Relevant bibliographies by topics / 060411 Population, Ecological and Evolutionary Genetics

Academic literature on the topic '060411 Population, Ecological and Evolutionary Genetics'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "060411 Population, Ecological and Evolutionary Genetics"

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Ferriere, Regis, and Stéphane Legendre. "Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1610 (January 19, 2013): 20120081. http://dx.doi.org/10.1098/rstb.2012.0081.

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Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.
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Pelletier, F., D. Garant, and A. P. Hendry. "Eco-evolutionary dynamics." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1523 (June 12, 2009): 1483–89. http://dx.doi.org/10.1098/rstb.2009.0027.

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Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.
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de Vries, Charlotte, and Hal Caswell. "Stage-Structured Evolutionary Demography: Linking Life Histories, Population Genetics, and Ecological Dynamics." American Naturalist 193, no. 4 (April 2019): 545–59. http://dx.doi.org/10.1086/701857.

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Ezard, Thomas H. G., Steeve D. Côté, and Fanie Pelletier. "Eco-evolutionary dynamics: disentangling phenotypic, environmental and population fluctuations." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1523 (June 12, 2009): 1491–98. http://dx.doi.org/10.1098/rstb.2009.0006.

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Decomposing variation in population growth into contributions from both ecological and evolutionary processes is of fundamental concern, particularly in a world characterized by rapid responses to anthropogenic threats. Although the impact of ecological change on evolutionary response has long been acknowledged, the converse has predominantly been neglected, especially empirically. By applying a recently published conceptual framework, we assess and contrast the relative importance of phenotypic and environmental variability on annual population growth in five ungulate populations. In four of the five populations, the contribution of phenotypic variability was greater than the contribution of environmental variability, although not significantly so. The similarity in the contributions of environment and phenotype suggests that neither is worthy of neglect. Population growth is a consequence of multiple processes, which strengthens arguments advocating integrated approaches to assess how populations respond to their environments.
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Westbury, Michael V., Diana Le Duc, David A. Duchêne, Arunkumar Krishnan, Stefan Prost, Sereina Rutschmann, Jose H. Grau, et al. "Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae." Molecular Biology and Evolution 38, no. 9 (February 24, 2021): 3884–97. http://dx.doi.org/10.1093/molbev/msab055.

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Abstract During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.
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Ross, Perran A., Michael Turelli, and Ary A. Hoffmann. "Evolutionary Ecology of Wolbachia Releases for Disease Control." Annual Review of Genetics 53, no. 1 (December 3, 2019): 93–116. http://dx.doi.org/10.1146/annurev-genet-112618-043609.

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Wolbachia is an endosymbiotic Alphaproteobacteria that can suppress insect-borne diseases through decreasing host virus transmission (population replacement) or through decreasing host population density (population suppression). We contrast natural Wolbachia infections in insect populations with Wolbachia transinfections in mosquitoes to gain insights into factors potentially affecting the long-term success of Wolbachia releases. Natural Wolbachia infections can spread rapidly, whereas the slow spread of transinfections is governed by deleterious effects on host fitness and demographic factors. Cytoplasmic incompatibility (CI) generated by Wolbachia is central to both population replacement and suppression programs, but CI in nature can be variable and evolve, as can Wolbachia fitness effects and virus blocking. Wolbachia spread is also influenced by environmental factors that decrease Wolbachia titer and reduce maternal Wolbachia transmission frequency. More information is needed on the interactions between Wolbachia and host nuclear/mitochondrial genomes, the interaction between invasion success and local ecological factors, and the long-term stability of Wolbachia-mediated virus blocking.
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Sadras, Victor O. "Evolutionary and ecological perspectives on the wheat phenotype." Proceedings of the Royal Society B: Biological Sciences 288, no. 1958 (September 8, 2021): 20211259. http://dx.doi.org/10.1098/rspb.2021.1259.

