Gene survival in the Asian wild horse (Equus przewalskii): II. Gene survival in the whole population,in subgroups,and through history

In populations with a known pedigree, exact joint probability distributions of numbers of surviving of genes from each founder can now be calculated for moderately large complex pedigrees (1,000–2,000 individuals and much inbreeding). The usefulness of such calculations is shown by our analysis of gene survival in the Asian wild horse (Equus przewalskii), a species now extinet in the wild with a captive population with 1,516 individuals in the known pedigree (12 generations). We calculate the genetic diversity of subsets of the current population interesting to the North American Species Survival Plan, trace the loss of genetic diversity in this species through its history in captivity, and determine genetically important individuals in the North American population—those with relatively high probabilities of having unique copy genes (genes not found in any other living individual in North America).     

Gene survival in the Asian wild horse (Equus przewalskii): I. Dependence of gene survival in the calgary breeding group pedigree

The joint probability distribution of the number of distinct (not identical by descent) genes from each founder of the Equus przewalskii population that survive in the five horses of the Calgary Zoological Gardens breeding group has been calculated. The dependence structure of this distribution is investigated, and informative marginal distributions are given, among them the distributions of the genetic contributions of each founder to the Calgary horses and the distribution of wild-type genes in these horses. The dependence pattern is found to be complex; there is no substitute for exact calculation of the full joint probability distribution of numbers of surviving genes. Probabilities of gene survival give a more complete summary of the genetic structure of a set of individuals than is provided by more routine measures such as heterozygosity or founder contributions. The feasibility of computing these probabilities for small groups of current individuals descended from few founders via long and complex pedigrees, provides a new approach to assessing such groups, and could be used also in selecting animals to form the founder stock of propagules for future reintroduction programs.     

Comparison of an exact and a simulation method for calculating gene extinction probabilities in pedigrees

A comparison is made between a much used simulation method, commonly called gene dropping, and the exact computational technique of peeling. These methods are illustrated using the problem of finding the distribution of the number of distinct ancestral genes surviving at an autosomal locus. Each method is used on several real zoo pedigrees, of varying size and complexity, and the results are compared. Gene dropping is found to be a good approximation to peeling, but for all but the most complex pedigrees surveyed, peeling is preferable. The relationship between heterozygosity and allelic variability is investigated.     

AlleleRetain: a program to assess management options for conserving allelic diversity in small,isolated populations

Preserving genetic health is an important aspect of species conservation. Allelic diversity is particularly important to conserve, as it provides capacity for adaptation and thus enables long‐term population viability. Allele retention is difficult to predict beyond one generation for real populations with complex demography and life‐history traits, so we developed a computer model to simulate allele retention in small populations. AlleleRetain is an individual‐based model implemented in r and can be applied to assess management options for conserving allelic diversity in small populations of animals with overlapping generations. AlleleRetain remedies the limitations of similar existing software, and its source code is freely available for further modification. AlleleRetain and its supporting materials can be downloaded from https://sites.google.com/site/alleleretain/ or CRAN ( http://cran.r-project.org ).     

Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses

The thoroughbred (TB) horse is one of the oldest breeds of domestic animals, with pedigree records spanning three centuries. Because the population is essentially closed, there is concern about loss of genetic variation. Here we report two parallel analyses. In the first, genetic variation in the current population is measured using data from 13 microsatellite loci in 211 horses with relationships calculated based on allele sharing. In the second analysis, pedigree information is used to calculate genetic relationships between animals based on shared ancestry. These two measures of relationship are compared and shown to be closely related. Together, they provide an estimate of the amount of genetic variation which existed in founder animals. This study confirms the narrow genetic base of the breed and provides comprehensive analysis of contributions of founder animals. Seventy-eight percent of alleles in the current population are derived from 30 founders, 27 of these male. Ten founder females account for 72% of maternal lineages, while one founder stallion is responsible for 95% of paternal lineages.     

