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Genetic Data (genetic + data)
Kinds of Genetic Data Terms modified by Genetic Data Selected AbstractsGenetic Data and the Listing of Species Under the U.S. Endangered Species ActCONSERVATION BIOLOGY, Issue 5 2007SYLVIA M. FALLON Acta de Especies en Peligro de E. U. A.; decisiones de enlistado; segmento poblacional distinto Abstract:,Genetic information is becoming an influential factor in determining whether species, subspecies, and distinct population segments qualify for protection under the U.S. Endangered Species Act. Nevertheless, there are currently no standards or guidelines that define how genetic information should be used by the federal agencies that administer the act. I examined listing decisions made over a 10-year period (February 1996,February 2006) that relied on genetic information. There was wide variation in the genetic data used to inform listing decisions in terms of which genomes (mitochondrial vs. nuclear) were sampled and the number of markers (or genetic techniques) and loci evaluated. In general, whether the federal agencies identified genetic distinctions between putative taxonomic units or populations depended on the type and amount of genetic data. Studies that relied on multiple genetic markers were more likely to detect distinctions, and those organisms were more likely to receive protection than studies that relied on a single genetic marker. Although the results may, in part, reflect the corresponding availability of genetic techniques over the given time frame, the variable use of genetic information for listing decisions has the potential to misguide conservation actions. Future management policy would benefit from guidelines for the critical evaluation of genetic information to list or delist organisms under the Endangered Species Act. Resumen:,La información genética se está convirtiendo en un factor influyente para determinar sí una especie, subespecie y segmentos poblacionales distintos califican para ser protegidos por el Acta de Especies en Peligro de E. U. A. Sin embargo, actualmente no hay estándares o lineamientos que definan como deben utilizar información genética las agencias federales que administran el acta. Examiné las decisiones de enlistado basadas en información genética tomadas en un período de 10 años (febrero 1996,febrero 2006). Hubo una amplia variación en los datos genéticos utilizados para informar las decisiones de enlistado en términos de cuáles genomas (mitocondrial vs. nuclear) fueron muestreados y el número de marcadores (o técnicas genéticas) y los loci evaluados. En general, las agencias federales identificaron diferencias genéticas entre unidades taxonómicas putativas o poblaciones dependiendo del tipo y cantidad de datos genéticos. Los estudios que se basaron en marcadores genéticos múltiples tuvieron mayor probabilidad de identificar distinciones, y esos organismos tuvieron mayor probabilidad de recibir protección, que los estudios basados en un solo marcador genético. Aunque los resultados pueden, en parte, reflejar la disponibilidad de técnicas genéticas para decisiones de enlistado en el período analizado, el uso variable de información genética para la toma de decisiones puede desinformar acciones de conservación. Las políticas de manejo futuras se beneficiarían de directrices para la evaluación crítica de información genética para enlistar o quitar de la lista a organismos bajo el Acta de Especies en Peligro. [source] Workplace Privacy and Discrimination Issues Related to Genetic Data: A Comparative Law Study of the European Union and the United StatesAMERICAN BUSINESS LAW JOURNAL, Issue 1 2006Nancy J. King [source] Genetic Diversity and Tests of the Hybrid Origin of the Endangered Yellow LarkspurCONSERVATION BIOLOGY, Issue 6 2001Jason A. Koontz The total number of individuals in these two populations is estimated to be <100. We used allozyme and random amplified polymorphic DNA ( RAPD) markers to (1) assess levels and patterns of genetic diversity in one wild population and two cultivated populations and (2) test the hypothesis that D. luteum is of hybrid origin between D. decorum and D. nudicaule. These data will be used to aid in developing a management plan to conserve the species. The wild population maintains high levels of genetic diversity. Genetic data indicate that both cultivated populations, especially the north Sonoma population, have several allozymes and RAPD markers not found in the wild population and could be used to establish new populations of D. luteum or to enhance the diversity and size of the wild population. The allozyme data did not reveal any fixed differences between D. decorum and D. nudicaule, although allele frequencies of the putative parental populations differed. At these loci, D. luteum resembled D. nudicaule more than D. decorum . Many unique RAPD markers distinguish each of the three species. The diagnostic markers from populations of D. nudicaule and D. decorum were not additive in the putative hybrid, and these data indicate that D. luteum is not of recent hybrid origin. Conservation of the yellow larkspur should include strategies that use the cultivated populations of D. luteum, but hybridizing D. decorum and D. nudicaule to "recreate"D. luteum is not recommended. Resumen:Delphidium luteum ( Ranunculaceae), un delfinio en peligro de extinción, está restringido a dos poblaciones silvestres cerca de Bodega Bay, California. Se estima que el total de individuos en estas dos poblaciones es de <100. Utilizamos marcadores de alozimas y RAPD para (1) evaluar los niveles y patrones de diversidad genética en una población silvestre y dos poblaciones cultivadas y (2) probar la hipótesis de que D. luteum es de origen híbrido entre D. decorum y D. nudicaule. Estos datos serán utilizados para ayudar a desarrollar un plan de manejo para conservar la especie. La población silvestre mantiene altos niveles de diversidad genética. Los datos genéticos indican que ambas poblaciones cultivadas, especialmente en la población de Sonoma norte, tienen varias alozimas y marcadores RAPD que no se encuentran en poblaciones silvestres y podrían utilizarse para establecer nuevas poblaciones de D. luteum o reforzar la diversidad y tamaño de la población silvestre. Los datos de alozimas no revelaron diferencias fijas entre D. decorum y D. nudicaule, aunque las frecuencias alélicas de las poblaciones parentales putativas fueron diferentes. En estos loci, D. luteum