Population Genetic Parameters Research Articles

Cross-amplification of ungulate microsatellite markers in the endemic Indian antelope or blackbuck (Antilope cervicapra) for population monitoring and conservation genetics studies in south Asia

The Indian antelope or blackbuck (Antilope cervicapra) is endemic to the Indian subcontinent, inhabiting scrublands and dry grasslands. Most of the blackbuck populations are small, isolated, and threatened by habitat fragmentation and degradation. Management of such disjunct populations requires genetic characterization, which is critical for assessing hazards of stochastic events and inbreeding. Addressing the scarcity of such information on the blackbuck, we describe a novel panel of microsatellite markers that could be used to monitor blackbuck demography and population genetic parameters using non-invasive faecal sampling. We screened microsatellites (n = 40) that had been reported to amplify in bovid and cervid species using faecal samples of the blackbuck collected from Kaimoor Wildlife Sanctuary, Uttar Pradesh, India and its vicinities. We selected 12 markers for amplification using faecal DNA extracts (n = 140) in three multiplex reactions. We observed a mean amplification success rate of 72.4% across loci (92.1-25.7%) with high allele diversity (mean number of alleles/locus = 8.67 ± 1.03). Mean genotyping error rates across the markers were low to moderate (allelic drop-out rate = 0.09; false allele rate = 0.11). The proportions of first- and second-order relatives in the study population were 0.69% and 6.21%, respectively. Based on amplification success, genotyping error rates and the probability of identity (PID), we suggest (i) a panel of five microsatellite markers (cumulative PID = 1.24 × 10-5) for individual identification and population monitoring and (ii) seven additional markers for conservation genetics studies. This study provides essential tools capable of augmenting blackbuck conservation strategies at the landscape level, integral to protecting the scrubland-grassland ecosystem.

Mitochondrial DNA Polymorphism in Zhejiang She Population Based on Next Generation Sequencing.

Objective To study the genetic polymorphism of whole mitochondrial DNA （mtDNA） genomes in She population in Zhejiang and to explore the maternal genetic structure of the She population. Methods Whole mtDNA genomes of 231 unrelated individuals from She population in Zhejiang Province were sequenced. The number of mutations and population genetics parameters such as, the haplotype diversity （HD）, discrimination power （DP）, and random match probabilities （RMP） were analyzed. The mtDNA haplogroups of Zhejiang She population were classified, and the maternal genetic relationships between She and nine other Chinese populations were estimated. Results In 231 Zhejiang She samples, 8 507 mutations （702 types） were observed and the samples were classified into 94 haplogroups. The HD, DP and RMP values were 0.998 6, 0.994 2 and 0.005 8, respectively. The lowest genetic differentiation degree （Fst=0.006 89） was detected between Zhejiang She population and southern Han population. Principal component analysis （PCA） and median-joining network analysis showed that the genetic distance of Zhejiang She population with Guangxi Yao, Yunnan Dai and Southern Han populations was relatively close, but the population still had some unique genetic characteristics. Conclusion The whole mtDNA genomes are highly polymorphic in Zhejiang She population. The Zhejiang She population contains complex and diverse genetic components and has a relatively close maternal genetic relationship with Guangxi Yao, Yunnan Dai and Southern Han populations. Meanwhile, Zhejiang She population has kept its unique maternal genetic components.

