bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography and natural selection in the Tenerife gecko Tarentola delalandii: testing historical and adaptive hypotheses
Authors: Gübitz T. , Thorpe R. S. , Malhotra A. 
Published: March 2003

AbstractCombining phylogeographic and matrix correspondence approaches in the analysis of geographical variation provides a fruitful approach to inferring the causes of molecular and morphological evolution within species. Here we present a study on the gecko Tarentola delalandii on the island of Tenerife, Canary Islands, which provides an outstanding model of an exceptionally high degree of phylogeographic differentiation in magnitude and pattern on a small spatial scale. We reconstruct the population history of T. delalandii using phylogeographic information, matrix correspondence tests and estimates of divergence times in conjunction with geological data. It appears that populations differentiated on three precursor islands and secondary contact followed the junction of these islands. The cytochrome b sequence appears to be evolving at least at ≈ 1% per million years in this species. Matrix correspondence tests indicate that morphological character systems may reflect ecological selection regimes (colour pattern), history (body dimensions) or both (scalation). The results imply that natural selection can override a historical legacy, but also underline the potential relevance of molecular phylogenetic data for the interpretation of geographical variation in morphology.
Dietary separation of sympatric carnivores identified by molecular analysis of scats
Authors: Farrell Laura E. , Roman Joseph , Sunquist Melvin E. 
Published: March 2003

AbstractWe studied the diets of four sympatric carnivores in the flooding savannas of western Venezuela by analysing predator DNA and prey remains in faeces. DNA was isolated and a portion of the cytochrome bgene of the mitochondrial genome amplified and sequenced from 20 of 34 scats. Species were diagnosed by comparing the resulting sequences to reference sequences generated from the blood of puma (Puma concolor), jaguar (Panthera onca), ocelot (Leopardus pardalus) and crab‐eating fox (Cerdocyon thous). Scat size has previously been used to identify predators, but DNA data show that puma and jaguar scats overlap in size, as do those of puma, ocelot and fox. Prey‐content analysis suggests minimal prey partitioning between pumas and jaguars. In field testing this technique for large carnivores, two potential limitations emerged: locating intact faecal samples and recovering DNA sequences from samples obtained in the wet season. Nonetheless, this study illustrates the tremendous potential of DNA faecal studies. The presence of domestic dog (Canis familiaris) in one puma scat and of wild pig (Sus scrofa), set as bait, in one jaguar sample exemplifies the forensic possibilities of this noninvasive analysis. In addition to defining the dietary habits of similar size sympatric mammals, DNA identifications from faeces allow wildlife managers to detect the presence of endangered taxa and manage prey for their conservation.
Microsatellite analysis of population structure and genetic differentiation within and between populations of the root vole,Microtus oeconomusin the Netherlands
Authors: Van De Zande L. , Van Apeldoorn R. C. , Blijdenstein A. F. , De Jong D. , Van Delden W. , Bijlsma R. 
Published: March 2003

AbstractEight microsatellite markers for the root vole (Microtus oeconomus) were developed to assess the amount of genetic variation for nine Dutch root vole populations from four different regions, and to evaluate the degree of differentiation and isolation. All eight microsatellite loci were found to be highly variable with observed heterozygosity values ranging from 0.61 to 0.82. These values are similar to those observed for more distant populations from Norway, Finland and Germany. Therefore, the populations seem not particularly depauperate of genetic variation at the microsatellite level. Genetically, the Dutch populations were found to have diverged considerably. Pairwise comparisons of all populations studied revealedFSTvalues significantly greater than zero for most comparisons. However, the magnitude of these values considerably depends on the compared population pair. The level of differentiation between local populations within Dutch regions is generally significantly lower than the differentiation between Dutch regions. The level of differentiation between Dutch regions, however, is not significantly different from that between populations of larger geographical distance. This implies that the regional Dutch populations are both isolated from each other and from other European populations. The observation that even local populations show low but significant genetic differentiation may be indicative for progressive isolation of these populations.
Differences in population structure of the anther smut fungus Microbotryum violaceum on two closely related host species, Silene latifolia and S. dioica
Authors: Bucheli E. , Gautschi B. , Shykoff J. A. 
Published: March 2003

