bluuebunny/crossref_metadata_2025_split huggingface dataset:
An unusual source of apparent mitochondrial heteroplasmy: duplicate mitochondrial control regions in Thalassarche albatrosses
Authors: ABBOTT CATHRYN L. , DOUBLE MICHAEL C. , TRUEMAN JOHN W. H. , ROBINSON ANNA , COCKBURN ANDREW 
Published: September 2005

AbstractMolecular ecologists, in search of suitable molecular markers, frequently PCR‐amplify regions of mitochondrial DNA from total DNA extracts. This approach, although common, is prone to the co‐amplification of nuclear copies of transposed DNA sequences (numts), which can then generate apparent mitochondrial sequence heteroplasmy. In this study we describe the discovery of apparent mitochondrial sequence heteroplasmy in Thalassarche albatrosses but eliminate the possibility of true sequence heteroplasmy and numts and instead reveal the source of the apparent heteroplasmy to be a duplicated control region. The two control regions align easily but are not identical in sequence or in length. Comparisons of functionally significant conserved sequence blocks do not provide evidence of degeneration in either duplicate. Phylogenetic analyses of domain I of both control region copies in five Thalassarche species indicate that they are largely evolving in concert; however, a short section within them is clearly evolving independently. To our knowledge this is the first time contrasting evolutionary patterns have been reported for duplicate control regions. Available evidence suggests that this duplication may be taxonomically widespread, so the results presented here should be considered in future evolutionary studies targeting the control region of all Procellariiformes and potentially other closely related avian groups.
A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad‐range North American conifer
Authors: GODBOUT JULIE , JARAMILLO‐CORREA JUAN P. , BEAULIEU JEAN , BOUSQUET JEAN 
Published: September 2005

AbstractJack pine (Pinus banksianaLamb.) is a broadly distributed North American conifer and its current range was covered by the Laurentian ice sheet during the last glacial maximum. To infer about the history and postglacial colonization of this boreal species, range‐wide genetic variation was assessed using a new and highly variable minisatellite‐like marker of the mitochondrial genome. Among the 543 trees analysed, 14 distinct haplotypes were detected, which corresponded to different repeat numbers of the 32‐nucleotide minisatellite‐like motif. Several haplotypes were rare with limited distribution, suggesting recent mutation events during the Holocene. At the population level, an average of 2.6 haplotypes and a mean haplotype diversity (H) of 0.328 were estimated. Population subdivision of genetic diversity was quite high withGSTandRSTvalues of 0.569 and 0.472, respectively. Spatial analyses identified three relatively homogeneous groups of populations presumably representative of genetically distinct glacial populations, one west and one east of the Appalachian Mountains in the United States and a third one presumably on the unglaciated northeastern coastal area in Canada. These results indicate the significant role of the northern part of the US Appalachian Mountains as a factor of vicariance during the ice age. A fourth distinct group of populations was observed in central Québec where the continental glacier retreated last. It included populations harbouring haplotypes present into the three previous groups, and it had higher level of haplotype diversity per population (H = 0.548) and lower population differentiation (GST = 0.265), which indicates a zone of suture or secondary contact between the migration fronts of the three glacial populations. Introgression fromPinus contortaDougl. var.latifoliaEngelm. was apparent in one western population from Alberta. Altogether, these results indicate that the mitochondrial DNA variation of jack pine is geographically highly structured and it correlates well with large‐scale patterns emerging from recent phylogeographical studies of other tree boreal species in North America.
Mating system, philopatry and patterns of kinship in the cooperatively breeding subdesert mesiteMonias benschi
Authors: SEDDON N. , AMOS W. , ADCOCK G. , JOHNSON P. , KRAAIJEVELD K. , KRAAIJEVELD‐SMIT F. J. L. , LEE W. , SENAPATHI G. D. , MULDER R. A. , TOBIAS J. A. 
Published: September 2005