ELEMENT OF SELECTION – STATE BOOKS OF BREEDING ANIMALS IN UKRAINE FOR THE PERIOD 2002–2010 YEARS

The issue of registration of breeding animals of different breeds is dealt with by organizations that keep state books of breeding animals. In Ukraine, the functions of keeping state books of breeding animals in cattle breeding, pig breeding, sheep breeding and horse breeding belong to the powers of the minister, which ensures the formation of state policy in the field of animal husbandry. The issue of animal breeding books is relevant because it is an ongoing process that requires a set of measures aimed at registration, maintenance and promotion of domestic breeding livestock.
 The purpose of research. To monitor the state books of breeding animals (SBBA) in dairy and meat cattle breeding, sheep breeding and pig breeding for the period 2002–2010. Also, establish the number of potential females that could be entered in the stud books.
 Materials and methods of research. The material for the study was data on the presence of breeding cows of dairy and meat production, sows and ewes of breeds registered in the State Register of Breeding Subjects in Animal Husbandry (until 2009, the State Breeding Register, SBR) during 2002–2019.
 The results of research. According to the SBR, 15 dairy breeds of cattle have been registered in Ukraine. During the study period, 15 volumes of SBBA of four breeds of dairy cattle were published in Ukraine, which included information on 12331 breeding animals, including 11477 cows. The largest number of recorded breeding animals of the Ukrainian Black-and-White dairy cattle, of which 144 breeding bulls and 4989 cows, are concentrated in six volumes. In second place is the Ukrainian Red-and-White dairy cattle, namely 4554 animals. Then there is the Simmental with 871 animals, of which 809 cows, and the red steppe 1773 heads, including 1609 cows.
 It is established that 48.7% of breeding animals were born in the period from 1990 to 1999. A small proportion, namely 0.3%, are animals born before 1979, and only 24% after 2000. Younger animals are recorded in the breeding books of Ukrainian Black-and-White dairy cattle and Ukrainian Red-and-White dairy cattle, and older – in the books of the red steppe.
 Of the 14 meat breeds used in Ukraine, only 5 have breeding animals that are registered with the SBBA. The total number of meat-producing animals recorded in the SBBA is 5586, including 4649 cows.
 Of the twelve breeds of pigs bred in Ukraine, only seven breeds, namely the Ukrainian white steppe (1451 heads) and Ukrainian spotted steppe (974), Myrhorod breed (123), Great Black (181), Landrace (727), Poltava meat breed (290) and Ukrainian meat breed (300) during the study period were published state pedigree books. Half (50.7%) of all recorded breeding pigs have a year of birth before 2000. Young (born in 2000) animals are recorded in the breeding books of the Landrace breed and the Ukrainian white steppe, Ukrainian meat breed and Poltava meat breed, where their share varies from 64 to 98%.
 During the study period, 9 volumes of state books of breeding sheep were published. In addition to Tsigai (884 goals), Askanian Karakul (700), fine-wool (1168), meat-wool with crossbred wool (1917) and Sokol (443), in 2003, 2004 and 2009 3 volumes of SBBA sheep of the Prekos breed were published.
 The calculation of potential females that could be recorded in the state breeding books revealed the presence of 1251102 breeding animals, including 100796 ewes, 70678 sows, 71341 beef cows and 1008287 dairy cows.
 The largest number of potential females of different breeds in cattle breeding, sheep breeding and pig breeding in the regions of Ukraine showed a certain pattern, namely the centers for dairy cattle breeding – Vinnytsia (83395 heads), Kyiv (111650), Khmelnytsky (64667), Cherkasy (68035) regions, beef cattle breeding – Volyn (13.466 head), Chernihiv (10.907 head), sheep breeding – Kherson (13.837), Odessa (19078) and pig breeding – Dnipropetrovsk (6452), Poltava (4621).
 The main goal for calculating potential females was to try to determine the size of the breed in dairy and beef cattle, sheep breeding and pigs breeding. Because the more animals included in the breeding model, the better the results of genetic improvement. In addition, it is possible to address the dynamics of the development of breeding traits, identify successful methods of selection and selection, assessment of population and genetic parameters over time and the creation of breeding programs with breeds of farm animals.
 Conclusion. State books of breeding animals are an important element of selection. Animal information databases help to estimate the populations of domestic and transboundary breeds in general by a set of characteristics, to determine the population-genetic parameters over time and to develop programs for the improvement of farm animals. Studies have identified a significant number (1251102 heads) of breeding cows, ewes and sows, which at one time could be recorded in the breeding books of the respective breeds.

