Relevant bibliographies by topics / Populations and conservation genetics

Academic literature on the topic 'Populations and conservation genetics'

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Published: 10 March 2023

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Journal articles on the topic "Populations and conservation genetics"

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FRANKHAM, RICHARD. "Quantitative genetics in conservation biology." Genetical Research 74, no. 3 (December 1999): 237–44. http://dx.doi.org/10.1017/s001667239900405x.

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Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.
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Armstrong, Graeme. "Conservation and the Genetics of Populations." Pacific Conservation Biology 14, no. 2 (2008): 146. http://dx.doi.org/10.1071/pc080146.

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I am sure many readers have experienced the excruciating situation of being involved in a conservation project that makes no effort to include a genetic component in the methodology. This is often due to a lack of understanding by managers compounded by an inability of biologists to remedy this situation by demonstrating the importance of genetics to the desired conservation outcome. The authors of Conservation and the Genetics of Populations have aimed their text at ?broadly trained biologists? to enable an understanding and application of genetic principles to conservation problems. If successful this would go a long way to alleviating this problem.
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Varvio, Sirkka-Liisa, Ranajit Chakraborty, and Masatoshi Nei. "Genetic variation in subdivided populations and conservation genetics." Heredity 57, no. 2 (October 1986): 189–98. http://dx.doi.org/10.1038/hdy.1986.109.

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Benirschke, Kurt. "Conservation and Genetics of Populations." Journal of Heredity 97, no. 6 (November 1, 2006): 612–13. http://dx.doi.org/10.1093/jhered/esl039.

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Priyono, Dwi Sendi, Dedy Duryadi Solihin, Achmad Farajallah, and Bambang Purwantara. "Genetic Diversity of the Endangered Endemic Anoa (Bubalus spp): Implication for Conservation." HAYATI Journal of Biosciences 29, no. 5 (May 17, 2022): 586–96. http://dx.doi.org/10.4308/hjb.29.5.586-596.

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Anoa is an endemic ungulate in Sulawesi and its status now is endangered because the population continues to decline. Conservation genetics is one of the crucial issues in the anoa conservation strategy and action plan 2013-2022 document, but this genetic data is not yet available. To investigate and provide valuable information for conservation genetics measures, thirteen polymorphic microsatellites were used to analyze 20 adult anoa. Anoa has relatively low genetic diversity within populations (HO = 0.58), and high genetic differentiation among populations (FST = 0157). Although the anoa population has a bottleneck signal (T.P.M: 0.019; P0.05), the bottleneck simulation results show that the loss of genetic diversity is being slow over the next 100 years (9.5%). We provide some recommendations for conservation genetics based on the findings in this paper, including monitoring and genetically mapping for other anoa populations due to bottleneck signals, establishing the founder of the ex-situ population by examining their genetic diversity status, maintaining and increasing the number of individuals in the ex-situ population to genetically safe population size, and managing anoa populations by avoiding inbreeding. In-situ and ex-situ conservation programs should be combined to maintain the genetic diversity of anoa.
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Sherwin, WB, and ND Murray. "Population and Conservation Genetics of Marsupials." Australian Journal of Zoology 37, no. 3 (1989): 161. http://dx.doi.org/10.1071/zo9890161.

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This article summarises current knowledge of marsupial population genetics, and discusses its relevance to the conservation of marsupial species. It has been suggested that there is much lower genetic variation within marsupial populations than in eutherian mammals. This trend is not evident in the electrophoretic data summarised here. However, genetic differentiation between populations, subspecies, and species of marsupials appears to be slightly lower than comparable values for eutherians. Genetic estimates of migration between populations are scarce at present, but show values that are comparable with eutherians. Some studies of marsupial population genetics have used non-electrophoretic characteristics, or have addressed the possibility of selection on the characters analysed. Although few, these studies indicate the suitability of marsupials for such investigations. Recent debate over the theories and applications of conservation genetics has made it clear that more research is required on individual species. Given the record of extinction of marsupials in the last 200 years, it is important to test the applicability of these theories to individual marsupial species. Several examples are discussed emphasising the need for ecological studies that estimate the effective number of reproducing individuals per generation. This figure, called the effective size, is the corner- stone of conservation genetics theory, being an important determinant of both the rate of loss of variation between individuals, and the rate of inbreeding. The effective size of the mainland population of the eastern barred bandicoot, Perameles gunnii, appears to be only about one-tenth of its census number. This result is comparable with estimates made in other vertebrates, and demonstrates that many marsupial species which appear to have an adequate census size on ecological grounds may face genetic problems resulting from small effective size.
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Scribner, Kim T. "Conservation genetics of managed ungulate populations." Acta Theriologica 38 (May 20, 1993): 89–101. http://dx.doi.org/10.4098/at.arch.93-44.

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Ouborg, N. Joop. "Integrating population genetics and conservation biology in the era of genomics." Biology Letters 6, no. 1 (September 2, 2009): 3–6. http://dx.doi.org/10.1098/rsbl.2009.0590.

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As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled ‘Integrating Population Genetics and Conservation Biology’ was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.
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Testroet, Philip, Dietmar Quandt, Arnoldo Santos Guerra, Kai Müller, and Wolfram Lobin. "Population genetics and conservation of Sideroxylon canariense (Sapotaceae) on the Canary Islands." Vieraea Folia scientiarum biologicarum canariensium 41, Vieraea 41 (2013): 319–32. http://dx.doi.org/10.31939/vieraea.2013.41.21.

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Genetic diversity patterns of different populations were studied in Sideroxylon canariense, a Canary Island endemic of conservation concern. The species range is composed of a number of very small and isolated populations. Genetic variation of these populations was analyzed using: (1) inter simple sequence repeats (ISSR), a common fingerprinting method in plant population genetics, and (2) nucleotide sequence analyses of the nuclear ITS region. While no intraspecific variation was detected among the ITS sequences, the ISSR data showed a very low degree of intraspecific genetic diversity among S. canariense populations on the Canaries, with very few genotypes. We believe that many of the populations consist of a single individual that propagates asexually. Action is urgently required to protect and propagate the highly endangered populations.
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Freeland, Joanna R., Joy Gillespie, Claudia Ciotir, and Marcel E. Dorken. "Conservation genetics of Hill’s thistle (Cirsium hillii)." Botany 88, no. 12 (December 2010): 1073–80. http://dx.doi.org/10.1139/b10-080.

