bluuebunny/crossref_metadata_2025_split huggingface dataset:
Island colonization and founder effects: the invasion of the Guadeloupe islands by ship rats (Rattus rattus)
Authors: ABDELKRIM J. , PASCAL M. , SAMADI S. 
Published: August 2005

AbstractThe stepwise colonization of islands within an archipelago is typically punctuated by successive founder effects, with each newly founded population being a subsample of the gene pool of the source island. Thus, the genetic signature of successive bottlenecks should be detected when analysing the genetic structure between islands of an archipelago. To test this prediction, we investigated introduced ship rat populations, Rattus rattus (Linnaeus, 1758), in the Guadeloupe Archipelago. Three different methods, commonly named the heterozygosity excess, the mode‐shift indicator and the M ratio method, were used to detect bottlenecks from genetic data obtained with eight microsatellite markers on Guadeloupe and two neighbouring islands, Petite‐Terre and Fajou. Moreover, a recent eradication failure on Fajou allowed us to test the accuracy of the methods in an ‘experimental‐like’ situation. The results indicate that rats were introduced on Guadeloupe first, which then became the source population for independent secondary colonization of Fajou and Petite‐Terre. Moreover, the heterozygosity excess and the mode‐shift indicator only detected bottlenecks for the recent colonization of Petite‐Terre and the eradication failure on Fajou. However, bottlenecks were detected for all the populations using the M ratio method. This could be interpreted as the remaining signature of the early introduction of the ship rat in the archipelago.
Phylogeography and demography of Guianan harlequin toads (Atelopus): diversification within a refuge
Authors: NOONAN BRICE P. , GAUCHER PHILIPPE 
Published: August 2005

AbstractWe investigated the genetic structure of populations of Guianan harlequin toads (genus Atelopus) and their evolutionary affinities to extra‐Guianan congeners. Phylogenetic analysis of mitochondrial cytochrome b (cyt b) and NADH dehydrogenase subunit 2 (ND2) gene sequences produced well‐supported clades largely corresponding to the four recognized taxa in the Guianas (Atelopus spumarius hoogmoedi, Atelopus spumarius barbotini, Atelopus franciscus, and Atelopus flavescens). Our findings suggest that the Guianan A. spumarius represent distinct evolutionary lineages that merit distinction from Amazonian conspecifics, and that the status of A. flavescens and A. franciscus is somewhat less clear. Approximately 69% of the observed genetic variation is accounted for by differences between these four recognized taxa. Coalescent‐based estimates of gene flow between taxa suggest that these lineages are largely isolated from one another. Negligible rates of migration between populations and significant divergence within such close proximity suggests that although the region inhabited by these taxa is almost entirely undisturbed, significant habitat heterogeneity exists as to have produced a remarkable diversification of Atelopus within the eastern Guiana Shield. These results contradict the commonly held view of the Guiana Shield as a ‘refuge’ whose stability during late Tertiary and Quaternary climatic fluctuations served as a biotic reservoir. Instead, we provide evidence that climatic fluctuations during this time had a diversifying effect within the Guianan region.
Barcoding generalist predators by polymerase chain reaction: carabids and spiders
Authors: GREENSTONE M. H. , ROWLEY D. L. , HEIMBACH U. , LUNDGREN J. G. , PFANNENSTIEL R. S. , REHNER S. A. 
Published: August 2005

AbstractIdentification of arthropod predators is challenging when closely related species are found at a given locality. Identification of the immature stages is especially problematic, because distinguishing morphological features are difficult to use or have not been described. We used polymerase chain reaction (PCR) to distinguish closely related carabids and spiders, and to match eggs and larvae (or nymphs) with identified adult parents. Within the Carabidae, we amplified species‐specific mitochondrial cytochrome oxidase I (COI) fragments for three species each in the genera Poecilus and Harpalus, and two each in Chlaenius and Bembidion. Within the Araneae, we amplified species‐specific COI fragments for two Hibana species (Anyphaenidae), Pardosa milvina and Rabidosa rabida (Lycosidae), Frontinella communis and Grammonota texana (Linyphiidae), and Cheiracanthium inclusum (Miturgidae). We are able to correctly identify all immature stages tested — eggs, larvae (or nymphs) and pupae — by comparison of the amplified fragments with those of the adults. Using COI markers as species identifiers is a tenet of the Barcode of Life initiative, an international consortium to provide a molecular identifier for every animal species.
Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan
Authors: RUDNICK JAMIE A. , KATZNER TODD E. , BRAGIN EVGENY A. , RHODES O. EUGENE , DEWOODY J. ANDREW 
Published: August 2005