AbstractWe investigated the genetic population structure of the sexually transmitted plant pathogen, the fungus Microbotryum violaceum, on the two closely related host species Silene latifolia and S. dioica using microsatellite markers. We found strong deviations from Hardy–Weinberg expectations, with significant heterozygote deficiency in almost all populations. Fungal strains from the two host species were differentiated, and these host races differed in amount of variation within populations and differentiation among populations. Anther smut from S. latifolia harboured significantly less microsatellite diversity and were more genetically differentiated from each other than those from S. dioica. Small effective population sizes, rapid population turnover, and less gene flow among populations could lead to this higher population differentiation and lower within population genetic diversity for anther smut populations on S. latifolia than on S. dioica. These results are in concordance with host ecology because S. latifolia grows in more disturbed habitats than S. dioica and may provide a shorter‐lived host environment.
Genetic population structure and introgression inAnopheles dirusmosquitoes in South‐east Asia
Authors: Walton Catherine , Handley Jane M. , Collins Frank H. , Baimai Visut , Harbach Ralph E. , Deesin Vanida , Butlin Roger K. 
Published: March 2003

AbstractGenetic structure and species relationships were studied in three closely related mosquito species,Anopheles dirusA, C and D in Thailand using 11 microsatellite loci and compared with previous mitochondrial DNA (mtDNA) data on the same populations. All three species were well differentiated from each other at the microsatellite loci. Given the almost complete absence of mtDNA differentiation betweenAn. dirusA and D, this endorses the previous suggestion of mtDNA introgression between these species. The high degree of differentiation between the northern and southern population ofAn. dirusC (RST = 0.401), in agreement with mtDNA data, is suggestive of incipient species. The lack of genetic structure indicated by microsatellites in four populations ofAn. dirusA across northern Thailand also concurs with mtDNA data. However, inAn. dirusD a limited but significant level of structure was detected by microsatellites over ~400 km in northern Thailand, whereas the mtDNA detected no population differentiation over a much larger area (>1200 km). There is prior evidence for population expansion in the mtDNA. If this is due to a selective sweep originating inAn. dirusD, the microsatellite data may indicate greater barriers to gene flow withinAn. dirusD than in species A. Alternatively, there may have been historical introgression of mtDNA and subsequent demographic expansion which occurred first inAn. dirusD so enabling it to accumulate some population differentiation. In the latter case the lack of migration‐drift equilibrium precludes the inference of absolute or relative values of gene flow inAn. dirusA and D.
Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago
Authors: Goodman Simon J. , Tamate Hidetoshi B. , Wilson Rebecca , Nagata Junko , Tatsuzawa Shirow , Swanson Graeme M. , Pemberton Josephine M. , McCullough Dale R. 
Published: March 2003

AbstractWe assessed genetic differentiation and diversity in 14 populations of sika deer (Cervus nippon) from Japan and four populations of sika deer introduced to the UK, using nine microsatellite loci. We observed extreme levels of differentiation and significant differences in diversity between populations. Our results do not support morphological subspecies designations, but are consistent with previous mitochondrial DNA analyses which suggest the existence of two genetically distinct lineages of sika deer in Japan. The source of sika introduced to the UK was identified as Kyushu. The underlying structure of Japanese populations probably derives from drift in separate glacial refugia and male dispersal limited by distance. This structure has been perturbed by bottlenecks and habitat fragmentation, resulting from human activity from the mid‐nineteenth century. Most current genetic differentiation and differences in diversity among populations probably result from recent drift. Coalescent model analysis suggests sika on each of the main Japanese islands have experienced different recent population histories. Hokkaido, which has large areas of continuous habitat, has maintained high levels of gene flow. In Honshu the population is highly fragmented and is likely to have been evolving by drift alone. In Kyushu there has been a balance between gene flow and drift but all the populations have experienced high levels of drift. Habitat fragment size was not significantly associated with genetic diversity in populations but there was a significant correlation between habitat fragment size and effective population size.
Intraspecific phylogeny and geographical variation of six species of northeastern AsiaticSorexshrews based on the mitochondrial cytochromebsequences
Authors: Ohdachi Satoshi , Dokuchaev Nikolai E. , Hasegawa Masami , Masuda Ryuichi 
Published: March 2003

