bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation
Authors: ALPERS D. L. , VAN VUUREN B. J. , ARCTANDER P. , ROBINSON T. J. 
Published: December 2004

AbstractThe roan antelope (Hippotragus equinus) is the second largest African antelope, distributed throughout the continent in sub‐Saharan savannah habitat. Mitochondrial DNA (mtDNA) control region sequencing (401 bp, n = 137) and microsatellite genotyping (eight loci, n = 137) were used to quantify the genetic variability within and among 18 populations of this species. The within‐population diversity was low to moderate with an average mtDNA nucleotide diversity of 1.9% and average expected heterozygosity with the microsatellites of 46%, but significant differences were found among populations with both the mtDNA and microsatellite data. Different levels of genetic resolution were found using the two marker sets, but both lent strong support for the separation of West African populations (samples from Benin, Senegal and Ghana) from the remainder of the populations studied across the African continent. Mismatch distribution analyses revealed possible past refugia for roan in the west and east of Africa. The West African populations could be recognized together as an evolutionarily significant unit (ESU), referable to the subspecies H. e. koba. Samples from the rest of the continent constituted a geographically more diverse assemblage with genetic associations not strictly corresponding to the other recognized subspecies.
Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method
Authors: NSUBUGA A. M. , ROBBINS M. M. , ROEDER A. D. , MORIN P. A. , BOESCH C. , VIGILANT L. 
Published: December 2004

AbstractGenetic analysis using noninvasively collected samples such as faeces continues to pose a formidable challenge because of unpredictable variation in the extent to which usable DNA is obtained. We investigated the influence of multiple variables on the quantity of DNA extracted from faecal samples from wild mountain gorillas and chimpanzees. There was a small negative correlation between temperature at time of collection and the amount of DNA obtained. Storage of samples either in RNAlater solution or dried using silica gel beads produced similar results, but significantly higher amounts of DNA were obtained using a novel protocol that combines a short period of storage in ethanol with subsequent desiccation using silica.
Isolation by distance and sharp discontinuities in gene frequencies: implications for the phylogeography of an alpine insect species, Carabus solieri
Authors: GARNIER S. , ALIBERT P. , AUDIOT P. , PRIEUR B. , RASPLUS J.‐Y. 
Published: December 2004

AbstractAnalysis of genetic isolation by distance (IBD) is of prime importance for the study of processes responsible for spatial population genetic structure and is thus frequently used in case studies. However, the identification of a significant IBD pattern does not necessarily imply the absence of sharp discontinuities in gene frequencies. Therefore, identifying barriers to gene flow and/or secondary contact between differentiated entities remains a major challenge in population biology. Geographical genetic structure of 41 populations (1080 individuals) of an alpine insect species, Carabus solieri, was studied using 10 microsatellite loci. All populations were significantly differentiated and spatially structured according to IBD over the entire range. However, clustering analyses clearly identified three main clusters of populations, which correspond to geographical entities. Whereas IBD also occurs within each cluster, population structure was different according to which group of populations was considered. The southernmost cluster corresponds to the most fragmented part of the range. Consistently, it was characterized by relatively high levels of differentiation associated with low genetic diversity, and the slope of the regression of genetic differentiation against geographical distances was threefold those of the two other clusters. Comparisons of within‐cluster and between‐cluster IBD patterns revealed barriers to gene flow. A comparison of the two approaches, IBD and clustering analyses, provided us with valuable information with which to infer the phylogeography of the species, and in particular to propose postglacial colonization routes from two potential refugia located in Italy and in southeastern France. Our study highlights strongly the possible confounding contribution of barriers to gene flow to IBD pattern and emphasizes the utility of the model‐based clustering analysis to identify such barriers.
Phylogeographic structure, gene flow and species status in blue grouse (Dendragapus obscurus)
Authors: BARROWCLOUGH GEORGE F. , GROTH JEFF G. , MERTZ LISA A. , GUTIÉRREZ R. J. 
Published: December 2004