fue más semejante a D. nudicaule que a D. decorum. Muchos marcadores RADP únicos distinguen a cada una de las tres especies. Los marcadores diagnóstico de poblaciones de D. decorum y D. nudicaule no fueron aditivos en el híbrido putativo, y estos datos indican que D. luteum no es de origen híbrido reciente. La conservación del delfinio amarillo debería incluir estrategias que usen las poblaciones cultivadas de D. luteum; sin embargo, no se recomienda la hibridación de D. decorum y D. nudicaule para "recrear" a D. luteum. [source] Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activityFEMS MICROBIOLOGY LETTERS, Issue 1 2001Nora Ausmees Abstract A conserved domain, called GGDEF (referring to a conserved central sequence pattern), is detected in many procaryotic proteins, often in various combinations with putative sensory-regulatory components. Most sequenced bacterial genomes contain several different GGDEF proteins. The function of this domain has so far not been experimentally shown. Through genetic complementation using genes from three different bacteria encoding proteins with GGDEF domains as the only element in common, we present genetic data indicating (a) that the GGDEF domain is responsible for the diguanylate cyclase activity of these proteins, and (b) that the activity of cellulose synthase in Rhizobium leguminosarum bv. trifolii and Agrobacterium tumefaciens is regulated by cyclic di-GMP as in Acetobacter xylinum. [source] Finding starting points for Markov chain Monte Carlo analysis of genetic data from large and complex pedigreesGENETIC EPIDEMIOLOGY, Issue 1 2003Yuqun Luo Abstract Genetic data from founder populations are advantageous for studies of complex traits that are often plagued by the problem of genetic heterogeneity. However, the desire to analyze large and complex pedigrees that often arise from such populations, coupled with the need to handle many linked and highly polymorphic loci simultaneously, poses challenges to current standard approaches. A viable alternative to solving such problems is via Markov chain Monte Carlo (MCMC) procedures, where a Markov chain, defined on the state space of a latent variable (e.g., genotypic configuration or inheritance vector), is constructed. However, finding starting points for the Markov chains is a difficult problem when the pedigree is not single-locus peelable; methods proposed in the literature have not yielded completely satisfactory solutions. We propose a generalization of the heated Gibbs sampler with relaxed penetrances (HGRP) of Lin et al., ([1993] IMA J. Math. Appl. Med. Biol. 10:1,17) to search for starting points. HGRP guarantees that a starting point will be found if there is no error in the data, but the chain usually needs to be run for a long time if the pedigree is extremely large and complex. By introducing a forcing step, the current algorithm substantially reduces the state space, and hence effectively speeds up the process of finding a starting point. Our algorithm also has a built-in preprocessing procedure for Mendelian error detection. The algorithm has been applied to both simulated and real data on two large and complex Hutterite pedigrees under many settings, and good results are obtained. The algorithm has been implemented in a user-friendly package called START. Genet Epidemiol 25:14,24, 2003. © 2003 Wiley-Liss, Inc. [source] Adaptive radiation in African weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and morphological approachJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2007P. G. D. FEULNER Abstract We combined multiple molecular markers and geometric morphometrics to revise the current taxonomy and to build a phylogenetic hypothesis for the African weakly electric fish genus Campylomormyrus. Genetic data (2039 bp DNA sequence of mitochondrial cytochrome b and nuclear S7 genes) on 106 specimens support the existence of at least six species occurring in sympatry. We were able to further confirm these species by microsatellite analysis at 16 unlinked nuclear loci and landmark-based morphometrics. We assigned them to nominal taxa by comparisons to type specimens of all Campylomormyrus species recognized so far. Additionally, we showed that the shape of the elongated trunk-like snout is the major source of morphological differentiation among them. This finding suggests that the radiation of this speciose genus might have been driven by adaptation to different food sources. [source] Conflicting estimates of connectivity among deep-sea coral populationsMARINE ECOLOGY, Issue 2010Karen Miller Abstract Genetic data were used as an indirect means of assessing connectivity among deep-sea coral populations on seamounts and slopes in the Australian and New Zealand region. We sequenced three DNA regions (16S, ITS and Control Region) in nine deep-sea coral species from sites spanning thousands of kilometers. Based on haplotype distributions and AMOVA, we found evidence of genetic subdivision across ocean expanses for three species: the scleractinian Desmophyllum dianthus, and the antipatharians Antipathes robillardi and Stichopathes variabilis. Levels of genetic variation were low for the remaining species, including the reef-forming Solenosmila variablis and Madrepora oculata, and more sensitive molecular markers may be needed to resolve their spatial structure properly. For two species (the scleractinian Stephanocyathus spiniger and the antipatharian Stichopathes filiformis), we found no evidence of genetic subdivision among sites within regions, suggesting sufficient gene flow occurs to maintain genetic homogeneity at scales of tens to hundreds of kilometers. Recognising that some seamount regions and coral populations are, or are not, effectively isolated will be a key component of successful management planning based on marine protected area networks , both within and beyond national jurisdictions. [source] The ClpX chaperone modulates assembly of the tubulin-like protein FtsZMOLECULAR MICROBIOLOGY, Issue 1 2005Richard B. Weart Summary Assembly of the tubulin-like cytoskeletal protein FtsZ into a ring structure establishes the location of the nascent division site in prokaryotes. Factors that modulate FtsZ assembly are essential for ensuring the precise spatial and temporal regulation of cytokinesis. We have identified ClpX, the substrate recognition subunit of the ClpXP protease, as an inhibitor of FtsZ assembly in Bacillus subtilis. Genetic data indicate that ClpX but not ClpP inhibits