AbstractIn the first molecular study of a member of the threatened avian family, Mesitornithidae, we used nine polymorphic microsatellite loci to elucidate parentage, patterns of within‐group kinship and occurrence of extra‐group paternity in the subdesert mesiteMonias benschi, of southwest Madagascar. We found this cooperatively breeding species to have a very fluid mating system. There was evidence of genetic monogamy and polygynandry: of the nine groups with multiple offspring, six contained one breeding pair with unrelated helpers and three contained multiple male and female breeders with related helpers. Although patterns of within‐group kinship varied, there was a strong positive relationship between group size and relatedness, suggesting that groups form by natal philopatry. There was also a strong positive correlation between within‐sex and between‐sex relatedness, indicating that unlike most cooperatively breeding birds, philopatry involved both sexes. In contrast to predictions of kin selection and reproductive skew models, all monogamous groups contained unrelated individuals, while two of the three polygynandrous groups were families. Moreover, although between‐group variation in seasonal reproductive success was related to within‐group female relatedness, relatedness among males and between the sexes had no bearing on a group's reproductive output. While kin selection may underlie helping behaviour in females, factors such as direct long‐term fitness benefits of group living probably determine helping in males. Of the 14 offspring produced by fully sampled groups, at least two were sired by males from neighbouring groups: one by a breeding male and one by a nonbreeding male, suggesting that males may augment their reproductive success through extra‐group paternity.
Worldwide structure of mtDNA diversity among Cuvier's beaked whales (Ziphius cavirostris): implications for threatened populations
Authors: DALEBOUT MEREL L. , ROBERTSON KELLY M. , FRANTZIS ALEXANDROS , ENGELHAUPT DAN , MIGNUCCI‐GIANNONI ANTONIO A. , ROSARIO‐DELESTRE RAUL J. , BAKER C. SCOTT 
Published: September 2005

AbstractWe present the first description of phylogeographic structure among Cuvier's beaked whales (Ziphius cavirostris) worldwide using mitochondrial DNA (mtDNA) control region sequences obtained from strandings (n = 70), incidental fisheries takes (n = 11), biopsy (n = 1), and whale‐meat markets (n = 5). Over a 290‐base pair fragment, 23 variable sites defined 33 unique haplotypes among the total of 87 samples. Nucleotide diversity at the control region was relatively low (π = 1.27%± 0.723%) compared to wide‐ranging baleen whales, but higher than strongly matrifocal sperm, pilot and killer whales. Phylogenetic reconstruction using maximum likelihood revealed four distinct haplotype groups, each of which displayed strong frequency differences among ocean basins, but no reciprocal monophyly or fixed character differences. Consistent with this phylogeographic pattern, an analysis of molecular variance showed high levels of differentiation among ocean basins (FST = 0.14, ΦST = 0.42; P < 0.001). Estimated rates of female migration among ocean basins were low (generally ≤ 2 individuals per generation). Regional sample sizes were too small to detect subdivisions within oceans except in the North Atlantic, where the Mediterranean Sea (n = 12) was highly differentiated due to the presence of two private haplotypes. One market product purchased in South Korea grouped with other haplotypes found only in the North Atlantic, suggesting a violation of current agreements banning international trade in cetacean species. Together, these results demonstrate a high degree of isolation and low maternal gene flow among oceanic, and in some cases, regional populations of Cuvier's beaked whales. This has important implications for understanding the threats of human impact, including fisheries by‐catch, direct hunting, and disturbance or mortality from anthropogenic sound.
Phylogeography of the Qinghai‐Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation
Authors: ZHANG Q. , CHIANG T. Y. , GEORGE M. , LIU J. Q. , ABBOTT R. J. 
Published: September 2005