AbstractIntraspecific phylogeny and genetic variation were investigated based on nucleotide sequences of the mitochondrial cytochromebgene in six soricine shrew species,Sorex unguiculatus,S. caecutiens,S. shinto,S. gracillimus,S. minutissimusandS. hosonoi, collected primarily from northeastern Asia. Maximum likelihood trees and a phylogenetic network were generated to estimate intraspecific phylogenies.S. minutissimusshowed high congruence between phylogenetic position and geographical origin andS. gracillimusshowed low congruence. In contrast, there was no congruence between phylogeny and geography inS. unguiculatusand theS. caecutiensfrom Sakhalin‐Eurasia. Positive correlation between genetic and geographical distances was found inS. minutissimusandS. gracillimus, but not in the other species (or regional populations). The results of the phylogenetic and genetic analyses suggest thatS. minutissimusandS. gracillimushave occupied their present ranges for a longer time than the other species if we assume a stepping‐stone model of population structure. In addition, there was no contradiction between the present investigations and the hypotheses of multiple immigration byS. gracillimusand a single immigration byS. unguiculatusinto Hokkaido Island. It is proposed that these six northeastern Asian species experienced different historical processes of range expansion and dispersal despite the fact that some of them currently show similar patterns of distribution.
The effects of mode of development on phylogeography and population structure of North Atlantic Crepidula (Gastropoda: Calyptraeidae)
Authors: Collin Rachel 
Published: March 2003

AbstractThe mode of development of marine invertebrates is thought to influence levels of population structure and the location of species range endpoints via differences in dispersal ability. To examine these effects, populations of three sympatric clades of sedentary, marine gastropods in the genus Crepidula were sampled along the Atlantic and Gulf coasts of North America. A haplotype tree was constructed for each clade based on 640 bp sequences of mitochondrial cytochrome oxidase c subunit I. Examination of the tree topology, and amova analysis show that species with direct development (those hatching as benthic juveniles) have higher levels of population structure than do species with planktonic development. Both species in the direct‐developing C. convexa clade have high levels of geographical differentiation, with most populations representing a discrete clade of haplotypes. The planktotrophic species C. fornicata contains two major haplotype clades, both of which include samples from throughout the Atlantic coast. In this species there is no geographical differentiation among haplotypes but amova analysis detects a small but statistically significant level of geographical structure. The population structure within the C. plana species complex appears also to vary with mode of development: C. atrasolea, a direct‐developing species, has higher levels of population structure than does C. depressa, a sympatric planktotrophic species. The coincident occurrence of range endpoints and genetic breaks along the east coast of Florida in both direct‐developing species and species with planktonic development indicates that this biogeographic break is not due to development‐specific mechanisms such as hydrographic effects on larval recruitment.
Population history of Manihot esculenta (Euphorbiaceae) inferred from nuclear DNA sequences
Authors: Olsen Kenneth M. 
Published: March 2003

