scholarly journals Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 306
Author(s):  
Maurizio Rossetto ◽  
Peter D. Wilson ◽  
Jason Bragg ◽  
Joel Cohen ◽  
Monica Fahey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
A Priori ◽  
Genetic Data ◽  
Environmental Data ◽  
Specific Data ◽  
Acacia Species ◽  
Simple Observation ◽  
Source Plant ◽  
Species Specific

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.

scholarly journals Long-term molecular evolutionary rate determines intraspecific genetic diversity

2019 ◽  
Author(s):  
Jiaqi Wu ◽  
Takahiro Yonezawa ◽  
Hirohisa Kishino
Keyword(s):  
Genetic Diversity ◽  
De Novo ◽  
Early Stage ◽  
Morphological Evolution ◽  
Biological Traits ◽  
Gene Trees ◽  
Intraspecific Genetic Diversity ◽  
Molecular Evolutionary Rates ◽  
Species Specific

AbstractWhat determines genetic diversity and how it connects to the various biological traits is unknown. In this work, we offer answers to these questions. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual genomes of human, chimpanzee, gorilla, mouse and dog/wolf, we found that intraspecific genetic diversity is determined by long-term molecular evolutionary rates, rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Expanding this new finding, we developed a method to detect fluctuations of species-specific selection on genes as the deviations of intra-species genetic diversity predicted from long-term rates. We show that the evolution of epithelial cells, rather than of connective tissue, mainly contributes to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps subjected by infectious diseases are most representative of adaptive evolution.

scholarly journals Inference with selection, varying population size and evolving population structure: Application of ABC to a forward-backward coalescent process with interactions

2019 ◽  
Author(s):  
Clotilde Lepers ◽  
Sylvain Billiard ◽  
Matthieu Porte ◽  
Sylvie Méléard ◽  
Viet Chi Tran
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
A Priori ◽  
Real Data ◽  
Genetic Data ◽  
Accurate Estimate ◽  
Asexual Population ◽  
Y Chromosomes ◽  
Population Structures ◽  
Approximate Bayesian

AbstractGenetic data are often used to infer history, demographic changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed a priori known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interaction to describe an asexual population, and we develop an inferential procedure for ecological, demographic and genetic parameters. We first show how genetic diversity and genealogies are related to birth and death rates, and to how individuals compete within and between strains. This leads us to propose an original model of phylogenies, with trait structure and interactions, that allows multiple merging. Second, we develop an Approximate Bayesian Computation framework to use our model for analyzing genetic data. We apply our procedure to simulated and real data. We show that the procedure give accurate estimate of the parameters of the model. We finally carry an illustration on real data and analyze the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia populations in order to test whether different social organizations show significantly different fertility.

scholarly journals Does marine geospatial/environmental variation affect genetic variation? A meta-analysis

2021 ◽  
Author(s):  
◽  
Daniel Cárcamo
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Meta Analysis ◽  
Environmental Variation ◽  
Environmental Data ◽  
Seascape Genetics ◽  
Species Specific

<p>Genetic information is important to inform management and conservation. However, few studies have tested the relationship between genetic variation and geospatial/environmental variation across marine species. Here, I test two genetics-based ideas in evolutionary theory using data from 55 New Zealand coastal marine taxa. The Core-Periphery Hypothesis (CPH) states that populations at the centre of a species’ distribution exhibit greater genetic variability than populations at the periphery (the ‘normal’ model). Variants of this model include the ‘ramped north’ (greatest variation in the north), the ‘ramped south’ (greatest variation in the south), and the ‘abundant edge’ (greatest variation at the distributional edges, least variation at the centre). The Seascape Genetics Test (SGT) null hypothesis predicts no association between genetic variation and environmental variation. I conducted a meta-analysis of published/unpublished material on population genetic connectivity and diversity and marine environmental data to test both hypotheses. To assess the CPH, genetic data were fitted to four models (Normal, Ramped North, Ramped South, Abundant Edge). I also conducted a descriptive analysis between the genetic outcomes of the CPH and abundance records for a subset of species. The SGT involved GLM analyses using eleven geospatial/environmental variables and species-specific FST-ΦST (genetic distance) estimates plus a smaller subset of genetic diversity data. The CPH results showed that 55 of 249 tests (evaluating on average 2.9 ± 1.3 genetic indices in each of the 84 studies) fitted at least one of the four models: Ramped North (10%), Ramped South (8%), Normal (2%) and Abundant Edge (2.4%). Species-specific abundance records followed the same patterns detected by the CPH. These results indicate that edge populations (Ramped North, Ramped South, Abundant Edge) exhibit greater genetic variability than central populations amongst marine taxa from New Zealand, but that most taxa do not conform to any model (~78% of all tests were not statistically significant). For the seascape genetics multi-species analysis (comprising 498 individual tests), the FST-ΦST estimates (genetic distance estimates between pairs of populations) were mostly affected by four factors related to sea surface temperature. For genetic diversity indices the most significant predictors were latitude and longitude. Whilst different factors (e.g., physical oceanography, food availability, life-history traits and harvesting), either acting alone or acting synergistically, are likely to be important in explaining patterns of genetic diversity in New Zealand’s marine coastal species, my results indicate that variables including SST and to a lesser extent the geospatial variables (latitude and longitude) explain much of the variation in the genetic indices tested here.</p>