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Technologies, from molecular genetics to precision agriculture, are outpacing theory, which is becoming a bottleneck for crop improvement. Here, we outline theoretical insights on the wheat phenotype from the perspective of three evolutionary and ecologically important relations—mother–offspring, plant–insect and plant–plant. The correlation between yield and grain number has been misinterpreted as cause-and-effect; an evolutionary perspective shows a striking similarity between crop and fishes. Both respond to environmental variation through offspring number; seed and egg size are conserved. The offspring of annual plants and semelparous fishes, lacking parental care, are subject to mother–offspring conflict and stabilizing selection. Labile reserve carbohydrates do not fit the current model of wheat yield; they can stabilize grain size, but involve trade-offs with root growth and grain number, and are at best neutral for yield. Shifting the focus from the carbon balance to an ecological role, we suggest that labile carbohydrates may disrupt aphid osmoregulation, and thus contribute to wheat agronomic adaptation. The tight association between high yield and low competitive ability justifies the view of crop yield as a population attribute whereby the behaviour of the plant becomes subordinated within that of the population, with implications for genotyping, phenotyping and plant breeding.
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Logares, Ramiro. "Population genetics: the next stop for microbial ecologists?" Open Life Sciences 6, no. 6 (December 1, 2011): 887–92. http://dx.doi.org/10.2478/s11535-011-0086-9.

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AbstractMicrobes play key roles in the functioning of the biosphere. Still, our knowledge about their total diversity is very limited. In particular, we lack a clear understanding of the evolutionary dynamics occurring within their populations (i.e. among members of the same biological species). Unlike animals and plants, microbes normally have huge population sizes, high reproductive rates and the potential for unrestricted dispersal. As a consequence, the knowledge of population genetics acquired from studying animals and plants cannot be applied without extensive testing to microbes. Next generation molecular tools, like High Throughput Sequencing (e.g. 454 and Illumina) coupled to Single Cell Genomics, now allow investigating microbial populations at a very fine scale. Such techniques have the potential to shed light on several ecological and evolutionary processes occurring within microbial populations that so far have remained hidden. Furthermore, they may facilitate the identification of microbial species. Eventually, we may find an answer to the question of whether microbes and multicellular organisms follow the same or different rules in their population diversification patterns.
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Coulson, T., T. G. Benton, P. Lundberg, S. R. X. Dall, B. E. Kendall, and J. M. Gaillard. "Estimating individual contributions to population growth: evolutionary fitness in ecological time." Proceedings of the Royal Society B: Biological Sciences 273, no. 1586 (December 6, 2005): 547–55. http://dx.doi.org/10.1098/rspb.2005.3357.

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Ecological and evolutionary change is generated by variation in individual performance. Biologists have consequently long been interested in decomposing change measured at the population level into contributions from individuals, the traits they express and the alleles they carry. We present a novel method of estimating individual contributions to population growth and changes in distributions of quantitative traits and alleles. An individual's contribution to population growth is an individual's realized annual fitness. We demonstrate how the quantities we develop can be used to address a range of empirical questions, and provide an application to a detailed dataset of Soay sheep. The approach provides results that are consistent with those obtained using lifetime estimates of individual performance, yet is substantially more powerful as it allows lifetime performance to be decomposed into annual survival and fecundity contributions.
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Pertoldi, C., L. A. Bach, J. C. Svenning, C. Damgaard, and M. Bayley. "Contributions from population genetics to ecotoxicology and stress ecology in light of transformation to the population genomic era." Archives of Biological Sciences 64, no. 2 (2012): 557–65. http://dx.doi.org/10.2298/abs1202557p.

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With the advent of the genomic era, which has partly been driven by advances in stress ecology, there is enormous growth in molecular and computer simulation techniques. Here we propose combining some of these techniques to give more elaborate risk assessments that include the effects of population variation in genotypes, phenotypes, and the way they link to aspects of life history and adaptive potential. We focused on ways to ascertain whether phenotypic plasticity or evolutionary responses constitute the basis for observed stress responses, as well as on the extrapolation problem, i.e. how do responses under controlled conditions correspond to those observed in natural ecological populations or in evolutionary end-points of interest? Additionally, we discuss the ways to integrate environmental variability into risk analysis and pest control predictions that include gene-environment interactions, focusing also on the importance of erosion of genetic diversity by toxic stressors to the risk of population extinction.
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Dissertations / Theses on the topic "060411 Population, Ecological and Evolutionary Genetics"

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Star, Bastiaan, and n/a. "Space matters : modeling selection in spatially heterogeneous environments." University of Otago. Department of Zoology, 2008. http://adt.otago.ac.nz./public/adt-NZDU20080507.151534.

