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At least 991 records · Page 55Linked to original sources
PubMed2003

Shell shape of the land snail Cornu aspersum in North Africa: unexpected evidence of a phylogeographical splitting.

Anatomical and molecular characters used to differentiate populations of the land snail Cornu aspersum (Helix aspersa) exhibit, in the western Mediterranean, definite and concordant patterns of correlation with geography. Scenarios involving Pliocene geological changes and postglacial expansion during the Pleistocene were proposed in previous studies to account for the establishment of this geographical structure. In the present work, we have performed a spatial analysis of variation in shell morphometrics, after the partitioning of the overall variation into size and shape components by means of a principal component-based approach (Cadima and Jolliffe, 1996). In order to know if the same historical events have also structured shell variation, the analysis includes all the populations from North Africa which were investigated for anatomical and molecular surveys. Contrary to shell size, which shows a significant spatial heterogeneity essentially related to environmental pressures, variation in shell shape components splits the populations according to a geographical pattern reflective of hypotheses suggested for molecular markers and genital anatomy. This implies that the selective forces often invoked to explain spatial changes in shell shape are not the deciding factors in the present case. Moreover, within each of the two geographical clusters defined, Mantel correlograms show that the similarity between populations declines according to an isolation by distance model. Because of the different allometric relationships between shell size and genitalia measurements in Western and Eastern entities of North Africa, mechanical constraints, possibly leading to a precopulatory isolation in the contact zone, are involved.

Africa, Northern↗
PubMed2006

The role of geographic setting on the diversification process among Tephritis conura (Tephritidae) host races.

We address the controversy over the processes causing divergence during speciation. Host races of the fruit fly Tephritis conura attack the thistles Cirsium oleraceum and Cirsium heterophyllum. By studying the genetic divergence of T. conura in areas where host plants are sympatric, parapatric and allopatric, we assessed the contribution of geography in driving host-race divergence. We also evaluated the relative importance of genetic drift and selection in the diversification process, by analysis of the geographic distribution of genetic variation. Host races were significantly diverged at five out of 13 polymorphic allozyme loci. Variance at two loci, Hex and Pep D, was almost exclusively attributable to host-plant affiliation in all geographic settings. However, Hex was significantly more differentiated between host races in sympatry/parapatry than in allopatry. This result might be explained by selection against hybridisation or against incorrect host choice in contact areas. Linkage disequilibrium tests suggest the latter: gene flow in contact areas may occur from males of the host-race C. heterophyllum to females of the host-race C. oleraceum, whereas incorrect oviposition events were never observed. The distinctive patterns of genetic differentiation at the two highly differentiated loci implicate the action of selection (acting directly or on linked loci) rather than genetic drift. Despite their restricted interactions in sympatry, we conclude that host races are stable and that the major diversification process took place before species arrived in today's geographical settings.

Animals↗
PubMed2002

Microarrays in ecology and evolution: a preview.

Microarray technology provides a new tool with which molecular ecologists and evolutionary biologists can survey genome-wide patterns of gene expression within and among species. New analytical approaches based on analysis of variance will allow quantification of the contributions of among individual variation, genotype, sex, microenvironment, population structure, and geography to variation in gene expression. Applications of this methodology are reviewed in relation to studies of mechanisms of adaptation and divergence; delineation of developmental and physiological pathways and networks; characterization of quantitative genetic parameters at the level of transcription ('quantitative genomics'); molecular dissection of parasitism and symbiosis; and studies of the diversification of gene content. Establishment of microarray resources is neither prohibitively expensive nor technologically demanding, and a commitment to development of gene expression profiling methods for nonmodel organisms could have a tremendous impact on molecular and genetic research at the interface of organismal and population biology.

Animals↗
PubMed2001

The zone of sympatry and hybridization of Mytilus edulis and M. galloprovincialis, as described by intron length polymorphism at locus mac-1.