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Populations at the edges of their geographical ranges are often characterized by reduced genetic diversity and increased genetic differentiation. These patterns may be exacerbated by specialized associations between plants and uncommon habitats. Together, reduced diversity and increased subdivision may increase the risk of population extirpation, an issue that is particularly important for plants classified as rare or threatened. Hill’s thistle (Cirsium hillii (Canby) Fernald), is a perennial herb endemic to the Great Lakes region and is considered threatened in Canada where its northernmost distribution occurs. We used microsatellite markers to genotype plants from 11 populations of Hill’s thistle that span the range of the species distribution within Canada. These data were used to investigate levels of genetic diversity within populations and genetic differentiation between populations, and to evaluate associations between patterns of genetic variation and those expected under ongoing habitat loss. Genetic differentiation among populations was low, although significant pairwise FST values, along with the presence of private alleles in most populations, was consistent with moderate to low gene flow. Nevertheless, in comparison with a congeneric rare species (Cirsium pitcheri) that occurs in the same geographical region in Canada, genetic diversity within most populations was high, and we suggest that this is at least partially attributable to this species’ combination of sexual and clonal reproduction. Despite high levels of genetic diversity, Hill’s thistle should probably remain a designated species at risk because of ongoing habitat loss; however, our data suggest that Hill’s thistle is unlikely to suffer from reduced genetic diversity in the foreseeable future.
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Dissertations / Theses on the topic "Populations and conservation genetics"

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Hipperson, Helen. "Conservation genetics in protected populations." Thesis, University of Sheffield, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.505563.

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Martien, Karen Kay Fear. "Conservation of spatially structured populations : lessons from population genetics /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9979969.

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Mäki-Petäys, H. (Hannaleena). "Conservation and management of populations in a fragmented forest landscape:behavioural ecology meets population genetics." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514283482.

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Abstract The effects of habitat loss and fragmentation on the genetic structure and vulnerability of populations strongly depend on the behaviour of a particular species. In this thesis, I examined the effects of forest fragmentation on genetic population structure with the aim of identifying and evaluating the different genetic and behavioural factors important for species conservation and management on different geographical scales. The species studied were the mound building red wood ants Formica lugubris and F. aquilonia, and a lekking bird, the capercaillie, Tetrao urogallus. Habitat loss and fragmentation affected the genetic structure in both wood ants and capercaillie. In general, the effects were related to the time since fragmentation and to the level of habitat loss and isolation from the other existing populations. The loss of genetic diversity due to population fragmentation was less observable than the differences in population structure. The response to habitat fragmentation was further dependent on species characteristics such as dispersal and mating behaviour. Sociality affected the genetic vulnerability of wood ant populations by decreasing gene diversity, increasing inbreeding depression and restricting gene flow between subpopulations. The results on the capercaillie in turn suggested that lekking behaviour restricts dispersal of both sexes, thus elevating the occurrence of inbreeding between individuals. The present study provided important information on species conservation and management in terms of better understanding species' biology and behaviour, as well as increased knowledge concerning the genetic issues that should be taken into account when planning conservation actions. By examining the genetic structure of the species it was possible to clarify the conservation status including the effective population size, the question of origin, and the genetic vulnerability (genetic diversity, inbreeding and inbreeding depression) of the populations and/or species. Overall, the results emphasised the importance of preserving the effective population size and the connectivity of habitat patches when planning species specific management strategies. There were great differences in conservation needs among the species, which should be taken into account especially in local management actions.
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Cain, Bradley. "Conservation genetics of enclosed black rhinoceros populations in Kenya." Thesis, Manchester Metropolitan University, 2012. http://e-space.mmu.ac.uk/315691/.

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Population size is a major determinant of extinction risk with small populations experiencing an inherently higher risk of extinction due to genetic threats and stochastic fluctuations in survival, fecundity and environmental conditions. For many species, natural populations are experiencing a dramatic decline in numbers and distribution as a direct result of human activities. The severity of the threats facing some species necessitates the movement of remaining individuals into protected areas or captive breeding programs where resources can be concentrated to promote recovery. Moreover, increasing levels of population fragmentation has led to metapopulation management being regarded as an integral part of many conservation strategies, particularly for large vertebrates. The translocation of individuals between populations across an inhospitable matrix is often needed to offset the detrimental effects of small population size and to maintain natural evolutionary processes. Whilst the benefits of active conservation management involving the mixing of individuals from hitherto isolated populations has been demonstrated in a number of cases, the impact on historic population structure and the potential for outbreeding depression is often poorly understood. Moreover an increasing body of theoretical and empirical work is demonstrating that mate selective choices are mediated not only by additive effects but by non-additive effects, most specifically the amount of genetic similarity between individuals. Recent studies on natural populations have demonstrated that there is a fitness cost associated with choosing maximally dissimilar mates and that even for intrapopulation breeding, individuals exercise a preference for mates of intermediate similarity. Populations subject to active conservation management are typically small admixed populations where individuals are presented with a limited number of potential mates, representing a greater spectrum of genetic divergence than would typically be present in non-managed populations. With many in situ and ex situ conservation programs reporting poor population growth rates linked to low or declining reproduction understanding the genetic influences on mate choice in these populations is potentially of great importance. This thesis examines (1) the effects of active conservation management on levels of genetic diversity and (2) historic population structure in the eastern black rhinoceros (Diceros bicornis michaeli). It also examines the relative influences of additive and non-additive effects on female mate choice in this actively managed conservation priority species. The eastern black rhinoceros (Diceros bicornis michaeli) has been subject to one viii of the severest human induced declines of any mammalian species. The subspecies formally ranged across East Africa from northern Tanzania to Somalia, with its largest populations in Kenya. A significant increase in poaching of rhinoceros for their horn during the 1970s and 1980s eliminated D. b. michaeli from Sudan, Ethiopia, Somalia, Uganda and Rwanda. Extensive populations in Tanzania were reduced to just two small populations and the subspecies was reduced from an estimated Kenyan population of 20,000 in 1970 to just 380 by 1987. In the face of the imminent extinction of the Kenyan population, the Kenya Wildlife Service (KWS) implemented a policy of moving all animals outside protected areas into fenced sanctuaries where resources could be concentrated to counter the poaching threat. The sanctuary system proved successful and as of 2006 Kenya had approximately 540 black rhinoceros protected within 14 separate populations. With the sanctuary system largely successful in countering the continued threat of poaching, emphasis has shifted to metapopulation management to ensure the viability of the small isolated populations within the sanctuary system. To assist in the effective metapopulation management of these isolated populations, data is presented here both on the current levels of genetic diversity and the range of historic genetic diversity captured within five enclosed sanctuary populations. A total of 166 individually identified black rhinoceros were genotyped for 9 microsatellite loci and a 507 bp segment of the mtDNA control region, with the majority of the genotyping conducted on DNA extracted from faeces. To assist in the identification of faecal samples from mixed sex pairings a simple, accurate, single-stage 5′-exonuclease assay for gender determination in the black rhinoceros from low-copy template DNA is presented. Genetic analysis and the examination of translocation records shows that the five sanctuaries are comprised of historic populations from three geographic regions within the country and that significant admixture has occurred between these historically divergent populations. These historically divergent populations are shown by molecular dating to have originated from the south of the country following an expansion which is putatively linked to the contraction of the Pleistocene forests approximately 300 KYA. Examination of mutation bias in the species reveals low levels of mutagenesis in concordance with other studies and evidence of ectopic gene conversion between eutherian sex chromosomes. The current metapopulation retains significant levels of genetic diversity for both nucleic (A = 5.0, HE = 0.689) and organellar (π = 0.007) genomes, with levels of diversity in individual populations related to ix the amount of admixture of former populations. Parentage analysis was undertaken for 107 individuals from three sanctuary populations representing approximately 16 years of successful reproductive activity in these populations. It is demonstrated that in the black rhinoceros male genetic diversity is a significant predictor of reproductive success and that females balance male genetic quality with intermediate levels of genetic similarity in admixed populations. This is the first time these effects have been investigated in a conservation priority species subject to active management and it is anticipated these results will have a profound impact on future management strategies for the species. In particular the overall results of this thesis provide a framework whereby the management of the Kenyan black rhinoceros metapopulation can be guided by the way rhinoceros are shown to manage their own reproductive success.
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Parda, Kriska F. I. G. "Long term fitness of hybridized populations of Drosophila." Thesis, California State University, Long Beach, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1528020.