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Selection in spatially heterogeneous environments is a convenient explanation for the high levels of genetic variation observed in natural populations. Indeed, theoretical studies predict that spatial heterogeneity leads to higher levels of variation in a variety of selection models. These models, however, have assumed quite restrictive parameters (e.g., two alleles, fixed gene flow and specific selection schemes). Therefore, the effect on spatial heterogeneity is still poorly understood for a wider range of parameters (e.g., multiple alleles, different levels of gene flow and more general selection schemes). We have relaxed some of the assumptions that have limited the previous models and studied the effect of spatial heterogeneity using simple single-locus viability selection models. First, we investigate the rarity of the parts of fitness space maintaining variation for multiple alleles and different levels of gene flow by randomly sampling that space using a "fitness space" approach. The volume of fitness space maintaining variation is always larger in a spatial model compared to a single-population model regardless of gene flow. Moreover, this volume is relatively larger for higher numbers of alleles, indicating that spatial heterogeneity is more efficient maintaining higher levels of variation. Second, we investigate the ease with which a more natural process of recurrent mutation and selection evolves to the particular area of fitness space maintaining variation using a "construction" approach. Depending on the amount of gene flow, the construction approach leads to both higher and lower levels of variation compared to a single-population model. Thus, spatial heterogeneity can both constrain and promote the ease with which a natural process of mutation and selection evolves to maintain variation. Also, the construction approach results in variation being maintained in a more stable subset of the volume of fitness space than the volume that resulted from the fitness space approach. Third, we investigate the effect of higher and lower levels of spatial environmental heterogeneity using the construction approach. The different levels of heterogeneity and gene flow interact to influence the amount of variation that is eventually maintained and this interaction effect is especially strong for intermediate levels of gene flow. More heterogeneous environments can maintain higher levels of variation, but selection in these environments also results in a higher level of migration load, lowering the final amount of adaptation that is achieved by the simulated evolutionary process. Finally, we investigate effect of genetic drift and finite populations using the construction approach. Interestingly, two different effects emerge for smaller and larger populations; in smaller populations genetic drift lowers the amount of variation as expected, whereas, more surprisingly, genetic drift increases the amount of variation in larger populations. Overall, spatial heterogeneity has profound effects on the outcome of selection, resulting in elevated levels of genetic variation for a wide variety of parameters.
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Inoue, Kentaro. "A Comprehensive Approach to Conservation Biology: From Population Genetics to Extinction Risk Assessment for Two Species of Freshwater Mussels." Miami University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=miami1437683696.

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(7023467), Charity Grace Owings. "Mediators of Fine-Scale Population Genetic Structure in the Black Blow Fly, Phormia regina (Meigen) (Diptera: Calliphoridae)." Thesis, 2019.

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Population genetic structure is difficult to assess in blow flies (Diptera: Calliphoridae) due to high connectivity and genetic diversity of subpopulations. Previous studies revealed high relatedness among individuals within wild samples of blow fly populations, however broad geographic structure was absent. The aim of this research was to determine if blow fly genetic structure exists at a fine spatiotemporal resolution and, if so, to elucidate the influence of environmental factors and resource availability on fly genetics. Specifically, blow fly population genetic patterns were tested against anull hypothesis that flies adhere to a patchy population model with high genetic diversity (i.e. no structure) and high resource availability. Samples of the black blow fly, Phormia regina Meigen (Diptera: Calliphoridae), were collected at six urban parks in Indiana, USA (=urban) in 2016 and 2017 (N = 14 and 16 timepoints, respectively). Additional sampling in different ecoregions was performed to determine if trends observed at a high-resolution scale were also present at a broad geographic scale. Therefore, P. regina were also collected at four sites within two national parks (the Great Smoky Mountains and Yellowstone National Parks) over a three-day period. Randomly selected females (N = 10) from each sample underwent the following analyses: 1) gut DNA extraction, 2) molecular analysis at 6 microsatellite loci, 3) vertebrate-specific 12S and 16S rRNA sequencing, and, 4) vertebrate fecal metabolite screening. Flies from the national parks and a comparable subset of urban data also underwent stable isotopeanalysis (SIA) to determine larval food source. Overall, strong seasonal population genetic structure was observed over both years in the urban environment (2016 F’ST= 0.47, 2017 F’ST0.34), however spatial structure was lacking, as seen in previous studies (2016 F’ST= 0.04, 2017 F’ST0.03). Weather conditions prior to and on the day of blow fly collections, interspecific competition, and resource availability greatly impacted the genetic diversity and kinship of P. regina. A total of 17 and 19 vertebrate species were detected by flies in 2016 and 2017, respectively, and many flies tested positive for vertebrate feces, suggesting that many varied resources are important for maintaining high gene flow among geographic locations. Genetic diversity was non-existent in flies collected from the Smokies (F’ST= 0.00), while very slight spatial structure existed in the Yellowstone populations (F’ST= 0.07). Environmental factors such as temperature, humidity, and wind speed were all statistically relevant in maximizing fly collections with vertebrate resources. In 720 min of total sampling time in the national parks and a subset of urban data, 28 vertebrate species were identified, and fecal resources appeared to be the most abundant in Yellowstone. Stable isotopeanalysis revealed a majority of larval resources in the national parks were herbivores, with a more even distribution of carnivore and herbivore carcasses present in the urban environment, which likely explains the high genetic diversity of adult flies in these regions. Overall, the null hypothesis that P. regina adheres to a patchy population model could not be rejected for the Smokies populations. However, the urban and Yellowstone populations appear to adhere to a Levins metapopulation model in which variable availability in resources leads to random bottleneck events in the local populations. Overall, environmental conditions, competition, and resource availability are all important factors influencing P. regina population genetic structure in different environments.
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(9720734), Rian R. Bylsma. "POPULATION GENETIC AND GENOMIC ANALYSES OF WESTERN MASSASAUGA (SISTRURUS TERGEMINUS SSP.): SUBSPECIES DELIMITATION AND CONSERVATION STATUS." Thesis, 2020.