AbstractThe nature of gene flow in plants — including the propensity for interspecific introgression — makes them interesting candidates for phylogeographical analysis. Plant phylogeography studies have been limited, however, by the availability of suitable intraspecific variation. In this study, DNA sequence variation from a nuclear gene [Glyceraldehyde 3‐phosphate dehydrogenase; (G3pdh)] was used to examine the population history of Manihot esculenta ssp. flabellifolia and a potentially hybridizing species, M. pruinosa. These species occur in the rainforest–savanna ecotone adjoining the Amazon basin, a region believed to have undergone major habitat shifts since the Pleistocene. Geographical distributions of the G3pdh haplotypes indicate genetic isolation‐by‐distance across the range of M. esculenta ssp. flabellifolia. However, there is greater genetic similarity between northeastern and western populations than would be expected given the present species distribution. A nested clade analysis suggests that northeastern and western populations were connected by gene flow until relatively recently, when they became fragmented. This inferred fragmentation event is consistent with post‐Pleistocene habitat shifts proposed for the Amazon basin. At the interspecific level, haplotype sharing with M. pruinosa may reflect either recent interspecific introgression or incomplete lineage sorting between these closely related species.
Sex‐specific genetic structure in Schistosoma mansoni: evolutionary and epidemiological implications
Authors: Prugnolle F. , De Meeûs T. , Durand P. , Sire C. , Théron A. 
Published: March 2003

AbstractWe studied the population genetic structure of 360 and 1247 adult Schistosoma mansoni using seven microsatellite and seven random amplified polymorphic DNA (RAPD) markers, respectively. Parasites were collected from their natural definitive host Rattus rattus in Guadeloupe (West Indies). We found a sex‐specific genetic structure, a pattern never before reported in a parasitic organism. Male genotypes were more randomly distributed among rats than female genotypes. This interpretation was consistent with a lower differentiation between hosts for males relative to females, the higher genetic similarity between females in the same host and the observed local (i.e. within‐individual‐host) differences in allele frequencies between the two sexes. We discuss our results using ecological and immunological perspectives on host–parasite relationships. These results change our view on the epidemiology of schistosomiasis, a serious disease affecting humans in African and American intertropical zones.
Individual female clutch identification through yolk protein electrophoresis in the communally breeding guira cuckoo (Guira guira)
Authors: Cariello Mariana O. , Schwabb Hubert G. , Lee Raymond W. , Macedo Regina H. F. 
Published: March 2003

AbstractAvian communal breeding systems generate alternative behavioural strategies for females, resulting in differences in reproductive success. Identifying eggs of different females in such systems is problematic, however, due to egg destruction before incubation, difficulty of capturing adults, and/or inaccuracy of egg identification based on egg morphometry. Here, we describe a technique that uses electrophoresis of yolk proteins to determine egg ownership, which we applied to communally breeding guira cuckoos (Guira guira). Validation of the method included identical yolk protein banding patterns in all eggs of the same female, but different patterns in eggs of different females in budgerigars (Melopsittacus undulatus), and identical patterns in yolk follicles of the same females in guira cuckoos. We applied the protocol to 195 guira cuckoo eggs from 34 joint nests in 2 years. All multiple guira cuckoo eggs laid on the same day in single nests had distinct banding patterns of yolk proteins, practically eliminating the possibility of more than one female being represented by the same pattern. Some identical banding patterns were repeated in different days within a nesting bout, indicating that some females laid several eggs in shared nests. Identical patterns occasionally occurred in renestings of groups, indicating that some females lay eggs in consecutive nestings. Yolk protein electrophoresis is a useful tool to identify egg maternity in other circumstances, such as polygynous mating systems with joint nests and intraspecific parasitism. Additionally, it is an alternative method for species where electrophoresis of egg white proteins does not show sufficient polymorphism.
Internal transcribed spacer repeat‐specific primers and the analysis of hybridization in the Glycine tomentella (Leguminosae) polyploid complex
Authors: Rauscher Jason T. , Doyle Jeff J. , Brown A. H. D. 
Published: March 2003