Patterns of Genetic Diversity and Mating Systems in a Mass-Reared Black Soldier Fly Colony.

The black soldier fly (BSF), Hermetia illucens, is a promising candidate for the emerging insect farming industry with favourable characteristics for both bioremediation and production of animal delivered nutritive and industrial compounds. The genetic management of commercial colonies will become increasingly important for the sustainability of the industry. However, r-selected life history traits of insects pose challenges to conventional animal husbandry and breeding approaches. In this study, the long-term genetic effects of mass-rearing were evaluated as well as mating systems in the species to establish factors that might influence genetic diversity, and by implication fitness and productivity in commercial colonies. Population genetic parameters, based on microsatellite markers, were estimated and compared amongst two temporal wild sampling populations and four generations (F28, F48, F52, and F62) of a mass-reared colony. Furthermore, genetic relationships amongst mate pairs were evaluated and parentage analysis was performed to determine the oc-currence of preferential mate choice and multiple paternity. The mass-reared colony showed a reduction in genetic diversity and evidence for inbreeding with significant successive generational genetic differentiation from the wild progenitor population. Population-level analysis also gave the first tentative evidence of positive assortative mating and genetic polyandry in BSF. The homoge-neity of the mass-reared colony seems to result from a dual action caused by small effective popu-lation size and increased homozygosity due to positive assortative mating. However, the high ge-netic diversity in the wild and a polyandrous mating system might suggest the possible restoration of diversity in mass-reared colonies through augmentation with the wild population.

How imputation can mitigate SNP ascertainment Bias

BackgroundPopulation genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays. The resulting bias in the estimation of allele frequency spectra and population genetics parameters like heterozygosity and genetic distances relative to whole genome sequencing (WGS) data is known as SNP ascertainment bias. Full correction for this bias requires detailed knowledge of the array design process, which is often not available in practice. This study suggests an alternative approach to mitigate ascertainment bias of a large set of genotyped individuals by using information of a small set of sequenced individuals via imputation without the need for prior knowledge on the array design.ResultsThe strategy was first tested by simulating additional ascertainment bias with a set of 1566 chickens from 74 populations that were genotyped for the positions of the Affymetrix Axiom™ 580 k Genome-Wide Chicken Array. Imputation accuracy was shown to be consistently higher for populations used for SNP discovery during the simulated array design process. Reference sets of at least one individual per population in the study set led to a strong correction of ascertainment bias for estimates of expected and observed heterozygosity, Wright’s Fixation Index and Nei’s Standard Genetic Distance. In contrast, unbalanced reference sets (overrepresentation of populations compared to the study set) introduced a new bias towards the reference populations. Finally, the array genotypes were imputed to WGS by utilization of reference sets of 74 individuals (one per population) to 98 individuals (additional commercial chickens) and compared with a mixture of individually and pooled sequenced populations. The imputation reduced the slope between heterozygosity estimates of array data and WGS data from 1.94 to 1.26 when using the smaller balanced reference panel and to 1.44 when using the larger but unbalanced reference panel. This generally supported the results from simulation but was less favorable, advocating for a larger reference panel when imputing to WGS.ConclusionsThe results highlight the potential of using imputation for mitigation of SNP ascertainment bias but also underline the need for unbiased reference sets.

Estimated genetic parameters for all genetically evaluated traits in Canadian Holsteins

Genetic improvement is a crucial tool to deal with the increasing demand for high quality, sustainably produced dairy. Breeding programs are based on genetic parameters, such as heritability and genetic correlations, for economically important traits in a population. In this study, we estimated population genetic parameters and genetic trends for 67 traits evaluated on heifers and first-lactation Canadian Holstein cows. The data consisted of approximately 500,000 records with pedigree information collected from 1980 to 2019. Genetic parameters were estimated using bivariate linear animal models under a Bayesian approach. Analyses for the 67 traits resulted in 2,211 bivariate combinations, from which the estimated genetic parameters are reported here. The most highly heritable traits were fat percent (0.66) and protein percent (0.69), followed by stature (0.47). Lowest heritabilities (0.01) were observed for disease-related traits, such as lameness and toe ulcer, and calf survival. The genetic correlations between gestation length, calf size, and calving ease measured on both heifer and cows were close to unity. On the other hand, traits such as body condition score and pin width, cystic ovaries and sole ulcer, rear teat placement, and toe ulcer were genetically unrelated. This study reports genetic parameters that have not been previously published for Canadian Holstein cows, and provides updates of those previously estimated. These estimates are useful for building new indexes, updating existing selection indexes, and for predicting correlated responses due to inclusion of novel traits in the breeding programs.

Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species

Microsatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.

Genome-scale data resolves the timing of divergence in Joshua trees.

Joshua trees (Yucca brevifolia and Y. jaegeriana) and their yucca moth pollinators (Tegeticula synthetica and T. antithetica) are a model system for studies of plant-pollinator coevolution and, they are thought to be one of the only cases in which there is compelling evidence for cospeciation driven by coevolution. Previous work attempted to evaluate whether divergence between the plant and their pollinators was contemporaneous. That work concluded that the trees diverged more than 5 million years ago-well before the pollinators. However, clear inferences were hampered by a lack of data from the nuclear genome and low genetic variation in chloroplast genes. As a result, divergence times in the trees could not be confidently estimated. We present an analysis of whole chloroplast genome sequence data and RADseq data from >5000 loci in the nuclear genome. We developed a molecular clock for the Asparagales and the Agavoideae using multiple fossil calibration points. Using Bayesian inference, we produced new estimates for the age of the genus Yucca and for Joshua trees. We used calculated summary statistics describing genetic variation and used coalescent-based methods to estimate population genetic parameters. We find that the Joshua trees are moderately genetically differentiated, but that they diverged quite recently (~100-200 kya), and much more recently than their pollinators. The results argue against the notion that coevolution directly contributed to speciation in this system, suggesting instead that coevolution with pollinators may have reinforced reproductive isolation following initial divergence in allopatry.

The mango seed weevil Sternochetus mangiferae (Fabricius) (Coleoptera: Curculionidae) is characterized by low genetic diversity and lack of genetic structure

The mango seed weevil Sternochetus mangiferae (Fabricius) is distributed across the major mango‐producing areas of the world and causes significant economic losses of mango fruit. Despite its importance as a crop pest, we have only limited information on the population genetics of the mango seed weevil. Here, we examined the genetic diversity of this important pest using specimens intercepted by Beijing Customs District P. R. in China from 41 countries and regions. We used segments of the mitochondrial gene cytochrome c oxidase subunit I and the nuclear gene elongation factor 1‐alpha to examine population genetic structure in this species. Our results showed that genetic diversity is low in S. mangiferae, with a mean genetic distance of 0.095–0.14%. Other population genetic parameters also indicated a low level of genetic diversity among samples from a large geographic range. Analysis of molecular variance revealed little population genetic structure, and mismatch distribution analyses provided evidence of a population expansion, although other demographic metrics of population expansion were nonsignificant. We suggest that the observed low level of genetic diversity and population genetic structure in S. mangiferae supports the hypothesis that the population genetics of this species has been impacted by anthropogenic transportation of mangoes and weevils.

Exploring underlying drivers of genotype by environment interactions in feed efficiency traits for dairy cattle with a mechanistic model involving energy acquisition and allocation

