bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating genetic drift and effective population size from temporal shifts in dominant gene marker frequencies
Authors: Jorde P. E. , Palm S. , Ryman N. 
Published: March 2003

AbstractMeasurement of temporal change in allele frequencies represents an indirect method for estimating the genetically effective size of populations. When allele frequencies are estimated for gene markers that display dominant gene expression, such as, e.g. random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers, the estimates can be seriously biased. We quantify bias for previous allele frequency estimators and present a new expression that is generally less biased and provides a more precise assessment of temporal allele frequency change. We further develop an estimator for effective population size that is appropriate when dealing with dominant gene markers. Comparison with estimates based on codominantly expressed genes, such as allozymes or microsatellites, indicates that about twice as many loci or sampled individuals are required when using dominant markers to achieve the same precision.
DNA fingerprinting reveals polygyny in the subterranean rodent Ctenomys talarum
Authors: Zenuto Roxana R. , Lacey Eileen A. , Busch Cristina 
Published: March 2003

AbstractDNA fingerprinting was used to characterize patterns of paternity in two populations of Ctenomys talarum from Buenos Aires Province, Argentina. The multilocus probe PV47–2 was used to detect variation in genomic DNA extracted from 12 females, their 32 offspring, and 14 putative sires. For 11 out of 12 litters examined, a single male capable of providing all nonmaternal bands was identified. Within each study population, individual males sired more than one litter, suggesting that C. talarum is polygynous. No evidence of multiple paternity of litters was found. High band‐sharing values among females suggest that further research is needed to assess the population genetic structure of this species.
The use of genetic markers in the identification and characterization of three recently discovered populations of a threatened plant species
Authors: Martín C. , González‐Benito M. E. , Iriondo J. M. 
Published: March 2003

Abstract Erodium paularense Fern. Gonz. & Izco (Geraniaceae) is a perennial, narrow endemic species of central Spain. Recently, three new populations have been found 160 km northwest of the first site, although the taxonomic status of the new populations has not yet been published. Random amplified polymorphic DNA (RAPD) markers were used to confirm that the new populations belong to E. paularense, and to evaluate the genetic diversity among individuals, populations and regions. The two regions were clearly differentiated through
upgma, whereas significant φST distances between all pairs of populations were obtained by
amova. Genetic distances between populations were partially explained by geographical distances. The clear genetic differentiation among regions, on top of the geographical distance and differences in geological substratum, supports a taxonomical discrimination of the regions at a subspecific level.
Mitochondrial phylogeography of the European pond turtle, Emys orbicularis (Linnaeus 1758)
Authors: Lenk P. , Fritz U. , Joger U. , Wink M. 
Published: March 2003

AbstractThe phylogeny and phylogeography of Emys orbicularis was inferred from mitochondrial nucleotide sequences of the cytochrome b gene analysed by DNA sequencing and RNA heteroduplex analysis. Within the family Emydidae the monotypic genus Emys is affiliated with the nearctic taxa Emydoidea blandingii and Clemmys marmorata. The analysis of 423 individuals of E. orbicularis, originating throughout its distribution range, revealed a remarkable intraspecific differentiation in 20 different haplotypes with distinct geographical ranges. Maximum parsimony analysis produced a star‐like phylogeny with seven main lineages which may reflect separations in the late Pliocene. The haplotype distribution examined by partial Mantel tests and analysis of molecular variance revealed a substantial effect of glacial periods. This historical perspective suggests the existence of multiple glacial refugia and considerable Holocene range expansion which was modulated by climatic traits. Further support is gained for the occurrence of long‐term parapatry in glacial refugia.
Disparate phylogeographic patterns of molecular genetic variation in four closely related South American small cat species
Authors: Johnson Warren E. , Slattery Jill Pecon , Eizirik Eduardo , Kim Jae‐Heup , Menotti Raymond Marilyn , Bonacic Cristian , Cambre Richard , Crawshaw Peter , Nunes Adauto , Seuánez Héctor N. , Martins Moreira Miguel Angelo , Seymour Kevin L. , Simon Faiçal , Swanson William , O’Brien Stephen J. 
Published: March 2003