AbstractWe investigated the genetic population structure and species status of a relatively sedentary bird that is a permanent resident of western North American forests, the blue grouse (Dendragapus obscurus). Phylogenetic analysis of complete mitochondrial control region DNA sequences resulted in the identification of three basal clades of haplotypes that were largely congruent with well‐known biogeographical regions. These clades corresponded to the parapatric sooty (D. o. fuliginosus) and dusky (D. o. obscurus) subspecies groups of blue grouse plus a previously unrecognized division between northern and southern dusky grouse populations; the latter does not correspond closely to any currently recognized subspecies boundary. Approximately 66% of the total genetic variation was distributed among these three regions. Maximum likelihood estimates of gene flow between the regions were low or asymmetric; gene flow has been insufficient to prevent genetic divergence between dusky and sooty grouse. Estimates of gene flow among populations within sooty grouse were large except across the Columbia River valley. Among populations of dusky grouse, estimates of gene flow were heterogeneous and asymmetrical, reflecting large‐scale fragmentation of the distribution due to landscape features and associated vegetation. Genetic, morphological and behavioural evidence suggest that sooty and dusky grouse are species‐level taxa; the specific status of a third clade remains ambiguous.
Population structure of loggerhead shrikes in the California Channel Islands
Authors: EGGERT LORI S. , MUNDY NICHOLAS I. , WOODRUFF DAVID S. 
Published: December 2004

AbstractThe 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.
The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis)
Authors: GOTTELLI DADA , MARINO JORGELINA , SILLERO‐ZUBIRI CLAUDIO , FUNK STEPHAN M. 
Published: December 2004

AbstractDuring the last glacial age, Afro‐alpine habitats were widespread across the highlands of Ethiopia. A wolf‐like canid ancestor is thought to have colonized this expanding habitat and given rise to a new species that was remarkably well adapted to the high altitude environment: the Ethiopian wolf Canis simensis. Here, we address the timing of genetic divergence and examine population genetic history and structure by investigating the distribution of mitochondrial DNA (mtDNA) sequence variation. The pattern of mtDNA variation and geographical distribution indicate an initial population expansion, probably immediately after divergence from the wolf‐like ancestor, around 100 000 years ago. The partition of mtDNA haplotypes that followed was most likely the result of habitat reduction and fragmentation at the onset of deglaciation ~ 15 000 years ago. Phylogenetic and geographical associations suggest that the most likely genetic partitioning corresponds to three mountain areas, Arsi/Bale, Wollo/Shoa and Simien/Mt. Guna. Although there is a degree of clustering of haplotypes from both sides of the Rift Valley, the lack of reciprocal monophyly does not support the taxonomic classification of two subspecies. This study highlights the importance of populations north of the Rift Valley for the maintenance of genetic variability within the species and has consequent implications for conservation.
Global population structure and taxonomy of the wandering albatross species complex
Authors: BURG T. M. , CROXALL J. P. 
Published: December 2004

AbstractA recent taxonomic revision of wandering albatross elevated each of the four subspecies to species. We used mitochondrial DNA and nine microsatellite markers to study the phylogenetic relationships of three species (Diomedea antipodensis, D. exulans and D. gibsoni) in the wandering albatross complex. A small number of samples from a fourth species, D. dabbenena, were analysed using mitochondrial DNA only. Mitochondrial DNA sequence analyses indicated the presence of three distinct groups within the wandering albatross complex: D. exulans, D. dabbenena and D. antipodensis/D. gibsoni. Although no fixed differences were found between D. antipodensis and D. gibsoni, a significant difference in the frequency of a single restriction site was detected using random fragment length polymorphism. Microsatellite analyses using nine variable loci, showed that D. exulans, D. antipodensis and D. gibsoni were genetically differentiated. Despite the widespread distribution of D. exulans, we did not detect any genetic differentiation among populations breeding on different island groups. The lower level of genetic differentiation between D. antipodensis and D. gibsoni should be reclassified as D. antipodensis. Within the context of the current taxonomy, these combined data support three species: D. dabbenena, D. exulans and D. antipodensis.
Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore
Authors: JONES MENNA E. , PAETKAU DAVID , GEFFEN ELI , MORITZ CRAIG 
Published: December 2004

AbstractGenetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide‐ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386–0.467) and allelic diversity (2.7–3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise FST), in agreement with movement data. At larger scales (150–250 km), gene flow is reduced (significant pairwise FST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well‐connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self‐assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model‐based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.
Climate and habitat barriers to dispersal in the highly mobile grey wolf
Authors: GEFFEN ELI , ANDERSON MARTI J. , WAYNE ROBERT K. 
Published: December 2004

AbstractWe reanalysed published data to evaluate whether climate and habitat are barriers to dispersal in one of the most mobile and widely distributed mammals, the grey wolf (Canis lupus). Distance‐based redundancy analysis (dbRDA) was used to examine the amount of variation in genetic distances that could be explained by an array of environmental factors, including geographical distance. Patterns in genetic variation were also examined using MDS plots among populations and relationships between genetic structure and individual environmental variables were further explored using the BIOENV procedure. We found that, contrary to a previous report, a pattern of isolation with distance is evident on a continental scale in the North American wolf population. This pattern is apparently related to climate and habitat. Specifically, vegetation types appear to play a role in the genetic dissimilarities among populations. When we controlled for the effect of spatial variation, climate was still associated with genetic distance. Further, partitioning of geographical distances into latitudinal and longitudinal axes revealed that the east–west gradient had the strongest relationship with genetic distance. We suggest two possible mechanisms by which environmental conditions may influence the dispersal decisions made by wolves.
Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes
Authors: MUTCH LESLEY A. , YOUNG J. PETER W. 
Published: December 2004

AbstractThe symbiotic partnerships between legumes and their root‐nodule bacteria (rhizobia) vary widely in their degree of specificity, but the underlying reasons are not understood. To assess the potential for host‐range evolution, we have investigated microheterogeneity among the shared symbionts of a group of related legume species. Host specificity and genetic diversity were characterized for a soil population of Rhizobium leguminosarum biovar viciae (Rlv) sampled using six wild Vicia and Lathyrus species and the crop plants pea (Pisum sativum) and broad bean (Vicia faba). Genetic variation among 625 isolates was assessed by restriction fragment length polymorphism (RFLP) of loci on the chromosome (ribosomal gene spacer) and symbiosis plasmid (nodD region). Broad bean strongly favoured a particular symbiotic genotype that formed a distinct phylogenetic subgroup of Rlv nodulation genotypes but was associated with a range of chromosomal backgrounds. Host range tests of 80 isolates demonstrated that only 34% of isolates were able to nodulate V. faba. By contrast, 89% were able to nodulate all the local wild hosts tested, so high genetic diversity of the rhizobial population cannot be ascribed directly to the diversity of host species at the site. Overall the picture is of a population of symbionts that is diversified by plasmid transfer and shared fairly indiscriminately by local wild legume hosts. The crop species are less promiscuous in their interaction with symbionts than the wild legumes.
Rivers influence the population genetic structure of bonobos (Pan paniscus)
Authors: ERIKSSON J. , HOHMANN G. , BOESCH C. , VIGILANT L. 
Published: December 2004

AbstractBonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current–day barriers, but not when straight‐line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.
Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe
Authors: HEUERTZ M. , FINESCHI S. , ANZIDEI M. , PASTORELLI R. , SALVINI D. , PAULE L. , FRASCARIA‐LACOSTE N. , HARDY O. J. , VEKEMANS X. , VENDRAMIN G. G. 
Published: December 2004