Feed efficiency (FE) is a complex phenotype made up of multiple traits for which there is potential for substantial genotype by environment interaction (G × E). The objective of this study is to evaluate the extent of G × E for FE traits with a simulation approach. We used a mechanistic model of the dairy cow that simulates trajectories of phenotypes throughout lifetime, depending on trajectories of resource acquisition and allocation, driven by 4 genetic scaling parameters, and depending on the nutritional environment (quantity and quality of feed resources). The cow model, calibrated for a grass-based farming system and seasonal calving, was combined with a genetic module. This simulated genetic variation in the 4 genetic scaling parameters related to resource acquisition and allocation, based on a simple balanced pedigree structure (200 paternal half-sib groups each of 100 daughters). The population of 20,000 cows generated was simulated in 4 nutritional environment scenarios, representing a gradient of feeding constraints. In each scenario, 6 traits derived from the model outputs were analyzed to obtain population genetic parameters. Genetic correlations between second-lactation production and FE were positive and high in all scenarios and increased as the nutritional environment became more constraining. A measure of lifetime FE was positively correlated with second-lactation production under a less constrained environment, but these correlations decreased as the environment became more constraining. The genetic correlation between body reserves at second calving, and lifetime FE was positive and low in the least constraining scenario and increased as the environment became more constraining. In addition to genetic parameters, we looked at the distributions of acquisition and allocation parameters among the best performing cows for lactation and life FE, in the 2 most contrasted scenarios. The 4 subpopulations of best cows had acquisition and allocation strategies different from the whole population. In conclusion, this simulation study identifies the potential underlying biological basis for important G × E in FE traits. This highlights the importance of having a balanced breeding goal when undertaking selection that should also be based on phenotypes relevant to the target performance environment.

Molecular characterization of two highly divergent Iranian johnsongrass mosaic virus isolates from Zea mays.

Iranian johnsongrass mosaic virus (IJMV, genus Potyvirus, family Potyviridae) is one of the most prevalent viruses causing maize mosaic disease in Iran. In this study, the complete genomes (9,618 and 9,543 nucleotides) of two highly divergent IJMV isolates (Maz2 and Maz3) were obtained from the metagenomic analysis of Zea mays RNAs using Illumina sequencing. The genome contained a single open reading frame (9,165 nucleotides) encoding a polyprotein of 3,054 amino acids, flanked by a 5'-untranslated region (UTR) of 216 and 143 nucleotides and a 3'-UTR of 237 and 235 nucleotides. A comparative analysis of the complete genome showed that IJMV-Maz2 and Maz3 had 85.99% nucleotide and 94.56% amino acid sequence identity with each other and shared 84.87-88.74% nt and 94.24-96.17% aa identity with those of two other IJMV isolates available in the GenBank. The coat protein of Maz2 and Maz3 showed 86.40-95.72% nt sequence identity (90.79-97.70% aa identity) to 12 other IJMV isolates available in GenBank. Our results indicated a relatively stable and conserved genomic composition with a low codon usage bias in all of the assayed IJMV coding sequences. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that purifying selection pressure was the major force acting upon the IJMV genome. The outcome of the study provides valuable insights on the evolution of IJMV genome, for which there are few genome sequences available, and informs the current breeding efforts towards resistance for IJMV.

Opportunities and challenges in assessing climate change vulnerability through genomics

By investigating how past selection has affected allele frequencies across space, genomic tools are providing new insights into adaptive evolutionary processes. Now researchers are considering how this genomic information can be used to predict the future vulnerability of species under climate change. Genomic vulnerability assessments show promise, but challenges remain.

New microsatellite markers for Ellipse, Venustaconcha ellipsiformis (Bivalvia: Unionidae), with notes on optimal sample size and cross-species amplification

Venustaconcha ellipsiformis (Unionidae) is a freshwater mussel species inhabiting small to medium streams of the Midwestern United States; however, its occurrence is rather sporadic and populations are often isolated. Due to anthropogenic habitat degradation and water pollution, this species is designated as some sort of conservation status in many states. To prioritize conservation strategies, highly variable genetic markers are necessary to assess population genetic structure and potential genetic erosion of V. ellipsiformis. Using whole genome sequence data, we developed and characterized microsatellite markers for V. ellipsiformis. Among 23 tetranucleotide loci tested, 14 loci were consistently amplified and showed polymorphism. Analyses performed on three populations in the upper Mississippi River basin showed that the number of alleles per locus ranged from 2 to 11 and the observed heterozygosity varied from 0.15 to 0.75. Based on genotypic and allelic rarefaction curves, these loci had adequate statistical power to genetically discriminate between individuals and the sample size was large enough to capture most alleles available in the populations at most loci. Finally, cross-species screening of the loci successfully amplified and showed polymorphism in six species in the tribe Lampsilini. The microsatellite loci developed in this study provide a valuable addition to extant genetic markers for freshwater mussels and can be useful to provide high-level resolution of population genetic parameters for V. ellipsiformis. Such information will be of great value for resource managers developing and prioritizing conservation strategies for imperiled mussel species.