AbstractTissue specimens from four species of Neotropical small cats (Oncifelis geoffroyi, N = 38; O. guigna, N = 6; Leopardus tigrinus, N = 32; Lynchailurus colocolo, N = 22) collected from throughout their distribution were examined for patterns of DNA sequence variation using three mitochondrial genes, 16S rRNA, ATP8, and NADH‐5. Patterns between and among O. guigna and O. geoffroyi individuals were assessed further from size variation at 20 microsatellite loci. Phylogenetic analyses using mitochondrial DNA sequences revealed monophyletic clustering of the four species, plus evidence of natural hybridization between L. tigrinus and L. colocolo in areas of range overlap and discrete population subdivisions reflecting geographical isolation. Several commonly accepted subspecies partitions were affirmed for L. colocolo, but not for O. geoffroyi. The lack of geographical substructure in O. geoffroyi was recapitulated with the microsatellite data, as was the monophyletic clustering of O. guigna and O. geoffroyi individuals. L. tigrinus forms two phylogeographic clusters which correspond to L.t. oncilla (from Costa Rica) and L.t. guttula (from Brazil) and which have mitochondrial DNA (mtDNA) genetic distance estimates comparable to interspecific values between other ocelot lineage species. Using feline‐specific calibration rates for mitochondrial DNA mutation rates, we estimated that extant lineages of O. guigna diverged 0.4 million years ago (Ma), compared with 1.7 Ma for L. colocolo, 2.0 Ma for O. geoffroyi, and 3.7 Ma for L. tigrinus.
Captive breeding, reintroduction, and the conservation genetics of black and white ruffed lemurs, Varecia variegata variegata
Authors: Wyner Yael M. , Amato George , DeSalle Rob 
Published: March 2003

AbstractA character‐based phylogenetic species concept approach was used to examine conservation unit status for three wild populations of black and white ruffed lemurs, Varecia vareigata variegata, from Betampona (N = 3), Manombo (N = 6), and Ranomafana (N = 14), Madagascar. Population aggregation analysis was performed on 548 bp from the control region (D‐loop) of the mitochondrial DNA (mtDNA). Twenty‐one diagnostic sites were found to differentiate the Betampona (northern) population from the Manombo/Ranomafana (southern) populations. Additionally, individuals from the North American captive population (N = 11) and from Parc Ivoloina, Madagascar (N = 6) were examined for the same mtDNA fragment. The captive animals more closely resembled the southern populations and the Parc Ivoloina animals were more similar to the northern population. However, the inclusion of these ex situ animals reduced the number of diagnostic sites differentiating the northern and southern populations. Our genetic data were used to assess the ongoing management strategy for reintroducing individuals into the Betampona population and for introducing new founders into the ex situ population. This study demonstrates the utility of combining genetic information with a consideration of conservation priorities in evaluating the implementation of management strategies.
Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)
Authors: Waits Lisette , Taberlet Pierre , Swenson Jon E. , Sandegren Finn , Franzén Robert 
Published: March 2003

AbstractIn the 1930s, the Scandinavian brown bear was close to extinction due to vigorous extermination programmes in Norway and Sweden. Increased protection of the brown bear in Scandinavia has resulted in the recovery of four subpopulations, which currently contain close to 1000 individuals. Effective conservation and management of the Scandinavian brown bear requires knowledge of the current levels of genetic diversity and gene flow among the four subpopulations. Earlier studies of mitochondrial DNA (mtDNA) diversity revealed extremely low levels of genetic variation, and population structure that grouped the three northern subpopulations in one genetic clade and the southernmost subpopulation in a second highly divergent clade. In this study, we extended the analysis of genetic diversity and gene flow in the Scandinavian brown bear using data from 19 nuclear DNA microsatellite loci. Results from the nuclear loci were strikingly different than the mtDNA results. Genetic diversity levels in the four subpopulations were equivalent to diversity levels in nonbottlenecked populations from North America, and significantly higher than levels in other bottlenecked and isolated brown bear populations. Gene flow levels between subpopulations ranged from low to moderate and were correlated with geographical distance. The substantial difference in results obtained using mtDNA and nuclear DNA markers stresses the importance of collecting data from both types of genetic markers before interpreting data and making recommendations for the conservation and management of natural populations. Based on the results from the mtDNA and nuclear DNA data sets, we propose one evolutionarily significant unit and four management units for the brown bear in Scandinavia.
Microsatellite and mitochondrial DNA polymorphism reveals life‐history dependent interbreeding between hatchery and wild brown trout (Salmo truttaL.)
Authors: Hansen Michael M. , Ruzzante Daniel E. , Nielsen Einar E. , Mensberg Karen‐lise D. 
Published: March 2003

