scholarly journals Peer Review #1 of "Effective population sizes and adaptive genetic variation in a captive bird population (v0.1)"

2018 ◽  
Keyword(s):  
Genetic Variation ◽  
Peer Review ◽  
Adaptive Genetic Variation ◽  
Effective Population ◽  
Bird Population ◽  
Captive Bird ◽  
Population Sizes

scholarly journals Effective population sizes and adaptive genetic variation in a captive bird population

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5803 ◽  
Author(s):  
Giridhar Athrey ◽  
Nikolas Faust ◽  
Anne-Sophie Charlotte Hieke ◽  
I. Lehr Brisbin
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Demographic History ◽  
Ex Situ ◽  
Adaptive Genetic Variation ◽  
Effective Population ◽  
B Locus ◽  
Captive Populations ◽  
Chain Of Custody ◽  
Population Sizes

Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral and adaptive loci in captive populations. In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.

scholarly journals Effective population sizes and adaptive genetic variation in a captive bird population

2018 ◽  
Author(s):  
Giridhar Athrey ◽  
Nikolas Faust ◽  
Anne-Sophie Charlotte Hieke ◽  
I. Lehr Brisbin
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Demographic History ◽  
Ex Situ ◽  
Adaptive Genetic Variation ◽  
Effective Population ◽  
B Locus ◽  
Captive Populations ◽  
Chain Of Custody ◽  
Population Sizes

AbstractCaptive populations are considered a key component of ex situ conservation programs. Research on multiple taxa have shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral, at adaptive loci in captive populations.In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population is represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike captive lab populations. Our analysis, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which are surprising in spite of the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.

Consequences of climatic change for distributions

2019 ◽  
pp. 165-184
Author(s):  
Brian Huntley
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Species Distributions ◽  
Climatic Changes ◽  
Adaptive Genetic Variation ◽  
Spatial Structuring ◽  
Modelling Studies ◽  
Population Sizes ◽  
Fossil Records

Species’ distributions, population sizes, and community composition are affected, directly and indirectly, by climatic changes, leading to changes in location, extent, and/or quality of distributions, range fragmentation or coalescence, and temporal discontinuities in suitable conditions. Quaternary fossil records document these responses, emphasizing individualism of species’ responses and impermanence of communities. Recent observations document similar changes attributable to recent climatic changes, including rapid decreases and increases in ranges and/or populations. Both also document extinctions associated with rapid climatic changes. Modelling studies predict substantial changes in species’ distributions, population sizes, and communities in response to future climatic changes. Implicit assumptions that genetic variation enabling adaptation is ubiquitous throughout species’ ranges, or that gene flow may be sufficiently rapid to allow adaptation, may be invalid. Work is needed to investigate spatial structuring of adaptive genetic variation and rates of gene flow, and to develop new models. Without this, species extinction risks may be severely underestimated.

Genetic variation in the greenback flounder Rhombosolea tapirina GÜnther (Teleostei, Pleuronectidae) and the implications for aquaculture

2000 ◽  
Vol 51 (1) ◽  
pp. 23 ◽  
Author(s):  
Tony van den Enden ◽  
Robert W. G. White ◽  
Nicholas G. Elliott
Keyword(s):  
Genetic Variation ◽  
New Zealand ◽  
Genetic Distance ◽  
West Coast ◽  
Gel Electrophoresis ◽  
Effective Population ◽  
Average Heterozygosity ◽  
The West ◽  
Order Of Magnitude ◽  
Population Sizes

Samples of the greenback flounder, Rhombosolea tapirina, were collected from five Tasmanian sites and from one site each off Victoria and New Zealand. Thirty enzyme-coding loci were analysed by gel electrophoresis. Seventeen loci were variable, nine of which were polymorphic in at least four samples. Average heterozygosity across all 30 loci was relatively high at 0.086 ± 0.032. There were significant genetic differences between the Australian and New Zealand samples, with a genetic distance of 0.041, which was an order of magnitude larger than that observed between any Australian samples. Samples from the west coast of Tasmania and from Victoria were genetically isolated from each other and from the remaining four Tasmanian samples; the latter showed little variation among themselves. Reductions in genetic variation (heterozygosity and alleles) were observed in two cultured cohorts when compared with the wild-caught samples, with corresponding low estimates of effective population sizes compared with putative breeding numbers. No genetic variation was detected between normal and malpigmented individuals from the same culture cohort.

scholarly journals Comparative losses of quantitative and molecular genetic variation in finite populations of Drosophila melanogaster