AbstractThe vegetation of the northeast Qinghai‐Tibetan Plateau is dominated by alpine meadow and desert‐steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT‐trnF and trnS‐trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (GST = 0.772, NST = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (NST > GST, P < 0.05). Eight of the nine disjunct populations surveyed on the high‐elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype‐rich plateau edge area and the almost haplotype‐uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present‐day spatial distribution of cpDNA haplotypes within the species.
Prevalence and penetrance variation of male‐killingWolbachiaacross Indo‐Pacific populations of the butterflyHypolimnas bolina
Authors: CHARLAT SYLVAIN , HORNETT EMILY A. , DYSON EMILY A. , HO PATRICK P. Y. , LOC NGUYEN THI , SCHILTHUIZEN MENNO , DAVIES NEIL , RODERICK GEORGE K. , HURST GREGORY D. D. 
Published: September 2005

AbstractMale‐killing bacteria are generally thought to attain low to intermediate prevalence in natural populations, with only mild effects on the host population sex ratio. This view was recently challenged by reports of extremely high infection frequencies in three butterfly species, raising the prospect that male killers, by making males rare, might drive many features of host ecology and evolution. To assess this hypothesis, it is necessary to evaluate how often male killers actually produce a highly female‐biased population sex ratio in nature, which requires both high prevalence of infection and high penetrance of action. To this end, we surveyed South Pacific and Southeast Asian populations ofHypolimnas bolina, a butterfly in which extreme prevalence of male‐killingWolbachiabacteria has recently been recorded. Our results indicate that highly female‐biased populations are common in Polynesia, with 6 out of 12 populations studied having in excess of 70% of females infected with a fully efficient male killer. However, heterogeneity is extreme in Polynesia, with the male‐killingWolbachiaabsent from three populations. In contrast to the Polynesian situation,Wolbachiadoes not kill males in any of the three Southeast Asian populations studied, despite its very high prevalence there. We conclude that male killers are likely to have significant ongoing ecological and evolutionary impact in 6 of the 15 populations surveyed. The causes and consequences of the observed spatial variation are discussed with respect to host resistance evolution, host ecology and interference with additional symbionts.
A novel approach to an old problem: tracking dispersed seeds
Authors: GRIVET DELPHINE , SMOUSE PETER E. , SORK VICTORIA L. 
Published: September 2005

AbstractAnimals are the principal vectors of dispersal for a large number of plant species. Unfortunately it is not easy to discern their movement patterns or the fate of their dispersed seeds. Many animals transport seeds by consuming them and then, some time later, defecating them. Others gather seeds and then store them for later consumption. Both circumstances lead to a set of seeds that have been dispersed in a clumped pattern, which offers a unique opportunity to assess seed movements. We introduce a novel approach that uses maternally inherited seed tissue to quantify the genetic structure of dispersed seed pools. This direct approach measures the genetic variability within and among seed pools, and estimates the scale of seed movement, without requiring a highly polymorphic battery of markers or the location and genotypes of all possible seed parents. We demonstrate this approach with the specific case of seed transport of valley oak (Quercus lobata) acorns by acorn woodpeckers (Melanerpes formicivorus). These territorial birds store acorns in drilled holes in the bark of trees, called granaries. We sampled stored acorns from different granaries, extracted DNA from the maternally inherited pericarp, and then assessed individuals for three microsatellite markers. We found extremely high genetic structure among granaries, a low number of effective seed donors per granary, and restricted seed movement. A maternity analysis performed on the same sample with seven microsatellites confirms acorn transport is limited to approximately 100‐m radius. Our findings provide insight into the foraging and seed‐dispersal behaviour of acorn woodpeckers, with an approach that can be widely extended to other systems.
Phylogeography of marine mutualists: parallel patterns of genetic structure between obligate goby and shrimp partners
Authors: THOMPSON ANDREW R. , THACKER CHRISTINE E. , SHAW EMILY Y. 
Published: September 2005