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In the practice of resource management conservation, it is common to introduce new members into small inbred populations in order to increase genetic diversity and reduce the negative effects of inbreeding. Although fitness often increases in the F1 generation immediately following intrapopulation hybridization, few studies have focused on the long-term fitness of such populations. The model organisms Drosophila melanogaster and D. simulans were used to investigate if heterosis, an increase in the fitness in the hybrid population, or outbreeding depression, a decline in the fitness in the hybrid population, occurs over an eight generation period. At each generation, a series of fitness related assays were performed to assess relative fitness. Results of this study were mixed. At best, only some hybridized populations showed slightly higher, but often nonsignificant increases in fitness, never in more than one assay. The lack of consistent strong persistent heterosis suggests that conservation efforts such as habitat preservation maybe be a better use of effort and money for assisting endangered species.

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Llorens, Tanya M. "Conservation genetics and ecology of two rare grevillea species." Department of Biological Sciences - Faculty of Science, 2004. http://ro.uow.edu.au/theses/374.

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Small and isolated plant populations have a higher probability of extinction – they are more susceptible to a range of environmental, demographic and genetic processes that may reduce population viability. In recent times, the number of populations and species that are susceptible to these processes has increased as a result of world-wide, human-induced habitat fragmentation. Habitat fragmentation typically reduces the formerly more continuous natural distribution of a species to a series of smaller and more isolated populations that occur in smaller and more isolated habitat patches. Such populations are often exposed to a range of additional processes that may threaten their viability, such as changes to disturbance regimes, environmental conditions and interactions with other species. However, our current understanding of the complex effects and interactions of these processes is poor. Species responses vary widely, studies are biased towards trees, herbs and self-incompatible species, and most studies investigate only one or two processes that may affect viability. Consequently, we are unable to make accurate predictions about the likely impacts of habitat fragmentation on population and species viability. I tested several hypotheses about the impact of habitat fragmentation, small population size, and population isolation on populations of two Grevillea species (Proteaceae) that occur in the Sydney region of New South Wales, Australia. These species provided an opportunity to investigate some of the ecological and genetic consequences of small population size and isolation, and to contrast them between a species for which the small size and isolation of its populations is the natural state (G. longifolia) and one for which it arose recently due to severe habitat fragmentation (G. caleyi). This comparative approach is important in identifying the processes involved in reducing population and species viability. The species share many aspects of their biology and ecology. Both are large, perennial shrubs that are self-compatible and naturally bird-pollinated. They are fire-sensitive and regenerate post-fire by mass germination from a long-lived, soil-stored seed bank. Both species consist of populations that vary dramatically in size and degree of isolation. I used microsatellite and AFLP markers to investigate aspects of the population genetics and mating system of these species, with the primary focus on G. caleyi. Both species showed a surprisingly large amount of genetic structuring among populations, although G. caleyi populations showed more structuring (FST = 0.46) than those of G. longifolia (FST = 0.33), despite being distributed over a much smaller area. In addition, for G. caleyi, most (63%) of the structuring was due to differences among recently-fragmented populations. By examining fine scale genetic structure within existing large populations, I determined that this was probably due to historic genetic structuring within formerly larger, more continuous populations. This has probably arisen due to both a lack of gene flow (no seed dispersal and limited pollen dispersal) and a large amount of inbreeding. Indeed, adult fixation indices were very high in G. caleyi (average f = 0.40, f > 0 in 16/18 populations). For both species, genetic diversity was not strongly correlated with population size. Genetic diversity was significantly lower in more isolated populations of G. caleyi, but this was probably due to a historic lack of gene flow to the more isolated parts of the species’ natural range, rather than to recent fragmentation. Levels of inbreeding (fixation indices) among adult plants did not vary with population size or isolation for either species. However, by genotyping fresh seeds from a range of small and large G. caleyi populations, I revealed that current outcrossing rates were much lower in small populations (t = 0.18 cf. 0.37). Observations of pollinator foraging indicated that this might be due to a very low visitation rate by birds and by a less diverse suite of species, resulting in a higher proportion of self-fertilisation. In contrast, even very small G. longifolia populations received many bird visits. In addition, G. caleyi plants in small populations were much smaller, had higher mortality, and produced fewer inflorescences and fruits, while this pattern was not apparent among G. longifolia populations. The contrast among the species in pollinator visits, plant vigour and reproduction may have been due to edge effects combined with the habitat degradation that was apparent at sites containing small G. caleyi populations. Small populations were typically found within very small and disturbed bush remnants, while small G. longifolia populations all occurred in relatively pristine habitat. Therefore, habitat quality rather than population size per se may be the most important factor that determines the mating system, plant vigour and fecundity in G. caleyi. The lack of obvious impacts of habitat fragmentation on the genetic haracteristics of adult G. caleyi plants may have been due to the soil-stored seed bank, which can contain seeds produced by at least two adult generations. Various authors have hypothesised that a persistent seed bank has the potential to reduce the rate of genetic change in a population. The seed banks of both G. caleyi and G. longifolia do appear to have this ability. I found that the seed bank of each species maintains the genetic characteristics of populations and stores genetic diversity and alleles that were not expressed in the extant adult plants. Nevertheless, the seed bank also showed greater spatial structuring than adults, which indicates that genetic changes may be occurring within these small populations despite the buffering power of the seed bank. Finally, I investigated some aspects of the ecology of G. caleyi and G. longifolia seed banks, with the aim of increasing our understanding of this important conservation resource. Soil sieving revealed that the seeds of both pecies occur at very low densities beneath adult plants (1 – 6 m-2), were vastly outnumbered by seed fragments, and were not found away from adult canopies. This supports previous evidence that indicated a lack of seed dispersal and very high rates of post-dispersal seed predation, which will restrict population size and extent. To some degree, the seed bank may buffer demographic changes that affected the previous adult generation – monitoring of post-fire seedling emergence revealed that population size typically increased, often dramatically, after a fire. Germination experiments showed that smoke elicited the greatest germination response from intact seeds of both species, and that dormancy polymorphism in the seed bank may allow both species to survive two fires in rapid succession and long inter-fire intervals. However, germination was low in field fire experiments, which may have been due to low fire intensity, and hence smoke production, resulting from a winter prescription burn. For both species, herefore, population viability may be compromised if the imposed fire regime includes fires that are too cool or too frequent. This study has demonstrated, for these species, that small populations that exist in recently fragmented habitat patches are far more likely to experience adverse ecological and genetic effects than those in continuous, relatively undisturbed, bushland. The process of demographic and genetic decline in small G. caleyi populations is likely to continue with the ongoing pressures of edge effects, habitat degradation and pollinator declines, and the increased isolation of some populations. The seed bank may buffer these declines to some extent, but this ability is limited by a lack of habitat for population expansion, which means that effective population sizes will remain very small or decrease further. The various differences detected between small and large G. caleyi populations emphasises the importance of large populations, and the ecological processes occurring within larger habitat patches, for the long-term conservation of the species.
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Ramakrishnan, Uma. "Conservation genetics of long-lived mammal populations : applications of individual-based models /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3071025.