AbstractThe effects of stocking hatchery trout into wild populations were studied in a Danish river, using microsatellite and mitochondrial DNA (mtDNA) markers. Baseline samples were taken from hatchery trout and wild trout assumed to be unaffected by previous stocking. Also, samples were taken from resident and sea trout from a stocked section of the river. Genetic differentiation between the hatchery strain and the local wild population was modest (microsatelliteFST = 0.06). Using assignment tests, more than 90% of individuals from the baseline samples were classified correctly. Assignment tests involving samples from the stocked river section suggested that the contribution by hatchery trout was low among sea trout (< 7%), but high (46%) among resident trout. Hybrid index analysis and a high percentage of mtDNA haplotypes specific to indigenous trout observed among resident trout that were assigned to the hatchery strain suggested that interbreeding took place between hatchery and wild trout. The latter result also indicated that male hatchery trout contributed more to interbreeding than females. We suggest that stronger selection acts against stocked hatchery trout that become anadromous compared to hatchery trout that become resident. As most resident trout are males this could also explain why gene flow from hatchery to wild trout appeared to be male biased. The results show that even despite modest differentiation at neutral loci domesticated trout may still perform worse than local populations and it is important to be aware of differential survival and reproductive success both between life‐history types and between sexes.
Spatial and temporal distribution of chloroplast DNA polymorphism in a tropical tree species
Authors: Caron H. , Dumas S. , Marque G. , Messier C. , Bandou E. , Petit R. J. , Kremer A. 
Published: March 2003

AbstractThe level and the spatial organization of chloroplast DNA polymorphism were investigated in Dicorynia guianensis Hamshoff (Caesalpiniaceae) at different spatial and temporal scales. D. guianensis is a canopy tree of the rain forest that is distributed throughout the Guiana plateau in small aggregates. Twelve different haplotypes were identified using restriction analysis of polymerase chain reaction (PCR) amplified fragments of the chloroplast genome. When populations from different areas of French Guiana were compared, a clear geographical pattern of haplotype frequencies was identified along the Atlantic coast. This pattern is most likely the result of the restriction–expansion dynamics of the tropical forest during the Quaternary. At the local level, D. guianensis was characterized by a high level of within population diversity. Maintenance of within population diversity results from the dynamics of the aggregates; stochastic demography associated with the turnover of aggregates generates genetic differentiation among them. At the stand level, a strong spatial aggregation of haplotypes persisted from the adult to the seedling cohort indicating limited seed flow. There was also a strong difference in levels of diversity between the cohorts which suggested that recruitment over several years is needed in order to maintain genetic diversity during regeneration.
Extra‐pair paternity in waved albatrosses
Authors: Huyvaert Kathryn P. , Anderson David J. , Jones Thomas C. , Duan Wenrui , Parker Patricia G. 
Published: March 2003