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The Western Massasauga (Sistrurus tergeminus) is a small, North American rattlesnake found west of the Mississippi River. Sistrurustergeminushas previously been divided into two putative subspecies, Desert (S. t. edwardsii) and Prairie Massasaugas (S. t. tergeminus) based upon qualitative variation in morphology, coloration, and habitat. The Desert Massasauga subspecies has been formally petitioned for federal listing under the U.S. Endangered Species Act. Ouroverarching goal was to evaluate genetic structure and genomic differentiation between specimens of the two putative subspecies in an effort to inform ongoing conservation assessments. To that end, we generated whole genome sequence data for both putativetaxa and then developed nearly 200 genetic markers from different fractions of the genome (~50 intergenic and ~50 genic markers from each of the two subspecies) to test for population structure across much of the Western Massasauga range. Mean genomic divergence between subspecies was only 0.0041 ± 0.0080 (Kimura’s 2-parameter distance) for nuclear sequences and 0.0175 ± 0.0031 for mitochondrial sequences, both exceedingly low values which approach the minimum of zero. Admixture analyses and F-statistics both indicated that regardless of how the markers were partitioned, genetic structure was oriented far more along a geographic axis (isolation-by-distance) than a taxonomic axis (i.e., between putative subspecies). Overall, our analyses provide little support that formal protection of the purported Desert Massasauga is warranted based on the homogeneity of the collective Western Massasauga gene pool.
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(9760598), Samarth Mathur. "AN EVOLUTIONARY GENOMICS STUDY FOR CONSERVATION OF THE MONTEZUMA QUAIL." Thesis, 2020.

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Humans have altered natural landscape since the agricultural revolution, but it has been most destructive since human globalization and rampant industrialization in the last two centuries. These activities deteriorate and fragments natural habitat of many wild species that creates small isolated populations that lose genetic diversity over time. Loss of genetic diversity reduces the adaptive capacity of a population to respond to future environmental change and increases their extinction risks. Implementing strategies for wildlife conservation is a challenge primarily because of our lack of understanding of the biology of many wild species, the risks they are currently facing, and their evolutionary histories. With the advent of genomic and computational techniques, it is now possible to address these concerns. In my research, I used genomics to study the evolutionary history of the Montezuma Quail (Cyrtonyx montezumae) and created monitoring tools that can be readily applied by wildlife managers for its conservation. Montezuma Quail is a small gamebird found mostly in Mexico with peripheral populations existing in Arizona, New Mexico, and Texas. Montezuma Quail are going through species wide decline in the United States and are listed as vulnerable in the state of Texas due to their small population sizes and geographic isolation from rest of the range. My results show that Texas quail are genetically distinct and significantly less diverse than Arizona quail. Analysis of whole genome sequences from multiple individuals show that due to small population sizes and isolation, Texas quail are significantly more inbred and genetic drift is the major contributor for loss of genetic diversity we see today. Inbreeding is negatively impacting Texas quail as they carry more deleterious alleles within their genome that reduce fitness of the individuals. Demographic models predict that both Arizona and Texas populations were formed via founding bottlenecks around 20,000 years ago. Texas populations have maintained small population sizes since its split from the ancestral populations and are less efficient in purging new deleterious mutations that arise post-bottleneck. The inferences from my research not only carries direct implications for Montezuma Quail conservationists, but also illustrate the power of evolutionary genomics in implementing targeted management strategies for any species that face existential threats in today’s waning world.