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Durant, Sarah Margaret. "Individual variation and dynamics of small populations : implications for conservation and management." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386390.

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Asher, Allison Marie. "CONSERVATION GENETICS OF PADDLEFISH: GENETIC EFFECTIVE POPULATION SIZE AND RANGEWIDE GENETIC STRUCTURE." OpenSIUC, 2019. https://opensiuc.lib.siu.edu/dissertations/1693.

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Paddlefish (Polyodon spathula) is a commercially and recreationally important species, with a native range that extends over 22 US states. This is a large, long-lived, highly mobile riverine species that has been negatively impacted by habitat fragmentation, historic overharvest, and hatchery supplementation. Dams are the primary cause of habitat fragmentation, blocking migration routes, flooding spawning grounds, and isolating populations. A common management action to mitigate the impacts of habitat fragmentation and maintain harvestable populations is hatchery propagation and stocking. Reduction in stock size, isolation of populations, and stocking can all negatively impact the genetic integrity of Paddlefish. I evaluated the impacts of isolation and hatchery supplementation on the effective population size (Ne) of Paddlefish as well as the range-wide genetic structure of Paddlefish.
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Halbert, Natalie Dierschke. "The utilization of genetic markers to resolve modern management issues in historic bison populations: implications for species conservation." Texas A&M University, 2003. http://hdl.handle.net/1969.1/1415.

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The saga of the American bison (Bison bison) is a well-known story of death, destruction, and greed circumvented by early conservationists. The foresight of 5 cattlemen and the Canadian and U.S. governments at the apex of the population bottleneck in the 1880s led to the eventual establishment of several federal bison populations, from which virtually all of the 300,000 extant bison are descended. A survey of 54 microsatellite loci spanning each autosomal and both sex chromosomes was used to compare levels of genetic variation among 10 of the 11 federal bison populations in the U.S. Although most populations contain moderate levels of genetic variation, the majority of genetic variation is contained within only 4 of the federal populations surveyed. The distribution and partitioning of genetic variation confirm historical records of founding lineages and transfers among populations. Previously published mitochondrial and nuclear markers were used to survey federal bison populations for evidence of domestic cattle introgression. While only 1 population was found to contain low levels of domestic cattle mitochondrial DNA, 7 of the 10 surveyed populations had detectable introgression of nuclear genes from domestic cattle. From this, 2 federal bison populations were identified that have both high levels of genetic variation and no evidence of introgression of domestic cattle genes. The data obtained from this study were used to examine consequences of past and present management practices in closed bison populations. In the case of the Texas State Bison Herd, observed chronic small population size, low levels of genetic variation, low natality rates, and high juvenile mortality rates combined with the results of population modeling indicate a high risk of extinction within the next 50 years unless new genetic variation is introduced into the herd. Alternatively, analysis of population substructure and nonrandom culling reveal the necessity for further investigation into the long-term effects of current management practices in the Yellowstone National Park bison population. This study illustrates that while bison may be considered a conservation success story, long-term survival of protected federal populations requires the development of effective genetic management strategies.
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Books on the topic "Populations and conservation genetics"

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Gordon, Luikart, and Aitken Sally N, eds. Conservation and the genetics of populations. 2nd ed. Hoboken: John Wiley & Sons, 2013.

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Conservation of wildlife populations: Demography, genetics, and management. 2nd ed. Hoboken, NJ: Wiley-Blackwell, 2013.

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Conservation of wildlife populations: Demography, genetics, and management. Malden, MA: Blackwell Pub., 2007.

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1950-, Loeschcke V., Tomiuk J, and Jain Subodh K. 1934-, eds. Conservation genetics. Basel: Birkhäuser Verlag, 1994.

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1965-, Young Andrew G., Clarke Geoffrey M. 1960-, Natural Heritage Trust, Commonwealth Scientific and Industrial Research Organization (Australia), and Zoological Society of London, eds. Genetics, demography and viability of fragmented populations. Cambridge, U.K: Cambridge University Press, 2000.

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C, Avise John, and Hamrick J. L. 1942-, eds. Conservation genetics: Case histories from nature. New York: Chapman & Hall, 1996.

