The Experts below are selected from a list of 15993 Experts worldwide ranked by ideXlab platform
Philip W. Hedrick - One of the best experts on this subject based on the ideXlab platform.
-
Conservation Genetics and North American Bison (Bison bison)
The Journal of heredity, 2009Co-Authors: Philip W. HedrickAbstract:The many millions of North American bison in the mid-19th century were reduced to near extinction by the middle 1880s. Plains bison, the subspecies found in the United States, were saved from extinction primarily by 5 private ranchers and the survival of a small herd in what is now Yellowstone National Park. This bottleneck resulted in the present-day plains bison population being descended from less than 100 founders. In addition, many Conservation herds have cattle ancestry because of hybridization promoted by these ranchers in the late 1800s and early 1900s. Today, although there are around 500,000 plains bison in North America, only 4% (20,000) are in Conservation herds. Only 1 Conservation herd with no known ancestry from cattle has an effective population size of more than 1000. Here I review and evaluate this situation and provide recommendations for the reduction of cattle ancestry, avoidance of inbreeding depression, and maintenance of genetic variation in the Conservation herds of bison.
-
Conservation Genetics where are we now
Trends in Ecology and Evolution, 2001Co-Authors: Philip W. HedrickAbstract:Genetic studies in endangered species have become widespread in the past decade, and with new information from various genome projects, new applications and insights are forthcoming. Generally, neutral variants are used for Conservation applications, and when combined with highly variable loci and/or many more markers, these approaches should become much more informative. Conservation Genetics is also concerned with detrimental and adaptive variation, which are more difficult to identify and characterize; however, the ability to predict the extent of such variation might become more successful and applied in future Conservation efforts. Neutral variants might be used to identify adaptive variants, but the overlay of different mutational processes and selective regimes suggests that extreme caution should be used in making such identifications.
-
Conservation Genetics techniques and fundamentals
Ecological Applications, 1992Co-Authors: Philip W. Hedrick, Philip S MillerAbstract:Conservation Genetics utilizes the tools and concepts of Genetics and applies them to problems in Conservation biology. For example, molecular genetic techniques, such as protein electrophoresis, and analysis of mitochondrial DNA and highly variable nuclear genes (including DNA fingerprinting), have been important in documenting the extent and pattern of genetic variation in endangered species. We review these techniques and their advantages and disadvantages, and give examples of their application to endan- gered species. For captive animal populations, pedigree analysis has become the basic approach to evaluate breeding priority of particular individuals. Several pedigree analysis techniques are commonly used, but peeling and gene dropping give the most information. We compare these techniques and illustrate their value with applications to the Guam Rail, Przewalski's horse, and other endangered captive animals. The rationale for much Conservation genetic interpretation is based in evolutionary Genetics. We discuss the avoidance of inbreeding depression and the maintenance of genetic variation-both primary Conservation genetic goals-from this perspective. In addition, we suggest aspects of these factors that deserve greater attention in their overall application to Conservation planning. Finally, we briefly mention three evolutionary topics-the relationship of heterozygosity and fitness, population bottlenecks, and outbreeding depression-that have implications for Conservation Genetics. Although simple interpretation in these areas is appealing, we feel that because they are only generally understood and often quite controversial, their application to endangered-species management should be carefully evaluated and moni- tored.
Thomas E Nichols - One of the best experts on this subject based on the ideXlab platform.
-
beyond bonferroni revisited concerns over inflated false positive research findings in the fields of Conservation Genetics biology and medicine
Conservation Genetics, 2019Co-Authors: Tonya White, Jan Van Der Ende, Thomas E NicholsAbstract:In 2006, Narum published a paper in Conservation Genetics emphasizing that Bonferroni correction for multiple testing can be highly conservative with poor statistical power (high Type II error). He pointed out that other approaches for multiple testing correction can control the false discovery rate (FDR) with a better balance of Type I and Type II errors and suggested that the approach of Benjamini and Yekutieli (BY) 2001 provides the most biologically relevant correction for evaluating the significance of population differentiation in Conservation Genetics. However, there are crucial differences between the original Benjamini and Yekutieli procedure and that described by Narum. After carefully reviewing both papers, we found an error due to the incorrect implementation of the BY procedure in Narum (Conserv Genet 7:783–787, 2006) such that the approach does not adequately control FDR. Since the incorrect BY approach has been increasingly used, not only in Conservation Genetics, but also in medicine and biology, it is important that the error is made known to the scientific community. In addition, we provide an overview of FDR approaches for multiple testing correction and encourage authors first and foremost to provide effect sizes for their results; and second, to be transparent in their descriptions of multiple testing correction. Finally, the impact of this error on Conservation Genetics and other fields will be study-dependent, as it is related to the number of true to false positives for each study.
-
beyond bonferroni revisited concerns over inflated false positives in Conservation Genetics Genetics and neuroscience
bioRxiv, 2018Co-Authors: Tonya White, Jan Van Der Ende, Thomas E NicholsAbstract:In 2006, Narum published a paper in Conservation Genetics that was motivated by the stringent nature of the Bonferroni approach for family wise error correction. It was suggested that the approach of Benjamini and Yekutieli in 2001 provided adequate correction and was more biologically relevant. However, there are crucial differences between the original Benjamini and Yekutieli 2001 procedure and that described by Narum. After carefully reviewing both papers, we believe that the Narum procedure is both different than the BY procedure and does not adequately control for family wise error. We provide an overview of approaches for FWE correction as well as evidence for the faulty implementation of the BY procedure by Narum using the equations from the respective papers, data from both papers, and the results of simulation.