FtsZ-ring formation in vivo. In vitro, ClpX inhibits FtsZ assembly in a ClpP-independent manner through a mechanism that does not require ATP hydrolysis. Together our data support a model in which ClpX helps maintain the cytoplasmic pool of unassembled FtsZ that is required for the dynamic nature of the cytokinetic ring. ClpX is conserved throughout bacteria and has been shown to interact directly with FtsZ in Escherichia coli. Thus, we speculate that ClpX functions as a general regulator of FtsZ assembly and cell division in a wide variety of bacteria. [source] Are behavioral differences among wild chimpanzee communities genetic or cultural?AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2010An assessment using tool-use data, phylogenetic methods Abstract Over the last 30 years it has become increasingly apparent that there are many behavioral differences among wild communities of Pan troglodytes. Some researchers argue these differences are a consequence of the behaviors being socially learned, and thus may be considered cultural. Others contend that the available evidence is too weak to discount the alternative possibility that the behaviors are genetically determined. Previous phylogenetic analyses of chimpanzee behavior have not supported the predictions of the genetic hypothesis. However, the results of these studies are potentially problematic because the behavioral sample employed did not include communities from central Africa. Here, we present the results of a study designed to address this shortcoming. We carried out cladistic analyses of presence/absence data pertaining to 19 tool-use behaviors in 10 different P. troglodytes communities plus an outgroup (P. paniscus). Genetic data indicate that chimpanzee communities in West Africa are well differentiated from those in eastern and central Africa, while the latter are not reciprocally monophyletic. Thus, we predicted that if the genetic hypothesis is correct, the tool-use data should mirror the genetic data in terms of structure. The three measures of phylogenetic structure we employed (the Retention Index, the bootstrap, and the Permutation Tail Probability Test) did not support the genetic hypothesis. They were all lower when all 10 communities were included than when the three western African communities are excluded. Hence, our study refutes the genetic hypothesis and provides further evidence that patterns of behavior in chimpanzees are the product of social learning and therefore meet the main condition for culture. Am J Phys Anthropol, 2010. © 2010 Wiley-Liss, Inc. [source] Phylogeography of the Angolan black and white colobus monkey, Colobus angolesnsis palliatus, in Kenya and TanzaniaAMERICAN JOURNAL OF PRIMATOLOGY, Issue 8 2010Monica M. McDonald Abstract Little is known about genetic variation in the 6,8 subspecies of Colobus angolensis, currently distinguished by pelage differences. We present a comparative genetic analysis of one of these subspecies, C. a. palliatus, in Kenya and Tanzania that assesses evolutionary relationships and patterns of mitochondrial genetic diversity in 103 individuals across its geographic range. Fecal samples from approximately 156 individuals were collected in four localities: (1) Diani Forest, Kenya; (2) Shimoni, Kenya; (3) Udzungwa Mountains National Park, Eastern Arc Mountains, Tanzania; and (4) Mount Rungwe, Southern Highlands, Tanzania. These samples represent at least six groups, with 5,15 samples from each. Comparative sequence analysis of a 1,795 base pair mtDNA fragment revealed 19 unique haplotypes in four populations. Phylogenetic analyses suggest that sampled Kenyan haplotypes are paraphyletic, with one Kenyan haplotype basal to all other sampled haplotypes. Analysis of molecular variance (AMOVA) suggests high levels of genetic variation among populations (,ST 0.72, P<0.001). Genetic data are concordant with a subspecies level differentiation between C. a. palliatus populations in Kenya and those in Central and southern Tanzania, as earlier suggested based on pelage differences. This study highlights the evolutionary distinctiveness of Kenyan populations of C. a. palliatus relative to Tanzanian populations. Although C. a. palliatus habitat in Tanzania is currently better protected than in Kenya, our results suggest Kenyan and Tanzanian populations should be considered distinct units, and the protection of C. a. palliatus habitat in Kenya, as well as habitat connectivity between Kenyan populations, should be prioritized for conservation and management. Am. J. Primatol. 72:715,724, 2010. © 2010 Wiley-Liss, Inc. [source] Genetic data in population viability analysis: case studies with ambystomatid salamandersANIMAL CONSERVATION, Issue 2 2010K. R. Greenwald Abstract Parameterization of population viability models is a complicated task for most types of animals, as knowledge of population demography, abundance and connectivity can be incomplete or unattainable. Here I illustrate several ways in which genetic data can be used to inform population viability analysis, via the parameterization of both initial abundance and dispersal matrices. As case studies, I use three ambysomatid salamander datasets to address the following question: how do population viability predictions change when dispersal estimates are based on genetic assignment test data versus a general dispersal,distance function? Model results showed that no local population was large enough to ensure long-term persistence in the absence of immigration, suggesting a metapopulation structure. Models parameterized with a dispersal,distance function resulted in much more optimistic predictions than those incorporating genetic data in the dispersal estimates. Under the dispersal,distance function scenario all local populations persisted; however, using genetic assignments to infer dispersal revealed local populations at risk of extinction. Viability estimates based on dispersal,distance functions should be interpreted with caution, especially in heterogeneous landscapes. In these situations I promote the idea of model parameterization using genetic assignment tests for a more accurate portrayal of real-world dispersal patterns. [source] Genetic data in population viability analysis: guidelines for future researchANIMAL CONSERVATION, Issue 2 2010K. R. Greenwald No abstract is available for this article. [source] Testing Hardy-Weinberg Equilibrium using Family Data from Complex SurveysANNALS OF HUMAN GENETICS, Issue 4 2009Dewei