bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world‐wide
Authors: BAKER C. S. , SLADE R. W. , BANNISTER J. L. , ABERNETHY R. B. , WEINRICH M. T. , LIEN J. , URBAN J. , CORKERON P. , CALMABOKIDIS J. , VASQUEZ O. , PALUMBI S. R. 
Published: April 2008

AbstractThe genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or ‘stocks’, world‐wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world‐wide genetic variation among oceanic populations, among subpopulations or ‘stocks’ within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south‐eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or ‘American’ stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long‐lived, mobile vertebrates in the marine ecosystem.
Species status and population genetic structure of the flightless chafer beetles Prodontria modesta and P. bicolorata (Coleoptera; Scarabaeidae) from South Island, New Zealand
Authors: EMERSON B. C. , WALLIS G. P. 
Published: April 2008

AbstractThis study uses isozyme electrophoresis to investigate the systematic status of two rare flightless chafer beetle species, Prodontria modesta and P. bicolorata, currently distinguished solely on the basis of colour. Seven polymorphic loci were analysed for the species in sympatry and allopatry. In sympatry, gene frequencies imply no genetic barrier between the two colour forms. Wright's hierarchical F‐statistics were calculated to determine how the genetic variation is partitioned across the geographic range of the two species. Strong geographic structuring occurs at the population level but there is little genetic differentiation attributable to species. Comparisons of morphological measurements are in support of the electrophoretic results. The systematic significance of the two distinct colour forms is thus questionable. Under the biological, recognition or phylogenetic species concepts, the genetic data suggest that there is only one species, polytypic for a colour pattern. Most of the genetic diversity of this group of beetles lies within and among populations, which differ quite markedly over their geographic range, rather than between the two named species.
DNA fingerprinting in Speke's gazelle: a test for genetic distinctness, and the correlation between relatedness and similarity
Authors: BUTLER M. A. , TEMPLETON A. R. , READ B. 
Published: April 2008

AbstractIn the absence of pedigree information, the determination of genetic distinctness of populations can only be made by genetic methods. Using DNA fingerprinting on the North American captive herd of Speke's gazelle Gazella spekei, we were able to address two hypotheses. First, two new individuals were found to have come from a genetically distinct population (P= 0.008, permutation test), and represent potential new founders to be added to the population. Secondly, genetic similarity was not significantly correlated with relatedness under extreme inbreeding and very close relationship (coefficient of relationship range 0.304‐0.717).
Genetic structure and mating system in the palila, an endangered Hawaiian honeycreeper, as assessed by DNA fingerprinting
Authors: FLEISCHER R. C. , TARR C. L. , PRATT T. K. 
Published: April 2008

AbstractWe conducted DNA fingerprinting analyses to ascertain the mating system and population genetic structure of the palila, an endangered Hawaiian honeycreeper, which occupies a fragmented range on the Mauna Kea volcano of the island of Hawai'i. DNA fingerprinting of twelve complete families from the Pu'u La'au population revealed no evidence of extrapair fertilization or intraspecific brood parasitism. Band‐sharing coefficients from fingerprints produced with two probes revealed that the large Pu'u La'au population on the southwest slope of Mauna Kea, and a smaller, geographically separate population on the east slope (at Kanakaleonui) had relatively high and virtually identical levels of minisatellite variability (mean S of 0.27 for each population based on combined data of M13 and Jeffreys 33.15 probes). The two populations also had nearly identical allele frequencies based on their mean corrected similarity, Sij, of 0.98. These data suggest that the two populations have not been fragmented long and/or have sufficient current gene flow to ameliorate any affects of genetic drift. We conclude that present levels of inbreeding are low within both populations, and that proposed translocations of individuals from Pu'u La'au to Kanakaleonui appear appropriate from a genetic standpoint.
Modelling problems in conservation genetics using Drosophila: consequences of fluctuating population sizes
Authors: WOODWORTH L. M. , MONTGOMERY M. E. , NURTHEN R. K. , BRISCOE D. A. , FRANKHAM R. 
Published: April 2008

AbstractMany natural populations fluctuate widely in population size. This is predicted to reduce effective population size, genetic variation, and reproductive fitness, and to increase inbreeding. The effects of fluctuating population size were examined in small populations of Drosophila melanogaster of the same average size, but maintained using either fluctuating (FPS) or equal (EPS) population sizes.FPS lines were maintained using seven pairs and one pair in alternate generations, and EPS lines with four pairs per generation. Ten replicates of each treatment were maintained. After eight generations, FPS had a higher inbreeding coefficient than EPS (0.60 vs. 0.38), a lower average allozyme heterozygosity (0.068 vs. 0.131), and a much lower relative fitness (0.03 vs. 0.25). Estimates of effective population sizes for FPS and EPS were 3.8 and 7.9 from pedigree inbreeding, and 4.9 vs. 7.1 from changes in average heterozygosities, as compared to theoretical expectations of 3.3 vs. 8.0. Results were generally in accordance with theoretical predictions. Management strategies for populations of rare and endangered species should aim to minimize population fluctuations over generations.
Applications of mitochondrial DNA analysis in conservation: a critical review
Authors: MORITZ C. 
Published: April 2008

