Genealogical Structure Research Articles

The influence of origin on milk productivity of cows

Holsteinized black-and-white cattle are used for milk production. The genealogical structure of the herd is represented by animals from the following genealogical lines: Vis Back Ideal 1013485, Reflection Sovering 198998, Montwick Cheiftain 95679, Pabst Governor 882933 and Annas Adema 30587. Animals of these types feature high milk productivity indices. In particular, the cows of all the researched lines have high milk productivity indices - more than 9,000 kg of milk per lactation. The highest milk yields are achieved by cows of the Montwick Cheiftain 95679 line. The yields are 16-339 kg higher than ones of the animals from the Annas Adema 30587 and Pabst Governor 882933 lines, respectively. According to the quality indices of milk, cows of all lines exceed the requirements of the breed standard. Data on amount of milk fat confirms the level of breeding value of the cattle breeding stock used in the farm. They exceed the breed standard in terms of milk fat yield by more than 2 times. The highest coefficient of the cows’ biological efficiency was recorded in the cows groups of Annas Adema 30587 and Montwick Cheiftain 95679 lines, and the biological full-value was confirmed for the Montwick Cheiftain 95679 and Pabst Governor 882933 lines.

Genealogical structure changes as range expansions transition from pushed to pulled

Range expansions accelerate evolution through multiple mechanisms, including gene surfing and genetic drift. The inference and control of these evolutionary processes ultimately rely on the information contained in genealogical trees. Currently, there are two opposing views on how range expansions shape genealogies. In invasion biology, expansions are typically approximated by a series of population bottlenecks producing genealogies with only pairwise mergers between lineages-a process known as the Kingman coalescent. Conversely, traveling wave models predict a coalescent with multiple mergers, known as the Bolthausen-Sznitman coalescent. Here, we unify these two approaches and show that expansions can generate an entire spectrum of coalescent topologies. Specifically, we show that tree topology is controlled by growth dynamics at the front and exhibits large differences between pulled and pushed expansions. These differences are explained by the fluctuations in the total number of descendants left by the early founders. High growth cooperativity leads to a narrow distribution of reproductive values and the Kingman coalescent. Conversely, low growth cooperativity results in a broad distribution, whose exponent controls the merger sizes in the genealogies. These broad distribution and non-Kingman tree topologies emerge due to the fluctuations in the front shape and position and do not occur in quasi-deterministic simulations. Overall, our results show that range expansions provide a robust mechanism for generating different types of multiple mergers, which could be similar to those observed in populations with strong selection or high fecundity. Thus, caution should be exercised in making inferences about the origin of non-Kingman genealogies.

Rising Inequality in Mothers' Employment Statuses: The Role of Intergenerational Transmission.

During the late twentieth century, U.S. mothers' propensities to hold full-time jobs became increasingly unequal across the distribution of socioeconomic status (SES). Consequently, daughters in high-SES households became more likely to be raised by working mothers than daughters in low-SES households. To what extent did this unequal exposure further shape maternal employment inequality in the twenty-first century-when these daughters had grown into adults and begun to raise their own children? Leveraging the genealogical structure of the Panel Study of Income Dynamics, this article estimates intergenerational employment coefficients on a sample of late twentieth century mothers and their daughters. It documents a much stronger intergenerational relationship in high-SES families than in low-SES families. Supplementary analyses reveal that being raised by a working mother significantly reduces the motherhood employment penalty among high-SES women but not among low-SES women. Unequal rates of mother-daughter employment transmission by SES can account for 36% of growing inequality in maternal employment across SES groups, observed in the Current Population Survey, between 1999 and 2016. These findings indicate that family-level transmission processes magnify the effects of structural forces on maternal employment inequality.