She Summary Genetic data collected during the second phase of the Third National Health and Nutrition Examination Survey (NHANES III) enable us to investigate the association of a wide variety of health factors with regard to genetic variation. The classic question when looking into the genetic variations in a population is whether the population is in the state of Hardy-Weinberg Equilibrium (HWE). Our objective was to develop test procedures using family data from complex surveys such as NHANES III. We developed six Pearson ,2 based tests for a diallelic locus of autosomal genes. The finite sample properties of the proposed test procedures were evaluated via Monte Carlo simulation studies and the Rao-Scott first order corrected test was recommended. Test procedures were applied to three loci from NHANES III genetic databases, i.e., ADRB2, TGFB1, and VDR. HWE was shown to hold at 0.05 level for all three loci when only families with genotypic information available for two parents and for one or more children were used in the analysis. [source] Do taxonomic divisions reflect genetic differentiation?BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009A comparison of morphological, Satyrinae, genetic data in Coenonympha tullia (Müller) Historically, morphological variation has been used to classify many species (and subspecies) of Lepidoptera. However, some of this variation may be unsuitable for inferring the recent evolutionary history of populations. Genetic data provide an alternative. We examine the morphological and genetic variation within and between British subspecies of Coenonympha tullia (Müller 1764) to test the hypothesis that neutral genetic variation corresponds to morphological variation. We find that most morphological and genetic variation occurs within populations and that those populations designated as subspecies based on morphological characters are not necessarily most closely related for mitochondrial DNA or nuclear DNA (amplified fragment length polymorphisms and allozymes). Thus, the notion that wing spot variation reflects population isolation and therefore genetic differentiation does not hold. The present study highlights the need for genetic data where taxonomy may be based on environmentally plastic or locally adapted characters because such characters will not reflect the true population genetic history. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 314,327. [source] Complex phylogeographical patterns, introgression and cryptic species in a lineage of Malagasy dung beetles (Coleoptera: Scarabaeidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009H. WIRTA Many taxa, including dung beetles, exhibit small-scale microendemism in Madagascar, which has contributed to the high level of species' diversity on the island. Species in the genus Nanos are numerically dominant in the dung beetle communities in rainforests in eastern Madagascar, but typically just one species occurs in any one locality. The two northern species, N. clypeatus and N. dubitatus, cannot be distinguished by either a mitochondrial or a nuclear genetic marker (cytochrome oxidase subunit I and internal transcription spacer 2). One population of the southern N. viettei is genetically highly divergent, although morphologically indistinguishable. Genetic data indicate that introgression occurred from N. dubitatus to N. viettei 1,2 Mya, and these species may continue to hybridize. Complex genetic patterns have mostly evolved within the last 2 Myr. During this time, the glacial cycles in the northern hemisphere were reflected in the oscillating climatic conditions in Africa, which repeatedly fragmented and re-united the rainforests in eastern Madagascar, possibly leading to the observed complex phylogeographical patterns in Nanos. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 942,955. [source] Genetic Data and the Listing of Species Under the U.S. Endangered Species ActCONSERVATION BIOLOGY, Issue 5 2007SYLVIA M. FALLON Acta de Especies en Peligro de E. U. A.; decisiones de enlistado; segmento poblacional distinto Abstract:,Genetic information is becoming an influential factor in determining whether species, subspecies, and distinct population segments qualify for protection under the U.S. Endangered Species Act. Nevertheless, there are currently no standards or guidelines that define how genetic information should be used by the federal agencies that administer the act. I examined listing decisions made over a 10-year period (February 1996,February 2006) that relied on genetic information. There was wide variation in the genetic data used to inform listing decisions in terms of which genomes (mitochondrial vs. nuclear) were sampled and the number of markers (or genetic techniques) and loci evaluated. In general, whether the federal agencies identified genetic distinctions between putative taxonomic units or populations depended on the type and amount of genetic data. Studies that relied on multiple genetic markers were more likely to detect distinctions, and those organisms were more likely to receive protection than studies that relied on a single genetic marker. Although the results may, in part, reflect the corresponding availability of genetic techniques over the given time frame, the variable use of genetic information for listing decisions has the potential to misguide conservation actions. Future management policy would benefit from guidelines for the critical evaluation of genetic information to list or delist organisms under the Endangered Species Act. Resumen:,La información genética se está convirtiendo en un factor influyente para determinar sí una especie, subespecie y segmentos poblacionales distintos califican para ser protegidos por el Acta de Especies en Peligro de E. U. A. Sin embargo, actualmente no hay estándares o lineamientos que definan como deben utilizar información genética las agencias federales que administran el acta. Examiné las decisiones de enlistado basadas en información genética tomadas en un período de 10 años (febrero 1996,febrero 2006). Hubo una amplia variación en los datos genéticos utilizados para informar las decisiones de enlistado en términos de cuáles genomas (mitocondrial vs. nuclear) fueron muestreados y el número de marcadores (o técnicas genéticas) y los loci evaluados. En general, las agencias federales identificaron diferencias genéticas entre unidades taxonómicas putativas o poblaciones dependiendo del tipo y cantidad de datos genéticos. Los