AbstractGenetic analyses on noninvasively collected samples have revolutionized how populations are monitored. Most noninvasive monitoring studies have used hair or scat for individual identification of elusive mammals, but here we utilize naturally shed feathers. The Eastern imperial eagle (EIE) is a species of conservation concern throughout Central Asia and, like most raptors, EIEs are inherently challenging to study because adults are difficult to capture and band using conventional techniques. Over 6 years, we noninvasively collected hundreds of adult feathers and directly sampled EIE chicks at a national nature reserve in Kazakhstan. All samples were genetically sexed and genotyped at a suite of microsatellite loci. Genetically profiled adult feathers identified and monitored the presence of individual eagles over time, enabling us to address a variety of issues related to the biology, demography, and conservation of EIEs. Specifically, we characterized (i) the genetic mating system, (ii) relatedness among mated pairs, (iii) chick sex ratios, and (iv) annual turnover in an adult breeding population. We show that EIEs are genetically monogamous and furthermore, there is no apparent relatedness‐based system of mate choice (e.g. inbreeding avoidance). Results indicate that annual adult EIE survivorship (84%) is lower than expected for a long‐lived raptor, but initial analyses suggest the current reproductive rate at our study site is sufficient to maintain a stable breeding population. The pristine habitat at our study site supports an EIE population that is probably the most demographically robust in the world; thus, our results caution that populations in marginal habitats may not be self‐sustaining.
Cryptic Neogene vicariance and Quaternary dispersal of the red‐spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas
Authors: JAEGER JEF R. , RIDDLE BRETT R. , BRADFORD DAVID F. 
Published: August 2005

AbstractWe define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid‐dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species’ range. Parsimony‐based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene–Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert–Colorado Plateau) and Western (Mojave–Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene–early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post‐Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene.
Genomic organization of molecular differentiation in Norway spruce (Picea abies)
Authors: ACHERÉ V. , FAVRE J. M. , BESNARD G. , JEANDROZ S. 
Published: August 2005

AbstractDiversity and differentiation among three populations representing the geographical domains commonly recognized within the natural distribution area of Picea abies were analysed by using a set of 292 AFLP (amplified fragment length polymorphism), SSR (single sequence repeat) and ESTP (expressed sequence tags polymorphism) markers. As usually observed in forest trees, results showed high within‐population diversity (HS reaching 0.79) and low among‐population differentiation (GST≈ 2%). The genomic organization of differentiation was then investigated on the basis of a subsample of 150 AFLP, SSR and ESTP mapped markers. The number of the loci differentiating the Baltico‐Nordic from the central European populations (25 loci) and, within the central European populations, the Alpine from the Hercyno‐Carpathian populations (12 loci), were different. These 37 differentiated loci, with individual GST values ranging from 0.008 to 0.20, were evenly distributed on all linkage groups and mostly followed the neutral expectations, suggesting genome‐wide effects on differentiation. Nine of them however behave as ‘outlier’ loci indicating possible locus‐specific selective effects. Contribution of ongoing evolutionary forces and historical effects to the geographical differentiation of the species are discussed.
Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?
Authors: SMITH CHRISTOPHER IRWIN , FARRELL BRIAN D. 
Published: August 2005