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(5931041), Stephanie Farmer. "An Exploration of Irish Surname History through Patrilineal Genetics." Thesis, 2020.

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Due to Ireland’s secluded geographical location, its genetic structure is a popular topic of study. The indigenous inhabitants of Ireland remained undisturbed for a long period time, allowing for a distinct genetic population to be created. This peace was disrupted by conflict with invading forces, such as the Nordic Vikings and Anglo-Norman forces. However, these historical events helped to shape both the culture of Ireland and the ancestry seen in the Irish population today. In Ireland, quite like many countries around the world, the male’s surname is passed from father to son, just as the Y-chromosome. The relationship between Irish surnames and their corresponding Y-haplogroups was examined to determine if common and rare Irish surnames can be genetically linked to the historical invasions listed above. The surnames chosen for this study were selected based on their prevalence in Ireland, rare or common, and their proposed historical origin, Irish, Norse or British. To discover any possible patterns in surnames and Y-chromosomal DNA, Y-haplogroups were generated from the DNA of 630 Irish male subjects using an assay specifically developed for the region. The assay contains twenty single-nucleotide polymorphisms (SNPs) that were selected to further resolve the R1b-L21 Y-haplogroup for Irish ancestry, the most prevalent haplogroup in Western Europe, and Ireland in particular. Additional Y-STR data was also generated to examine recent surname history within the collected individuals. Each surname was examined to determine whether one haplogroup occurred more frequently and with this method, distinct patterns in Irish surnames and geographical locations were discovered. In addition to resolving Y-surname history patterns, it is also believed that this assay may be beneficial in determining if an unknown DNA sample is of Western European origin and even in some cases, if a more specific Irish origin can be predicted.

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"Evolution Under Our Feet: Anthony David Bradshaw (1926–2008) and the Rise of Ecological Genetics." Doctoral diss., 2015. http://hdl.handle.net/2286/R.I.30014.

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abstract: How fast is evolution? In this dissertation I document a profound change that occurred around the middle of the 20th century in the way that ecologists conceptualized the temporal and spatial scales of adaptive evolution, through the lens of British plant ecologist Anthony David Bradshaw (1926–2008). In the early 1960s, one prominent ecologist distinguished what he called “ecological time”—around ten generations—from “evolutionary time”— around half of a million years. For most ecologists working in the first half of the 20th century, evolution by natural selection was indeed a slow and plodding process, tangible in its products but not in its processes, and inconsequential for explaining most ecological phenomena. During the 1960s, however, many ecologists began to see evolution as potentially rapid and observable. Natural selection moved from the distant past—a remote explanans for both extant biological diversity and paleontological phenomena—to a measurable, quantifiable mechanism molding populations in real time. The idea that adaptive evolution could be rapid and highly localized was a significant enabling condition for the emergence of ecological genetics in the second half of the 20th century. Most of what historians know about that conceptual shift and the rise of ecological genetics centers on the work of Oxford zoologist E. B. Ford and his students on polymorphism in Lepidotera, especially industrial melanism in Biston betularia. I argue that ecological genetics in Britain was not the brainchild of an infamous patriarch (Ford), but rather the outgrowth of a long tradition of pastureland research at plant breeding stations in Scotland and Wales, part of a discipline known as “genecology” or “experimental taxonomy.” Bradshaw’s investigative activities between 1948 and 1968 were an outgrowth of the specific brand of plant genecology practiced at the Welsh and Scottish Plant Breeding stations. Bradshaw generated evidence that plant populations with negligible reproductive isolation—separated by just a few meters—could diverge and adapt to contrasting environmental conditions in just a few generations. In Bradshaw’s research one can observe the crystallization of a new concept of rapid adaptive evolution, and the methodological and conceptual transformation of genecology into ecological genetics.
Dissertation/Thesis
Doctoral Dissertation Biology 2015
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(6630767), Ian M. Silver-Gorges. "Evidence for Hierarchical Structuring and Large-Scale Connectivity in Eastern Pacific Olive ridley Sea Turtles (Lepidochelys olivacea)." Thesis, 2019.