Multiple evolutionary lineages for the main vector of Leishmania guyanensis, Lutzomyia umbratilis (Diptera: Psychodidae), in the Brazilian Amazon

Lutzomyia umbratilis is the main vector of Leishmania guyanensis in the Brazilian Amazon and in neighboring countries. Previous biological and molecular investigations have revealed significant differences between L. umbratilis populations from the central Brazilian Amazon region. Here, a phylogeographic survey of L. umbratilis populations collected from nine localities in the Brazilian Amazon was conducted using two mitochondrial genes. Statistical analyses focused on population genetics, phylogenetic relationships and species delimitations. COI genetic diversity was very high, whereas Cytb diversity was moderate. COI genealogical haplotypes, population structure and phylogenetic analyses identified a deep genetic differentiation and three main genetic groups. Cytb showed a shallower genetic structure, two main haplogroups and poorly resolved phylogenetic trees. These findings, allied to absence of isolation by distance, support the hypothesis that the Amazon and Negro Rivers and interfluves are the main evolutionary forces driving L. umbratilis diversification. The main three genetic groups observed represent three evolutionary lineages, possibly species. The first lineage occurs north of the Amazon River and east of Negro River, where Le. guyanensis transmission is intense, implying that L. umbratilis is an important vector there. The second lineage is in the interfluve between north of Amazon River and west of Negro River, an area reported to be free of Le. guyanensis transmission. The third lineage, first recorded in this study, is in the interfluve between south of Amazon River and west of Madeira River, and its involvement in the transmission of this parasite remains to be elucidated.

Genealogical structure of the Belarusian black-and-white breed based on the microsatellite analysis of the lines bred at gene pool enterprises

The methods of molecular genetic analysis are widely used to assess the genetic structure and to study the dynamics of population-genetic processes in populations of domestic animals. I n particular, these are the highly polymorphic genetic markers – the microsatellites that are the most common molecular markers in genetic and genomic research. The aim of the research was to develop the genealogical structure of the Belarusian black-and-white breed based on the microsatellite analysis of the lines bred at a gene pool enterprise. The research was carried out with the animals bred at the JSC “SGC “Zarechye”. For the microsatellite analysis of boars of the Belarusian black-and-white breed, the DNA testing was carried out at 9 STR-loci (SО155, SО355, SО386, SО005, SW72, SW951, SО101, SW240, and SW857). In all studied lines, the largest number of effective alleles was at the SО005 locus – 4.00–5.14. The lines of animals with heterozygosity can be used in various breeding schemes, both in purebred breeding (in pedigree pig breeding) and in crossing (in industrial pig breeding). Polymorphism determines the degree of genetic variation in populations. The locus is classified as polymorphic when the frequency of the most common allele of this locus does not exceed 95% (р ≤ 95). The revealed polymorphism of loci in the lines Maket, Tik, and Veseliy indicates the presence of genetic variability in them, which allows using them in breeding and breed-forming processes. Based on the studies made, the genealogical structure of the Belarusian black-and-white breed, consisting of one subcluster and two branches, has been developed, which makes it possible to assess the state and degree of relation of structural units (lines), and reflects the prospect of their further use.

Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

Evaluation of genetic diversity of subdivided genealogical groups in Lithuanian Trakehner horse population using immunogenetic tools

The objective of this study was to evaluate the inter-breed genetic diversity of Lithuanian Trakehner horses. The current population in Lithuania numbers 1 039 Trakehner horses. The study included the immunogenetic data analysis of 316 blood samples. Pedigree was traced back to 7–11 generations. The horses were assigned to genealogical clusters originating from East Prussian Trakehner Stud, Thoroughbred and Arab sires. The first two clusters were subdivided into nine-horse groups according to the most important ancestors. The evaluation of genetic diversity was based on six blood groups and five protein polymorphism systems. The differences between genealogical groups were confirmed by principal component analysis and applied cluster analysis. According to the allelic frequency, the Trakehner population changed very slightly through a 30-year period, and only one rare (0.013) allele Tf<sup>RR</sup> (frequent in other Trakehner populations), has been newly found. The analysis of genetic polymorphism systems based on a very low rate of alleles Q<sup>abc</sup> (0.093) and D<sup>dkl</sup> (0.046), which are typical of other populations, indicated the exclusivity of the Trakehner population in Lithuania. The average expected heterozygosity by blood protein polymorphism and blood groups were 0.409 and 0.441, respectively. The genetic clustering diverged by observed heterozygosity of blood groups and by pedigree data in Pilger through Egoist, Bay Ronald through Dark Ronald and Dampfross through Hyperion subgroups. The determined distinctiveness of subdivided Trakehner horse groups suggests reconsidering the breeding strategies and conservation programme of Trakehner horses. Breeding and selection of subdivided sire lines could be among the appropriate solutions for the maintenance and extension of the genealogical structure.