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G, Cloud Joseph, Thorgaard Gary H, North Atlantic Treaty Organization. Scientific Affairs Division., and NATO Advanced Study Institute on Genetic Conservation of Salmonid Fishes (1991 : Moscow, Idaho, and Pullman, Wash.), eds. Genetic conservation of salmonid fishes. New York: Plenum Press, 1993.

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Höglund, Jacob. Evolutionary conservation genetics. Oxford: Oxford University Press, 2009.

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Evolutionary conservation genetics. Oxford: Oxford University Press, 2009.

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Giorgio, Bertorelle, ed. Population genetics for animal conservation. New York: Cambridge University Press, 2009.

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Book chapters on the topic "Populations and conservation genetics"

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Vrijenhoek, R. C. "Genetic diversity and fitness in small populations." In Conservation Genetics, 37–53. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_5.

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Olesen, J. M., and S. K. Jain. "D: Fragmented plant populations and their lost interactions." In Conservation Genetics, 417–26. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_35.

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Tomiuk, J., and V. Loeschcke. "A: The genetic monitoring of primate populations for their conservation." In Conservation Genetics, 401–6. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_32.

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Hansen, M. M., and V. Loeschcke. "Effects of releasing hatchery-reared brown trout to wild trout populations." In Conservation Genetics, 273–89. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_22.

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Hauser, T. P., C. Damgaard, and V. Loeschcke. "Effects of inbreeding in small plant populations: Expectations and implications for conservation." In Conservation Genetics, 115–29. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_11.

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Noordwijk, A. J. "The interaction of inbreeding depression and environmental stochasticity in the risk of extinction of small populations." In Conservation Genetics, 131–46. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_12.

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Altukhov, Yu P. "The principles of population monitoring for conservation genetics." In Conservation Genetics, 337–50. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_26.

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Lawrence, M. J., and D. F. Marshall. "Plant population genetics." In Plant Genetic Conservation, 99–113. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-009-1437-7_6.

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Jong, G., J. R. Ruiter, and R. Haring. "Genetic structure of a population with social structure and migration." In Conservation Genetics, 147–64. Basel: Birkhäuser Basel, 1994. http://dx.doi.org/10.1007/978-3-0348-8510-2_13.

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Baker, C. Scott, and Stephen R. Palumbi. "Population Structure, Molecular Systematics, and Forensic Identification of Whales and Dolphins." In Conservation Genetics, 10–49. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4757-2504-9_2.

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Conference papers on the topic "Populations and conservation genetics"

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Sipra, Katherine. "Snow Leopard Population Genetics and Diet Analysis in the Baltistan Region of Northern Pakistan." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/108618.

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Ganea, Anatolie. "Conservarea in situ a agrobiodiversității vegetale – factor de reușită în promovarea agriculturii durabile." In VIIth International Scientific Conference “Genetics, Physiology and Plant Breeding”. Institute of Genetics, Physiology and Plant Protection, Republic of Moldova, 2021. http://dx.doi.org/10.53040/gppb7.2021.58.

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The article gives brief information on inventorying of some crop wild relatives in the forest ecosystems of different soil-climatic zones of Republic of Moldova, and collection of accessions of the local forms of cultivated plants on farms. It was found that natural populations of 5 pilot species – wild cherry, wild pear, cornelian cherry, wild apple and hazelnut are degrading under the influence of envi-ronmental stresses. It is noted that the range of social-economic and political factors of the past 60-70 years has led to significant genetic erosion of the local gene pool of agricultural crops. Elaboration of the effective methods for in situ conservation of agrobiodiversity will facilitate the greening of agricultural production and introduction of the elements of sustainable agriculture.
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Kurland, Sara, Nils Ryman, Ola Hössjer, and Linda Laikre. "CANCELLED: Loss of natural Baltic salmon populations can severely reduce metapopulation capacity for retaining genetic variation." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/107735.

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Đuretanović, Simona, Tijana Veličković, Aleksandra Milošković, Milena Radenković, Marijana Nikolić, Ivana Maguire, and Vladica Simić. "PRELIMINARY RESULTS REGARDING PHYLOGENY OF THE NOBLE CRAYFISH (DECAPODA, ASTACIDAE, „ASTACUS ASTACUS“) IN SERBIA." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.222dj.

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The noble crayfish is one of the three autochthonous species that inhabit the freshwater ecosystems of Serbia, along with stone and Danube crayfish. The noble crayfish has a complex historical and genetic status shaped by geological events, habitat loss, pollution, translocations, and reintroductions of both autochthonous and allochthonous crayfish species. That led to the disruption of the species genetic structure, mixing, and loss of populations across Europe. According to recent data, its populations in the freshwater ecosystems of Serbia are significantly reduced, so it has the status of a "strictly protected species". The genetic structure of the species must be known for endangered species conservation. Unfortunately, there is lack of such data for the territory of Serbia, which due to its position on the Balkan Peninsula, was an important refuge during the glaciation period. In this paper, the genetic structure of seven crayfish populations in freshwater ecosystems of Serbia was examined. Analyzes were performed on the COI and 16S rRNA genes of mitochondrial DNA. The study results showed a significant diversity of COI and 16S rRNA haplotypes compared to already described haplotypes. Three haplotypes were detected, of which Hap26 is the most common and was detected in five studied populations. Haplotypes Hap47 and Hap49 were detected in one and two populations, respectively. The results obtained in this study, together with previously published morphometric data, represent a good starting point for further genetic and population research, which are the basis for the proposal of conservation measures.
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Ostroverkhova, N. V. "DARK FOREST BEE APIS MELLIFERA MELLIFERA L. IN SIBERIA: CURRENT STATE AND WAYS OF POPULATION CONSERVATION." In V International Scientific Conference CONCEPTUAL AND APPLIED ASPECTS OF INVERTEBRATE SCIENTIFIC RESEARCH AND BIOLOGICAL EDUCATION. Tomsk State University Press, 2020. http://dx.doi.org/10.17223/978-5-94621-931-0-2020-56.

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Screening studies of the honey bee in Siberia made it possible to identify the dark forest bee Apis mellifera mellifera populations in the Tomsk region, Krasnoyarsk and Altai territories, and the Altai Republic. A comparative analysis of the genetic diversity of the dark forest bee populations of Siberia, the Urals and Europe, carried out according to the data of the molecular genetic study of the mitochondrial and nuclear genomes, suggests the existence of the Siberian ecotype of the Middle Russian breed. The studied bee colonies are characterized by a high adaptive potential (high degree of "acclimatization") and good economically significant indicators. To preserve the gene pool of the Middle Russian breed of Siberian populations, monitoring studies, ecological and genetic analysis of bee colonies as well as selection and breeding work in the Tomsk bee farm are carried out.
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Samokhvalova, Natalia. "Genetic diversity of populations of the rare species Cypripedium calceolus L. in Belarus." In 79th International Scientific Conference of the University of Latvia. University of Latvia, 2022. http://dx.doi.org/10.22364/iarb.2021.08.