AbstractAlthough it has been suggested that Pleistocene climate changes drove population differentiation and speciation in many groups of organisms, population genetic evidence in support of this scenario has been ambiguous, and it has often been difficult to distinguish putative vicariance from simple isolation by distance. The sky island communities of the American Southwest present an ideal system in which to compare late Pleistocene range fragmentations documented by palaeoenvironmental studies with population genetic data from organisms within these communities. In order to elucidate the impact of Pleistocene climate fluctuations on these environments, biogeographic patterns in the flightless longhorn cactus beetle, Moneilema appressum were examined using mitochondrial DNA sequence data. Gene tree relationships between haplotypes were inferred using parsimony, maximum‐likelihood, and Bayesian analysis. Nested clade analysis, Mantel tests, and coalescent modelling were employed to examine alternative biogeographic scenarios, and to test the hypothesis that Pleistocene climate changes drove population differentiation in this species. The program mdiv was used to estimate migration and divergence times between populations, and to measure the statistical support for isolation over ongoing migration. These analyses showed significant geographic structure in genetic relationships, and implicated topography as a key determinant of isolation. However, although the coalescent analyses suggested that a history of past habitat fragmentation underlies the observed geographic patterns, the nested clade analysis indicated that the pattern was consistent with isolation by distance. Estimated divergence times indicated that range fragmentation in M. appressum is considerably older than the end of the most recent glacial, but coincided with earlier interglacial warming events and with documented range expansions in other, desert‐dwelling species of Moneilema.
Detection, identification and geographical distribution of European corn borer larval parasitoids using molecular markers
Authors: AGUSTÍ N. , BOURGUET D. , SPATARO T. , DELOS M. , EYCHENNE N. , FOLCHER L. , ARDITI R. 
Published: August 2005

AbstractBiological control requires specific tools for the accurate detection and identification of natural enemies, and to detect unusual variations in their density, which may follow changes in agricultural practices. Here we have developed specific molecular markers to detect Lydella thompsoni (Herting) and Pseudoperichaeta nigrolineata (Walker) (Diptera: Tachinidae) within the European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae). Primers amplifying fragments of the mitochondrial COI gene were designed following alignment of comparable sequences for a range of parasitoid and host species. Each of the primer pairs proved to be species specific to a tachinid species, amplifying DNA fragments of 191 and 91 bp in length for L. thompsoni and P. nigrolineata, respectively. This DNA‐based technique allowed molecular evaluation of parasitism in O. nubilalis natural populations. In order to study the geographical distribution of both species in France, O. nubilalis diapausing larvae in maize stalks were collected from 12 locations over the whole country. The molecular evaluation of parasitism was compared with the traditional method of maintaining O. nubilalis populations in controlled conditions before breaking off the diapause. The percentage parasitism found in both species of tachinids was higher — approximately three times — using the molecular method, suggesting an underestimation by the traditional rearing protocol. Tachinid parasitism on O. nubilalis was not significantly different between geographical areas (south, central and north France) for both species. This study shows that molecular methods are very promising for the correct detection and identification of tachinid parasitoids in natural field populations.
Clonal and spatial genetic structures of aspen (Populus tremuloides Michx.)
Authors: NAMROUD MARIE‐CLAIRE , PARK ANDREW , TREMBLAY FRANCINE , BERGERON YVES 
Published: August 2005

AbstractTo portray aspen clonal and spatial genetic structures, we mapped and genotyped trees in two 1‐ha plots, each containing three aspen cohorts originating from fire or subsequent secondary disturbances. We used four microsatellite loci to identify aspen clones and increment core analysis to determine tree age. Clonal dimensions were measured by the maximum distance between two ramets and the number of ramets per genet. Standard normal deviate (SND) was used to assess the spatial distribution of aspen genets and cohorts, and multivariate spatial genetic autocorrelations to assess the spatial distribution of aspen genetic variation. Most aspen genets consisted of only one ramet (> 75%). Median clonal dimensions were 19 and 29 m (maxima: 104 and 72 m in the two plots). No segregation was observed between clones. Aspen cohorts were spatially segregated but trees were spatially aggregated within old and medium‐aged cohorts. In contrast, trees were more randomly distributed within the youngest cohorts. This coincided with a spatial genetic autocorrelation at small scales (up to 30 m) in the older cohorts and a more random genetic distribution in the youngest ones. Our results suggest that aspen spatial genetic structuring reflects the spatial patterns produced by the regeneration of discrete cohorts at different stages of succession. Vegetative reproduction leads to aspen genetic spatial structuring at small scales (few metres) until midsuccession. However, as the stand gets older, the spatial distribution of aspen trees and genetic structure evolve from a structured pattern to a more random one under a gap disturbances regime.
Ten years of AFLP in ecology and evolution: why so few animals?
Authors: BENSCH STAFFAN , ÅKESSON MIKAEL 
Published: August 2005