普通小麦Genomic-SSR和EST-SSR分子标记遗传差异及其与系谱遗传距离的比较研究

采用Genomic-SSR和EST—SSR标记技术,对来自我国北方冬麦区的18份普通小麦品种(系)的遗传多样性进行了探讨,并与系谱遗传距离进行了比较分析。研究发现,平均每个Genomic—SSR检测到的等位基因数为3．34个,明显高于EST-SSR的2．31个。遗传距离(GD)计算结果显示,18个小麦基因型之间的EST—SSR平均遗传距离较小,仅为0．3996,低于Genomic—SSR的GD平均值0．5458。尽管EST-SSR揭示出的多态性明显低于Genomic-SSR,但系谱分析和聚类结果均表明,与Genomic—SSR相比,EST—SSR标记能更准确地反映出不同小麦基因型之间的遗传和亲缘关系。据此可以认为,EST—SSR是评价小麦遗传多样性的一种理想标记形式。研究还证实,一个骨干亲本与由其衍生出来的品种(系)之间的遗传差异一般较小,并对拓宽普通小麦遗传基础的策略和方法进行了讨论。     

An improvement on the maximum likelihood reconstruction of pedigrees from marker data

Many methods have been proposed to reconstruct the pedigree of a sample of individuals from their multilocus marker genotypes. These methods, like those in other fields of statistical inferences, may suffer from both type I (falsely related) and type II (falsely unrelated) errors. In sibship reconstruction, type I errors come from the spurious fusion of two or more small sibships into a single sibship, and type II errors originate from the spurious splitting of a large sibship into two or more small sibships. In this study I investigate the tendencies of both types of errors made by the likelihood methods in sibship reconstruction, using both analytical and simulation approaches. I propose an improvement on the likelihood methods to reduce sibship splitting, and thus type II errors by downscaling the number of inferred siblings sharing the same genotype at a locus. Simulations are then conducted to compare the accuracy of the original and improved likelihood methods in sibship reconstruction of a large sample of individuals in full-sib families of the same small size, the same large size and highly variable sizes, using a variable number of loci with a variable number of alleles per locus. The methods were also applied to the analysis of a salmon data set. I show that my scaling scheme prevents effectively the splitting of large sibships, and reduces type II errors greatly with little increase in type I errors. As a result, it improves the overall accuracy of sibship assignments, except when sibships are expected to be uniformly small or marker information is unrealistically scarce.     

Pedigree analysis of the Turkish Arab horse population: structure,inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N_e), the effective number of founders (f_e), the effective number of ancestors (f_a) and the number of founder genome equivalents (f_g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the meanFand AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and thef_e,f_aandf_gwere 342, 223, 40, 22 and 9.6 for the RP. The large differences observed betweenf_e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability.N_eestimated via an individual increase in inbreeding per generation (${\overline{N}}_{\text{e}}$), and paired increase in coancestry$\left(\text{}{\overline{N}}_{eC}\right)$, were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.     

Change in genetic size of small-closed populations: Lessons from a domestic mammal population

The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, N(e) ), as well as measures based on probability of gene origin (effective number of founders, f(e) , effective number of founder genomes, f(g) , and effective number of non-founder genomes, f(ne) ). Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that N(e) decreased from 263 to 93. The observed trend for f(e) was irregular throughout the experiment in a way that f(e) was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f(g) , the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD) which was obtained from estimates of f(g) , decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f(ne) from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f(e) to f(g) indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f(ne) was much higher than f(e) , thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f(e) > f(ne) . The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.     