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Studying the level and structure of the genetic diversity of rare species is important for creating an effective strategy for their conservation. Using iPBS markers in our study, it was found that C. calceolus genotypes have a rather low level of genetic diversity. Genetic differentiation was found mainly within coenopopulations, which may be caused by the phenomenon of cross-pollination. The genetic distance between coenopopulations corresponded to their geographic location.
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Zhongbao Li, Jin Chen, and Yuanyu Cao. "Notice of Retraction: Genetic diversity and conservation strategies of amphioxus Branchiostoma belcheri (gray) populations." In 2010 2nd Conference on Environmental Science and Information Application Technology (ESIAT 2010). IEEE, 2010. http://dx.doi.org/10.1109/esiat.2010.5568536.

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Chernetskaya, A. G., T. V. Yunkevich, and T. V. Kalenchuk. "ADDITIONAL METHODS FOR PRESERVING THE GENE POOL OF POPULATIONS OF RARE SPECIES OF MEDICINAL PLANTS." In SAKHAROV READINGS 2021: ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. International Sakharov Environmental Institute of Belarusian State University, 2021. http://dx.doi.org/10.46646/sakh-2021-2-371-374.

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To effectively conserve the gene pool of protected plants ex situ, a wide range of methods and approaches is used, each of which has its own advantages and disadvantages. To date, considerable experience has been gained in the preservation of plant genetic resources, which are important mainly for the agricultural sector, using different temperature regimes; gene banks have been created all over the world. Unfortunately, cryopreservation of seeds and various other plant material is successfully used mainly for agricultural crops, and experiments to preserve the gene pool of rare and endangered plant species are not so widespread. It is necessary to investigate the possibility of sustainable reproduction of the gene pool of certain rare and endangered species. The use of microclonal reproduction of protected plants is an additional way to preserve their gene pool and a prerequisite for the repаtriation of species that are disappearing in nature. The development of effective methods of microclonal reproduction is the basis of work on the creation of in vitro genetic banks of rare and endangered plant species, as well as one of the promising directions for the conservation of biodiversity in general.
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Oreha, Jelena, and Natalja Škute. "The Present Genetic Structure of Vendace (Coregonus albula (L.)): Populations in Latvian Lakes as a Result of Its Management and Conservation." In SIBIC 2022. Basel Switzerland: MDPI, 2022. http://dx.doi.org/10.3390/blsf2022013110.

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Lira, S. M. A., R. Schwamborn, C. Falcão, T. Silva, and R. A. Torres. "GENETIC DIVERSITY AND CONNECTIVITY OF ISOLATED POPULATIONS OF THE LAND CRAB JOHNGARTHIA LAGOSTOMA (BRACHYURA: GECARCINIDAE): IMPLICATIONS FOR ITS CONSERVATION IN THE TROPICAL ATLANTIC." In X Congresso Brasileiro sobre Crustáceos. Sociedade Brasileira de Carcinologia, 2018. http://dx.doi.org/10.21826/2178-7581x2018234.

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Reports on the topic "Populations and conservation genetics"

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Michelmore, Richard, Eviatar Nevo, Abraham Korol, and Tzion Fahima. Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7573075.bard.

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Genetic resistance is often the least expensive, most effective, and ecologically-sound method of disease control. It is becoming apparent that plant genomes contain large numbers of disease resistance genes. However, the numbers of different resistance specificities within a genepool and the genetic mechanisms generating diversity are poorly understood. Our objectives were to characterize diversity in clusters of resistance genes in wild progenitors of cultivated lettuce in Israel and California in comparison to diversity within cultivated lettuce, and to determine the extent of gene flow, recombination, and genetic instability in generating variation within clusters of resistance genes. Genetic diversity of resistance genes was analyzed in wild and cultivated germplasm using molecular markers derived from lettuce resistance gene sequences of the NBS-LRR type that mapped to the major cluster if resistance genes in lettuce (Sicard et al. 1999). Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR- encoding regions, were developed from sequences of resistance gene homologs at the Dm3 cluster (RGC2s) in lettuce. Variation for these markers was assessed in germplasm including 74 genotypes of cultivated lettuce, L. saliva and 71 accessions of the three wild Lactuca spp., L. serriola, L. saligna and L. virosa that represent the major species in the sexually accessible genepool for lettuce. Diversity was also studied within and between natural populations of L. serriola from Israel and California. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. We documented a variety of genetic events occurring at clusters of resistance genes for the second objective (Sicard et al., 1999; Woo el al., in prep; Kuang et al., in prepb). The diversity of resistance genes in haplotypes provided evidence for gene duplication and unequal crossing over during the evolution of this cluster of resistance genes. Comparison of nine resistance genes in cv. Diana identified 22 gene conversion and five intergenic recombinations. We cloned and sequenced a 700 bp region from the middle of RGC2 genes from six genotypes, two each from L. saliva, L. serriola, and L. saligna . We have identified over 60 unique RGC2 sequences. Phylogenetic analysis surprisingly demonstrated much greater similarity between than within genotypes. This led to the realization that resistance genes are evolving much slower than had previously been assumed and to a new model as to how resistance genes are evolving (Michelmore and Meyers, 1998). The genetic structure of L. serriola was studied using 319 AFLP markers (Kuang et al., in prepa). Forty-one populations from Turkey, Armenia, Israel, and California as well as seven European countries were examined. AFLP marker data showed that the Turkish and Armenian populations were the most polymorphic populations and the European populations were the least. The Davis, CA population, a recent post-Columbian colonization, showed medium genetic diversity and was genetically close to the Turkish populations. Our results suggest that Turkey - Armenia may be the center of origin and diversity of L. serriola and may therefore have the greatest diversity of resistance genes. Our characterization of the diversity of resistance genes and the genetic mechanisms generating it will allow informed exploration, in situ and ex situ conservation, and utilization of germplasm resources for disease control. The results of this project provide the basis for our future research work, which will lead to a detailed understanding of the evolution of resistance genes in plants.
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Emily Cavill, Emily Cavill. Conservation Genetics of the Endangered Seychelles Magpie-Robin (Copsychus sechellarum). Experiment, October 2016. http://dx.doi.org/10.18258/8213.

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Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.