Intron-size variation at the actin gene locus mac-1 was used to characterize mussel, Mytilus spp., populations in the approximately 2000-km wide zone of contact and hybridization ('hybrid zone') between M. edulis and M. galloprovincialis in western Europe. Twenty-five samples were collected in 1995-99 in locations within the hybrid zone and from reference populations of each species. We used correspondence analysis on the matrix of allelic frequencies to determine which alleles are characteristic of each species, and to characterize samples along the genetic gradient between M. edulis and M. galloprovincialis. In the hybrid zone, some samples exhibited mac-1 allele frequencies that were typical of M. edulis; other samples were distributed along the M. edulis/M. galloprovincialis gradient and displayed variable levels of intergradation that were not correlated with geography. Some of the latter samples exhibited significant heterozygote deficiencies. The simple admixture hypothesis (Wahlund effect) could not be rejected for two-fifths of the samples. The hybrid zone thus appeared as a mosaic of populations which are either pure M. edulis, or hybrid between M. galloprovincialis and M. edulis, or a mixture of the foregoing with M. galloprovincialis individuals. These results were consistent with published allozyme data, suggesting that they can be extended to the entire nuclear genome. M. edulis mac-1 alleles were present at moderate frequency in Atlantic M. galloprovincialis, and at significantly lower frequency in some Mediterranean samples. This pattern was homogeneous over a broad geographical range within each basin. It was not evident that introgression of M. edulis into M. galloprovincialis presently occurs south of the zone of contact. We propose that the distinctness of the Atlantic M. galloprovincialis population results from past introgression by M. edulis alleles.

Actins↗
PubMed2000

Species relationships and population structure of Littorina saxatilis Olivi and L. tenebrosa Montagu in Ireland using single-strand conformational polymorphisms (SSCPs) of cytochrome b fragments.

Littorina saxatilis is a ubiquitous snail of intertidal habitats in the North Atlantic. Shell type in littorinids is extremely polymorphic and defined by habitat. Taxonomy based upon shell type has been revised in the light of anatomic and genetic information, but uncertainties remain. In this study, the population structure of L. saxatilis and L. tenebrosa was studied at 11 sites in Ireland using single-strand conformational polymorphisms of a 375-bp portion of the cytochrome b gene, and the status of L. tenebrosa, the small, fragile-shelled, brackish water type, was considered. The genetic patterns among L. saxatilis and L. tenebrosa populations were examined over varying distances and L. tenebrosa was compared with adjacent L. saxatilis populations at four sites on the west coast of Ireland and one site on the east coast. Haplotype diversity was high with 32 haplotypes present among 995 individuals. Pairwise tests suggest gene flow over small scales among and between habitat types and may reflect the stochastic legacy of postglacial recolonization over larger scales. In AMOVA tests, geography explained nearly twice as much of the variance (30%) as habitat type (18%), indicating that gene flow is more restricted by distance than by habitat type, and supporting the status of L. tenebrosa as an ecotype of L. saxatilis rather than a separate species.

Analysis of Variance↗
PubMed2000

Nested cladistic analysis, phylogeography and speciation in the Timarcha goettingensis complex (Coleoptera, chrysomelidae).

The Timarcha goettingensis complex is a monophyletic assemblage of closely related leaf beetles (Chrysomelidae), distributed from the north half of the Iberian Peninsula to Central Europe. Oligophagy, mountainous habitat and apterism are factors which are assumed to promote speciation in these beetles. We have used cytochrome oxidase subunit II mitochondrial DNA genealogies obtained from 31 sampling localities and a nested geographical distance analysis to assess the population structure and demographic factors explaining the geographical distributions of the mtDNA haplotypes in the T. goettingensis complex. The results show that there is a significant association between genetic structuring and geography. Inferences about the historical population processes in the species complex are discussed, being in general in accordance with contiguous range expansions and past fragmentations. The use of the cohesion species concept approach suggests the existence of several systematic ranks among the different T. goettingensis populations, which is in part supported by ecological traits such as trophic selection and altitudinal distribution.

Animals↗
PubMed2001

Using phylogeographic analyses of gene trees to test species status and processes.

A gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra- and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.

Animals↗
PubMed2001

Speciation, hybrid zones and phylogeography - or seeing genes in space and time.

The origins and development of the study of speciation, hybrid zones and phylogeography are outlined using evolutionary iconography. This traces the ideas in this field from Lamarck and Darwin through to the present as represented in diagrams and figures. A 'tree of trees' summarizes this growth and current vitality. The new facility to use various DNA sequences from nuclear, mitochondrial and chloroplast genomes to determine genetic variation throughout a species range is examined particularly. There is great genomic subdivision across species distributions, which can be interpreted in the light of the recent demonstrations of severe palaeoclimatic oscillations. Refugia and postglacial colonization routes are proposed for several organisms across Europe. The role of geography in speciation through the Pleistocene is considered. These emerging principles and analyses are applied to data available on a variety of organisms in other regions of the world, such as the Arctic, North America and the Tropics, and including the progress of Homo sapiens through the last ice age. Some suggestions are made for future research directions.

Animals↗
PubMed2003

Phylogeography of the endangered darkling beetle species of Pimelia endemic to Gran Canaria (Canary Islands).