中国玉米遗传单一性的经济影响

广泛采用少数优良种质资源,可能会引起作物遗传多样性下降,降低品种的抗病和抗逆能力,影响作物的产量。本研究采用系谱分析方法,研究了我国20个主产省玉米遗传单一性的变化及其对我国玉米生产的影响。结果表明,遗传单一性与玉米单产之间呈显著的负相关关系：遗传单一性每增加1%,玉米平均单产将降低13%;研究同时也表明遗传单一性和品种单一性是两个相互独立的变量,品种单一性不一定导致遗传基础的单一性。政府应从调节育种人员行为上制定相应的政策,防止遗传基础单一化,在增加作物遗传多样性的同时,选育优质高产的品种。     

European pig genetic diversity: a minireview

An evaluation of the European pig diversity has been carried on by several countries, with the support of the European Union over the period of 1994 to 2000. This article presents an overview of the results of this investigation, focussing on two genetic marker techniques, namely microsatellites (MS) and amplification of fragment length polymorphism (AFLP). Nearly 200 loci were characterised on about 50 individuals from each of 59 to 71 breeds, according to the marker considered. The analysis of diversity, based on genetic distances, led to similar conclusions for the two marker types (MS and AFLP), in spite of a markedly lower total diversity of AFLP compared to MS. The analysis of the MS loci showed that the allelic diversity pattern among breeds was quasi-independent from the diversity pattern based on allele frequencies. Genetic distances showed no particular clustering of local with international breeds, confirming the genetic uniqueness of the European local breeds compared to mainstream international breeds. The taxonomy of the local breeds revealed a cluster of the Iberian type breeds, in contrast with a wider dispersal of the breeds from other countries. Phylogeny often disagreed with documented breeds' history, showing the complex migration/admixture patterns which underlie the breeds' relationships. Methodologies developed in this investigation as well as the database and the DNA depository created should provide support for further innovative research in the field of domestic animal diversity management.     

Microevolution in Solatopupa landsnails (Pulmonata Chondrinidae): genetic diversity and founder effects

Enzyme variability at 28 presumptive gene loci was studied, by standard starch gel electrophoresis, in 30 populations belonging to the five recognized species of the landsnail Solatopupa from its entire NW Mediterranean range.
Six genetically differentiated groups can be identified among the 30 populations sampled. These are distinguished by two to 19 diagnostic loci, different levels of genetic variability and populations genetics. They are also significantly different as far as the D values are considered. There is no evidence of gene flow among them. Genetically inferred groups correspond in four cases to morphologically distinguished species. In contrast, S. similis , as identified by morphological features, is likely to be a complex of at least two cryptic species.
Populations and species of Solatopupa are characterized by: high fixation of alternative alleles both within and between species; medium-lo-low levels of genie variation; heterozygote deficiency; sharp genetic differentiation among population within species; restricted gene flow; and high genetic distances. Genetic variability is partly associated with climatic factors related to moisture.
Both deterministic and stochastic processes may play a part in the genetic differentiation of Solatopupa snails. Founder events seem to be the main factor affecting the genetic structure of populations and perhaps also speciation. Solatopupa populations display many attributes of populations that may be expected to undergo speciation events involving reorganization of the whole genome after a founder event.     

Modeling problems in conservation genetics using captive Drosophila populations: Consequences of equalizing founder representation

Equalizing founder representation is a recommended practice for maintaining captive populations. However, this procedure has not been subject to controlled experimental evaluation. The effects on inbreeding, genetic variation, and reproductive fitness of maintaining small captive populations by equalizing founder representation (EFR) versus randomly choosing parents (RC) were compared. Ten replicate lines were created with unequal founder representations, split into EFR and RC lines, and maintained for a further eight generations. Founder representations computed from pedigrees were closer to equality in the EFR lines than in the RC lines or the base population, most of the changes being evident after one generation. Significant benefits of EFR were found in lowered inbreeding (mean inbreeding coefficients of 0.35 and 0.41, respectively, for EFR and RC lines) and average heterozygosity (0.141 for EFR, 0.084 for RC, compared with 0.216 in the base population). However, EFR was not significantly better than RC in moving allele frequencies towards equalized founder representation. No significant difference was found in reproductive fitness between EFR and RC (relative fitnesses compared to the base population were 0.179 for EFR and 0.182 for RC). The use of equalization of founder representation for a few generations can be recommended in the genetic management of captive populations derived from a small number of founders that contribute unequally. © 1992 Wiley-Liss, Inc.     