AbstractPatterns of variation in mitochondrial DNA (mtDNA) increasingly are being investigated in threatened or managed species, but not always with clearly defined goals for conservation. In this review I identify uses of mtDNA analysis which fall into two different areas: (i) ‘gene conservation’ ‐ the identification and management of genetic diversity, and (ii) ‘molecular ecology’ ‐ the use of mtDNA variation to guide and assist demographic studies of populations. These two classes of application have different conceptual bases, conservation goals and time‐frames. Gene conservation makes extensive use of phylogenetic information and is, in general, most relevant to long‐term planning. Appropriate uses here include identification of Evolutionarily Significant Units and assessment of conservation priority of taxa or areas from an evolutionary perspective. Less appropriate are inferences about fitness from within‐population diversity and about species boundaries. Molecular ecology makes more use of allele frequencies and provides information useful for short‐term management of populations. Powerful applications are to identify Management Units and to define and use naturally occurring genetic tags. Estimating demographic parameters, e.g migration rate and population size, from patterns of mtDNA diversity is fraught with difficulty, particularly where populations are fluctuating, and is unlikely to produce quantitative estimates sufficiently accurate to be useful for practical management of contemporary populations. However, through comparative studies, mtDNA analysis can provide qualitative signals of population changes, allowing efficient targeting of resource‐intensive ecological studies. Thus, there are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long‐term planning and short‐term execution of species recovery plans.
Development of RAPD markers in two introduced fire ants,Solenopsis invictaandS. richteri, and their application to the study of a hybrid zone
Authors: SHOEMAKER D. DEWAYNE , ROSS K. G. , ARNOLD M. L. 
Published: April 2008

AbstractWe developed RAPD DNA markers useful in distinguishing the fire antsSolenopsis invictaandS. richteri.An initial survey of 200 primers revealed seven informative markers; family studies allowed us to determine expression patterns and to confirm Mendelian inheritance of these markers. The seven RAPD markers, one of which is inherited as a codominant marker, were employed along with three allozyme markers to describe the structure of a hybrid zone that has formed between the two species in the USA, where they have been introduced. The data suggest minor introgression of alleles from one parental species (S. richteri) into the other (S. invicta), which most likely reflects the documented recent movement of this hybrid zone. This pattern is interpreted as interspecific introgression rather than shared intraspecific polymorphism on the basis of comparisons with samples from native, non‐hybridizing populations in South America that lack such polymorphism. The data further reveal that the structure of the hybrid zone in the USA varies geographically. One parental species (S. invicta) and the hybrids exhibit a mosaic distribution in the east; a gradual transition between the parental species occurs in the centre, with a large intervening area of hybrid genotypes only; and there is apparent contact between parental populations with a small or no intervening zone of hybridization in the west. These differing patterns in the structure of the hybrid zone presumably reflect the unique histories of colonization in different parts of the range of introduced fire ants.
Phylogeny of mitochondrial DNA clones in tassel‐eared squirrels Sciurus aberti
Authors: WETTSTEIN P. J. , LAGER P. , JIN L. , STATES J. , LAMB T. , CHAKRABORTY R. 
Published: April 2008

AbstractThe tassel‐eared squirrel, Sciurus aberti, includes six subspecies which occupy restrictive and apparently identical habitats in Ponderosa pine forests in the south‐western United States and Mexico; the strict habitat requirement of this species is based on dietary requirements which are only fulfilled in these forests. To examine evolutionary relationships among certain subspecies of S. aberti, we obtained estimates of nucleotide diversity within subspecies as well as nucleotide divergence between subspecies using mitochondrial DNA (mtDNA) analysis. Restriction site polymorphisms were identified in samples of the four US subspecies: S. a. aberti (Abert), S. a. kaibabensis (Kaibab), S. a. ferreus (Ferreus), and S. a. chuscensis (Chuska) Fourteen mtDNA clones were resolved that were, with one exception, uniquely subspecific. Dendrograms constructed by neighbour‐joining and maximum parsimony methods revealed two major assemblages: (1) an Abert/Kaibab group; and (2) a Ferreus/Chuska group. The Abert vs. Ferreus clones exhibited the greatest net nucleotide divergence, with a lineage separation estimate approximating 572 000 years ago assuming a nucleotide substitution rate of 7.15 × 10‐9/year/site. Five out of ten Chuska squirrels shared a clone with one Abert sample; the relative sizes of these two populations and their respective ranges as well as their close proximity support the proposal for relatively recent intermixing of Abert and Chuska populations resulting in what appears to be Abert → Chuska migration. Nucleotide diversity within subspecies ranked as Kaibab < Ferreus < Abert < Chuska; the relatively high diversity for the Chuska sample is based on the apparent introgression of Abert mtDNA. The relative diversity exhibited by Kaibab, Ferreus and Aberti samples corresponds to the range size of the respective subspecies.
The establishment of a hybrid zone between red and sika deer (genusCervus)
Authors: ABERNETHY K. 
Published: April 2008