AbstractResearchers in the field of molecular ecology and evolution require versatile and low‐cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start‐up time before data can be generated is often less than a week. Built‐in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA‐AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.
Genetic resistance to bovine tuberculosis in the Iberian wild boar
Authors: ACEVEDO‐WHITEHOUSE KARINA , VICENTE JOAQUÍN , GORTAZAR CHRISTIAN , HÖFLE URSULA , FERNÁNDEZ‐DE‐MERA ISABEL G. , AMOS WILLIAM 
Published: August 2005

AbstractBovine tuberculosis (bTB) is an important re‐emerging zoonotic disease, causing major economic losses and constraining international trade of animals and their products. Despite eradication programmes, some countries continue to encounter outbreaks, mainly due to wildlife acting as primary hosts or reservoirs. While the genetic component of tuberculosis in humans and cattle is well documented, the role of genetic factors as modulators of bTB resistance remains unclear for natural populations. To address this issue, we investigated the relative contribution of host genetic variability to susceptibility to bTB infection and disease progression in wild boars from southern Spain. We found that genetic heterozygosity is an important predictor of bTB, not only modulating resistance to infection but also influencing containment of disease progression in infected individuals. Our results provide further evidence that host genetic variability plays a central role in natural populations. Testing each marker separately reveals evidence of both general and single‐locus associative effects on bTB and several loci reveal high homology to regions of the genome with known immune function. Our results may prove to be crucial for understanding outbreaks of bTB in wildlife that could potentially affect domestic livestock and humans.
The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe
Authors: BRITO PATRÍCIA H. 
Published: August 2005

AbstractThe glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree‐nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well‐supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.
Thymoma‐associated exfoliative dermatitis in a rabbit
Authors: FLORIZOONE KOENRAAD 
Published: August 2005

Abstract A 5‐year‐old rabbit with generalized scaling is presented. Multiple skin scrapings and acetate tape impressions were negative for mites andMalassezia. Culture for dermatophytes was also negative. Skin biopsies showed similarities with sebaceous adenitis described in rabbits (absence of sebaceous glands, perifollicular lymphocytic infiltrate at the level of the absent sebaceous glands, lymphocytic mural folliculitis, interface dermatitis). The owners refused any treatment and 2 months later the rabbit was euthanized due to anorexia. At necropsy a mass was found in the anterior mediastinum. Histopathology confirmed a diagnosis of thymoma. A possible paraneoplastic skin disease was suspected, based on similarities with thymoma‐associated exfoliative dermatitis in cats.
Humoral measurement of type‐1 hypersensitivity reactions to a commercialMalasseziaallergen
Authors: FARVER K. , MORRIS D. O. , SHOFER F. , ESCH B. 
Published: August 2005

Abstract Malassezia pachydermatisis considered to be a contributing factor to canine atopic dermatitis (AD). The purpose of this study was to investigate the humoral response to a commercially producedM. pachydermatisextract. Fifteen atopic dogs withMalasseziaovergrowth on the skin (MD), 16 atopic dogs without MD, three atopic dogs with overgrowth ofMalasseziain the ears only (MO), and 12 normal dogs were intradermally tested withM. pachydermatisextract at 50, 100, 250, 500, 1000, 2000 and 4000 PNU mL−1. All dogs were evaluated cytologically by cutaneous tape strip and bilateral ear exudate sampling to determine presence of MD or MO. Each had serum evaluated for anti‐MalasseziaIgE using threeMalasseziaextracts with an ELISA assay. The irritant threshold concentration at which healthy nonatopic dogs ceased to react was 1000 PNU mL−1. There was a significant difference in intradermal test reactivity between the atopic groups. At this dilution, 93% (14/15) of the atopic MD group, 31% (5/16) of the atopic group without MD or MO, and 100% (3/3) of the atopic MO only group reacted. There were no significant differences in the serum IgE levels as measured by the Greer ELISA assay, between any groups using any of the three extracts. These results support that Greer'sM. pachydermatisextract is useful for intradermal testing of dogs with an allergic phenotype, and that atopics with MD are more likely to have a type‐1Malasseziahypersensitivity than those without. The ELISA assay may require further development in order to be useful for the diagnosis ofMalasseziahypersensitivity.