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Inferring genetic population structure in endangered, highly migratory species such as sea turtles is a necessary but difficult task in order to design conservation and management plans. Genetically discrete populations are not obvious in highly migratory species, yet require unique conservation planning due to unique spatial and behavioral life-history characteristics. Population structure may be inferred using slowly evolving mitochondrial DNA (mtDNA), but some populations may have diverged recently and are difficult to detect using mtDNA. In these cases, rapidly evolving nuclear microsatellites may better elucidate population structuring. Bayesian inference and ordination may be useful for assigning individuals to inferred populations when populations are unknown. It is important to carefully examine population inference results to detect hierarchical population structuring, and to use multiple, mathematically diverse methods when inferring and describing population structure from genetic data. Here I use Bayesian inference, ordination, and multiple genetic analyses to investigate population structure in Olive ridley sea turtles (ORs; Lepidochelys olivacea) nesting in northwestern Costa Rica (NWCR) and across the entire Eastern Tropical Pacific (ETP). Mitochondrial DNA did not show structure within NWCR, and existing data from prior studies are not appropriately published to compare NWCR to Mexican ORs. In NWCR, Bayesian inference suggested one population, but ordination suggested four moderately structured populations with high internal relatedness, and moderate to high levels of connectivity. In the ETP, Bayesian inference suggested a Mexican and Central American population, but hierarchical analysis revealed a third subpopulation within Mexico. Ordination revealed nine cryptic clusters across the ETP that primarily corresponded to Mexican and Central American populations but contained individuals from both populations, some from other, distant nesting sites. The subpopulation within Mexico was well-defined after ordination, and all clusters displayed high 10 internal relatedness and moderate genetic differentiation. Bottlenecks were detected in both putative populations, at seven Mexican and two Central American nesting beaches, and in six out of nine inferred clusters, including three out of four Mexican clusters. Bottleneck events may have played some role in cluster differentiation. Migration was significant from Mexico to Central America at multiple levels, but did not necessarily agree with potential migrants elucidated by ordination. Migration was generally lower between ordination-inferred clusters than between nesting sites or Bayesian-inferred clusters. Phylogenetic trees generally supported structuring by ordination, rather than by Bayesian inference. Structuring in ordination not tied to bottleneck events could be due to mating behaviors or patterns of nesting beach colonization dictated by environmental features. In this study, ordination provided a more practical and nuanced framework for defining MUs and DIPs in ETP ORs than did STRUCTURE. This may be due to hierarchical structuring within ETP ORs that may be present in other sea turtle populations and species. In the case of ETP ORs, hierarchical structure may be an artefact of recent population bottlenecks and subsequent recolonization of nesting beaches, or due to mating at foraging grounds or along migratory routes. Bayesian inference may not be the best method for population inference in highly migratory species such as sea turtles, which have a high potential for broad scale genetic connectivity, and therefore may display hierarchical population structuring not easily related to nesting sites. Future studies, and perhaps published studies, should incorporate Bayesian inference and ordination, as well as other measures of population divergence and descriptive statistics, when searching for population structure in highly migratory species such as sea turtles.
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Collett, Michael Anthony. "Cloning, characterisation and evolutionary relationships of two pyr4 genes from an Acremonium endophyte of perennial ryegrass : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Molecular Genetics at Massey University, Palmerston North, New Zealand." 1994. http://hdl.handle.net/10179/1300.