Phylogenetic and geographical nested clade analysis (NCA) methods were applied to mitochondrial DNA sequences of Pimelia darkling beetles (Coleoptera, Tenebrionidae) endemic to Gran Canaria, an island in the Canary archipelago. The three species P. granulicollis, P. estevezi and P. sparsa occur on the island, the latter with three recognized subspecies. Another species, P. fernandezlopezi (endemic to the island of La Gomera) is a close relative of P. granulicollis based on partial Cytochrome Oxidase I mtDNA sequences obtained in a previous study. Some of these beetles are endangered, so phylogeographical structure within species and populations can help to define conservation priorities. A total of about 700 bp of Cytochrome Oxidase II were examined in 18 populations and up to 75 individuals excluding outgroups. Among them, 22 haplotypes were exclusive to P. granulicollis and P. estevezi and 31 were from P. sparsa. Phylogenetic analysis points to the paraphyly of Gran Canarian Pimelia, as the La Gomera P. fernandezlopezi haplotypes are included in them, and reciprocal monophyly of two species groups: one constituted by P. granulicollis, P. estevezi and P. fernandezlopezi (subgenus Aphanaspis), and the other by P. sparsa'sensu lato'. The two species groups show a remarkably high mtDNA divergence. Within P. sparsa, different analyses all reveal a common result, i.e. conflict between current subspecific taxonomic designations and evolutionary units, while P. estevezi and P. fernandezlopezi are very close to P. granulicollis measured at the mtDNA level. Geographical NCA identifies several cases of nonrandom associations between haplotypes and geography that may be caused by allopatric fragmentation of populations with some cases of restriction of gene flow or range expansion. Analyses of molecular variance and geographical NCA allow definition of evolutionary units for conservation purposes in both species-groups and suggest scenarios in which vicariance caused by geological history of the island may have shaped the pattern of the mitochondrial genetic diversity of these beetles.

Animals↗
PubMed2003

Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish, Polynemus sheridani.

We assayed mtDNA haplotype [300 base pairs (bp) control region] geography and genealogy in the Indo-Pacific tasselfish, Polynemus sheridani from its contiguous estuarine distribution across northern Australia (n = 169). Eight estuaries were sampled from three oceanographic regions (Timor Sea, Gulf of Carpentaria and the Coral Sea) to assess the impact of Pleistocene sea level changes on the historical connectivity among P. sheridani populations. Specifically, we investigated the genetic consequences of disruption to Indian-Pacific Ocean connectivity brought about by the closure of the Torres Strait. Overall there was significant population subdivision among estuaries (FST = 0.161, PhiST = 0.187). Despite a linear distribution, P. sheridani did not show isolation by distance over the entire sampled range because of genetic similarity of estuaries greater than 3000 km apart. However, significant isolation by distance was detected between estuaries separated by less than 3000 km of coastline. Unlike many genetic studies of Indo-Pacific marine species, there was no evidence for an historical division between eastern and western populations. Instead, phylogeographical patterns were dominated by a starlike intraspecific phylogeny coupled with evidence for population expansion in both the Gulf of Carpentaria and the Coral Sea but not the Timor Sea. This was interpreted as evidence for recent west to east recolonization across of northern Australia following the last postglacial marine advance. We argue that although sufficient time has elapsed postcolonization for populations to approach gene flow-drift equilibrium over smaller spatial scales (< 3000 km), the signal of historical colonization persists to obscure the expected equilibrium pattern of isolation by distance over large spatial scales (> 3000 km).

Animals↗
PubMed2003

Genetic variation among interconnected populations of Catostomus occidentalis: implications for distinguishing impacts of contaminants from biogeographical structuring.

Exposure to contaminants can affect survivorship, recruitment, reproductive success, mutation rates and migration, and may play a significant role in the partitioning of genetic variation among exposed and nonexposed populations. However, the application of molecular population genetic data to evaluate such influences has been uncommon and often flawed. We tested whether patterns of genetic variation among native fish populations (Sacramento sucker, Catostomus occidentalis) in the Central Valley of California were consistent with long-term pesticide exposure history, or primarily with expectations based on biogeography. Field sampling was designed to rigorously test for both geographical and contamination influences. Fine-scale structure of these interconnected populations was detected with both amplified fragment length polymorphisms (AFLP) and microsatellite markers, and patterns of variation elucidated by the two marker systems were highly concordant. Analyses indicated that biogeographical hypotheses described the data set better than hypotheses relating to common historical pesticide exposure. Downstream populations had higher genetic diversity than upstream populations, regardless of exposure history, and genetic distances showed that populations from the same river system tended to cluster together. Relatedness among populations reflected primarily directions of gene flow, rather than convergence among contaminant-exposed populations. Watershed geography accounted for significant partitioning of genetic variation among populations, whereas contaminant exposure history did not. Genetic patterns indicating contaminant-induced selection, increased mutation rates or recent bottlenecks were weak or absent. We stress the importance of testing contaminant-induced genetic change hypotheses within a biogeographical context. Strategic application of molecular markers for analysis of fine-scale structure, and for evaluating contaminant impacts on gene pools, is discussed.