AbstractWe estimated the rate of extra‐pair fertilizations (EPFs) in waved albatrosses (Phoebastria irrorata) on Isla Española, Galápagos, Ecuador, using multilocus minisatellite DNA fingerprinting. Waved albatrosses are socially monogamous, long‐lived seabirds whose main population is on Española. Aggressive extra‐pair copulation (EPC) attempts have been observed in the breeding colony during the days preceding egg‐laying. Our genetic analyses of 16 families (single chicks and their attending parents) revealed evidence of EPFs in four families. In all cases males were the excluded parent. These data suggest that waved albatrosses have an unusually high rate of EPF relative to taxa with similar life histories. Future behavioural observations will determine the extent to which forced vs. unforced EPCs contribute to this high EPF rate.
Phylogeography of colonially nesting seabirds, with special reference to global matrilineal patterns in the sooty tern (Sterna fuscata)
Authors: Avise John C. , Nelson William S. , Bowen Brian W. , Walker Deette 
Published: March 2003

AbstractSooty tern (Sterna fuscata) rookeries are scattered throughout the tropical oceans. When not nesting, individuals wander great distances across open seas, but, like many other seabirds, they tend to be site‐faithful to nesting locales in successive years. Here we examine the matrilineal history of sooty terns on a global scale. Assayed colonies within an ocean are poorly differentiated in mitochondrial DNA sequence, a result indicating tight historical ties. However, a shallow genealogical partition distinguishes Atlantic from Indo‐Pacific rookeries. Phylogeographic patterns in the sooty tern are compared to those in other colonially nesting seabirds, as well as in the green turtle (Chelonia mydas), an analogue of tropical seabirds in some salient aspects of natural history. Phylogeographic structure within an ocean is normally weak in seabirds, unlike the pronounced matrilineal structure in green turtles. However, the phylogeographic partition between Atlantic and Indo‐Pacific rookeries in sooty terns mirrors, albeit in shallower evolutionary time, the major matrilineal subdivision in green turtles. Thus, global geology has apparently influenced historical gene movements in these two circumtropical species.
A molecular analysis of ground sloth diet through the last glaciation
Authors: Hofreiter M. , Poinar H. N. , Spaulding W. G. , Bauer K. , Martin P. S. , Possnert G. , Pääbo S. 
Published: March 2003

AbstractDNA was extracted from five coprolites, excavated in Gypsum Cave, Nevada and radiocarbon dated to approximately 11 000, 20 000 and 28 500 years bp. All coprolites contained mitochondrial DNA sequences identical to a DNA sequence determined from a bone of the extinct ground sloth Nothrotheriops shastensis. A 157‐bp fragment of the chloroplast gene for the large subunit of the ribulosebisphosphate carboxylase (rbcL) was amplified from the boluses and several hundred clones were sequenced. In addition, the same DNA fragment was sequenced from 99 plant species that occur in the vicinity of Gypsum Cave today. When these were compared to the DNA sequences in GenBank, 69 were correctly (two incorrectly) assigned to taxonomic orders. The plant sequences from the five coprolites as well as from one previously studied coprolite were compared to rbcL sequences in GenBank and the contemporary plant species. Thirteen families or orders of plants that formed part of the diet of the Shasta ground sloth could be identified, showing that the ground sloth was feeding on trees as well as herbs and grasses. The plants in the boluses further indicate that the climate 11 000 years bp was dryer than 20 000 and 28 500 years bp. However, the sloths seem to have visited water sources more frequently at 11 000 bp than at earlier times.
Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north‐eastern Australia
Authors: Hurwood David A. , Hughes Jane M. 
Published: March 2003

AbstractThe freshwater shrimp, Caridina zebra, is endemic to montane rainforest streams of the Atherton Tableland, north‐eastern Australia. As the confluences of many of the headwater streams are in unsuitable habitat, dispersal is expected to be highly restricted. Results from a previous allozyme survey for this species suggested that historical dispersal between separate river drainages had occurred due to rearrangements of the drainage lines at some stage in the recent past. The aim of this study was to use temporal information from the mitochondrial cytochrome oxidase subunit I (CO‐I) gene to determine whether the observed genetic structure was a result of historical processes, or alternatively, due to low levels of terrestrial dispersal. The mitochondrial DNA (mtDNA) data were analysed using nested clade analysis, which can differentiate between historical fragmentation and range expansion vs. contemporary restricted gene flow. The results displayed three divergent clades that were likely to have arisen in allopatry. One widespread clade, with individuals in more than one river drainage, reflected a pattern of restricted gene flow. This suggests that this species is capable of terrestrial dispersal.
Small genets of Lactarius xanthogalactus, Russula cremoricolor and Amanita francheti in late‐stage ectomycorrhizal successions
Authors: Redecker Dirk , Szaro Timothy M. , Bowman Ryan J. , Bruns Thomas D. 
Published: March 2003