estudios que se basaron en marcadores genéticos múltiples tuvieron mayor probabilidad de identificar distinciones, y esos organismos tuvieron mayor probabilidad de recibir protección, que los estudios basados en un solo marcador genético. Aunque los resultados pueden, en parte, reflejar la disponibilidad de técnicas genéticas para decisiones de enlistado en el período analizado, el uso variable de información genética para la toma de decisiones puede desinformar acciones de conservación. Las políticas de manejo futuras se beneficiarían de directrices para la evaluación crítica de información genética para enlistar o quitar de la lista a organismos bajo el Acta de Especies en Peligro. [source] Effectiveness of Conservation Targets in Capturing Genetic DiversityCONSERVATION BIOLOGY, Issue 1 2003Maile C. Neel We used empirical data from four rare plant taxa to assess these consequences in terms of how well allele numbers ( all alleles and alleles occurring at a frequency openface>0.05 in any population ) and expected heterozygosity are represented when different numbers of populations are conserved. We determined sampling distributions for these three measures of genetic diversity using Monte Carlo methods. We assessed the proportion of alleles included in the number of populations considered adequate for conservation, needed to capture all alleles, and needed to meet an accepted standard of genetic-diversity conservation of having a 90,95% probability of including all common alleles. We also assessed the number of populations necessary to obtain values of heterozygosity within ±10% of the value obtained from all populations. Numbers of alleles were strongly affected by the number of populations sampled. Heterozygosity was only slightly less sensitive to numbers of populations than were alleles. On average, currently advocated conservation intensities represented 67,83% of all alleles and 85,93% of common alleles. The smallest number of populations to include all alleles ranged from 6 to 17 ( 42,57% ), but <0.2% of 1000 samples of these numbers of populations included them all. It was necessary to conserve 16,29 ( 53,93% ) of the sampled populations to meet the standard for common alleles. Between 20% and 64% of populations were needed to reliably represent species-level heterozygosity. Thus, higher percentages of populations are needed than are currently considered adequate to conserve genetic diversity if populations are selected without genetic data. Resumen: Cualquier acción de conservación que preserve algunas poblaciones y no otras tendrá consecuencias genéticas. Utilizamos datos empíricos de cuatro taxones de plantas raras para evaluar estas consecuencias en términos de lo bien representados que están los números de alelos ( todos los alelos ocurriendo a una frecuencia>0.05 en cualquier población ) y la heterocigosidad esperada cuando se conservan diferentes números de poblaciones. Las distribuciones de muestreo de estas tres medidas de la diversidad genética fueron determinadas utilizando métodos Monte Carlo. Evaluamos la proporción de alelos incluida en números de poblaciones: consideradas adecuadas para la conservación; requeridas para capturar todos los alelos; y las requeridas para alcanzar un estándar de conservación de diversidad genética aceptable del 90,95% de probabilidad de incluir todos los alelos comunes. También evaluamos el número de poblaciones necesarias para obtener valores de heterocigosidad que caigan dentro de ±10% del valor obtenido de todas las poblaciones. Los números de alelos fueron afectados significativamente por el número de poblaciones muestreadas. La heterocigosidad solo fue ligeramente menos sensible a los números de poblaciones de lo que fueron los alelos. Las intensidades de conservación propugnadas actualmente representaron en promedio el 67,83% de todos los alelos y el 85,93% de los alelos comunes. El menor número de poblaciones para incluir a todos los alelos varió de 6 a 17 ( 42,57% ), pero <0.2% de 1000 muestras de esos números de poblaciones los incluyó a todos. Fue necesario conservar de 16 a 29 ( 53,93% ) de las poblaciones muestreadas para alcanzar el estándar para los alelos comunes. Se requirió entre 20% y 64% de las poblaciones para representar la heterocigosidad a nivel de especie confiablemente. Por lo tanto, se requieren mayores porcentajes de poblaciones que los actualmente considerados adecuados para conservar la diversidad genética si las poblaciones son seleccionadas sin datos genéticos. [source] Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic dataECOGRAPHY, Issue 5 2009Niko Balkenhol The goal of landscape genetics is to detect and explain landscape effects on genetic diversity and structure. Despite the increasing popularity of landscape genetic approaches, the statistical methods for linking genetic and landscape data remain largely untested. This lack of method evaluation makes it difficult to compare studies utilizing different statistics, and compromises the future development and application of the field. To investigate the suitability and comparability of various statistical approaches used in landscape genetics, we simulated data sets corresponding to five landscape-genetic scenarios. We then analyzed these data with eleven methods, and compared the methods based on their statistical power, type-1 error rates, and their overall ability to lead researchers to accurate conclusions about landscape-genetic relationships. Results suggest that some of the most commonly applied techniques (e.g. Mantel and partial Mantel tests) have high type-1 error rates, and that multivariate, non-linear methods are better suited for landscape genetic data analysis. Furthermore, different methods generally show only moderate levels of agreement. Thus, analyzing a data set with only one method could yield method-dependent results, potentially leading to erroneous conclusions. Based on these findings, we give recommendations for choosing optimal combinations of statistical methods, and identify future research needs for landscape genetic data analyses. [source] Interspecific and intraspecific differences in two Liriomyza leafminer species in CaliforniaENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, Issue 2 2002Stuart R. Reitz Abstract In recent years, the pest status of Liriomyza trifolii (Burgess) and L. huidobrensis (Blanchard) (Diptera: Agromyzidae) has changed in California, as well as other areas of the world. In California, L. huidobrensis