AbstractThe survival of many organisms depends on interspecific, mutualistic interactions. Hence, it is important to assess the phylogeography of multiple mutualistic species simultaneously to gain insight into how their metapopulations persist, spread and recover from disturbance. Consequently, we sequenced mitochondrial DNA (cytochrome b) from a gobiid fish (Ctenogobiops feroculus) and its mutualistic partner, an alpheid snapping shrimp (Alpheus djeddensis). These obligate mutualists are common in shallow coral reef lagoons, and we collected individuals from 11 Indo‐Pacific islands that were likely exposed to different disturbance histories due to sea level fluctuations associated with glaciation events [geological studies indicate that eastern oceanic islands (Cook Islands, French Polynesia) were more disturbed than western continental plate islands that have deeper, more extensive lagoons (Okinawa, Fiji)]. Both phylogenetic and population genetic analyses indicated that gobies from Okinawa and Fiji were genetically distinct both from each other and those in the Cook Islands and French Polynesia. Shrimp, by contrast, grouped into two distinct genetic groups that showed no geographic structure. Restricting the analysis to one clade of shrimp, which contained two‐thirds of the individuals, showed that these shrimp had very similar phylogeographical structure to the gobies. Mismatch distributions demonstrated that both gobies and shrimp experienced a recent, rapid population expansion into French Polynesia. Finally, nucleotide and haplotype diversities per sample location were significantly correlated between mutualists and tended to be higher on western continental than eastern oceanic islands. Our results suggest that these mutualists recovered from a major disturbance by colonizing South Pacific islands in synchrony.
Rapidly declining fine‐scale spatial genetic structure in female red deer
Authors: NUSSEY D. H. , COLTMAN D. W. , COULSON T. , KRUUK L. E. B. , DONALD A. , MORRIS S. J. , CLUTTON‐BROCK T. H. , PEMBERTON J. 
Published: September 2005

AbstractA growing literature now documents the presence of fine‐scale genetic structure in wild vertebrate populations. Breeding population size, levels of dispersal and polygyny — all hypothesized to affect population genetic structure — are known to be influenced by ecological conditions experienced by populations. However the possibility of temporal or spatial variation in fine‐scale genetic structure as a result of ecological change is rarely considered or explored. Here we investigate temporal variation in fine‐scale genetic structure in a red deer population on the Isle or Rum, Scotland. We document extremely fine‐scale spatial genetic structure (< 100 m) amongst females but not males across a 24‐year study period during which resource competition has intensified and the population has reached habitat carrying capacity. Based on census data, adult deer were allocated to one of three subpopulations in each year of the study. Global FST estimates for females generated using these subpopulations decreased over the study period, indicating a rapid decline in fine‐scale genetic structure of the population. Global FST estimates for males were not different from zero across the study period. Using census and genetic data, we illustrate that, as a consequence of a release from culling early in the study period, the number of breeding females has increased while levels of polygyny have decreased in this population. We found little evidence for increasing dispersal between subpopulations over time in either sex. We argue that both increasing female population size and decreasing polygyny could explain the decline in female population genetic structure.
Specificity of the mutualistic association between actinomycete bacteria and two sympatric species of Acromyrmex leaf‐cutting ants
Authors: POULSEN M. , CAFARO M. , BOOMSMA J. J. , CURRIE C. R. 
Published: September 2005