scholarly journals Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population

2021 ◽  
Author(s):  
Mikael Åkesson ◽  
Øystein Flagstad ◽  
Jouni Aspi ◽  
Ilpo Kojola ◽  
Olof Liberg ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Canis Lupus ◽  
Animal Species ◽  
Allelic Richness ◽  
A Priori ◽  
Management Actions ◽  
Viable Population ◽  
Population Sizes ◽  
Source Populations

AbstractTransboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.

Data Management at CEDA

2020 ◽  
Author(s):  
Kate Winfield
Keyword(s):  
Data Management ◽  
Best Practice ◽  
Climate Models ◽  
Good Practice ◽  
Environmental Data ◽  
Observation Data ◽  
Specific Data ◽  
Share Data ◽  
Earth Observation Data

&lt;p&gt;Sending data to a secure long-term archive is increasingly a necessity for science projects due to the funding body and publishing requirements. It is also good practice for long term scientific aims and to enable the preservation and re-use of valuable research data. The Centre for Environmental Data Analysis (CEDA) hosts a data archive holding vast atmospheric and earth observation data from sources including aircraft campaigns, satellites, pollution, automatic weather stations, climate models, etc. The CEDA archive currently holds 14 PB data, in over 250 millions of files, which makes it challenging to discover and access specific data. In order to manage this, it is necessary to use standard formats and descriptions about the data. This poster will explore best practice in data management in CEDA and show tools used to archive and share data.&lt;/p&gt;

scholarly journals Does marine geospatial/environmental variation affect genetic variation? A meta-analysis

2021 ◽  
Author(s):  
◽  
Daniel Cárcamo
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Meta Analysis ◽  
Environmental Variation ◽  
Environmental Data ◽  
Seascape Genetics ◽  
Species Specific

<p>Genetic information is important to inform management and conservation. However, few studies have tested the relationship between genetic variation and geospatial/environmental variation across marine species. Here, I test two genetics-based ideas in evolutionary theory using data from 55 New Zealand coastal marine taxa. The Core-Periphery Hypothesis (CPH) states that populations at the centre of a species’ distribution exhibit greater genetic variability than populations at the periphery (the ‘normal’ model). Variants of this model include the ‘ramped north’ (greatest variation in the north), the ‘ramped south’ (greatest variation in the south), and the ‘abundant edge’ (greatest variation at the distributional edges, least variation at the centre). The Seascape Genetics Test (SGT) null hypothesis predicts no association between genetic variation and environmental variation. I conducted a meta-analysis of published/unpublished material on population genetic connectivity and diversity and marine environmental data to test both hypotheses. To assess the CPH, genetic data were fitted to four models (Normal, Ramped North, Ramped South, Abundant Edge). I also conducted a descriptive analysis between the genetic outcomes of the CPH and abundance records for a subset of species. The SGT involved GLM analyses using eleven geospatial/environmental variables and species-specific FST-ΦST (genetic distance) estimates plus a smaller subset of genetic diversity data. The CPH results showed that 55 of 249 tests (evaluating on average 2.9 ± 1.3 genetic indices in each of the 84 studies) fitted at least one of the four models: Ramped North (10%), Ramped South (8%), Normal (2%) and Abundant Edge (2.4%). Species-specific abundance records followed the same patterns detected by the CPH. These results indicate that edge populations (Ramped North, Ramped South, Abundant Edge) exhibit greater genetic variability than central populations amongst marine taxa from New Zealand, but that most taxa do not conform to any model (~78% of all tests were not statistically significant). For the seascape genetics multi-species analysis (comprising 498 individual tests), the FST-ΦST estimates (genetic distance estimates between pairs of populations) were mostly affected by four factors related to sea surface temperature. For genetic diversity indices the most significant predictors were latitude and longitude. Whilst different factors (e.g., physical oceanography, food availability, life-history traits and harvesting), either acting alone or acting synergistically, are likely to be important in explaining patterns of genetic diversity in New Zealand’s marine coastal species, my results indicate that variables including SST and to a lesser extent the geospatial variables (latitude and longitude) explain much of the variation in the genetic indices tested here.</p>

Nesting Expectations: What Can the Mexican and Argentinean Cash Transfers Tell Us about the Development of Development?