has become the predominant Liriomyza species in valleys along the central coast, while L. trifolii remains the predominant species in southern California. To investigate possible reasons for this change in status, differences in host plant use and reproductive success of intraspecific populations were examined for Liriomyza trifolii and L. huidobrensis from both central and southern California. The southern L. trifolii fed, oviposited and reproduced successfully on all five hosts tested, but the central population fed significantly less on all hosts and was restricted to reproducing on pepper only. With the exception of pepper, southern L. trifolii had significantly greater larval survival on all hosts than central L. trifolii. In contrast, the central L. huidobrensis population had greater reproductive success than the southern population of that species on all hosts plants tested. However, pepper was not a suitable host for either L. huidobrensis population. Both species showed positive assortative mating, with homotypic mating occurring more frequently than heterotypic mating; however, the difference between L. trifolii populations was much more pronounced than between L. huidobrensis populations. These data indicate that central and southern California populations of each species are distinct biotypes. Furthermore when coupled with previous genetic data, our results suggest the possible existence of cryptic species within L. trifolii. [source] ESCI award lecture: from a little mouse to rationale medicine for bone lossEUROPEAN JOURNAL OF CLINICAL INVESTIGATION, Issue 10 2009A. Leibbrandt Abstract Completion of the human genome is one of the many significant milestones in the new era of systems biology. The current phase of genomic studies is focused upon parsing this new found genetic data with respect to scientific interest, and economic and health impact applications. As the sequences are now available and whole genome single nucleotide polymorphism maps for multiple human diseases will be available with the advent of modern genomics, the big challenge is to determine the function of these genes in the context of the entire organism. The emphasis is therefore on functional genomic analysis that represents the new front-line and limiting factor for realizing potential benefits of genome-based science. Defined gene targeting has been proven to be particularly useful as loss of expression mutants can reveal essential functions of molecules and the pathogenesis of disease. Using gene-targeted mice, my group has over the years identified genes that control heart and lung functions [1,5]; apoptosis [6,9]; lymphocyte activation [10,14]; cancer [15,17]; pain [18]; diabetes [19]; fertility [20] or wound healing [21]. In this study, I would like to review our work on RANKL in more detail. [source] Increased numbers of mononuclear cells from blood and CSF expressing interferon-gamma mRNA in multiple sclerosis are from both the CD4+ and the CD8+ subsetsEUROPEAN JOURNAL OF NEUROLOGY, Issue 1 2000E. Wallström Activated, cytokine-producing lymphocytes may regulate central nervous system (CNS) inflammation in multiple sclerosis (MS). We utilize a novel combination of in situ hybridization (ISH) and immunocytochemical staining of peripheral blood lymphocytes (PBLs) to identify spontaneously interferon-gamma (IFN,) mRNA expressing cells as CD4+ or CD8+. A major proportion of the IFN, mRNA expressing lymphocytes belonged to the CD4+ lineage, which concords with the cellular composition of MS brain lesions, findings in experimental models and the HLA class II haplotype association in MS. There were also significantly more CD8+ IFN, mRNA expressing lymphocytes in the MS patients compared with healthy controls, further suggesting the contribution of activated cells from this lineage in the inflammatory response in MS. Both CD4+ and CD8+ IFN, mRNA expressing cells were enriched in the cerebrospinal fluid (CSF) as compared with the peripheral blood of the MS patients. Combined with emerging genetic data on HLA class I influences, our data argues for a joint role of activated CD8+ and CD4+ cells in the pathogenesis of MS. [source] LIKELIHOOD-BASED INFERENCE IN ISOLATION-BY-DISTANCE MODELS USING THE SPATIAL DISTRIBUTION OF LOW-FREQUENCY ALLELESEVOLUTION, Issue 11 2009John Novembre Estimating dispersal distances from population genetic data provides an important alternative to logistically taxing methods for directly observing dispersal. Although methods for estimating dispersal rates between a modest number of discrete demes are well developed, methods of inference applicable to "isolation-by-distance" models are much less established. Here, we present a method for estimating ,,2, the product of population density (,) and the variance of the dispersal displacement distribution (,2). The method is based on the assumption that low-frequency alleles are identical by descent. Hence, the extent of geographic clustering of such alleles, relative to their frequency in the population, provides information about ,,2. We show that a novel likelihood-based method can infer this composite parameter with a modest bias in a lattice model of isolation-by-distance. For calculating the likelihood, we use an importance sampling approach to average over the unobserved intraallelic genealogies, where the intraallelic genealogies are modeled as a pure birth process. The approach also leads to a likelihood-ratio test of isotropy of dispersal, that is, whether dispersal distances on two axes are different. We test the performance of our methods using simulations of new mutations in a lattice model and illustrate its use with a dataset from Arabidopsis thaliana. [source] CONTEMPORARY ISOLATION-BY-DISTANCE, BUT NOT ISOLATION-BY-TIME, AMONG DEMES OF EUROPEAN GRAYLING (THYMALLUS THYMALLUS, LINNAEUS) WITH RECENT COMMON ANCESTORSEVOLUTION, Issue 2 2009Nicola J. Barson The development of isolation by distance (IBD) and isolation by time (IBT) was contrasted among demes of European grayling (Thymallus thymallus) that have diverged within the last 25 generations following colonization of a lake (Lesjaskogsvatnet). We find low but significant levels of genetic differentiation among spawning tributaries and a pattern of IBD among them. We do not, however, find evidence for IBT despite an up to four-week difference in spawning date between "warm/early" and "cold/late" spawning demes and differences in the incubation temperatures experienced