Eric J. Routman - One of the best experts on this subject based on the ideXlab platform.
-
Phylogeography and Conservation Genetics of the hellbender salamander (Cryptobranchus alleganiensis)
Conservation Genetics, 2008Co-Authors: Stephen J. Sabatino, Eric J. RoutmanAbstract:We investigated hellbender phylogeography through phylogenetic analyses of individuals sampled from 16 locations throughout their range in the eastern United States. Analyses were conducted on concatenated cytochrome-oxidase I (COI), cytochrome- b (Cyt b ) and NADH dehydrogenase subunit 4 (ND4) mtDNA sequence, totaling 2160 nucleotides. Hellbender haplotypes differed by 0.1 to 5.8% maximum likelihood (ML) corrected sequence divergence. Phylogenetic analyses reveal that hellbenders are separated into 8 reciprocally monophyletic populations or clades differentiated by a minimum of 0.7 to 5.4% sequence divergence, each of which constitutes a separate Management Unit (MU). High among population divergence and reciprocal monophyly suggest that female-mediated gene flow is severely restricted or non-existent among each MU. Hellbenders are currently divided into two subspecies, Cryptobranchus alleganiensis alleganiensis and C. a. bishopi based on morphological characters. The phylogenetic analyses presented here strongly indicate that these subspecies are paraphyletic. Management priorities for the hellbender should be reconsidered in light of these new molecular data. Results from Bayesian rooting indicate the root of the hellbender mtDNA tree lies on the branch leading to hellbender haplotypes from the Current, Eleven Point and New Rivers. The rooted tree suggests that a common ancestor in the southern Ozarks and/or southern Appalachians gave rise to northern hellbender populations, consistent with a Pleistocene refuge hypothesis.
Gordon Luikart - One of the best experts on this subject based on the ideXlab platform.
-
genomics and the future of Conservation Genetics
Nature Reviews Genetics, 2010Co-Authors: Fred W Allendorf, Paul A Hohenlohe, Gordon LuikartAbstract:We will soon have complete genome sequences from thousands of species, as well as from many individuals within species. This coming explosion of information will transform our understanding of the amount, distribution and functional significance of genetic variation in natural populations. Now is a crucial time to explore the potential implications of this information revolution for Conservation Genetics and to recognize limitations in applying genomic tools to Conservation issues. We identify and discuss those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity. We also provide guidance on which genomics tools and approaches will be most appropriate to use for different aspects of Conservation.
-
advancing ecological understandings through technological transformations in noninvasive Genetics
Molecular Ecology Resources, 2009Co-Authors: Albano Bejapereira, Gordon Luikart, Rita Oliveira, Paulo C Alves, Michael K SchwartzAbstract:Noninvasive genetic approaches continue to improve studies in molecular ecology, Conservation Genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological advances continue to make noninvasive approaches among the most used and rapidly advancing areas in Genetics. Here, we review recent advances in noninvasive Genetics and how they allow us to address important research and management questions thanks to improved techniques for DNA extraction, preservation, amplification and data analysis. We show that many advances come from the fields of forensics, human health and domestic animal health science, and suggest that molecular ecologists explore literature from these fields. Finally, we discuss how the combination of advances in each step of a noninvasive Genetics study, along with fruitful areas for future research, will continually increase the power and role of noninvasive Genetics in molecular ecology and Conservation Genetics.
Nicolas Hubert - One of the best experts on this subject based on the ideXlab platform.
-
Identifying spatially concordant evolutionary significant units across multiple species through DNA barcodes: Application to the Conservation Genetics of the freshwater fishes of Java and Bali
Global Ecology and Conservation, 2018Co-Authors: Aditya Hutama, Hadi Dahruddin, Frédéric Busson, Sopian Sauri, Philippe Keith, Renny Kurnia Hadiaty, Robert Hanner, Bambang Suryobroto, Nicolas HubertAbstract:Delineating Evolutionary Significant Units for Conservation purposes is a crucial step in Conservation. Across a distribution range, species frequently display population structure that drives the distribution of genetic diversity. These patterns of genetic structure and diversity result from intricate interactions between biogeographic history and demographic dynamics. Prior biogeographic knowledge, however, is scarcely available, a trend particularly pronounced in the tropics where the taxonomic impediment is hampering biogeographic studies and Conservation efforts. DNA barcoding has been initially proposed to foster taxonomic studies through the development of an automated molecular system of species identification. While its utility for species identification is increasingly acknowledged, its usefulness for fast and large-scale delineation of ESU remains to be explored. If proved to be useful for that purpose, DNA barcoding may also open new perspectives in Conservation by quickly providing preliminary information about population Conservation status. The present study aims at assessing the utility of DNA barcoding for the delineation of ESUs among the most common freshwater fish species of Java and Bali through the comparison of population genetic structures and diversification patterns across multiple species. Substantial levels of cryptic diversity are discovered among the three widely distributed freshwater fish species analyzed with a total of 21 evolutionary independent mitochondrial lineages (BINs) observed in Barbodes binotatus, Channa gachua and Glyptothorax platypogon. The maximum genetic distance for each coalescent tree ranges from 6.78 to 7.76 K2P genetic distances for C. gachua and G. platypogon, respectively. Diversification and population genetic analyses support a scenario of allopatric differentiation. The analysis of the BINs spatial distribution indicates concordant distribution patterns among the three species that allow identifying 18 ESUs. Implications for the Conservation Genetics of these species are discussed at the light of the history of the region.