AbstractWe used chloroplast polymerase chain reaction‐restriction‐fragment length polymorphism (PCR‐RFLP) and chloroplast microsatellites to assess the structure of genetic variation and postglacial history across the entire natural range of the common ash (Fraxinus excelsior L.), a broad‐leaved wind‐pollinated and wind‐dispersed European forest tree. A low level of polymorphism was observed, with only 12 haplotypes at four polymorphic microsatellites in 201 populations, and two PCR‐RFLP haplotypes in a subset of 62 populations. The clear geographical pattern displayed by the five most common haplotypes was in agreement with glacial refugia for ash being located in Iberia, Italy, the eastern Alps and the Balkan Peninsula, as had been suggested from fossil pollen data. A low chloroplast DNA mutation rate, a low effective population size in glacial refugia related to ash's life history traits, as well as features of postglacial expansion were put forward to explain the low level of polymorphism. Differentiation among populations was high (GST = 0.89), reflecting poor mixing among recolonizing lineages. Therefore, the responsible factor for the highly homogeneous genetic pattern previously identified at nuclear microsatellites throughout western and central Europe (Heuertz et al. 2004) must have been efficient postglacial pollen flow. Further comparison of variation patterns at both marker systems revealed that nuclear microsatellites identified complex differentiation patterns in south‐eastern Europe which remained undetected with chloroplast microsatellites. The results suggest that data from different markers should be combined in order to capture the most important genetic patterns in a species.
Breeding system and demography shape population genetic structure across ecological and climatic zones in the African freshwater snail,Bulinus forskalii(Gastropoda, Pulmonata), intermediate host for schistosomes
Authors: GOW J. L. , NOBLE L. R. , ROLLINSON D. , MIMPFOUNDI R. , JONES C. S. 
Published: December 2004

AbstractThe role of breeding system and population bottlenecks in shaping the distribution of neutral genetic variation among populations inhabiting patchily distributed, ephemeral water bodies was examined for the hermaphroditic freshwater snailBulinus forskalii, intermediate host for the medically important trematodeSchistosoma guineensis. Levels of genetic variation at 11 microsatellite loci were assessed for 600 individuals sampled from 19 populations that span three ecological and climatic zones (ecozones) in Cameroon, West Africa. Significant heterozygote deficiencies and linkage disequilibria indicated very high selfing rates in these populations. Despite this and the large genetic differentiation detected between populations, high levels of genetic variation were harboured within these populations. The high level of gene flow inferred from assignment tests may be responsible for this pattern. Indeed, metapopulation dynamics, including high levels of gene flow as well as extinction/contraction and recolonization events, are invoked to account for the observed population structuring, which was not a consequence of isolation‐by‐distance. BecauseB. forskaliipopulations inhabiting the northern, Sahelian area are subject to more pronounced annual cycles of drought and flood than the southern equatorial ones, they were expected to be subject to population bottlenecks of increased frequency and severity and, therefore, show reduced genetic variability and elevated population differentiation. Contrary to predictions, the populations inhabiting the most northerly ecozone exhibited higher genetic diversity and lower genetic differentiation than those in the most southerly one, suggesting that elevated gene flow in this region is counteracting genetic drift.
Phylogeography recapitulates topography: very fine‐scale local endemism of a saproxylic ‘giant’ springtail at Tallaganda in the Great Dividing Range of south–east Australia
Authors: GARRICK R. C. , SANDS C. J. , ROWELL D. M. , TAIT N. N. , GREENSLADE P. , SUNNUCKS P. 
Published: December 2004

AbstractComparative phylogeography can reveal processes and historical events that shape the biodiversity of species and communities. As part of a comparative research program, the phylogeography of a new, endemic Australian genus and species of log‐dependent (saproxylic) collembola was investigated using mitochondrial sequences, allozymes and anonymous single‐copy nuclear markers. We found the genetic structure of the species corresponds with five a priori microbiogeographical regions, with population subdivision at various depths owing to palaeoclimatic influences. Closely related mtDNA haplotypes are codistributed within a single region or occur in adjacent regions, nuclear allele frequencies are more similar among more proximate populations, and interpopulation migration is rare. Based on mtDNA divergence, a late Miocene–late Pliocene coalescence is likely. The present‐day distribution of genetic diversity seems to have been impacted by three major climatic events: Pliocene cooling and drying (2.5–7 million years before present, Mybp), early Pleistocene wet‐dry oscillations (c. 1.2 Mybp) and the more recent glacial‐interglacial cycles that have characterized the latter part of the Quaternary (< 0.4 Mybp).