Abstract Acromyrmex leaf‐cutting ants maintain two highly specialized, vertically transmitted mutualistic ectosymbionts: basidiomycete fungi that are cultivated for food in underground gardens and actinomycete Pseudonocardia bacteria that are reared on the cuticle to produce antibiotics that suppress the growth of Escovopsis parasites of the fungus garden. Mutualism stability has been hypothesized to benefit from genetic uniformity of symbionts, as multiple coexisting strains are expected to compete and, thus, reduce the benefit of the symbiosis. However, the Pseudonocardia symbionts are likely to be involved in Red‐Queen‐like antagonistic co‐evolution with Escovopsis so that multiple strains per host might be favoured by selection provided the cost of competition between bacterial strains is low. We examined the genetic uniformity of the Pseudonocardia symbionts of two sympatric species of Acromyrmex ants by comparing partial sequences of the nuclear Elongation Factor‐Tu gene. We find no genetic variation in Pseudonocardia symbionts among nest mate workers, neither in Acromyrmex octospinosus, where colonies are founded by a single queen, nor in Acromyrmex echinatior, where mixing of bacterial lineages might happen when unrelated queens cofound a colony. We further show that the two ant species maintain the same pool of Pseudonocardia symbionts, indicating that horizontal transmission occasionally occurs, and that this pool consists of two distinct clades of closely related Pseudonocardia strains. Our finding that individual colonies cultivate a single actinomycete strain is in agreement with predictions from evolutionary theory on host–symbiont conflict over symbiont mixing, but indicates that there may be constraints on the effectiveness of the bacterial symbionts on an evolutionary timescale.
Naturally occurring variation in high temperature induced floral bud abortion across Arabidopsis thaliana accessions
Authors: WARNER RYAN M. , ERWIN JOHN E. 
Published: September 2005

ABSTRACTA system to study the basis of high temperature‐induced floral bud abortion using naturally occurring variation for heat‐tolerance of floral development among Arabidopsis thaliana (L.) Heynh. wild‐collected accessions is described. High temperature‐induced floral bud abortion was dependent on both temperature and duration of exposure. Normalizing high temperature exposures to degree‐hours (°C‐h) above 33 °C indicated that abortion of flower buds increased as exposure increased between 200 and 300 °C‐h above 33 °C and exposures > 300 °C‐h above 33 °C resulted in abortion of the entire primary inflorescence. Thirteen wild‐collected Arabidopsis accessions representing a latitudinal gradient were screened for variation in high temperature‐induced floral bud abortion, and Col‐0 and No‐0 were selected as models for heat‐tolerance and ‐sensitivity for flower development, respectively. No‐0 flower buds were heat‐sensitive across a wider range of developmental stages (stages 9–12, compared to stage 12 for Col‐0 flower buds). Exposing the inflorescence alone to high temperature was sufficient to induce floral bud abortion, and Col‐0 and No‐0 photosynthetic rates were similar during high temperature exposure and recovery, indicating that high temperature induced floral abortion is not simply due to reductions in carbon assimilation under high temperatures. Determining that exposing floral buds alone to high temperature is sufficient to induce abortion and identifying the stages of floral development sensitive to high temperature‐induced abortion will aid in identifying the developmental events subject to disruption under high temperatures.
Ca2+ and AtCaM3 are involved in the expression of heat shock protein gene in Arabidopsis
Authors: LIU HONG‐TAO , SUN DA‐YE , ZHOU REN‐GANG 
Published: September 2005

ABSTRACTThe involvement of calcium and different calmodulin isoforms (Ca2+‐CaM) in heat shock (HS) signal transduction in Arabidopsis (Arabidopsis thaliana) was investigated. Using transgenic Arabidopsis plants which have the AtHsp18.2 promoter/GUS fusion gene, it was found that the level of β‐glucuronidase (GUS) activity was up‐regulated by the addition of CaCl2 and down‐regulated by the calcium ion chelator EGTA, the calcium ion channel blockers LaCl3 and verapamil, or the CaM antagonists N‐(6‐aminohexyl)‐5‐chloro‐1‐naphthalenesulfonamide (W7), chlorpromazine (CPZ) and trifluoperazine (TFP). CaCl2 not only increased the GUS activity after HS, but also up‐regulated the GUS activity under non‐HS conditions. These results provide additional support for the involvement of the Ca2+‐CaM signalling system in HSP gene expression. The expression of nine CaM genes (AtCaM1–9) from Arabidopsis was differentially regulated by HS at 37 °C. The expression of AtCaM3 and AtCaM7 genes increased during HS. The temporal expression of the AtCaM3, AtCaM7 and hsp18.2 genes demonstrated that up‐regulation of AtCaM3 expression occurred earlier than that of AtCaM7 or hsp18.2.