PECULIARITIES OF FORMATION OF GENEALOGICAL STRUCTURE OF UKRAINIAN BLACK-AND-WHITE DAIRY BREED IN SUMY REGION AND RESEARCH OF ITS INFLUENCE ON THE GENOTYPE OF COWS BY CAPA-CASEIN

PECULIARITIES OF FORMATION OF GENEALOGICAL STRUCTURE OF UKRAINIAN BLACK-AND-WHITE DAIRY BREED IN SUMY REGION AND RESEARCH OF ITS INFLUENCE ON THE GENOTYPE OF COWS BY CAPA-CASEIN

GROWTH AND DEVELOPMENT OF HEIFERS OF THE CREATED SIMМENTAL MEAT BREED

GROWTH AND DEVELOPMENT OF HEIFERS OF THE CREATED SIMМENTAL MEAT BREED

ANALYSIS OF THE GENEALOGICAL LINES OF THE HERD OF CATTLE OF THE ABERDEEN-ANGUS BREED IN THE SAE "MAIN BREEDING CENTER OF UKRAINE"

ANALYSIS OF THE GENEALOGICAL LINES OF THE HERD OF CATTLE OF THE ABERDEEN-ANGUS BREED IN THE SAE "MAIN BREEDING CENTER OF UKRAINE"

Dependence of productive qualities of cows of brown Swiss breed on their physiological devel-opment

The brown Swiss breed of cattle, which is currently being bred in the Smolensk region for dairy and meat productivity, is of interest from the point of view of its production feasibility and competitiveness, and the biological properties of livestock. The research was carried out in a breeding reproducer for the breeding of brown Swiss cattle of the Smolensk region, in the conditions of the farm, the age of fruitful insemination, physiological development, linear affiliation and productive qualities were analyzed (n=384). According to the terms of fertilization, the animals were conditionally divided into three groups: - early-maturing 46 heads (12%) live weight of the first insemination 329 kg, medium-maturing 191 heads (49.7%) live weight 388 kg and late-maturing 147 heads (38.3%) live weight 429 kg. The genealogical structure of the analyzed livestock includes descendants of the related groups Meridian 90827 (46.3%), Concentrate 106157 (25.4%), Master 106902 (25.4%) and line Laird 71151 (2.9%). The highest milk yield and fat for the first (4520 kg) and highest lactation (5022 kg, 3.97 %) in late-maturing animals. The group of first-calf cows of medium precocity in terms of milk yield occupies an intermediate position (4334 kg). The difference in live weight between the third and first groups is significant (P<0.05). There were no significant differences in milk fat and protein between the groups of cows. From these studies, it follows that the larger the live weight at the first insemination, the more productive they are.

On conditioning a self-similar growth-fragmentation by its intrinsic area

The genealogical structure of self-similar growth-fragmentations can be described in terms of a branching random walk. The so-called intrinsic area A arises in this setting as the terminal value of a remarkable additive martingale. Motivated by connections with some models of random planar geometry, the purpose of this work is to investigate the effect of conditioning a self-similar growth-fragmentation on its intrinsic area. The distribution of A is a fixed point of a useful smoothing transform which enables us to establish the existence of a regular density a and to determine the asymptotic behavior of a(r) as r→∞ (this can be seen as a local version of Kesten–Grincevicius–Goldie theorem’s for random affine fixed point equations in a particular setting). In turn, this yields a family of martingales from which the formal conditioning on A=r can be realized by probability tilting. We point at a limit theorem for the conditional distribution given A=r as r→∞, and also observe that such conditioning still makes sense under the so-called canonical measure for which the growth-fragmentation starts from 0.

MtDNA <italic>COⅠ</italic> sequence diversity of <italic>Gerres limbatus</italic> in coastal waters of China