COMPUTER PROGRAMS: nessi: a program for numerical estimations in sporophytic self-incompatibility genetic systems

nessi is a computer program generating predictions about allelic and genotypic frequencies at the S-locus in sporophytic self-incompatibility systems under finite and infinite populations. For any pattern of dominance relationships among self-incompatibility alleles, nessi computes deterministic equilibrium frequencies and estimates distributions in samples from finite populations of the number of alleles at equilibrium, allelic and genotypic frequencies at equilibrium and allelic and genotypic frequency changes in a single generation. These predictions can be used to rigorously test the impact of negative frequency-dependent selection on diversity patterns in natural populations.     

hp‐rare 1.0: a computer program for performing rarefaction on measures of allelic richness

The number of alleles in a sample (allelic richness) is a fundamental measure of genetic diversity. However, this diversity measure has been difficult to use because large samples are expected to contain more alleles than small samples. The statistical technique of rarefaction compensates for this sampling disparity. Here I introduce a computer program that performs rarefaction on private alleles and hierarchical sampling designs.     

Selective recovery of founder genetic diversity in aquacultural broodstocks and captive, endangered fish populations

Hatchery broodstocks used for genetic conservation or aquaculture may represent their ancestral gene pools rather poorly. This is especially likely when the fish that found a broodstock are close relatives of each other. We re-analysed microsatellite data from a breeding experiment on red sea bream to demonstrate how lost genetic variation might be recovered when gene frequencies have been distorted by consanguineous founders in a hatchery. A minimal-kinship criterion based on a relatedness estimator was used to select subsets of breeders which represented the maximum number of founder lineages (i.e., carried the fewest identical copies of ancestral genes). UPGMA clustering of Nei's genetic distances grouped these selected subsets with the parental gene pool, rather than with the entire, highly drifted offspring generation. The selected subsets also captured much of the expected heterozygosity and allelic diversity of the parental gene pool. Independent pedigree data on the same fish showed that the selected subsets had more contributing parents and more founder equivalents than random subsets of the same size. The estimated mean coancestry was lower in the selected subsets, meaning that inbreeding in subsequent generations would be lower if they were used as breeders. The procedure appears suitable for reducing the genetic distortion due to consanguineous and over-represented founders of a hatchery gene pool.     

fptest: a sas routine for testing differences in allelic count

Allelic count is an important measure of genetic diversity, but it is a function of sample size. This size-dependent property may not only introduce bias in its estimation, but also cause difficulty in testing the significance of its difference between samples. Here we present a sas routine of random permutation that can assist in the assessment of allelic count differences among groups of variable size. An example is given to examine the statistical significance of the differences in allelic count among eight breeding periods of Canadian oat cultivars.     

Effective population size in the captive breeding program of the Lake Victoria cichlid Paralabidochromis chilotes

Microsatellite DNA markers were used to monitor levels of genetic variation in 3 generations of the American Zoo and Aquarium Association [AZA] Species Survival Plan [SSP] captive breeding program for the Lake Victoria cichlid Paralabidochromis chilotes. Temporal changes in the frequency of 15 alleles, across four polymorphic loci, were used to estimate effective population size (N_e). The upper limit of the 95% confidence interval for N_e never exceeded eight individuals, with all of the corresponding N_e/N ratios falling below 0.15. A test of the proportion of expected heterozygous individuals between the F₁ and F₃ generations indicated a significant decline in expected heterozygosity of 5% per generation. Alternative husbandry protocols, including subdividing the captive population, are addressed to reduce the further loss of genetic variation. Zoo Biol 18:215–222, 1999. © 1999 Wiley‐Liss, Inc.     

A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current‐day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that these bottlenecks may have occurred prior to 2003. A greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. However, populations differed significantly between sampling years for resistance: some populations maintained high resistance between the sampling years whereas others exhibited increased or decreased resistance. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We probably uncovered only modest increases in resistance on average between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that nonresistant migrants germinate from the seed bank.