means. Mite nest ectoparasites negatively affected fledgling weight, and the effects were stronger in female than male fledglings. There was no effect of parasitism on the tarsus length in males, as previously reported in retrospective analyses performed without knowledge of sex until recruitment. Overall, selection on fledgling viability on the basis of morphological traits and hatching date was not confounded by an individual's gender.
High levels of genetic monogamy in the group‐living Australian lizardEgernia stokesii
Authors: Gardner M. G. , Bull C. M. , Cooper S. J. B. 
Published: March 2003

AbstractThe Australian lizardEgernia stokesiilives in spatially and temporally stable groups of up to 17 individuals. We have recently shown that these groups are comprised of breeding partners, their offspring and, in some cases, highly related adults, providing the first genetic evidence of a family structure in any lizard species. Here we investigated the mating system ofE. stokesiiusing data from up to eight polymorphic microsatellite loci and tested the hypothesis that breeding partners are monogamous both within and between mating seasons. Among 16 laboratory‐born litters from field collected gravid females from two sites in South Australia, 75% had a single male parent and no male contributed to more than one litter, indicating a high level of genetic monogamy within a season. Additional analyses of field caught individuals, captured between 1994 and 1998, enabled assignment of parentage for 70 juveniles and subadults. These data showed that most young (88.6%) had both parents from within the same group and that high proportions of males (88.9%) and females (63.6%) have multiple cohorts of offspring only with the same partner. Our results suggest that monogamy both within and between seasons is a common mating strategy ofE. stokesiiand that breeding partners maintain stable associations together and with multiple cohorts of their offspring over periods of up to at least 5 years.
Likely multiple origins of a diploid hybrid sunflower species
Authors: Schwarzbach A. E. , Rieseberg L. H. 
Published: March 2003

AbstractThe recurrent origin of diploid hybrid species is theoretically improbable because of the enormous diversity of hybrid genotypes generated by recombination. Recent greenhouse experiments, however, indicate that the genomic composition of hybrid lineages is shaped in part by deterministic forces, and that recurrent diploid hybrid speciation may be more feasible than previously believed. Here we use patterns of variation from chloroplast DNA (cpDNA), nuclear microsatellite loci, cross‐viability and chromosome structure to assess whether a well‐characterized diploid hybrid sunflower species,Helianthus anomalus, was derived on multiple occasions from its parental species,H. annuusandH. petiolaris. Chloroplast DNA and crossability data were most consistent with a scenario in whichH. anomalusarose three times: three differentH. anomalusfertility groups were discovered, each with a unique cpDNA haplotype. In contrast, there was no clear signature of multiple, independent origins from the microsatellite loci. Given the age ofH. anomalus(> 100 000 years bp), it may be that microsatellite evidence for recurrent speciation has been eroded by mutation and gene flow through pollen.
Population genetic structure of the cyclic snowshoe hare (Lepus americanus) in southwestern Yukon, Canada
Authors: Burton Cole , Krebs Charles J. , Taylor Eric B. 
Published: March 2003

AbstractSpatial population structure has important ecological and evolutionary consequences. Little is known about the population structure of snowshoe hares (Lepus americanus), despite their ecological importance in North American boreal forests. We used seven variable microsatellite DNA loci to determine the spatial genetic structure of snowshoe hares near Kluane Lake, Yukon during a cyclic population peak. We sampled 317 hares at 12 sites separated by distances ranging from 3 to 140 km, and used 46 additional samples from Alaska and Montana. The level of genetic variation was high (13.4 alleles/locus, 0.67 expected heterozygosity) and the distribution of alleles and genotypes was not homogeneous across the sites. The degree of differentiation was low among Yukon sites (FST = 0.015) and between Yukon and Alaska (FST = 0.012), but the Montana site was highly differentiated (FST = 0.20). A weak pattern of isolation by distance was found over the Yukon study area, with an indication that local genetic drift may be important in shaping the regional genetic structure. Landscape barriers expected to influence gene flow did not consistently affect genetic structure, although there was evidence for a partial barrier effect of Kluane Lake. The high level of inferred gene flow confirms that snowshoe hare dispersal is widespread, successful and equal between the sexes. A stepping‐stone model of gene flow, potentially influenced by the synchronous density cycle, appears to best explain the observed genetic structure. Our results suggest that despite their dramatic fluctuations in density, snowshoe hares in the northern boreal forest have a large evolutionary effective population size and are not strongly subdivided by either physical or social barriers to gene flow.
Mitochondrial and nuclear DNA phylogeography of Thymallus spp. (grayling) provides evidence of ice‐age mediated environmental perturbations in the world's oldest body of fresh water, Lake Baikal
Authors: Koskinen Mikko T. , Knizhin Igor , Primmer Craig R. , Schlötterer Christian , Weiss Steven 
Published: March 2003