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Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.
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Laura Melissa Guzman, Laura Melissa Guzman. Bridging the conservation genetics knowledge gap in the Spanish speaking Global South. Experiment, January 2022. http://dx.doi.org/10.18258/24078.

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Fahima, Tzion, and Jorge Dubcovsky. Map-based cloning of the novel stripe rust resistance gene YrG303 and its use to engineer 1B chromosome with multiple beneficial traits. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598147.bard.

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Research problem: Bread wheat (Triticumaestivum) provides approximately 20% of the calories and proteins consumed by humankind. As the world population continues to increase, it is necessary to improve wheat yields, increase grain quality, and minimize the losses produced by biotic and abiotic stresses. Stripe rust, caused by Pucciniastriiformisf. sp. tritici(Pst), is one of the most destructive diseases of wheat. The new pathogen races are more virulent and aggressive than previous ones and have produced large economic losses. A rich source for stripe-rust resistance genes (Yr) was found in wild emmer wheat populations from Israel. Original Project goals: Our long term goal is to identify, map, clone, characterize and deploy in breeding, novel wild emmer Yr genes, and combine them with multiple beneficial traits. The current study was aiming to map and clone YrG303 and Yr15, located on chromosome 1BS and combine them with drought resistance and grain quality genes. Positional cloning of YrG303/Yr15: Fine mapping of these genes revealed that YrG303 is actually allelic to Yr15. Fine genetic mapping using large segregating populations resulted in reduction of the genetic interval spanning Yr15 to less than 0.1 cM. Physical mapping of the YrG303/Yr15 locus was based on the complete chromosome 1BS physical map of wheat constructed by our group. Screening of 1BS BAC library with Yr15 markers revealed a long BAC scaffold covering the target region. The screening of T. dicoccoidesaccession-specific BAC library with Yr15 markers resulted in direct landing on the target site. Sequencing of T. dicoccoidesBAC clones that cover the YrG303/Yr15 locus revealed a single candidate gene (CG) with conserved domains that may indicate a role in disease resistance response. Validation of the CG was carried out using EMS mutagenesis (loss-of- function approach). Sequencing of the CG in susceptible yr15/yrG303 plants revealed three independent mutants that harbour non-functional yr15/yrG303 alleles within the CG conserved domains, and therefore validated its function as a Pstresistance gene. Evaluation of marker-assisted-selection (MAS) for Yr15. Introgressions of Yr15 into cultivated wheat are widely used now. Recently, we have shown that DNA markers linked to Yr15 can be used as efficient tools for introgression of Yr15 into cultivated wheat via MAS. The developed markers were consistent and polymorphic in all 34 tested introgressions and are the most recommended markers for the introgression of Yr15. These markers will facilitate simultaneous selection for multiple Yr genes and help to avoid escapees during the selection process. Engineering of improved chromosome 1BS that harbors multiple beneficial traits. We have implemented the knowledge and genetic resources accumulated in this project for the engineering of 1B "super-chromosome" that harbors multiple beneficial traits. We completed the generation of a chromosome including the rye 1RS distal segment associated with improved drought tolerance with the Yr gene, Yr15, and the strong gluten allele 7Bx-over-expressor (7Bxᴼᴱ). We have completed the introgression of this improved chromosome into our recently released variety Patwin-515HP and our rain fed variety Kern, as well as to our top breeding lines UC1767 and UC1745. Elucidating the mechanism of resistance exhibited by Yr36 (WKS1). The WHEAT KINASE START1 (WKS1) resistance gene (Yr36) confers partial resistance to Pst. We have shown that wheat plants transformed with WKS1 transcript are resistant to Pst. WKS1 is targeted to the chloroplast where it phosphorylates the thylakoid-associatedascorbateperoxidase (tAPX) and reduces its ability to detoxify peroxides. Based on these results, we propose that the phosphorylation of tAPX by WKS1 reduces the ability of the cells to detoxify ROS and contributes to cell death. Distribution and diversity of WKS in wild emmer populations. We have shown that WKS1 is present only in the southern distribution range of wild emmer in the Fertile Crescent. Sequence analysis revealed a high level of WKS1 conservation among wild emmer populations, in contrast to the high level of diversity observed in NB-LRR genes. This phenomenon shed some light on the evolution of genes that confer partial resistance to Pst. Three new WKS1 haplotypes displayed a resistance response, suggesting that they can be useful to improve wheat resistance to Pst. In summary, we have improved our understanding of cereals’ resistance mechanisms to rusts and we have used that knowledge to develop improved wheat varieties.
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Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.

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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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Nott, M. P., and Nicole Michel. Management Strategies for Reversing Declines in Landbirds of Conservation Concern on Military Installations: Predictive Modeling of Landbird Populations on Military Installations. Fort Belvoir, VA: Defense Technical Information Center, June 2005. http://dx.doi.org/10.21236/ada541508.

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Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597923.bard.

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Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explore the response of the duplicate peanut pod transcriptome to drought stress. Study how entire duplicated PF regulatory processes are networked within a polyploid organism. Discover locus-specific SNP markers and map pod quality traits under different environments. The research included genotypes and segregating populations from Israel and US that are varied in PF, SF and their tolerance to water deficit. Initially, an extensive field trial was conducted to investigate the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Significant irrigation and genotypic effect was observed for the two main PF related traits, "seed ratio" and "dead-end ratio", demonstrating that reduction in irrigation directly influences the developing pods as a result of low water potential. Although the Irrigation × Genotype interaction was not statistically significant, one genotype (line 53) was found to be more sensitive to low irrigation treatments. Two RNAseq studies were simultaneously conducted in IL and the USA to characterize expression changes that accompany shell ("source") and seed ("sink") biogenesis in peanut. Both studies showed that SF and PF processes are very dynamic and undergo very rapid change in the accumulation of RNA, nutrients, and oil. Some genotypes differ in transcript accumulation rates, which can explain their difference in SF and PF potential; like cvHanoch that was found to be more enriched than line 53 in processes involving the generation of metabolites and energy at the beginning of seed development. Interestingly, an opposite situation was found in pericarp development, wherein rapid cell wall maturation processes were up-regulated in line 53. Although no significant effect was found for the irrigation level on seed transcriptome in general, and particularly on subgenomic assignment (that was found almost comparable to a 1:1 for A- and B- subgenomes), more specific homoeologous expression changes associated with particular biosynthesis pathways were found. For example, some significant A- and B- biases were observed in particular parts of the oil related gene expression network and several candidate genes with potential influence on oil content and SF were further examined. Substation achievement of the current program was the development and application of new SNP detection and mapping methods for peanut. Two major efforts on this direction were performed. In IL, a GBS approach was developed to map pod quality traits on Hanoch X 53 F2/F3 generations. Although the GBS approach was found to be less effective for our genetic system, it still succeeded to find significant mapping locations for several traits like testa color (linkage A10), number of seeds/pods (A5) and pod wart resistance (B7). In the USA, a SNP array was developed and applied for peanut, which is based on whole genome re-sequencing of 20 genotypes. This chip was used to map pod quality related traits in a Tifrunner x NC3033 RIL population. It was phenotyped for three years, including a new x-ray method to phenotype seed-fill and seed density. The total map size was 1229.7 cM with 1320 markers assigned. Based on this linkage map, 21 QTLs were identified for the traits 16/64 weight, kernel percentage, seed and pod weight, double pod and pod area. Collectively, this research serves as the first fundamental effort in peanut for understanding the PF and SF components, as a whole, and as influenced by the irrigation level. Results of the proposed study will also generate information and materials that will benefit peanut breeding by facilitating selection for reduced linkage drag during introgression of disease resistance traits into elite cultivars. BARD Report - Project4540 Page 2 of 10
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LeDuc, Jamie, Ryan Maki, Tom Burri, Joan Elias, Jay Glase, Brenda Moraska Lafrancois, Kevin Peterson, David Vandermeulen, and Ben Vondra. Voyageurs National Park interior lakes status and impact assessment. National Park Service, February 2022. http://dx.doi.org/10.36967/nrr-2289923.