Analysis of Variance↗
PubMed2003

Genetic mosaic in a marine species flock.

We used molecular approaches to study the status of speciation in coral reef fishes known as hamlets (Serranidae: Hypoplectrus). Several hamlet morphospecies coexist on Caribbean reefs, and mate assortatively with respect to their strikingly distinct colour patterns. We provide evidence that, genetically, the hamlets display characteristics common in species flocks on land and in freshwaters. Substitutions within two mitochondrial DNA (mtDNA) protein-coding genes place hamlets within a monophyletic group relative to members of two related genera (Serranus and Diplectrum), and establish that the hamlet radiation must have been very recent. mtDNA distances separating hamlet morphospecies were slight (0.6 +/- 0.04%), yielding a coalescent estimate for the age of the hamlet flock of approximately 430 000 years. Morphospecies did not sort into distinct mtDNA haplotype phylogroups, and alleles at five hypervariable microsatellite loci were shared broadly across species boundaries. None the less, molecular variation was not distributed at random. Analyses of mtDNA haplotype frequencies and nested clades in haplotype networks revealed significant genetic differences between geographical regions and among colour morphospecies. We also observed significant microsatellite differentiation between geographical regions and in Puerto Rico, among colour morphospecies; the latter providing evidence for reproductive isolation between colour morphospecies at this locale. In our Panama collection, however, colour morphospecies were mostly genetically indistinguishable. This mosaic pattern of DNA differentiation implies a complex interaction between population history, mating behaviour and geography and suggests that porous boundaries separate species in this flock of brilliantly coloured coral reef fishes.

Animals↗
PubMed2003

Phylogeography of the circumpolar Paranoplocephala arctica species complex (Cestoda: Anoplocephalidae) parasitizing collared lemmings (Dicrostonyx spp.).

The Paranoplocephla arctica complex (Cyclophyllidea, Anoplocephalidae), host-specific cestodes of collared lemmings Dicrostonyx, include two morphospecies P. arctica and P. alternata, whose taxonomical status now must be considered ambiguous. The genetic population structure and phylogeography of the P. arctica complex was studied from 83 individuals sampled throughout the Holarctic distribution range using 600 bp of the mitochondrial cytochrome c oxidase subunit I gene (COI). The mitochondrial DNA (mtDNA) phylogeny divides the species complex into one main Nearctic and one main Palaearctic phylogroup, corresponding to the main phylogenetic division of the hosts. In the Palearctic phylogroup, the parasite clades correspond to the host clades although the parasites from Wrangel Island form an exception as the host on this island, D. groenlandicus, belongs to the Nearctic phylogroup. In the Nearctic, northern refugia beyond the ice limit of the Pleistocene glaciations are proposed for the hosts. All reconstructions of parasite phylogeny show a genetically differentiated population structure that in the Canadian Arctic lacks strict congruence between phylogeny and geography. The parasite phylogeny does not show complete congruence with host relationships, suggesting a history of colonization and secondary patterns of dispersal from Beringia into the Canadian Arctic, an event not proposed by the host phylogenies alone.

Animals↗
PubMed2005

The clustering of other chronic inflammatory diseases in inflammatory bowel disease: a population-based study.

BACKGROUND & AIMS: We aimed to discern the relative risk for several chronic inflammatory conditions in patients with ulcerative colitis (UC) and Crohn's disease. METHODS: We used the population-based University of Manitoba IBD Database that includes longitudinal files on all patients from all health system contacts identified by International Classification of Diseases, 9th revision, Clinical Modification codes for visit diagnosis. From the provincial database we extracted a control cohort matching the IBD patients 10:1 by age, sex, and geography. We considered a potential comorbid disease to be present if the patient had 5 or more health system contacts for that diagnosis. The comorbid disease period prevalence was analyzed separately for patients with UC and Crohn's disease and a prevalence ratio was calculated comparing the IBD populations with the matched cohort. RESULTS: There were 8072 cases of IBD from 1984 to 2003, including UC (n = 3879) and Crohn's disease (n = 4193). There was a mean of approximately 16 person-years of coverage for both patients and control patients. Both UC and Crohn's disease patients had a significantly greater likelihood of having arthritis, asthma, bronchitis, psoriasis, and pericarditis than population controls. An increased risk for chronic renal disease and multiple sclerosis was noted in UC but not Crohn's disease patients. The most common nonintestinal comorbidities identified were arthritis and asthma. CONCLUSIONS: The finding of asthma as the most common comorbidity increased in Crohn's disease patients compared with the general population is novel. These may be diseases with common causes or complications of one disease that lead to the presentation with another. Studies such as this should encourage further research into the common triggers in the organ systems that lead to autoimmune diseases.