AbstractJapanese sika deer (Cervus nippon nippon) were introduced to Scotland around 80 years (20 generations) ago. The sika phenotype is expanding its range and hybridizing extensively with native red deer (Cervus elaphus) leading to the establishment of a hybrid zone. This zone is currently moving and cannot be considered to be at equilibrium. Cervid genotypes and mitochondrial haplotypes were mapped across the sika phenotype range, using diagnostic protein isozymes, microsatellite nuclear DNA markers and RFLPs in mtDNA. These were analysed to estimate heterozygote deficits and nuclear linkage disequilibria and cytonuclear disequilibria in relation to gene frequencies and time since contact. Introgression was found in both taxa and strong linkage disequilibria and heterozygote deficits characterize the populations longest exposed to hybridization. Populations further from the introduction site, where hybridization is facilitated by the dispersal of sika‐like stags, show low values for linkage disequilibria and heterozygote deficit. The observed patterns in genotype are explained in terms of assortative mating and a selective advantage of the sika genotype. The genetic integrity of the Scottish mainland red deer is shown to be at risk from the invasion of sika.
Analysis of population genetic structure with RAPD markers
Authors: LYNCH M. , MILLIGAN B. G. 
Published: April 2008

AbstractRecent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD (random amplified polymorphic DNA) method is one such technique that has attracted widespread interest. The analysis of population structure with RAPD data is hampered by the lack of complete genotypic information resulting from dominance, since this enhances the sampling variance associated with single loci as well as induces bias in parameter estimation. We present estimators for several population‐genetic parameters (gene and genotype frequencies, within‐ and between‐population heterozygosities, degree of inbreeding and population subdivision, and degree of individual relatedness) along with expressions for their sampling variances. Although completely unbiased estimators do not appear to be possible with RAPDs, several steps are suggested that will insure that the bias in parameter estimates is negligible. To achieve the same degree of statistical power, on the order of 2 to 10 times more individuals need to be sampled per locus when dominant markers are relied upon, as compared to codominant (RFLP, isozyme) markers. Moreover, to avoid bias in parameter estimation, the marker alleles for most of these loci should be in relatively low frequency. Due to the need for pruning loci with low‐frequency null alleles, more loci also need to be sampled with RAPDs than with more conventional markers, and some problems of bias cannot be completely eliminated.
Paternity exclusion by DNA fingerprinting, and mate guarding in the hooded seal Cystophora cristata
Authors: McRAE S. B. , KOVACS K. M. 
Published: April 2008

AbstractHooded seal Cystophora cristata trios consist of an adult female, her pup, and an attending adult male. Using DNA fingerprinting, we excluded the possibility that the attending males within hooded seal trios were the fathers of the pups, proving that these hooded seals did not remain paired from one breeding season to the next. Behavioural observations of the trios after capture and release revealed that male hooded seals displace one another in attending nursing females. Mate guarding appears to be the preferred mating strategy available to male hooded seals given intense competition for females, a very brief nursing period, and oestrus occuring soon after weaning, but its effectiveness remains unclear.
Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles
Authors: HAIG S. M. , BALLOU J. D. , CASNA N. J. 
Published: April 2008

