A unified approach to characterize and conserve adaptive and neutral genetic diversity in subdivided populations

SummaryAs extinction of local domestic breeds and of isolated subpopulations of wild species continues, and the resources available for conservation programs are limited, prioritizing subpopulations for conservation is of high importance to halt the erosion of genetic diversity observed in endangered species. Current approaches usually only take neutral genetic diversity into account. However, adaptation of subpopulations to different environments also contributes to the diversity found in the species. This paper introduces two notions of adaptive variation. The adaptive diversity in a trait is the excess of variance found in genotypic values relative to the variance that would have been expected in the absence of selection. The adaptivity coverage of a set of subpopulations quantifies how well the subpopulations could adapt to a large range of environments within a limited time span. Additionally, genome-based notions of neutral diversities were obtained that correspond to well known pedigree-based definitions. The values of subpopulations for conservation of adaptivity coverage were compared with their conservation values for adaptive diversity and neutral diversities using simulated data. Conservation values for adaptive diversity and neutral diversities were only slightly correlated, but the values for conservation of adaptivity coverage showed a reasonable correlation with both kinds if the time span was chosen appropriately. Hence, maintaining adaptivity coverage is a promising approach to prioritize subpopulations for conservation decisions.

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Characterization and conservation of genetic diversity in subdivided populations

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2005.1680 ◽

2005 ◽

Vol 360 (1459) ◽

pp. 1367-1378 ◽

Cited By ~ 105

Author(s):

M.A Toro ◽

A Caballero

Keyword(s):

Genetic Diversity ◽

Genetic Analysis ◽

Population Genetic ◽

Quantitative Variation ◽

Population Variation ◽

Conservation Priorities ◽

Population Genetic Analysis ◽

Subdivided Populations ◽

Points Of View ◽

Conservation Decisions

We review the available tools for analysing genetic diversity in conservation programmes of subdivided populations. Ways for establishing conservation priorities have been developed in the context of livestock populations, both from the classical population genetic analysis and from the more recent Weitzman's approach. We discuss different reasons to emphasize either within or between-population variation in conservation decisions and the methodology to establish some compromise. The comparison between neutral and quantitative variation is reviewed from both theoretical and empirical points of view, and the different procedures for the dynamic management of conserved subdivided populations are discussed.

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Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

Reproduction in Domestic Animals ◽

10.1111/rda.13991 ◽

2021 ◽

Author(s):

Eddington Gororo ◽

Fungayi Primrose Chatiza ◽

Farisai Chidzwondo ◽

Stanley Marshall Makuza

Keyword(s):

Genetic Diversity ◽

Quantitative Variation ◽

Neutral Genetic Diversity

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Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

PLoS ONE ◽

10.1371/journal.pone.0245965 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0245965

Author(s):

Catherine Kiwuka ◽

Eva Goudsmit ◽

Rémi Tournebize ◽

Sinara Oliveira de Aquino ◽

Jacob C. Douma ◽

...

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Allelic Variation ◽

Coffea Canephora ◽

Ex Situ ◽

Negative Effects ◽

Robusta Coffee ◽

Genetic Diversity And Structure ◽

Adaptive Diversity ◽

Southern Central

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

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The Coalescent in a Continuous, Finite, Linear Population

Genetics ◽

10.1093/genetics/161.2.873 ◽

2002 ◽

Vol 161 (2) ◽

pp. 873-888

Author(s):

Jon F Wilkins ◽

John Wakeley

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Simulated Data ◽

Restricted Gene Flow ◽

Demographic Parameters ◽

Common Ancestry ◽

Linear Habitat ◽

Mean Time ◽

Finite Linear

Abstract In this article we present a model for analyzing patterns of genetic diversity in a continuous, finite, linear habitat with restricted gene flow. The distribution of coalescent times and locations is derived for a pair of sequences sampled from arbitrary locations along the habitat. The results for mean time to coalescence are compared to simulated data. As expected, mean time to common ancestry increases with the distance separating the two sequences. Additionally, this mean time is greater near the center of the habitat than near the ends. In the distant past, lineages that have not undergone coalescence are more likely to have been at opposite ends of the population range, whereas coalescent events in the distant past are biased toward the center. All of these effects are more pronounced when gene flow is more limited. The pattern of pairwise nucleotide differences predicted by the model is compared to data collected from sardine populations. The sardine data are used to illustrate how demographic parameters can be estimated using the model.

