bluuebunny/crossref_metadata_2025_split huggingface dataset:
European colonization by the spined loach (Cobitis taenia) from Ponto‐Caspian refugia based on mitochondrial DNA variation
Authors: CULLING MARK A. , JANKO KAREL , BORON ALICJA , VASIL’EV VICTOR P. , CÔTÉ ISABELLE M. , HEWITT GODFREY M. 
Published: December 2005

AbstractIn the last 20 years, new species, asexual reproduction, polyploidy and hybridization have all been reported within the genus Cobitis. An understanding of the current distribution and baseline phylogeographical history of ‘true’ nonhybrid Cobitis species is crucial in order to unravel these discoveries. In the present work, we investigated the phylogeography of the spined loach, Cobitis taenia, using 1126 bp of the mitochondrial cytochrome b gene from 174 individuals collected at 47 sites. In total, 51 haplotypes that differed at 49 positions (4.35%) were detected. We deduce that C. taenia survived European glaciations in at least three refuges in the Ponto‐Caspian area. Two of these refuges each provided a major lineage that recolonized Europe in separate directions: one westward to England and the other spreading north into Russia before moving west. A third (minor) lineage that contributed little to the recolonization of Europe was also revealed — remaining near its Black Sea refuge. However, more recent history was difficult to resolve with colonization from a more western refugium during the last glacial maximum (LGM) a distinct possibility. Nested clade analysis indicates a pattern of restricted gene flow with isolation by distance at the first two levels and overall. Unlike many other European freshwater fish species, the Danube is not part of the current distribution of C. taenia, nor was it used as either a refuge or a source of colonization of Europe. Low genetic diversity within C. taenia suggests that its colonization of Europe is relatively recent. Demographic analyses revealed a history of recent expansion and isolation by distance.
A tale of two siblings: multiple paternity in big brown bats (Eptesicus fuscus) demonstrated using microsatellite markers
Authors: VONHOF M. J. , BARBER D. , FENTON M. B. , STROBECK C. 
Published: December 2005

AbstractIn many bat species, the opportunity for sperm competition or other mechanisms of post‐copulatory paternity biasing is thought to be great, due to the long delay between copulation and fertilization, demonstrated sperm storage capabilities, and observed promiscuity. We present the results of the first study to assess whether litters of big brown bats (Eptesicus fuscus) containing dizygotic twins share the same father. We sampled 26 mother–offspring triads from three colonies in Indiana and Illinois, as well as 299 additional adults (237 females and 62 males) from these colonies and six other maternity colonies in the same area in 1997–1998. All individuals were genotyped at nine highly variable autosomal microsatellite loci and one X‐linked locus. We assessed multiple paternity using autosomal and X‐linked locus exclusions, and using maximum‐likelihood methods. All methods confirmed multiple paternity within litters, and the maximum‐likelihood analyses indicated that almost half of the sampled litters were composed of maternal half‐siblings rather than full‐siblings. Our results highlight the potential importance of post‐copulatory mechanisms of paternity determination in the mating system of big brown bats, and have important implications for gene flow and population structuring in this species.
Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon
Authors: ROBERGE CHRISTIAN , EINUM SIGURD , GUDERLEY HELGA , BERNATCHEZ LOUIS 
Published: December 2005

AbstractFarmed salmon strains have been selected to improve growth rates as well as other traits of commercial interest but the 2 million farmed salmon escaping annually may enhance the risk of extinction of wild populations through genetic and ecological interactions. Here, we compare the transcription profiles of 3557 genes in the progeny of farmed and wild Atlantic salmon from Norway and Canada grown in controlled conditions, and demonstrate that five to seven generations of artificial selection led to heritable changes in gene transcription profiles, the average magnitude of the differences being 25% and 18% for at least 1.4% and 1.7% of the expressed genes in juvenile salmon from Norway and Canada, respectively. Moreover, genes showing significant transcription profile differences in both farmed strains (16%) all exhibited parallel changes. These findings, along with the identification of several genes whose expression profiles were modified through artificial selection, provide new insights into the molecular basis of parallel evolution, and suggest how gene flow from farmed escapees may affect the genetic integrity of wild populations.
Bayesian analyses of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite loci
Authors: LECIS R. , PIERPAOLI M. , BIRÒ Z. S. , SZEMETHY L. , RAGNI B. , VERCILLO F. , RANDI E. 
Published: December 2005