Population data for 23 autosomal STR loci in White British population.

We report allele frequencies and standard population genetics parameters for 23 forensic autosomal STR loci tested among White British population. In addition, we use generated allele frequency data to compare the extent of genetic variation with 19 other European populations.

Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

Key messageBrazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity ({H}_{o}), effective population size estimate widehat{{(N}_{e}}) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Evaluating the genetic diversity in two tropical leguminous trees, Dalbergia cochinchinensis and D. nigrescens, in lowland forests in Cambodia and Thailand using MIG-seq.

It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and FST were computed. The estimates calculated from the data obtained by MIG-seq were compared to those obtained by Sanger sequencing of nine nuclear coding genes in D. cochinchinensis in our previous study. The nucleotide diversity at the MIG-seq loci was slightly higher than that at silent sites in the coding loci, whereas the FST values at the MIG-seq loci were generally lower than those at the coding loci, although the differences were not significant. Moreover, nucleotide diversities within populations of the two species were similar to each other, at approximately 0.005. Three and four population clusters were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were differentiated from each other, the levels of differentiation among them, as measured by FST, were higher in D. cochinchinensis than in D. nigrescens. This indicates higher levels of gene flow between the populations in the latter species. We recommend using MIG-seq for quick surveys of genetic variation because it is cost-effective and results in smaller variance in the estimates of population genetic parameters.

Exploring the Genetic Consequences of Clonality in Haplodiplontic Taxa.

Partially clonality is an incredibly common reproductive mode found across all the major eukaryotic lineages. Yet, population genetic theory is based on exclusive sexuality or exclusive asexuality, and partial clonality is often ignored. This is particularly true in haplodiplontic eukaryotes, including algae, ferns, mosses, and fungi, where somatic development occurs in both the haploid and diploid stages. Haplodiplontic life cycles are predicted to be correlated with asexuality, but tests of this prediction are rare. Moreover, there are unique consequences of having long-lived haploid and diploid stages in the same life cycle. For example, clonal processes uncouple the life cycle such that the repetition of the diploid stage via clonality leads to the loss of the haploid stage. Here, we surveyed the literature to find studies that had genotyped both haploid and diploid stages and recalculated population genetic summary metrics for seven red algae, one green alga, three brown algae, and three mosses. We compared these data to recent simulations that explicitly addressed the population genetic consequences of partial clonality in haplodiplontic life cycles. Not only was partial clonality found to act as a homogenizing force, but the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetic indices. We found remarkably similar patterns across commonly used population genetic metrics between our empirical and recent theoretical expectations. To facilitate future studies, we provide some recommendations for sampling and analyzing population genetic parameters for haplodiplontic taxa.

Inference of population genetic parameters from an irregular time series of seasonal influenza virus sequences.