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Subtle human impacts on neutral genetic diversity and spatial patterns of genetic variation in European beech (Fagus sylvatica)

Forest Ecology and Management ◽

10.1016/j.foreco.2014.02.003 ◽

2014 ◽

Vol 319 ◽

pp. 138-149 ◽

Cited By ~ 32

Author(s):

K.C. Rajendra ◽

Sarah Seifert ◽

Kathleen Prinz ◽

Oliver Gailing ◽

Reiner Finkeldey

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Spatial Patterns ◽

Fagus Sylvatica ◽

Human Impacts ◽

European Beech ◽

Neutral Genetic Diversity

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Numerical Modeling and Design of Thermoelectric Cooling Systems

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.110-116.2639 ◽

2011 ◽

Vol 110-116 ◽

pp. 2639-2646 ◽

Cited By ~ 2

Author(s):

Rong Yuan Jou

Keyword(s):

Numerical Modeling ◽

Large Range ◽

Cooling System ◽

Thermoelectric Module ◽

Simulated Data ◽

Good Precision ◽

Thermoelectric Cooling ◽

Cooling Systems ◽

Thermoelectric Coolers ◽

Internal Parameters

Thermoelectric coolers are often used as reliable energy converters in a large range of applications. For design considerations, it is crucial to establish an effective methodology to determine and optimize the TEC performance within the cooling system constraints. For this purpose, firstly, three approaches are used to obtain the internal parameters of a given thermoelectric module. For these three estimating procedures, the simulated pumping powers are in the sequence of method III < method II < method I for each temperature difference. Hence, good precision of the simulated data are obtained by averaging the results of these three methods. Then, design optimizations of a thermoelectric assembly are conducted to obtain the device parameter, efficiency, and maximum power, respectively. Results show it is simple and effective way for design of a thermoelectric cooling system.

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Landscape prerequisites for the survival of a modelled metapopulation and its neutral genetic diversity are affected by climate change

Landscape Ecology ◽

10.1007/s10980-011-9676-1 ◽

2011 ◽

Vol 27 (2) ◽

pp. 227-237 ◽

Cited By ~ 10

Author(s):

Marleen M. P. Cobben ◽

Jana Verboom ◽

Paul F. M. Opdam ◽

Rolf F. Hoekstra ◽

René Jochem ◽

...

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Neutral Genetic Diversity

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Rejection of a serial founder effects model of genetic and linguistic coevolution

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.2296 ◽

2012 ◽

Vol 279 (1736) ◽

pp. 2281-2288 ◽

Cited By ~ 20

Author(s):

Keith Hunley ◽

Claire Bowern ◽

Meghan Healy

Keyword(s):

Genetic Diversity ◽

Negative Correlation ◽

Microsatellite Loci ◽

Population Genetic ◽

Evolutionary Process ◽

Founder Effects ◽

Genetic Studies ◽

Neutral Genetic Diversity ◽

Genetic Pattern ◽

Autosomal Microsatellite Loci

Recent genetic studies attribute the negative correlation between population genetic diversity and distance from Africa to a serial founder effects (SFE) evolutionary process. A recent linguistic study concluded that a similar decay in phoneme inventories in human languages was also the product of the SFE process. However, the SFE process makes additional predictions for patterns of neutral genetic diversity, both within and between groups, that have not yet been tested on phonemic data. In this study, we describe these predictions and test them on linguistic and genetic samples. The linguistic sample consists of 725 widespread languages, which together contain 908 distinct phonemes. The genetic sample consists of 614 autosomal microsatellite loci in 100 widespread populations. All aspects of the genetic pattern are consistent with the predictions of SFE. In contrast, most of the predictions of SFE are violated for the phonemic data. We show that phoneme inventories provide information about recent contacts between languages. However, because phonemes change rapidly, they cannot provide information about more ancient evolutionary processes.

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The Effect of Mating System Differences on Nucleotide Diversity at the Phosphoglucose Isomerase Locus in the Plant Genus Leavenworthia

Genetics ◽

10.1093/genetics/151.1.343 ◽

1999 ◽

Vol 151 (1) ◽

pp. 343-357 ◽

Cited By ~ 14

Author(s):

F Liu ◽

D Charlesworth ◽

M Kreitman

Keyword(s):

Genetic Diversity ◽

Nucleotide Diversity ◽

Phosphoglucose Isomerase ◽

Self Incompatibility ◽

Background Selection ◽

Selective Sweeps ◽

Balanced Polymorphism ◽

Neutral Genetic Diversity ◽

Low Diversity ◽

High Diversity

AbstractTo test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.

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