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A fragment of the Claviceps purpurea pyr4 gene, encoding the enzyme orotidine-5'-monophosphate decarboxylase (OMPdecarboxylase) was used to screen a genomic library to an isolate (designated Lp1) of an Acremonium sp. which grows as an endophyte in perennial ryegrass (Lolium perenne). Four positive clones, λMC11, λMC12, λMC14 and λMC20 were isolated. Three of these clones, λMC12, λMC14 and λMC20 were overlapping clones from the same locus, while λMC11 was from a different locus. Fragments of these clones which hybridised with C. purpurea pyr4 were sequenced and found to have similarity with pyr4 from other fungi of the Pyrenomycetes and related Deuteromycetes, suggesting that Lp1 has evolved from a sexual Pyrenomycetes species. The pyr4 from λMC12, λMC14 and λMC20 was designated pyr4-1 and that from λMC11 was designated pyr4-2. The predicted ORFs of the two genes were highly conserved and the 5' non-coding nucleotide sequences were the least conserved regions. RT-PCR and northern analysis of total RNA from Lp1 demonstrated that transcripts approximately 1.4 kb in length were produced from the two genes and present at similar levels. Genomic fragments containing pyr4-1 or pyr4-2 were transformed into a strain of Aspergillus nidulans which has a mutation in the pyrG gene (encoding OMPdecarboxylase). Both of the Lp1 pyr4 complemented a pyrG mutation in Aspergillus nidulans, confirming that both pyr4-1 and pyr4-2 encode functional OMPdecarboxylases. Comparisons of pyr4 restriction fragment length polymorphisms (RFLPs) from Lp1 and isolates of Epichloë typhina, E. festucae, A. lolii, A. uncinatum, and three endophyte taxonomic groupings from Festuca arundinacea: FaTG-1 (=A. coenophialum), FaTG-2 and FaTG-3 suggested that pyr4-1 originated from E. typhina, the ryegrass choke pathogen, and pyr4-2 originated from A. lolii, another endophyte from perennial ryegrass. This suggested that Lp1 is an interspecific hybrid, between E. typhina and A. lolii. Comparisons of the variable 5' non-coding nucleotide sequences from pyr4 of Lp1 and other isolates demonstrated that E. typhina, and A. lolii or E. festucae were the most likely ancestors of the two pyr4 found in Lp1. The A. lolii and E. festucae sequences were very similar, suggesting they are closely related. A. lolii has most probably evolved from an E. festucae, and in the process lost the sexual cycle. Analysis of single spore purified isolates of Lp1 revealed that Lp1 was a homokaryon for pyr4. A Southern blot of a CHEF gel of Lp1 and these single spored isolates was hybridised to a pyr4 probe and demonstrated that pyr4-1 and pyr4-2 were present on either two chromosomes of similar size, or one chromosome. The hybridisation that gave rise to Lp1 was concluded to have been a relatively recent event, given the similarity of pyr4-1 and pyr4-2 nucleotide sequences to those of their probable ancestors, and the fact that both genes are expressed and functional. Interspecific hybridisation is probably widespread in the asexual endophytes, and may be an important event in their evolution, and the evolution of other fungal species.
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Books on the topic "060411 Population, Ecological and Evolutionary Genetics"

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

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1933-, Parsons P. A., ed. Evolutionary genetics and environmental stress. Oxford: Oxford University Press, 1991.

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Hoffmann, Ary A. Evolutionary genetics and environmental stress. Oxford: Oxford University Press, 1993.

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Walsh, Bruce, and Michael Lynch. Evolution and Selection of Quantitative Traits. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.001.0001.

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Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.
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Allendorf, Fred W., W. Chris Funk, Sally N. Aitken, Margaret Byrne, Gordon Luikart, and Agostinho Antunes. Conservation and the Genomics of Populations. 3rd ed. Oxford University Press, 2022. http://dx.doi.org/10.1093/oso/9780198856566.001.0001.

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Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genomics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or commercial importance. New molecular techniques, statistical methods, and computer programs, genetic principles, and methods are becoming increasingly useful in the conservation of biological diversity. Using a balance of data and theory, coupled with basic and applied research examples, this book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, the interpretation of genetic data from natural populations, and how these can be applied to conservation. The book includes examples from plants, animals, and microbes in wild and captive populations. This third edition has been thoroughly revised to include advances in genomics and contains new chapters on population genomics, genetic monitoring, and conservation genetics in practice, as well as new sections on climate change, emerging diseases, metagenomics, and more. More than one-third of the references in this edition were published after the previous edition. Each of the 24 chapters and the Appendix end with a Guest Box written by an expert who provides an example of the principles presented in the chapter from their own work. This book is essential for advanced undergraduate and graduate students of conservation genetics, natural resource management, and conservation biology, as well as professional conservation biologists and policy-makers working for wildlife and habitat management agencies. Much of the book will also interest nonprofessionals who are curious about the role of genetics in conservation and management of wild and captive populations.
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Book chapters on the topic "060411 Population, Ecological and Evolutionary Genetics"

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Murphy, Michael, and John A. Sved. "The Effects of Natural and Artificial Selection on Dysgenic Potential of a Wild Population of Drosophila melanogaster." In Ecological and Evolutionary Genetics of Drosophila, 87–98. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4684-8768-8_7.