2005 ◽  
Vol 85 (1) ◽  
pp. 47-55 ◽  
Author(s):  
DEAN M. GILLIGAN ◽  
DAVID A. BRISCOE ◽  
RICHARD FRANKHAM
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Molecular Genetic ◽  
Neutral Theory ◽  
Similar Rate ◽  
Sampling Errors ◽  
Effective Population ◽  
Quantitative Genetic ◽  
Population Sizes ◽  
Molecular Genetic Variation

Quantitative genetic variation, the main determinant of the ability to evolve, is expected to be lost in small populations, but there are limited data on the effect, and controversy as to whether it is similar to that for near neutral molecular variation. Genetic variation for abdominal and sternopleural bristle numbers and allozyme heterozygosity were estimated in 23 populations of Drosophila melanogaster maintained at effective population sizes of 25, 50, 100, 250 or 500 for 50 generations, as well as in 19 highly inbred populations and the wild outbred base population. Highly significant negative regressions of proportion of initial genetic variation retained on inbreeding due to finite population size were observed for both quantitative characters (b=−0·67±0·14 and −0·58±0·11) and allozyme heterozygosity (b=−0·79±0·10), and the regression coefficients did not differ significantly. Thus, quantitative genetic variation is being lost at a similar rate to molecular genetic variation. However, genetic variation for all traits was lost at rates significantly slower than predicted by neutral theory, most likely due to associative overdominance. Positive, but relatively low correlations were found among the different measures of genetic variation, but their low magnitudes were attributed to large sampling errors, rather than differences in the underlying processes of loss.

scholarly journals Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size

2021 ◽  
Author(s):  
Michaela Halsey ◽  
John Stuhler ◽  
Natalia J Bayona-Vasquez ◽  
Roy N Platt ◽  
Jim R Goetze ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Population Fluctuations ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Single Nucleotide ◽  
Demographic Dynamics ◽  
Population Sizes

Organisms with low effective population sizes are at greater risk of extinction because of reduced genetic diversity.   Dipodomys elator  is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread  D. ordii  is thought to exhibit relative geographic and demographic stability. Genetic variation between  D. elator  and  D. ordii  samples was assessed using 3RAD, a modified restriction site associated sequencing approach. It was hypothesized that  D. elator  would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to  D. ordii . Also of interest was identifying population structure within contemporary samples of  D. elator  and detecting genetic variation between temporal samples that could indicate demographic dynamics. Up to 61,000 single nucleotide polymorphisms were analyzed. It was determined that genetic variability and effective population size in contemporary  D. elator  populations were lower than that of  D. ordii, that there is only slight, if any, structure within contemporary  D. elator  populations, and there is little genetic differentiation between spatial or temporal historical samples suggesting little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of  D. elator  has remained stable despite claims of reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract any immediate decrease in fitness.

Effective population size of koala populations under different population management regimes including contraception

2009 ◽  
Vol 36 (7) ◽  
pp. 601 ◽  
Author(s):  
Mark M. Tanaka ◽  
Romane Cristescu ◽  
Desmond W. Cooper
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Equal Opportunity ◽  
Management Strategies ◽  
Effective Population ◽  
Population Sizes ◽  
Wildlife Populations ◽  
Population Genetic Variation

Context. The management of wildlife populations aiming to control population size should also consider the preservation of genetic diversity. Some overabundant koala populations, for example, have low genetic variation. Different management strategies will affect population genetic variation differently. Aims. Here, we compare four strategies with respect to their effects on the effective population size, Ne , and therefore on genetic variation. Methods. The four strategies of interest are: (1) sterilisation or culling (which have the same effect on genetic variation); (2) random contraception of females with replacement; (3) random contraception of females without replacement; and (4) regular contraception, giving every female equal opportunity to reproduce. We develop mathematical models of these alternative schemes to evaluate their impact on Ne . We also consider the effect of changing population sizes by investigating a model with geometric population growth in which females are removed by sterilisation or culling. Key results. We find that sterilisation/culling at sexual maturity has the most detrimental effect on Ne , whereas regular contraception has no impact on Ne . Random contraception lies between these two extremes, leading to a moderate reduction in Ne . Removal of females from a growing population results in a higher Ne than the removal of females from a static population. Conclusions. Different strategies for controlling a population lead to different effective population sizes. Implications. To preserve genetic diversity in a wildlife population under control, the effective population size should be kept as large as possible. We suggest that a suitable approach in managing koala populations may be to prevent reproduction by all females older than a particular age.

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