AbstractKin structure among founders can have a significant effect on subsequent population structure. Here we use the correlation between DNA profile similarity and relatedness calculated from pedigrees to test hypotheses regarding kin structure among founders to the captive Guam rail (Rallus owstoni) population. Five different pedigrees were generated under the following hypotheses: (i) founders are unrelated; (ii) founders are unrelated except for same‐nest chicks; (iii) founders from the same major site are siblings; (iv) founders from the same local site are siblings; and (v) founders are related as defined by a UPGMA cluster analysis of DNA similarity data. Relatedness values from pedigrees 1, 2 and 5 had the highest correlation with DNA similarity but the correlation between relatedness and similarity were not significantly different among pedigrees. Pedigree 5 resulted in the highest correlation overall when using only relatedness values that changed as a result of different founder hypotheses. Thus, founders were assigned relatedness based on pedigree 5 because it had the highest correlations with DNA similarity, was the most conservative approach, and incorporated all field data. The analyses indicated that estimating relatedness using DNA profiles remains problematic, therefore we compared mean kinship, a measure of genetic importance, with mean DNA profile similarity to determine if genetic importance among individuals could be determined via use of DNA profiles alone. The significant correlation suggests this method may provide more information about population structure than was previously thought. Thus, DNA profiles can provide a reasonable explanation for founder relatedness and mean DNA profile similarity may be helpful in determining relative genetic importance of individuals when detailed pedigrees are absent.
DNA fingerprinting reveals significant amounts of genetic variation in a wild raspberry Rubus idaeus population
Authors: ANTONIUS K. , NYBOM H. 
Published: April 2008

AbstractEstablishing the genotypic distribution in natural plant populations is an important part of ecological studies concerning plant growth, reproduction and turn‐over. Restriction enzyme‐digested DNA samples, isolated from 24 plants of a natural Rubus idaeus population, were analysed with DNA fingerprinting using the M13 repeat sequence as well as a synthetic (AC)/(TG) polydinucleotide as hybridization probes. All the examined samples exhibit unique DNA fingerprint patterns, suggesting that vegetative reproduction may be considerably more restricted in wild R. idaeus populations than previously assumed. By comparison, all samples of the apomictic blackberry species Rubus nessensis, collected on the same location, were completely identical.
The local distribution of highly divergent mitochondrial DNA haplotypes in toque macaques Macaca sinica at Polonnaruwa, Sri Lanka
Authors: HOELZER G. A. , DITTUS W. P. J. , ASHLEY M. V. , MELNICK D. J. 
Published: April 2008

AbstractSurveys of mitochondrial DNA (mtDNA) variation in macaque monkeys have revealed extremely high levels of intraspecific divergence among haplotypes. One consistent pattern that has emerged from these studies is that divergent haplotypes are geographically segregated so that sampling a few matrilines from a given region shows them to be identical, or a closely related subset of haplotypes. Geographically structured mtDNA variation has also been commonly observed in other taxa. In this study, haplotype variation and distribution are studied in detail within a local population of toque macaques. The results show that highly divergent haplotypes, differing by 3.1% in their nucleotide sequences, coexist in this population and that they may be spatially segregated even on this micro‐geographic scale. Furthermore, these differences are maintained between social groups that exchange male migrants, and thus nuclear genes, frequently.
Fluorescent Pseudomonas species categorized by using polymerase chain reaction (PCR)/restriction fragment analysis of 16S rDNA
Authors: LAGUERRE G. , RIGOTTIER‐GOIS L. , LEMANCEAU P. 
Published: April 2008

AbstractA rapid procedure for the identification of fluorescent pseudomonads, based on the polymerase chain reaction (PCR) and restriction fragment analysis of 16S rDNA genes is described. Thirty‐one strains belonging to 10 different Pseudomonas species of the Pseudomonas fluorescens rRNA branch were characterized. Amplified rDNA was digested with 13 different restriction endonucleases. The combined data from restriction analysis enabled the definition of 17 different 16S rDNA genotypes. All type strains belonging to different species were differentiated. The good correlation between grouping obtained using restriction analysis with other molecular classification criteria demonstrates the value of the described method to characterize rapidly fluorescent Pseudomonas strains at the species level.
Molecular biogeography of clonal lineages in a high‐Arctic apomictic Daphnia complex
Authors: WEIDER L. J. , HOBAEK A. 
Published: April 2008

AbstractAn electrophoretic survey of 81 populations of arctic Daphnia pulex from around the Svalbard archipelago revealed the presence of 49 unique allozyme clones (N= 3357). Two closely related clones accounted for 66% of the total sample, and were widespread across the archipelago. Restriction fragment length polymorphisms (RFLPs) of a 2.1‐kb fragment of mtDNA (NADH‐4 and NADH‐5 subunits), amplified using the polymerase chain reaction (PCR), revealed the presence of eight mtDNA haplotypes. One haplotype was particularly widespread, and the two most abundant allozyme clones shared this haplotype. Nonrandom distribution patterns of clones were observed, and are most likely the result of historical events (i.e. founder effects) related to the past glacial history of the archipelago. The data are discussed with reference to past glaciation events, and attempts are made to discern the colonization history of this apomictic complex.