Allozyme diversity in the endangered shrub Linderamelissifolia (Lauraceae) and its widespread congener Linderabenzoin

1996 ◽  
Vol 26 (12) ◽  
pp. 2080-2087 ◽  
Author(s):  
Mary Jo W. Godt ◽  
J.L. Hamrick
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Southeastern United States ◽  
Genotypic Diversity ◽  
Allozyme Variation ◽  
Effective Population ◽  
Allozyme Diversity ◽  
Dioecious Species ◽  
Population Sizes ◽  
Low Levels

Allozyme diversity was assessed in 15 populations of the endangered clonal shrub Linderamelissifolia (Walt.) Blume (pondberry; Lauraceae) throughout its range in the southeastern United States and in five populations of spicebush (Linderabenzoin (L.) Blume), a sexually reproducing, co-occurring congener. Low levels of allozyme variation characterize both dioecious species. Although genetic diversity was moderately high (HT = 0.239) at polymorphic loci for L. benzoin, few of the 42 loci were polymorphic (Ps = 35%; Pp = 25%), and thus overall estimates of genetic diversity were relatively low (Hes = 0.083; Hep = 0.070). Little genetic variation was detected at 27 loci within L. melissifolia (Hes = 0.025; Hep = 0.015). Nine L. melissifolia loci (33%) were polymorphic but genetic diversity was low (HT = 0.074) at these loci, and few were polymorphic within populations (mean = 6.7%). The number of multilocus genotypes detected in L. melissifolia populations ranged from 1 to 18, with a mean of 4.5. Mean genetic identities between populations within each species were high (I = 0.98 and 0.99 for L. benzoin and L. melissifolia, respectively), a result of the high numbers of monomorphic loci. Despite the high genetic similarity of populations, estimates of gene flow were low to moderate (Nm = 0.82 and 1.25 for L. melissifolia and L. benzoin, respectively). The lower genetic diversity within L. melissifolia may be primarily due to bottlenecks during its evolutionary history. The recent loss of populations and of genets within populations have probably further eroded genetic diversity. To reduce the risk of extinction, effective population sizes of L. melissifolia could be enhanced by increasing genotypic diversity within populations.

Population genetic structure in duckweed (Lemna minor, Lemnaceae)

1996 ◽  
Vol 74 (2) ◽  
pp. 222-230 ◽  
Author(s):  
Christopher T. Cole ◽  
Martin I. Voskuil
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic ◽  
Lemna Minor ◽  
Vegetative Reproduction ◽  
Low Frequency ◽  
Morphological Differentiation ◽  
Genotypic Diversity ◽  
Allozyme Variation ◽  
Low Levels

Allozyme variation in 11 Minnesota populations of Lemna minor L. was studied, using 11 enzyme systems, resolving 16 putative loci from 285 plants. Significant deviations from Hardy–Weinberg frequencies occurred in several populations that had excesses of heterozygotes at several loci. While genotypic diversity and evenness measures are similar to other vegetatively reproducing plants (D = 0.541, E = 0.607), very few multilocus genotypes per population were found (mean = 4.0). Substantial population structure was evident (FST = 0.407), apparently reflecting low levels of gene flow (Nm = 0.30) despite the capacity of this species for dispersal of plantlets. This low level of gene flow and apparent low frequency of sexual reproduction has produced substantial levels of genetic divergence among populations, despite an absence of morphological differentiation. Keywords: allozymes, genetic structure, hydrophily, Lemna, vegetative dispersal, vegetative reproduction.

scholarly journals Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

scholarly journals Challenges to assessing connectivity between massive populations of the Australian plague locust

2011 ◽  
Vol 278 (1721) ◽  
pp. 3152-3160 ◽  
Author(s):  
Marie-Pierre Chapuis ◽  
Julie-Anne M. Popple ◽  
Karine Berthier ◽  
Stephen J. Simpson ◽  
Edward Deveson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Large Population ◽  
Movement Ecology ◽  
Effective Population ◽  
Continental Scale ◽  
Australian Continent ◽  
Population Structuring ◽  
Population Sizes ◽  
Approximate Bayesian ◽  
Australian Plague Locust

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera , is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m , that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations.

scholarly journals Coalescent models at small effective population sizes and population declines are positively misleading

2019 ◽  
Author(s):  
M. Elise Lauterbur
Keyword(s):  
Genetic Diversity ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Relationships ◽  
Population Decline ◽  
Population Declines ◽  
Effective Population ◽  
Analytical Approximations ◽  
Population Sizes

AbstractPopulation genetics employs two major models for conceptualizing genetic relationships among individuals – outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

scholarly journals Continent-wide effects of urbanization on bird and mammal genetic diversity

2019 ◽  
Author(s):  
C. Schmidt ◽  
M. Domaratzki ◽  
R.P. Kinnunen ◽  
J. Bowman ◽  
C.J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Bird Species ◽  
Population Level ◽  
Natural Environments ◽  
Population Declines ◽  
Effective Population ◽  
Human Footprint ◽  
Rate Of Increase ◽  
Population Sizes

AbstractUrbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

scholarly journals Population diversity and relatedness in Sugarbirds (Promeropidae:Promeropsspp.)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5000
Author(s):  
Evan S. Haworth ◽  
Michael J. Cunningham ◽  
Kathleen M. Calf Tjorve
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Gene ◽  
Conservation Status ◽  
Tail Length ◽  
Population Diversity ◽  
Breeding Systems ◽  
Effective Population ◽  
Socially Monogamous ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops caferandP. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data,P. gurneyiare in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity inP. caferfrom Helderberg Nature Reserve andP. gurneyifrom Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.

scholarly journals Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

2017 ◽  
Vol 60 (2) ◽  
pp. 137-143
Author(s):  
José Fernando Vázquez-Armijo ◽  
Gaspar Manuel Parra-Bracamonte ◽  
Miguel Abraham Velazquez ◽  
Ana María Sifuentes-Rincón ◽  
José Luis Tinoco-Jaramillo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
The Other ◽  
Genetic Integrity ◽  
Effective Population ◽  
South Central ◽  
Microsatellite Dna Markers ◽  
Quarter Horse ◽  
Population Sizes

Abstract. The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL) horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

scholarly journals Molecular evolutionary consequences of island colonisation

2015 ◽  
Author(s):  
Jennifer James ◽  
Robert Lanfear ◽  
Adam Eyre-Walker
Keyword(s):  
Genetic Diversity ◽  
Population Bottleneck ◽  
Surprising Result ◽  
Population Bottlenecks ◽  
Adaptive Potential ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Evolutionary Consequences ◽  
The Relationship

Island endemics are likely to experience population bottlenecks; they also have restricted ranges. Therefore we expect island species to have small effective population sizes (Ne) and reduced genetic diversity compared to their mainland counterparts. As a consequence, island species may have inefficient selection and reduced adaptive potential. We used both polymorphisms and substitutions to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne. We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that had undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of effectiveness of selection or mutation rate. Our evidence suggests that island colonisation has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.

scholarly journals Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations ( Mimus spp.)

2010 ◽  
Vol 365 (1543) ◽  
pp. 1127-1138 ◽  
Author(s):  
Paquita E. A. Hoeck ◽  
Jennifer L. Bollmer ◽  
Patricia G. Parker ◽  
Lukas F. Keller
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Genetic Drift ◽  
Bird Species ◽  
Effective Population ◽  
Island Size ◽  
Island Populations ◽  
Population Sizes ◽  
Spatio Temporal

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.

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