AbstractTheories on the hydrological history of Lake Baikal, the world's oldest and deepest body of freshwater, and its surrounding great rivers, are currently based solely on geological evidence and are conflicting. Baikal is inhabited by numerous zoogeographical enigmas but their high level of endemism has hindered phylogeographic inferences. We provide a biological perspective of the region's palaeo‐hydrological development based on the demographic and genealogical history of the widespread Thymallus spp. (grayling). Phylogenetic reconstruction reveals that old lineages of grayling (pre‐Pleistocene) currently inhabit the Enisey, Lena and Amur River basins. For Lake Baikal however, we conclude that a mid‐Pleistocene colonization (110 000–450 000 years ago) of an unoccupied niche has occurred. Population genetic inferences support an Enisey–Angara river route of colonization into Baikal, corresponding to the cataclysmic palaeo‐hydrological event that led to the formation of the lake's only contemporary outlet, and a subsequent range expansion several thousand kilometres into the uppermost reaches of the Selenga River basin. The evolutionary history of Lake Baikal grayling is congruent with the controversial hypothesis of repeated glaciation. However, considering the extraordinary levels of endemism and proposed Miocene or Oligocene coalescence of other faunal lineages, a less profound but equally consequential cycle of environmental perturbations may have taken place. Bi‐parentally inherited microsatellite DNA loci supported the phylogenetic relationships of Thymallus spp. and the geographical expansion of Baikal grayling strikingly well. A Markov Chain Monte Carlo modelling approach suggested severe contemporary population decline during the last century, possibly reflecting the influence of an uncontrolled fishery on this treasured ecosystem. These complementary pictures of the demographic history of grayling underscore the breadth of historical inquiry that can be entertained through the modelling of sufficient molecular data, and may significantly alter the zoogeographical and limnological perspectives of Baikal's history.
Fine‐scaled geographical population structuring in a highly mobile marine species: the Atlantic cod
Authors: Knutsen H. , Jorde P. E. , André C. , Stenseth N. CHR. 
Published: March 2003

AbstractCompared with many terrestrial and freshwater environments, dispersal and interbreeding is generally much less restricted in the marine environment. We studied the tendency for a marine species, the Atlantic cod, to be sub‐structured into genetically differentiated populations on a fine geographical scale. We selected a coastal area free of any obvious physical barriers and restricted sampling to a 300‐km region, well within the dispersal ability of this species. Screening 10 polymorphic microsatellite loci in 6 samples we detected a weak, but consistent, differentiation at all 10 loci. The average FST over loci was small (0.0023) but highly significant statistically, demonstrating that genetically differentiated populations can arise and persist in the absence of physical barriers or great distance. We found no geographical pattern in the genetic differentiation and there was no apparent trend of isolation by distance along the coastline. These findings lend support to the notion that low levels of differentiation are due to passive transport of eggs or larvae by the ocean currents rather than to adult dispersal, the latter being strongly dependent on distance.
Lizards in ‘nuclear families’: a novel reptilian social system in Egernia saxatilis (Scincidae)
Authors: O'Connor D. , Shine R. 
Published: March 2003

AbstractRecent research has revealed unsuspected complexity in social organization among squamate reptiles. In particular, large Australian scincid lizards of the genus Egernia have been reported to occur in large aggregations of closely related individuals. However, the ‘nuclear family’ structure found in many other ‘social’ organisms (especially birds) has not been reported from reptiles. Our field studies on black rock skinks (Egernia saxatilis) in southeastern Australia document exactly this pattern. We quantified group composition using behavioural observations at regular intervals over three field seasons, and took tissue samples for parentage analysis. On the focal rock outcrop 72% of lizards were typically found as part of a stable social grouping, with individuals physically associated with other group members in a third of observations. Eighty‐five per cent of juveniles lived in social groups, 65% in family groups with at least one of their parents (including 39% with both parents as revealed by parentage analysis of five microsatellite loci). Broader sampling in surrounding areas revealed similar patterns of group size, composition and relatedness. Overall, of the groups that contained more than one adult, 83% contained a single adult pair. Long‐term monogamy and group stability were evident from our genetic data, with up to three annual cohorts of full‐sib offspring living with their biological parents. Our data expand the range of social systems known for reptiles, and reveal strong convergence towards ‘nuclear family’ systems in distantly related vertebrates.
SoxR‐dependent response to oxidative stress and virulence of Erwinia chrysanthemi: the key role of SufC, an orphan ABC ATPase
Authors: Nachin Laurence , El Hassouni Mohammed , Loiseau Laurent , Expert Dominique , Barras Frédéric 
Published: March 2003

Erwinia chrysanthemi causes soft‐rot disease in a great variety of plants. In addition to the depolymerizing activity of plant cell wall‐degrading enzymes, iron acquisition and resistance to oxidative stress contribute greatly to the virulence of this pathogen. Here, we studied the pin10 locus originally thought to encode new virulence factors. The sequence analysis revealed six open reading frames that were homologous to the Escherichia coli sufA, sufB, sufC, sufD, sufS and sufE genes. Sequence similarity searching predicted that (i) SufA, SufB, SufD, SufS and SufE proteins are involved in iron metabolism and possibly in Fe–S cluster assembly; and (ii) SufC is an ATPase of an ABC transporter. The reverse transcription–polymerase chain reaction procedure showed that the sufABCDSE genes constitute an operon. Expression of a sufB::uidA fusion was found to be induced in iron‐deficient growth conditions and to be repressed by the iron‐sensing Fur repressor. Each of the six suf genes was inactivated by the insertion of a cassette generating a non‐polar mutation. The intracellular iron level in the sufA, sufB, sufC, sufS and sufE mutants was higher than in the wild type, as assessed by increased sensitivity to the iron‐activated antibiotic streptonigrin. In addition, inactivation of sufC and sufD led to increased sensitivity to paraquat. Virulence tests showed that sufA and sufC mutants exhibited reduced ability to cause maceration of chicory leaves, whereas a functional sufC gene was necessary for the bacteria to cause systemic invasion of Saintpaulia ionantha. The E. coli sufC homologue was inactivated by reverse genetic. This mutation was found to modify the soxR‐dependent induction of soxS gene expression. We discuss the possibility that SufC is a versatile ATPase that can associate either with the other Suf proteins to form a Fe–S cluster‐assembling machinery or with membrane proteins encoded elsewhere in the chromosome to form an Fe–S ABC exporter. Overall, these results stress the importance of the connection between iron metabolism and oxidative stress during the early steps of infection by E. chrysanthemi.