by offspring. It appears that IBD has developed more rapidly than IBT in this system and that adaptive divergence has been initiated in the absence of IBT. Although analysis of selected loci could reveal reduced recombination in parts of the genome associated with temporal divergence, our analysis of neutral genetic data suggests that IBD is a more important isolating mechanism in the early stages of adaptive divergence in European grayling. [source] NATURAL SELECTION ALONG AN ENVIRONMENTAL GRADIENT: A CLASSIC CLINE IN MOUSE PIGMENTATIONEVOLUTION, Issue 7 2008Lynne M. Mullen We revisited a classic study of morphological variation in the oldfield mouse (Peromyscus polionotus) to estimate the strength of selection acting on pigmentation patterns and to identify the underlying genes. We measured 215 specimens collected by Francis Sumner in the 1920s from eight populations across a 155-km, environmentally variable transect from the white sands of Florida's Gulf coast to the dark, loamy soil of southeastern Alabama. Like Sumner, we found significant variation among populations: mice inhabiting coastal sand dunes had larger feet, longer tails, and lighter pigmentation than inland populations. Most striking, all seven pigmentation traits examined showed a sharp decrease in reflectance about 55 km from the coast, with most of the phenotypic change occurring over less than 10 km. The largest change in soil reflectance occurred just south of this break in pigmentation. Geographic analysis of microsatellite markers shows little interpopulation differentiation, so the abrupt change in pigmentation is not associated with recent secondary contact or reduced gene flow between adjacent populations. Using these genetic data, we estimated that the strength of selection needed to maintain the observed distribution of pigment traits ranged from 0.0004 to 21%, depending on the trait and model used. We also examined changes in allele frequency of SNPs in two pigmentation genes, Mc1r and Agouti, and show that mutations in the cis -regulatory region of Agouti may contribute to this cline in pigmentation. The concordance between environmental variation and pigmentation in the face of high levels of interpopulation gene flow strongly implies that natural selection is maintaining a steep cline in pigmentation and the genes underlying it. [source] GENETICS AND RECENT HUMAN EVOLUTIONEVOLUTION, Issue 7 2007Alan R. Templeton Starting with "mitochondrial Eve" in 1987, genetics has played an increasingly important role in studies of the last two million years of human evolution. It initially appeared that genetic data resolved the basic models of recent human evolution in favor of the "out-of-Africa replacement" hypothesis in which anatomically modern humans evolved in Africa about 150,000 years ago, started to spread throughout the world about 100,000 years ago, and subsequently drove to complete genetic extinction (replacement) all other human populations in Eurasia. Unfortunately, many of the genetic studies on recent human evolution have suffered from scientific flaws, including misrepresenting the models of recent human evolution, focusing upon hypothesis compatibility rather than hypothesis testing, committing the ecological fallacy, and failing to consider a broader array of alternative hypotheses. Once these flaws are corrected, there is actually little genetic support for the out-of-Africa replacement hypothesis. Indeed, when genetic data are used in a hypothesis-testing framework, the out-of-Africa replacement hypothesis is strongly rejected. The model of recent human evolution that emerges from a statistical hypothesis-testing framework does not correspond to any of the traditional models of human evolution, but it is compatible with fossil and archaeological data. These studies also reveal that any one gene or DNA region captures only a small part of human evolutionary history, so multilocus studies are essential. As more and more loci became available, genetics will undoubtedly offer additional insights and resolutions of human evolution. [source] Evolution of the nose and nasal skeleton in primatesEVOLUTIONARY ANTHROPOLOGY, Issue 4 2007Timothy D. Smith Abstract One traditional diagnostic feature of the Order Primates is a decreased emphasis on olfaction.1, 2 Some authors attribute this feature only to tarsiers and anthropoids, either through convergence or as a common feature of haplorhines.2,4 Other authors de-emphasize olfaction relative to vision,5,7 which does not necessarily denote olfactory reduction per se. There are lengthy roots to this discussion. The importance of the sense of smell to at least some primates, humans in particular, has long been viewed as secondary to the importance of visual, auditory, and tactile senses. Smell, or olfaction, is viewed as the primitive special sense, the stimuli perceived in an unconscious manner, submerged relative to higher neural functions,1 and a sense that has been increasingly reduced during the course of primate evolution.1,8 Anatomical structures related to olfaction differ profoundly in proportions and complexity between higher taxonomic groups of primates (Haplorhini, Strepsirrhini). These anatomical differences are beyond dispute (Box 1). However, the relationship between the anatomical differences and primate sensory abilities, and hence the validity of using them to group primates into "microsmatic" or "macrosmatic" categories,9, 10 is less clear when we examine the physiological and genetic data on primate olfaction. [source] Genetic population structure of marine fish: mismatch between biological and fisheries management unitsFISH AND FISHERIES, Issue 4 2009Henning Reiss Abstract An essential prerequisite of a sustainable fisheries management is the matching of biologically relevant processes and management action. In fisheries management and assessment, fish stocks are the fundamental biological unit, but the reasoning for the operational management unit is often indistinct and mismatches between the biology and the management action frequently occur. Despite the plethora of population genetic data on marine fishes, to date little or no use is made of the information, despite the fact that the detection of genetic differentiation may indicate reproductively distinct populations. Here, we discuss key aspects of genetic population differentiation in the context of their importance for fisheries management. Furthermore, we evaluate the population structure