Asthma↗
PubMed2003

Racial, ethnic, and geographic disparities in rates of knee arthroplasty among Medicare patients.

BACKGROUND: There are large variations in the use of knee arthroplasty among Medicare enrollees according to race or ethnic group and sex. Are racial and ethnic disparities more pronounced in some regions than in others, and if so, why? METHODS: We used all Medicare fee-for-service claims data for 1998 through 2000 to determine the incidence of knee arthroplasty according to Hospital Referral Region, sex, and race or ethnic group. A total of 430,726 knee arthroplasties were performed during the three-year study period. RESULTS: At the national level, the annual rate of knee arthroplasty was higher for non-Hispanic white women (5.97 procedures per 1000) than for Hispanic women (5.37 per 1000) and black women (4.84 per 1000). The rate for non-Hispanic white men (4.82 procedures per 1000) was higher than that for Hispanic men (3.46 per 1000) and more than double that for black men (1.84 per 1000). The rates were significantly lower for black men than for non-Hispanic white men in nearly every region of the country (P<0.05). For the Hispanic population and for black women, racial or ethnic disparities at the national level were due in part to geographic differences rather than to differences in the rates for different racial and ethnic groups within geographic areas. Residential segregation and low income levels contributed to racial and ethnic disparities in arthroplasty rates. CONCLUSIONS: In the Medicare population, the rate of surgical treatment for osteoarthritis of the knee varies dramatically according to sex, race or ethnic group, and region. These variations underscore the importance of geography and sex in determining racial or ethnic barriers to health care.

Arthroplasty, Replacement, Knee↗
PubMed1989

The generation of spatial population distributions from census centroid data.

"Census data are commonly used in geographical analysis and to inform planning purposes, though at the disaggregate level the basis of enumeration poses difficulties. In this paper an approach to surface generation is described that offers the prospect of revealing an underlying population distribution from centroid-based data which is independent of zonal geography. It is suggested that this can serve a wide variety of analytical, cartographic, and policy purposes, including the creation of spatial indicators of economic and social conditions and enhancing the value of census data. The approach is illustrated by reference to an analysis of part of the valleys of South Wales, in the United Kingdom."

Censuses↗
PubMed1995

Constructing an urban deprivation index: a way of meeting the need for flexibility.

The authors examine the use of census data to construct an urban deprivation index for the United Kingdom, with special attention given to the need for flexibility. "A single index is rejected in favour of a matrix of results which captures the complex geography of deprivation. The matrix of districts includes measures of the degree of deprivation, its spatial extent, its intensity, and the spatial distribution of deprivation at the enumeration district scale. The profiles of various districts are discussed to illustrate the use of the matrix."

Censuses↗
PubMed2004

Giant tortoises are not so slow: rapid diversification and biogeographic consensus in the Galápagos.

Isolated oceanic archipelagos have played a major role in the development of evolutionary theory by offering a unique setting for studying spatial and temporal patterns of biological diversification. However, the evolutionary events that cause associations between genetic variation and geography in archipelago radiations are largely unknown. This finding is especially true in the Galápagos Islands, where molecular studies have revealed conflicting biogeographic patterns. Here, we elucidate the history of diversification of giant Galápagos tortoises by using mtDNA sequences from 802 individuals representing all known extant populations. We test biogeographic predictions based on geological history and assess the roles of volcano emergence and island formation in driving evolutionary diversification. Patterns of colonization and lineage sorting appear highly consistent with the chronological formation of the archipelago. Populations from older islands are composed exclusively of endemic haplotypes that define divergent monophyletic clades. Younger populations, although currently differentiated, exhibit patterns of colonization, demographic variation and genetic interchange shaped by recent volcanism. Colonization probably occurs shortly after a volcano emerges through range expansion from older volcanoes. Volcanism can also create temporal shifts from historical to recurrent events, such as promoting gene flow by creating land bridges between isolated volcanoes. The association of spatial and temporal patterns of genetic variation with geophysical aspects of the environment can best be attributed to the limited dispersal and migration of tortoises following an oceanographic current. The endangered giant Galápagos tortoises represent a rapid allopatric radiation and further exemplify evolutionary processes in one of the world's greatest natural laboratories of evolution.

Animals↗