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Genetic Data Set (genetic + data_set)
Selected AbstractsHabitat heterogeneity influences connectivity in a spatially structured pest populationJOURNAL OF APPLIED ECOLOGY, Issue 2 2006G. S. HAMILTON Summary 1Patterns of connectivity influence pest population system dynamics, and it is essential to consider connectivity when planning effective management strategies. Traditional connectivity models often consider populations embedded in a matrix of unsuitable habitat. This approach is unlikely to be applicable to those pest species that can utilize most of the landscape in which they live. There is therefore a need for a simple and flexible tool to assess connectivity in such systems. 2In this study, we developed a new model in which contiguous resource patches that differ in quality, and landscape elements that impede dispersal, impact on connectivity within a population system. The model was applied to a wild rabbit population system, a well-studied pest species in Australia. An independent population genetic data set was used to validate the model. 3There was a highly significant association between pairwise population connectivity and the genetic data (Mantel test, r=,0·502, P= 0·002). As predicted, two populations that showed very low connectivity were strongly isolated genetically. These sites appeared to be substantially isolated because of forests, which acted to impede rabbit dispersal. When these sites were excluded from analysis, connectivity indices again explained the pattern of genetic data (Mantel test, r=,0·46, P= 0·037). This showed that both spatial variation in resource quality and forests influenced connectivity in this system. Sensitivity analyses confirmed that the distribution and extent of forests was important in limiting connectivity to some sites. The model was relatively robust to changes in population parameters. 4Synthesis and applications. Connectivity among wild rabbit populations in this system was strongly influenced by habitat heterogeneity, rather than factors such as geographical distance or major landscape elements such as rivers, both of which are traditionally considered to influence system dynamics. This may have substantial implications for many pest systems, and suggests that the impact of habitat heterogeneity on connectivity should be considered when planning efficient management strategies. [source] ORIGINAL ARTICLE: Coalescent analyses support multiple mainland-to-island dispersals in the evolution of Malagasy Triaenops bats (Chiroptera: Hipposideridae)JOURNAL OF BIOGEOGRAPHY, Issue 6 2008Amy L. Russell Abstract Aim, We investigate the directionality of mainland-to-island dispersals, focusing on a case study of an African-Malagasy bat genus, Triaenops (Hipposideridae). Taxa include T. persicus from east Africa and three Triaenops species from Madagascar (T. auritus, T. furculus, and T. rufus). The evolution of this bat family considerably post-dated the tectonic division of Madagascar from Africa, excluding vicariance as a viable hypothesis. Therefore, we consider three biogeographical scenarios to explain these species' current ranges: (A) a single dispersal from Africa to Madagascar with subsequent speciation of the Malagasy species; (B) multiple, unidirectional dispersals from Africa to Madagascar resulting in multiple, independent Malagasy lineages; or (C) early dispersal of a proto-species from Africa to Madagascar, with later back-dispersal of a descendant Malagasy taxon to Africa. Location, East Africa, Madagascar, and the Mozambique Channel. Methods, We compare the utility of phylogenetic and coalescent methodologies to address the question of directionality in a mainland-to-island dispersal event for recently diverged taxa. We also emphasize the application of biologically explicit demographic systems, such as the non-equilibrium isolation-with-migration model. Here, these methods are applied to a four-species haploid genetic data set, with simulation analyses being applied to validate this approach. Results, Coalescent simulations favour scenario B: multiple, unidirectional dispersals from Africa to Madagascar resulting in multiple, independent Malagasy bat lineages. From coalescent dating, we estimate that the genus Triaenops was still a single taxon approximately 2.25 Ma. The most recent Africa to Madagascar dispersal occurred much more recently (c. 660 ka), and led to the formation of the extant Malagasy species, T. rufus. Main conclusions, Haploid genetic data from four species of Triaenops are statistically most consistent with multiple, unidirectional dispersals from mainland Africa to Madagascar during the late Pleistocene. [source] How to track and assess genotyping errors in population genetics studiesMOLECULAR ECOLOGY, Issue 11 2004A. BONIN Abstract Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies. [source] Fossil evidence and phylogeography of temperate species: ,glacial refugia' and post-glacial recolonizationJOURNAL OF BIOGEOGRAPHY, Issue 11 2009Robert S. Sommer Abstract We present a short synthesis of the Pleistocene distribution dynamics and phylogeographic recolonization hypotheses for two temperate European mammal species, the red deer (Cervus elaphus) and the roe deer (Capreolus capreolus), for which high-resolution patterns of fossil evidence and genetic data sets are available. Such data are critical to an understanding of the role of hypothesized glacial refugia. Both species show a similar pattern: a relatively wide distribution in the southern part of Central Europe 60,000,25,000 years ago, and a strong restriction to areas in southern Europe for nearly 10,000 years during the Last Glacial Maximum (LGM) and the early Late Glacial (25,000,14,700 years ago). With the beginning of Greenland Interstadial 1 (Bølling/Allerød warming, c. 14,700,11,600 years ago) a sudden range expansion into Central Europe is visible, but the colonization of most of Central Europe, including the northern European Lowlands, only began in the early Holocene. In a European context, regions where the species were distributed during the LGM and early Late Glacial are most relevant as potential origins of recolonization processes, because during these c. 10,000 years distribution ranges were smaller than at any other time in the Late Quaternary. As far as the present distribution of temperate species and their genetic lineages is concerned, so-called ,cryptic refugia' are important only if the species are actually confirmed there during the LGM, as otherwise they could not possibly have contributed to the recolonization that eventually resulted in the present distribution ranges. [source] Human cranial anatomy and the differential preservation of population history and climate signaturesTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 12 2006Katerina Harvati Abstract Cranial morphology is widely used to reconstruct evolutionary relationships, but its reliability in reflecting phylogeny and population history has been questioned. Some cranial regions, particularly the face and neurocranium, are believed to be influenced by the environment and prone to convergence. Others, such as the temporal bone, are thought to reflect more accurately phylogenetic relationships. Direct testing of these hypotheses was not possible until the advent of large genetic data sets. The few relevant studies in human populations have had intriguing but possibly conflicting results, probably partly due to methodological differences and to the small numbers of populations used. Here we use three-dimensional (3D) geometric morphometrics methods to test explicitly the ability of cranial shape, size, and relative position/orientation of cranial regions to track population history and climate. Morphological distances among 13 recent human populations were calculated from four 3D landmark data sets, respectively reflecting facial, neurocranial, and temporal bone shape; shape and relative position; overall cranial shape; and centroid sizes. These distances were compared to neutral genetic and climatic distances among the same, or closely matched, populations. Results indicate that neurocranial and temporal bone shape track neutral genetic distances, while facial shape reflects climate; centroid size shows a weak association with climatic variables; and relative position/orientation of cranial regions does not appear correlated with any of these factors. Because different cranial regions preserve population history and climate signatures differentially, caution is suggested when using cranial anatomy for phylogenetic reconstruction. Anat Rec Part A, 2006. © 2006 Wiley-Liss, Inc. [source] | ||||||||||