of all 32 managed marine fish species in the north-east Atlantic and relate this structure to current management units and practice. Although a large number of studies on genetic population structure have been published in the last decades, data are still rare for most exploited species. The mismatch between genetic population structure and the current management units found for six species (Gadus morhua, Melanogrammus aeglefinus, Merlangius merlangus, Micromesistius poutassou, Merluccius merluccius and Clupea harengus), emphasizes the need for a revision of these units and questions the appropriateness of current management measures. The implementation of complex and dynamic population structures into novel and less static management procedures should be a primary task for future fisheries management approaches. [source] Seascape genetics and the spatial ecology of marine populationsFISH AND FISHERIES, Issue 4 2008Kimberly A Selkoe Abstract Molecular tools perform at their best when integrated with other data and approaches. The value of integrating approaches is especially high when the underlying genetic signal is relatively weak, as occurs in many marine species. Recently, studies combining genetic, oceanographic, behavioural and modelling approaches have provided new insights into the spatial ecology of marine populations, in particular regarding larval migration, barriers to dispersal and source-sink population dynamics. In this perspectives piece, we explore the advantages of a multidisciplinary approach to marine population genetics by (i) providing a synthesis of what has been learned about connectivity from studies that combine genetic data with other tools, (ii) discussing how incorporation of ecological and oceanographic information into alternative hypotheses can boost inference when genetic power is low, and (iii) summarizing recent innovations in statistical population genetics that enable seamless integration of ecological, environmental and genetic data. These topics are covered in the context of how genetic inferences of connectivity and dispersal can contribute to pressing questions facing marine conservation and management. [source] Constraints on recovery: using molecular methods to study connectivity of aquatic biota in rivers and streamsFRESHWATER BIOLOGY, Issue 4 2007JANE M. HUGHESArticle first published online: 2 MAR 200 Summary 1. The ,Field of Dreams Hypothesis' states ,if we build it, they will come', referring to the assumption that if habitats are restored, species will recolonise them. However, the ability of a species to recolonise a restored site will depend not only on the appropriate habitat being present, but also on the ability to get there. This is likely to depend on both the species' dispersal behaviour and the position of a site in the landscape. 2. Animals with good potential for dispersal are more likely to be able to disperse to newly restored sites. Similarly, sites in lowland streams with limited altitudinal differences between sites may be easier to reach than upstream sites. This is because upstream sites are connected to one another via lowland streams that have different characteristics and therefore may be difficult for animals to traverse. 3. In this paper, genetic data from a range of freshwater species that have been analysed in my laboratory are used to assess the importance of life cycle and position in the landscape (i.e. upland versus lowland streams) on connectivity patterns (and thus recolonisation potential) among populations. 4. In general, contemporary dispersal across catchment boundaries is negligible, except for aquatic insects with an adult flight stage. Dispersal among streams within catchments appears to be more limited than was predicted from knowledge on life histories, except for fish in lowland rivers and streams. 5. As predicted, dispersal of fish, crustaceans and molluscs among streams within catchments is significantly greater in lowland rivers than in upland streams. 6. Overall, these analyses suggest that, with the exception of most insects, and fishes in lowland rivers, natural recolonisation of restored sites is only likely from sites within the same stream. If a species has disappeared from the whole stream, then restoration of habitat alone may not be sufficient for its re-establishment. [source] Use of longitudinal data in genetic studies in the genome-wide association studies era: summary of Group 14GENETIC EPIDEMIOLOGY, Issue S1 2009Berit Kerner Abstract Participants analyzed actual and simulated longitudinal data from the Framingham Heart Study for various metabolic and cardiovascular traits. The genetic information incorporated into these investigations ranged from selected single-nucleotide polymorphisms to genome-wide association arrays. Genotypes were incorporated using a broad range of methodological approaches including conditional logistic regression, linear mixed models, generalized estimating equations, linear growth curve estimation, growth modeling, growth mixture modeling, population attributable risk fraction based on survival functions under the proportional hazards models, and multivariate adaptive splines for the analysis of longitudinal data. The specific scientific questions addressed by these different approaches also varied, ranging from a more precise definition of the phenotype, bias reduction in control selection, estimation of effect sizes and genotype associated risk, to direct incorporation of genetic data into longitudinal modeling approaches and the exploration of population heterogeneity with regard to longitudinal trajectories. The group reached several overall conclusions: (1) The additional information provided by longitudinal data may be useful in genetic analyses. (2) The precision of the phenotype definition as well as control selection in nested designs may be improved, especially if traits demonstrate a trend over time or have strong age-of-onset effects. (3) Analyzing genetic data stratified for high-risk subgroups defined by a unique development over time could be useful for the detection of rare mutations in common multifactorial diseases. (4) Estimation of the population impact of genomic risk variants could be more precise. The challenges and computational complexity demanded by genome-wide single-nucleotide polymorphism data were also discussed. Genet. Epidemiol. 33 (Suppl. 1):S93,S98, 2009. © 2009 Wiley-Liss, Inc. [source] | |||||||||||||||||||||||||||||||||||||||||||