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Kawecki, Tadeusz J. "Ecological and Evolutionary Consequences of Source-Sink Population Dynamics." In Ecology, Genetics and Evolution of Metapopulations, 387–414. Elsevier, 2004. http://dx.doi.org/10.1016/b978-012323448-3/50018-0.

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Stepien, Carol, Jasminca Behrmann-Godel, and Louis Bernatchez. "Evolutionary Relationships, Population Genetics, and Ecological and Genomic Adaptations of Perch (Perca)." In Biology of Perch, 7–46. CRC Press, 2015. http://dx.doi.org/10.1201/b18806-3.

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"Evolutionary Relationships, Population Genetics, and Ecological and Genomic Adaptations of Perch (Perca)." In Biology of Perch, 17–56. CRC Press, 2015. http://dx.doi.org/10.1201/b18806-5.

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"Paddlefish: Ecological, Aquacultural, and Regulatory Challenges of Managing a Global Resource." In Paddlefish: Ecological, Aquacultural, and Regulatory Challenges of Managing a Global Resource, edited by Michael R. Schwemm, Allison M. Asher, Edward J. Heist, Thomas F. Turner, and Anthony A. Echelle. American Fisheries Society, 2019. http://dx.doi.org/10.47886/9781934874530.ch2.

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<i>Abstract</i>.—Long-term sustainability of the Paddlefish <i>Polyodon spathula</i> will require effective consideration and application of genetic principles and tools by fisheries managers. Paddlefish migration patterns, harvest, and fish culture and stocking for mitigation collectively influence stock structure and genetic resources. Studies since the early 1980s have indicated that Paddlefish showed higher levels of genetic diversity and gene flow in open rivers, but that diversity and gene flow have typically been reduced within geographically isolated and impounded reaches, a result consistent with reduced migratory behavior, river fragmentation, and demographic bottlenecks. Concurrent hatchery propagation methods and broodstock selection probably also contributed to unintentional genetic changes in stocked Paddlefish populations (Gavins Point, South Dakota-Nebraska). We present case studies depicting how stocking has altered the genetic structure of populations and reduced within-population diversity. Documented genetic changes have resulted from 1) annual stocking and low natural reproduction leading to a low effective population size (Table Rock Lake, Missouri), 2) introgression by hatchery-reared broodstock from a distant source population (Gavins Point, South Dakota-Nebraska into Kaw Lake, Oklahoma), and 3) subsampling of genetic diversity in a stocked population (Oologah Lake, Verdigris River, Oklahoma) relative to the broodstock source (Grand Lake, Grand/Neosho River, Oklahoma). We present two other case studies of population genetics issues from Grand Lake, the first suggesting a population bottleneck due to impoundment by dam approximately 80 years ago, and the second detailing the potential genetic effects of episodic recruitment on genetic effective size. Paddlefish in some areas have fortunately retained genetic variation and avoided immediate concerns of inbreeding, due in part to life-history attributes and prudent management. Increased consideration of genetic structure both within states and across jurisdictional boundaries will additionally improve range-wide management decisions. These case studies offer several general conclusions useful to guide future management of Paddlefish populations in order to maintain evolutionary potential and local adaptation, important considerations for conservation and sustainable harvest in modified river systems.
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DeLong, John P. "Selection on Functional Response Parameters." In Predator Ecology, 65–78. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780192895509.003.0006.

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In this chapter I show why there should be selection on traits associated with functional response parameters. I describe this using standard quantitative genetics techniques to show how a classic evolutionary arms race arises and how it depends on key features of the functional response. I suggest this arms race is more aptly described as a tug-of-war. I then show that selection on the predator and prey components of space clearance rate is synchronous for predator and prey through population cycles but alternating between predator and prey for handling time. I suggest that trade-offs, ecological pleiotropy, and phenotypic plasticity can slow natural selection on traits that influence functional response parameters.
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