AbstractMethods recently developed to infer population structure and admixture mostly use individual genotypes described by unlinked neutral markers. However, Hardy–Weinberg and linkage disequilibria among independent markers decline rapidly with admixture time, and the admixture signals could be lost in a few generations. In this study, we aimed to describe genetic admixture in 182 European wild and domestic cats (Felis silvestris), which hybridize sporadically in Italy and extensively in Hungary. Cats were genotyped at 27 microsatellites, including 21 linked loci mapping on five distinct feline linkage groups. Genotypes were analysed with structure 2.1, a Bayesian procedure designed to model admixture linkage disequilibrium, which promises to assess efficiently older admixture events using tightly linked markers. Results showed that domestic and wild cats sampled in Italy were split into two distinct clusters with average proportions of membership Q > 0.90, congruent with prior morphological identifications. In contrast, free‐living cats sampled in Hungary were assigned partly to the domestic and the wild cat clusters, with Q < 0.50. Admixture analyses of individual genotypes identified, respectively, 5/61 (8%), and 16–20/65 (25–31%) hybrids among the Italian wildcats and Hungarian free‐living cats. Similar results were obtained in the past using unlinked loci, although the new linked markers identified additional admixed wildcats in Italy. Linkage analyses confirm that hybridization is limited in Italian, but widespread in Hungarian wildcats, a population that is threatened by cross‐breeding with free‐ranging domestic cats. The total panel of 27 loci performed better than the linked loci alone in the identification of domestic and known hybrid cats, suggesting that a large number of linked plus unlinked markers can improve the results of admixture analyses. Inferred recombination events led to identify the population of origin of chromosomal segments, suggesting that admixture mapping experiments can be designed also in wild populations.
Spatial dynamics of supercolonies of the invasive yellow crazy ant,Anoplolepis gracilipes, on Christmas Island, Indian Ocean
Authors: Abbott K. L. 
Published: December 2005

ABSTRACTKey to the management of invasive species is an understanding of the scope of an invasion, the rate of proliferation and the rate at which invaded habitats become degraded. This study examines the spatial dynamics of high‐density supercolonies of the invasive yellow crazy ant,Anoplolepis gracilipes, on Christmas Island, Indian Ocean, and the associated impacts at their boundaries. Since the early 1990s,A. gracilipessupercolonies have occupied over 30% of the 10,000 ha of rainforest on Christmas Island. Thirty‐four discrete high‐density supercolonies formed between 1989 and 2003, ranging in size across nearly three orders of magnitude from 0.9 to 787 ha. Supercolonies boundaries are diffuse, and ants were observed in low densities in some cases up to 200 m from the main high‐density supercolony. The 13 boundaries examined were all dynamic over a 10–20 observation month period: nine boundaries expanded, and the maximum rate of spread was 0.5 m day−1. Across boundary transition zones, between high‐density supercolonies and intact rainforest, yellow crazy ants reduced other ant species richness, occupied red crab burrows and killed resident red crabs, which was the trigger for ‘invasional meltdown’ on Christmas Island. The highly variable and unpredictable nature ofA. gracilipesboundaries poses a challenge for incorporation into a predictive framework, as well as for their management.
Regional and local influence of grazing activity on the diversity of a semi‐arid dung beetle community
Authors: Lobo Jorge M. , Hortal Joaquín , Cabrero‐Sañudo Francisco J. 
Published: December 2005

ABSTRACTThis study analyses the effect of resource availability (i.e. sheep dung) on dung beetle communities in an arid region of Central Spain, both at regional and at local scales. A total of 18 sites within 600 km2were sampled for the regional analysis and 16 sites within the 30 km2of an Iberian municipality were sampled for the local analysis. Spatial and environmental characteristics of sampling sites were also compiled at both scales, including measures of grazing activity (livestock density at regional scale, and two counts of rabbit and sheep dung at local scale). At a regional scale, any environmental or spatial variable can help to explain the variation in abundance. However, species richness was related to summer precipitation and composition was related to elevation. At local scale, abundance is not significantly related to any of the environmental variables, but species richness was related to the local amount of sheep dung (27% of variance). The amount of dung in a 2‐km buffer around the site accounts for 27–32% of variance in abundance and 60–65% of variance in species richness. The presence of the flock with the highest sheep density explains 53% of abundance variability and 73% of species richness variance. A cluster analysis of localities identified two main groups, one characterized by a lower abundance and species richness that can be considered a nested subsample of the species‐rich group. The mean and maximum amount of sheep dung in the sites separated by less than 2 km are the only significant explanatory variables able to discriminate both groups.These results suggest that grazing intensity (and the associated increase in the amount of trophic resources) is a key factor in determining local variation in the diversity and composition of dung beetle assemblages. However, dung beetle assemblages are not spatially independent at the analysed resolution, and the amount of dung in the surroundings seems to be more important for locally collected species than the dung effectively found in the site. Although differences in the availability and quantity of trophic resources among nearby sites could be affecting the population dynamics and dispersion of dung beetles within a locality, sites with larger populations, and greater species numbers would not be able to exercise enough influence as to bring about a complete local faunistic homogenization.
Do body size and diet breadth affect partitioning of species diversity? A test with forest Lepidoptera
Authors: Summerville Keith S. , Wilson Tiffany D. , Veech Joseph A. , Crist Thomas O. 
Published: December 2005