AbstractPolyploid and diploid hybridization is a ubiquitous and evolutionarily important phenomenon in the plant world. Determining the parental species of a hybrid, however, is difficult. Molecular markers such as the nuclear ribosomal DNA gene complex, particularly its internal transcribed spacer (ITS) region, have proved powerful in determining hybrid parentage. In some cases, population and genomic phenomena, such as genetic drift and concerted evolution, result in the loss of all or many of the tandemly repeated copies derived from one parental species, making the recovery of hybrid history difficult or impossible. Methods such as direct sequencing and cloning are typically used to find ITS sequences contributed from parental species, but are limited in their ability to detect rare repeat types. Here we report that repeat‐specific polymerase chain reaction primers can recover rare parental ITS sequences in the Glycine tomentella polyploid complex. In three allopolyploid lineages of this complex, repeat‐specific primers reliably detected rare repeats that both direct sequencing and the screening of many cloned sequences failed to detect. Other strategies, such as the use of exclusion primers, may detect rare parental repeat types in hybrids when previous hypotheses regarding the second parental species are lacking.
Sperm length influences fertilization success during sperm competition in the snail Viviparus ater
Authors: Oppliger A. , Naciri‐Graven Y. , Ribi G. , Hosken D. J. 
Published: March 2003

AbstractSperm form and size is tremendously variable within and across species. However, a general explanation for this variation is lacking. It has been suggested that sperm size may influence sperm competition, and there is evidence for this in some taxa but not others. In addition to normal fertilizing sperm, a number of molluscs and insects produce nonfertile sperm that are also extremely morphologically variable, and distinct from fertilizing forms. There is evidence that nonfertile sperm play an indirect role in sperm competition by decreasing female remating propensity in Lepidopterans, but in most taxa the function of parasperm is unknown. We investigated the role of nonfertile (oligopyrene) sperm during sperm competition in the fresh water snail Viviparus ater. Previous studies found that the proportion of oligopyrene sperm increased with the risk of sperm competition, and hence it seems likely that these sperm influence fertilization success during competitive matings. In mating experiments in which females were sequentially housed with males, we examined a range of male characteristics which potentially influence fertilization success. We found that the size of oligopyrene sperm was the best predictor of fertilization success, with males having the longer sperm siring the highest proportion of offspring. Furthermore, we found a positive shell size and sperm concentration effect on paternity, and females with multiply sired families produced more offspring than females mating with only one male. This result suggests polyandry is beneficial for female snails.
Regulation of immunity to the two‐component lantibiotic, lacticin 3147, by the transcriptional repressor LtnR
Authors: McAuliffe Olivia , O'Keeffe Triona , Hill Colin , Ross R. Paul 
Published: March 2003

Lacticin 3147 is a membrane‐active, two‐component lantibiotic produced by Lactococcus lactis ssp. lactis DPC3147. In this study, the promoters of the lacticin 3147 gene cluster were mapped to the intergenic region between ltnR and ltnA1 (the genes encoding the regulatory protein LtnR and the first structural gene, LtnA1), and Northern analyses revealed that the biosynthetic and immunity genes are divergently transcribed in two operons, ltnA1A2M1TM2D and ltnRIFE respectively. Although the promoter controlling biosynthesis (Pbac) appears to be constitutive, characterization of a downstream β‐galactosidase (β‐gal) fusion beyond an intragenic stem–loop structure in ltnM1 confirmed that this putative transcriptional attenuator allows limited readthrough to the downstream biosynthetic genes, thus maintaining the correct stoichiometry between structural peptides and biosynthetic machinery. The promoter of the ltnRIFE operon (Pimm) was shown to be regulated by the transcriptional repressor LtnR. A mutant with a truncated ltnR gene exhibited a hyperimmune phenotype, whereas overexpression of ltnR resulted in cells with increased sensitivity to lacticin 3147. Gel mobility shift analysis indicated that LtnR binds to the Pimm promoter region, and fusion of this promoter to the β‐gal gene of pAK80 revealed that expression from Pimm is significantly reduced in the presence of LtnR. Thus, we have demonstrated that lacticin 3147 uses a regulatory mechanism not previously identified in lantibiotic systems.