1969 ◽  
Vol 59 (1) ◽  
pp. 157-169
Author(s):  
Andrés Dapuez
Keyword(s):  
Latin America ◽  
Latin American ◽  
A Priori ◽  
Cash Transfers ◽  
Conditional Cash Transfers ◽  
Cash Transfer ◽  
Short Term ◽  
Transfer Programs

Latin American cash transfer programs have been implemented aiming at particular anticipatory scenarios. Given that the fulfillment of cash transfer objectives can be calculated neither empirically nor rationally a priori, I analyse these programs in this article using the concept of an “imaginary future.” I posit that cash transfer implementers in Latin America have entertained three main fictional expectations: social pacification in the short term, market inclusion in the long term, and the construction of a more distributive society in the very long term. I classify and date these developing expectations into three waves of conditional cash transfers implementation.

scholarly journals Frame me if you must: PrEP framing and the impact on adherence to HIV Pre-exposure Prophylaxis

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S439-S439
Author(s):  
Eric Ellorin ◽  
Jill Blumenthal ◽  
Sonia Jain ◽  
Xiaoying Sun ◽  
Katya Corado ◽  
...  
Keyword(s):  
A Priori ◽  
Social Groups ◽  
Continuous Measure ◽  
Gay Community ◽  
Randomized Controlled ◽  
Exposure Prophylaxis ◽  
The Impact ◽  
Actual Prevalence ◽  
Tenofovir Diphosphate

Abstract Background “PrEP whore” has been used both as a pejorative by PrEP opponents in the gay community and, reactively, by PrEP advocates as a method to reclaim the label from stigmatization and “slut-shaming.” The actual prevalence and impact of such PrEP-directed stigma on adherence have been insufficiently studied. Methods CCTG 595 was a randomized controlled PrEP demonstration project in 398 HIV-uninfected MSM and transwomen. Intracellular tenofovir-diphosphate (TFV-DP) levels at weeks 12 and 48 were used as a continuous measure of adherence. At study visits, participants were asked to describe how they perceived others’ reactions to them being on PrEP. These perceptions were categorized a priori as either “positively framed,” “negatively framed,” or both. We used Wilcoxon rank-sum to determine the association between positive and negative framing and TFV-DP levels at weeks 12 and 48. Results By week 4, 29% of participants reported perceiving positive reactions from members of their social groups, 5% negative, and 6% both. Reporting decreased over 48 weeks, but positive reactions were consistently reported more than negative. At week 12, no differences in mean TFV-DP levels were observed in participants with positively-framed reactions compared with those reporting no outcome or only negatively-framed (1338 [IQR, 1036-1609] vs. 1281 [946-1489] fmol/punch, P = 0.17). Additionally, no differences were observed in those with negative reactions vs. those without (1209 [977–1427] vs. 1303 [964–1545], P = 0.58). At week 48, mean TFV-DP levels trended toward being higher among those that report any reaction, regardless if positive (1335 [909–1665] vs. 1179 [841–1455], P = 0.09) or negative (1377 [1054–1603] vs. 1192 [838–1486], P = 0.10) than those reporting no reaction. At week 48, 46% of participants reported experiencing some form of PrEP-directed judgment, 23% reported being called “PrEP whore,” and 21% avoiding disclosing PrEP use. Conclusion Over 48 weeks, nearly half of participants reported some form of judgment or stigmatization as a consequence of PrEP use. However, individuals more frequently perceived positively framed reactions to being on PrEP than negative. Importantly, long-term PrEP adherence does not appear to suffer as a result of negative PrEP framing. Disclosures All authors: No reported disclosures.

scholarly journals Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 126
Author(s):  
Emily K. Latch ◽  
Kenneth L. Gee ◽  
Stephen L. Webb ◽  
Rodney L. Honeycutt ◽  
Randy W. DeYoung ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Wildlife Management ◽  
Field Observations ◽  
Adaptive Potential ◽  
Population Isolation ◽  
Potential Benefits ◽  
Wildlife Populations ◽  
Mtdna Diversity

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

Sign in / Sign up

Export Citation Format

Share Document