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Voyageurs National Park (VNP) is a water-based park that includes part or all of four large lakes and twenty-six smaller lakes commonly referred to as “interior lakes”. The 26 interior lakes of VNP are important aquatic resources with differing size and depth, water chemistry, trophic status, fish communities, and visitor use. Despite the remote location of these lakes, they have been impacted by multiple stressors, including contaminants and non-native species. This assessment provides key information in support of a science-based management plan for these lakes. The objectives of this assessment were to: 1) assess the status of each of the interior lakes and categorically rank the lakes from least to most impacted; 2) use the results to make specific science-based management and restoration recommendations for the most impacted lakes; and 3) make general recommendations that may be useful in managing all of Voyageurs National Park’s interior lakes. When all factors considered in this analysis (water quality, fish mercury concentrations, and fish community characteristics) were combined and assessed, thirteen lakes were classified as most impacted, nine as moderately impacted, and three as least impacted. Although nearly half of the lakes were classified as most impacted in this assessment, many of these lakes are in excellent condition compared to other lakes in the region. The factor-by-factor impact status of the lakes was considered to help describe the condition of the lakes and the potential for restoration. No local management options were identified to mitigate the mercury contamination in these lakes as research has shown the sources of the contamination to arrive from regional and global sources. Similarly, no management actions were identified to reduce nutrient concentrations in the lakes ranked most impacted for nutrient conditions as these are remote lakes with minimal or no development within their watersheds, and it was also noted that paleolimnological studies have shown that the nutrient status of the interior lakes was relatively unchanged from pre-European settlement conditions. Finally, for the lakes in which presumed introduced fish species are present, piscicides were considered as a potential management action. Piscicides were not recommended as a strategy to eradicate introduced fish species as it was determined that genetic conservation of the populations of native fish species still present in these lakes was more valuable than eradicating the introduced species.
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10

Elizur, Abigail, Amir Sagi, Gideon Hulata, Clive Jones, and Wayne Knibb. Improving Crustacean Aquaculture Production Efficiencies through Development of Monosex Populations Using Endocrine and Molecular Manipulations. United States Department of Agriculture, June 2010. http://dx.doi.org/10.32747/2010.7613890.bard.

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Background Most of Australian prawn aquaculture production is based on P. monodon. However, the Australian industry is under intense competition from lower priced overseas imports. The availability of all-female monosex populations, by virtue of their large size and associated premium prize, will offer competitive advantage to the industry which desperately needs to counteract competitors within this market. As for the redclaw production in Israel, although it is at its infancy, the growers realized that the production of males is extremely advantageous and that such management strategy will change the economic assumptions and performances of this aquaculture to attract many more growers. Original objectives (as in original proposal) Investigating the sex inheritance mechanism in the tiger prawn. Identification of genes expressed uniquely in the androgenic gland (AG) of prawns and crayfish. The above genes and/or their products will be used to localize the AG in the prawn and manipulate the AG activity in both species. Production of monosex populations through AG manipulation. In the prawn, production of all-female populations and in the crayfish, all-male populations. Achievements In the crayfish, the AG cDNA library was further screened and a third AG specific transcript, designated Cq-AG3, had been identified. Simultaneously the two AG specific genes, which were previously identified, were further characterized. Tissue specificity of one of those genes, termed Cq-AG2, was demonstrated by northern blot hybridization and RNA in-situ hybridization. Bioinformatics prediction, which suggested a 42 amino acid long signal anchor at the N-terminus of the deduced Cq-AG2, was confirmed by immunolocalization of a recombinant protein. Cq-IAG's functionality was demonstrated by dsRNA in-vivo injections to intersex crayfish. Cq-IAGsilencing induced dramatic sex-related alterations, including male feature feminization, reduced sperm production, extensive testicular apoptosis, induction of the vitellogeningene expression and accumulation of yolk proteins in the ovaries. In the prawn, the AG was identified and a cDNA library was created. The putative P. monodonAG hormone encoding gene (Pm-IAG) was identified, isolated and characterized for time of expression and histological localization. Implantation of the AG into prawn post larvae (PL) and juveniles resulted in phenotypic transformation which included the appearance of appendix masculina and enlarged petasma. The transformation however did not result in sex change or the creation of neo males thus the population genetics stage to be executed with Prof. Hulata did not materialized. Repeated AG implantation is currently being trialed. Major conclusions and Implications, both scientific and agricultural Cq-IAG's involvement in male sexual differentiation had been demonstrated and it is strongly suggested that this gene encodes an AG hormone in this crayfish. A thorough screening of the AG cDNA library shows Cq-IAG is the prominent transcript within the library. However, the identification of two additional transcripts hints that Cq-IAG is not the only gene mediating the AG effects. The successful gene silencing of Cq-IAG, if performed at earlier developmental stages, might accomplish full and functional sex reversal which will enable the production of all-male crayfish populations. Pm-IAG is likely to play a similar role in prawns. It is possible that repeated administration of the AG into prawn will lead to the desired full sex reversal, so that WZ neo males, crossed with WZ females can result in WW females, which will form the basis for monosex all-female population.
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