AbstractWe determined the size of genets of late‐stage ectomycorrhizal fungi in field sites in coastal Northern California. Basidiocarps were collected, mapped and subjected to genetic fingerprinting using amplified fragment length polymorphisms (AFLPs). The minimum size estimates for the largest genets of Amanita francheti, Lactarius xanthogalactus and Russula cremoricolor were 1.5, 9.3 and 1.1 m2, respectively. The molecular markers also showed that R. cremoricolor is dimorphic, with red‐ and white‐capped morphotypes of this species forming a continuous population. Our results suggest that spore propagation plays a much more important role in the life history of the Russulaceae in undisturbed forest settings than previously recognized. Fungi appearing late in the succession sequence and systems without obvious disturbance therefore do not necessarily colonize primarily by mycelium.
Microsatellite analysis of the inbreeding grass weed Barren Brome (Anisantha sterilis) reveals genetic diversity at the within‐ and between‐farm scales
Authors: Green J. M. , Barker J. H. A. , Marshall E. J. P. , Froud‐Williams R. J. , Peters N. C. B. , Arnold G. M. , Dawson K. , Karp A. 
Published: March 2003

AbstractNine microsatellites were used to screen 131 samples of Barren Brome (Anisantha sterilis: synonym Bromus sterilis) collected from within the fields of three English farms [from Oxfordshire (Oxon), Leicestershire (Leics) and Wiltshire (Wilts)] and eight seeds taken from samples of each of 10 farms across England, UK. Most individuals (~97%) were homozygous. Polymorphism occurred at all nine loci in all three farms sampled at the field scale, and at most loci for nine of the other 10 farm samples. Between three and 11 alleles were found per locus. Gene diversity (D = 1 − ∑pi2) ranged from 0.088 to 0.760. Polymorphism occurred among individuals within and among fields, and farms. Some alleles were found in only one farm. On the basis of the alleles at all nine loci in the 211 sampled plants, a total of 92 (44%) different genotypes was identified. Clustering analysis using the unweighted pair group method with arithmetic averages (upgma) for the combined Oxon, Wilts and Leics samples did not cluster them into their respective farms. Similarly, a phenogram of samples from all 10 farms showed considerable mixing of individuals with respect to farm origins. Identification of genotypes on field plans showed evidence of both spatial localization and mixing. Previous reports have suggested that A. sterilis is strictly inbreeding with little intrapopulation variation at the genetic level. Our data reveal that A. sterilis exists as numerous separate and genetically different lines, which are maintained by inbreeding but which very occasionally outcross. Possible explanations for this pattern of high genetic diversity are discussed.
Haplotype (mtDNA) diversity of brown trout Salmo trutta in tributaries of the Austrian Danube: massive introgression of Atlantic basin fish — by man or nature?
Authors: Weiss S. , Schlötterer C. , Waidbacher H. , Jungwirth M. 
Published: March 2003

AbstractMitochondrial haplotype diversity in 27 populations of brown trout, Salmo trutta L., in Austria was investigated by sequencing the 5′ end of the mitochondrial DNA (mtDNA) control region. Although all populations are within the Danube drainage, 44% of all individuals carried Atlantic basin haplotypes. It is argued that the presence of these haplotypes in Austria primarily reflects introgression stemming from the stocking of hatchery‐reared fish. However, several lines of evidence suggest that some natural colonization from Atlantic lineages may have contributed to the present haplotype diversity. Nonetheless, the more diverse Danubian clade is represented by regionally distinct haplotype diversity that should be protected from the continued introduction of domesticated strains of exogenous fish.