ABSTRACTTwo of the major themes resulting from recent macroecological research are the central roles that body size and niche breadth may play as determinants of species geographical distribution. Unanswered questions, however, linger regarding how similarities in body size or niche breadth affect the allocation of α‐ and β‐diversity across spatial scales. Using data on moth diversity in the eastern deciduous forest of North America, we tested the predictions that smaller‐bodied and diet‐restricted species would have lower levels of α‐diversity within forest stands and greater β‐diversity at higher sampling scales compared to larger or more generalist species. Moths were sampled using a nested sampling design consisting of three hierarchical levels: 20 forest stands, 5 sites and 3 ecoregions. Body size for 492 species was estimated as mean forewing length, and diet breadth was assessed from the published literature. Moth species were then classified according to body size (small or large) or diet breadth (generalist or restricted), and partitioning was conducted on each group. Diversity partitions for large‐ and small‐bodied species yielded similar patterns. When observed diversity components differed from those derived from our null model, a consistent pattern was observed: α‐diversity was greater than expected, β‐diversity among forest stands was less than expected, and β‐diversity among sites and ecoregions was higher than expected. In contrast, diet‐restricted moths contributed significantly less to stand‐level α‐diversity than generalist feeders. Furthermore, specialists contributed to a greater proportion of β‐diversity across scales compared to generalist moths. Because absolute measures of β‐diversity among stands were greater for generalists than for restricted feeders, we suggest that regional β‐diversity of forest moths may be influenced by several possible factors: intraspecific aggregation of diet‐restricted species, local fluctuations in population size of eruptive generalists and small geographical distributions of generalist moths than predicted by the geographical extent of putative host plants
Reconstructing ancestral ecologies: challenges and possible solutions
Authors: Hardy Christopher R. 
Published: December 2005

ABSTRACTThere are several ways to extract information about the evolutionary ecology of clades from their phylogenies. Of these, character state optimization and ‘ancestor reconstruction’ are perhaps the most widely used despite their being fraught with assumptions and potential pitfalls. Requirements forrobustinferences of ancestral traits in general (i.e. those applicable to all types of characters) include accurate and robust phylogenetic hypotheses, complete species‐level sampling and the appropriate choice of optimality criterion. Ecological characters, however, also require careful consideration of methods for accounting for intraspecific variability. Such methods include ‘Presence Coding’ and ‘Polymorphism Coding’ for discrete ecological characters, and ‘Range Coding’ and ‘MaxMin Coding’ for continuously variable characters. Ultimately, however, historical inferences such as these are, as with phylogenetic inference itself, associated with a degree of uncertainty. Statistically based uncertainty estimates are available within the context of model‐based inference (e.g. maximum likelihood and Bayesian); however, these measures are only as reliable as the chosen model is appropriate. Although generally thought to preclude the possibility of measuring relative uncertainty or support for alternative possible reconstructions, certain useful non‐statistical support measures (i.e. ‘Sharkey support’ and ‘Parsimony support’) are applicable to parsimony reconstructions.
What can phylogenetics tell us about speciation in the Cape flora?
Authors: Barraclough Timothy G. 
Published: December 2005

ABSTRACTThe spectacular diversity of the Cape flora has promoted wide speculation on the evolutionary processes behind its origins, but until recently these ideas could not be tested rigorously due to the almost complete absence of a fossil record for the region. Now, molecular phylogenetic approaches, combined with analyses of ecological and biogeographical information, offer the potential to test key hypotheses about speciation of so‐called Cape clades of flowering plants. We outline the main theories and how they might be tested by phylogenetic approaches. One conclusion is that population level studies of particular species complexes are now needed to complement the growing volume of phylogenetic information for Cape clades and to provide better understanding of mechanisms of population divergence in the Cape. Another is that comparisons between Cape and non‐Cape clades are needed to confirm whether speciation is indeed faster in the Cape region. An alternative possibility, that extinction rates are lower, should also be considered in these comparisons. By virtue of the ongoing, coordinated efforts by a global team of botanists, the Cape is now uniquely placed for exploring the origins and assembly of a regional assemblage or biome.
Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies
Authors: Hawkins J. A. 
Published: December 2005