Basic summary statistics that quantify the population genetic structure of influenza virus are important for understanding and inferring the evolutionary and epidemiological processes. However, the sampling dates of global virus sequences in the last several decades are scattered nonuniformly throughout the calendar. Such temporal structure of samples and the small effective size of viral population hampers the use of conventional methods to calculate summary statistics. Here, we define statistics that overcome this problem by correcting for the sampling-time difference in quantifying a pairwise sequence difference. A simple linear regression method jointly estimates the mutation rate and the level of sequence polymorphism, thus providing an estimate of the effective population size. It also leads to the definition of Wright's FST for arbitrary time-series data. Furthermore, as an alternative to Tajima's D statistic or the site-frequency spectrum, a mismatch distribution corrected for sampling-time differences can be obtained and compared between actual and simulated data. Application of these methods to seasonal influenza A/H3N2 viruses sampled between 1980 and 2017 and sequences simulated under the model of recurrent positive selection with metapopulation dynamics allowed us to estimate the synonymous mutation rate and find parameter values for selection and demographic structure that fit the observation. We found that the mutation rates of HA and PB1 segments before 2007 were particularly high and that including recurrent positive selection in our model was essential for the genealogical structure of the HA segment. Methods developed here can be generally applied to population genetic inferences using serially sampled genetic data.

Populációgenetikai paraméterek, tenyészértékek, fenotípusos és genetikai trendek limousin tehenek első ellési életkorára

Some environmental effects, population genetic parameters, breeding value of Limousin breeding bulls, also phenotypic and genetic trends in the age at first calving (AFC) of cows between 1992 and 2013 were estimated. Data were served by the Limousin and Blonde d’Aquitaine Breeders Association, in Hungary. The study was extended to three herds and 1157 cows. GLM method was used for the study of different effects, the BLUP animal model for estimation of population genetic parameters and breeding values (BV), and one-way linear regression analysis for trend calculations. The overall mean value of the AFC was estimated to be 34.7±0.4 months. The contribution of the evaluated factors to the phenotype was as follows: herd 73.51%, birth year of cow 13.02%, sire 6.74%, birth season of cow 1.62%. The heritability of AFC proved to be low (h2 = 0.08±0.07 and h2 = 0.01±0.04). There were relatively small differences in the estimated BV of the studied sires for the AFC. Based on the phenotypic trend calculation, the AFC of cows decreased by an average of 0.33 months per year, however no significant change was found in the genetic trend during the study period.

Distributional characterizations and testing for differences of relatedness and inbreeding of a subpopulation of American Hereford bulls.

Beta distributions are characterized by two determining parameters and a parameter space from 0 to 1, and may be useful for examining population genetic parameters such as the relationship or inbreeding coefficients. Often subpopulations exist within breeds that are congregated around particular lineages of cattle or ancestors that breeders value. These subpopulations are more related to each other than to the majority of other animals; they may have higher inbreeding as well. Value may be added to these subpopulations because of their relatedness with important or renowned ancestors. The objectives of this work were to compare the relatedness and inbreeding of a group of 26 modern bulls from a subpopulation of the American Hereford breed relative to 1) 30 males with the most descendants present in the pedigree, 2) 15 renowned American Hereford bulls considered important individuals in the breed’s history, and 3) 19 prominent subpopulation male ancestors. Conformance of the mean relationship coefficients of the bulls with the three groups and the mean inbreeding coefficient with all pedigree animals to beta distributions was assessed by 1) visually determining the parameters of the beta distributions based on the entire pedigree, 2) testing the mean relationship coefficient or inbreeding coefficient of the group of subpopulation bulls for its positional inclusion in those distributions, and 3) bootstrap sampling methodology. The mean relationship coefficients of the 26 Trask bulls with the 30 bulls with the most descendants, the 15 renowned ancestors, and the 19 Trask male ancestors were 0.15, 0.132, and 0.208, respectively. Testing of these means in beta distributions indicated that the group of 26 Trask bulls were no more related to the three groups of bulls than all of the animals in the pedigree (0.06 < P < 0.25). Bootstrap sampling indicated that the 26 bulls were more related to the three groups of male ancestors than the remainder of the animals in the pedigree (P < 0.0001). The mean inbreeding coefficient of the 26 bulls (0.13) did not differ from the overall inbreeding coefficient (0.056) when tested using a beta distribution; however, bootstrap sampling indicated otherwise (P < 0.0001). Results may indicate the inadequacy of visually parameterizing a beta distribution. Quantification of pedigree relatedness of a group of animals to key ancestors, especially with no DNA available, may add value to that group and individuals.