In order to contribute information on genetic background of <italic>Gerres limbatus</italic> in coastal waters of China, 652 bp mtDNA <italic>COⅠ</italic> sequences of 140 individuals from 9 geographic populations were analyzed. 14 mutation sites were found and 13 haplotypes were identified, of which 9 were unique haplotypes and 4 were shared haplotypes. The overall haplotype and nucleotide diversity were low ( <italic>H</italic>_d=0.276±0.050, π =0.000 5±0.000 1 ), of which genetic diversity of populations from the east part of the Qiongzhou Strait ( <italic>H</italic>_d = 0.338-0.456, π = 0.000 6-0.001 1 ) was higher than those in the western Beibu Gulf ( <italic>H</italic>_d =0-0.295, π =0-0.000 5 ). Haplotype network diagrams did not show obvious genealogical and geographic structure. Genetic differentiation coefficicent(<italic>F</italic>_st) showed that there was indistinctively low-middle genetic differentiation between Naozhou population and other populations ( <italic>F</italic>_st= 0.0773-0.1696). No obvious differentiation was found among other populations ( <italic>F</italic>_st=-0.041 5-0.061 2). AMOVA analysis also showed that 95% population variation originated from within the group. The negative overall value of the neutrality test (Tajima’s <italic>D</italic>=-2.254 9; Fu’s <italic>F</italic>_s=-16.472 5 ) and a significant single peak in the nucleotide mismatch distribution were consistent with demographic expansion in the past, and deduced expansion time ranged from about 0.130 4 to 0.043 5 million years ago. Since the overall genetic diversity of the population was less than 0.5 and nucleotide diversity was less than 0.005, it was speculated that <italic>Gerres limbatus</italic> population in coastal waters of China had recently encountered a severe bottleneck effect. The nucleotide diversity of the Ningde and Naozhou populations was relatively high and had a conservation priority. As genetic diversity of populations in the Beibu Gulf was extremely low, measures should be taken to avoid further decline in genetic diversity.

Genealogical lines of breeding mares as biological resources of a thoroughbred horse breed bred in the Stavropol Krai

Tribal horse breeding is one of the priority areas of livestock in the Stavropol Territory. The article provides an analysis of the population of purebred horse breeding mares bred in the leading farms of the Stavropol Territory (OOO “SKHP Svobodnyi trud”, OOO “SKHP Novomarevskoe”, FGUP “Rassvet-Stavropole”). An assessment of the mares of the pedigree core of purebred horse breed showed that their genealogical structure is represented by 12 lines. It should be noted that the 5 lines of Norsen Dancer, Native Dancer, Nazrullah, Fairway and Tern-Tu go back to the same ancestor – the Falaris line, which is 82.6 % of the total number of breeding mares. The data obtained correspond to the general trend that is observed in the global structure of purebred horse breed. An analysis of the genealogical lines of the pedigree nucleus of purebred horse mares in the Stavropol Krai revealed their optimal linear and age structure. A zootechnical assessment showed that according to measurements and indices, the mares of the farms analyzed correspond to the breed standard. The research results can be recommended as educational material for students and undergraduates of universities studying in the areas of preparation of zootechnical profile.

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.

Создание племенных стад в белорусском заводском типе свиней породы йоркшир на основе новых заводских линий с использованием микросателлитных маркеров

Based on the conducted studies using DNA testing and microsatellite markers, the genealogical structure and microsatellite profile of breeding herds of White-Russian factory-type Yorkshire pigs created in JSC «SGC «Zapadny» and SE «Zhodinoagroplemelita» were developed, which are based on the new lines Drug6805 and Dobry 2313. The average number of private alleles in loci in boars of different lines was 0,111–0,593. The created breeding herds and new lines will serve as the basis for the breeding of the factory type of pigs in the Yorkshire breed.

СЕЛЕКЦИОННАЯ РАБОТА СО СТАДОМ ТРАНСГЕННЫХ КОЗ В РЕСПУБЛИКЕ БЕЛАРУСЬ

Genealogical structure of the livestock of goats producing the bio-analogue of human lactoferrin has been studied for the fi rst time in the Republic of Belarus. Successors of lines and families have been determined, and a comparative assessment of using various selection profi les for obtaining goats and dams of the stock of genetically engineered animals has been carried out.