ABSTRACTPhylogenetic methods hold great promise for the reconstruction of the transition from precursor to modern flora and the identification of underlying factors which drive the process. The phylogenetic methods presently used to address the question of the origin of the Cape flora of South Africa are considered here. The sampling requirements of each of these methods, which include dating of diversifications using calibrated molecular trees, sister pair comparisons, lineage through time plots and biogeographical optimizations, are reviewed. Sampling of genes, genomes and species are considered. Although increased higher‐level studies and increased sampling are required for robust interpretation, it is clear that much progress is already made. It is argued that despite the remarkable richness of the flora, the Cape flora is a valuable model system to demonstrate the utility of phylogenetic methods in determining the history of a modern flora.
Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times
Authors: Rutschmann Frank 
Published: December 2005

ABSTRACTThis article reviews the most common methods used today for estimating divergence times and rates of molecular evolution. The methods are grouped into three main classes: (1) methods that use a molecular clock and one global rate of substitution, (2) methods that correct for rate heterogeneity, and (3) methods that try to incorporate rate heterogeneity. Additionally, links to the most important literature on molecular dating are given, including articles comparing the performance of different methods, papers that investigate problems related to taxon, gene and partition sampling, and literature discussing highly debated issues like calibration strategies and uncertainties, dating precision and the calculation of error estimates.
Investigating the evolution of floras: problems and progress — An introduction
Authors: Linder H. P. 
Published: December 2005

ABSTRACTThe Cape flora of southern Africa is a remarkable hotspot for plant species diversity and endemism. At a meeting in Zurich in 2004 progress in understanding the evolution of this diversity was reviewed. In this symposium, four papers presenting several of the methods used in this investigation were reported. These papers deal with molecular dating methods, the reconstruction of ancestral habitats, with possible speciation scenarios for the Cape flora, and the importance of the correct sampling strategies.
Using niche‐based modelling to assess the impact of climate change on tree functional diversity in Europe
Authors: Thuiller Wilfried , Lavorel Sandra , Sykes Martin T. , Araújo Miguel B. 
Published: December 2005

ABSTRACTRapid anthropogenic climate change is already affecting species distributions and ecosystem functioning worldwide. We applied niche‐based models to analyse the impact of climate change on tree species and functional diversity in Europe. Present‐day climate was used to predict the distributions of 122 tree species from different functional types (FT). We then explored projections of future distributions under one climate scenario for 2080, considering two alternative dispersal assumptions: no dispersal and unlimited dispersal. The species‐rich broadleaved deciduous group appeared to play a key role in the future of different European regions. Temperate areas were projected to lose both species richness and functional diversity due to the loss of broadleaved deciduous trees. These were projected to migrate to boreal forests, thereby increasing their species richness and functional diversity. Atlantic areas provided an intermediate case, with a predicted reduction in the numbers of species and occasional predicted gains in functional diversity. This resulted from a loss in species within the broadleaved deciduous FT, but overall maintenance of the group. Our results illustrate the fact that both species‐specific predictions and functional patterns should be examined separately in order to assess the impacts of climate change on biodiversity and gain insights into future ecosystem functioning.
Spider diversity in a tropical habitat gradient in Chiapas, Mexico
Authors: Pinkus‐Rendón Miguel Angel , León‐Cortés Jorge Leonel , Ibarra‐Núñez Guillermo 
Published: December 2005

ABSTRACTThis paper presents an assessment of spider diversity in a complex landscape of southern Mexico. Eighteen different habitats were identified, measured and mapped across this fragmented landscape. Habitat types were characterized by measuring various features, including number of plant forms, tree cover and litter depth. Each month from February to April (dry season) and from June to August 2002 (wet season), spiders were sampled on each habitat by using pitfall traps and direct collection. Correlations between spider diversity and habitat characteristics were carried out to explore the relative contribution of each habitat variable as related to changes in spider composition and richness. In total, 115 spider species were recorded in 18 habitat types, and the mean number and density of species per habitat were 21 (± 3, standard error of mean) and 57 (± 9), respectively. The species recorded represent 41% of the fauna recorded in the Mexican state of Chiapas and 4% of the fauna recorded in Mexico. Relatively pristine habitats (e.g. deciduous forest) contained an important proportion of spider diversity in this fragmented landscape. Epigean spider diversity was significantly correlated with tree cover and with the diversity of plant forms during the rainy season. No correlation was detected between soil spider diversity and the habitat variables measured for any season. The results of this work suggest that in highly fragmented tropical landscapes, some habitat types (e.g. coffee plantations, hedgerows) might play an important role for the persistence of spider populations. The prevalence of relatively stable conditions in some of these habitats can allow spiders species (e.g. Nephila clavipes) to overcome adverse conditions such as a decrease in humidity and dramatic changes in temperature and wind exposure, allowing them to recolonize when favourable conditions return.