THE PARAMETERS OF SELECTION, THE GENEALOGICAL STRUCTURE AND METHODS OF BREEDING UKRAINIAN RIDING HORSE BREED

The Ukrainian Riding Horse breed is the leading breed of horses in Ukraine in the direction of the sport of working capacity. A long period of breeding improvement requires the establishment of breeding parameters that will continue the breeding process, taking into account the modern needs of classical equestrian sports. Studies were conducted on the entire livestock of the breed, which is kept by breeding subjects and private owners. Quantitative indicators of the breed are established, which are: the total number of 672 heads, including breeding mares of reproductive age – 266 heads. The established parameters of breeding, according to which it is necessary to conduct further improvement of the Ukrainian Riding Horse breed: purpose-breeding horses mainly for purebred breeding, horses with universal sport activity; breeding methods-purebred by lines, crossing at the level of blood flow with the original and other sports breeds, conditional blood capacity for the original breeds - ¾, for others – ½; breeding core should be at least 800 purebred mares; the number of genealogical lines should remain at the current level – 7 or increase; number of breeding stallions in lines-not less than 5, mares – 30 heads; measurement indicators (2 – year-old age: 160-158-178-20 cm (Stallions), 157-155-177-20 cm (mares); 3-year-old age: 163-162-186-21 (Stallions), 161-160-184-20.5 cm (mares); 4 – year – old age and older: 165-165-192-21 cm (stallions), 163-163-190-20.5 cm (mares); the class of young animals at the first bonus should be: elite – 85%, 1 class – 15 % (stallions); Elite - 90%, 1 class – 10 % (mares); the average score for sports performance of 2-year-old young animals should not be lower than: 8 points (Stallions), 7 points (mares); the proportion of horses that have passed factory and Inter – factory tests of sports qualities: stud farms – 80 %; breeding loudspeakers – 70 %; height of overcoming obstacles when testing jumping qualities in freedom (without a rider): at the age of 2 years – 130 cm; at the age of 3 years – 140 cm; at the age of 4 years and older –150 cm. The given breeding parameters are justified by the results of the selection assessment of the entire recorded livestock of the Ukrainian Riding Horse breed. The genealogical structure of the breed consists of 8 lines, mainly – Hobot (24.4 %) and Bespechny (20.5 %). Highly rated for its typicality and exterior stallions line Huguenot, Bespechny and Khrustal, in terms of measurements of the body - the stallions of lines Vodopad and of Raufbold. The greatest number of mares refers to the lines Raufbold (25.1 %) and Factotum (22.0 %). The breed was 23 uterine families. The largest number of representatives in uterine families Tema, Infra II, Bilinka, Eureka, Asaliya. The top number of offspring of the highest sports class estimated breeding family of Arizona, Cathedra, Tema, Bilinka and Tina. Evaluation of models the selection of which received horses showed that most stallions – Champions of competitions at the national level and winners of international competitions obtained in the model selection with inbreeding on one ancestor: Bespechny III-III; VI, IV-IV; V, IV-II; V, IV-IV; Huguenot V-IV; Plastic V-III; Raufbold III-III. The analysis of pedigrees of horses - winners and prize-winners in competitions of the international and national level established that the majority of horses from selection were purebred and came from classical lines of the Ukrainian Riding Horse breed (52.0 %). Among the crossbred descendants of the first generation the highest number of winners of competitions at the national level obtained from crosses with Trakenen breed (61.2 %), winners of international competitions – from stallions of the Thoroughbred riding breed (14.7%).

Analysis of the genealogical structure of the breeding herd of Holstein cattle at Agricultural Farm named after Ilyich

Analysis of the genealogical structure of the breeding herd of Holstein cattle at Agricultural Farm named after Ilyich

Immunogenetic status and breeding value of Holstein cows

In the genealogical structure of the breeding stock, the highest specific weight is occupied by the Reflection Sovering and Vis bek Aydiala lines, accounting for 56.8 and 39.9% of animals, respectively. The study results of Holstein cattle blood-group factors can be used to monitor its gene pool, genetic intrabreed differentiation, assess selection parameters, and conduct targeted selection of parental pairs. It was determined that in EAA blood group system in Holstein cows of reproduction from the USA, the frequency of A1 antigen is 58.7%, and in domestic reproduction animals, this antigen is found with a lower frequency of 50.7%. At the same time, in the specified system of blood groups in both groups of experimental animals, antigen “a” is characterized by the highest frequency, the lowest occurrence is A2 antigen, and animals with A1 antigen took an intermediate position. In EAB system, the US Holstein cows have a higher frequency of such antigens as Е3/, О3 и I1 compared to the reproductive animals of Agro-Soyuz LLC. The EAF blood group system is represented by two antigens, where F antigen frequency in both groups of experimental animals is 100%. Of all the blood group systems, the greatest differences between compared groups of animals were detected for the antigens of EAZ blood group system.