scholarly journals Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 839 ◽  
Author(s):  
Andrea Giontella ◽  
Irene Cardinali ◽  
Hovirag Lancioni ◽  
Samira Giovannini ◽  
Camillo Pieramati ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Resource ◽  
High Variability ◽  
Pedigree Information ◽  
Pedigree Data ◽  
Local Breed ◽  
Ancient Population ◽  
Mitochondrial Haplotypes ◽  
Multiple Sampling ◽  
Genealogical Data

The Maremmano horse is considered one of the most important Italian warmblood breeds which originated from an ancient population. In 1980, the National Association of Maremmano Breeders established the first Studbook that recorded 440 dams and four sire founders. In this study, we selected the most significant maternal lines in terms of offspring (for a total of 74 lineages and 92 Maremmano horses) and analyzed their mitochondrial DNA control regions. We found a high variability, reflecting the importance of this local breed as a genetic resource to be preserved. Through multiple sampling, we then verified the pedigree information for 12 dam lines by matching genealogical data with mitochondrial haplotypes. A complete concordance was demonstrated in nine lineages, while for the other we highlighted a different number of haplotypes for each line (three in Fiorella, two in Nizza I, and two in Pomposina), thus suggesting that the information recorded in the Studbook could be wrong and the samples do not descend from the same maternal founder. Our combined analysis provides the opportunity to confirm the ancestry of animals and could be employed to prevent errors in pedigree data also for other breeds and species.

scholarly journals Evidence for non-neutrality of mitochondrial DNA haplotypes in Drosophila pseudoobscura.

Genetics ◽  
1988 ◽  
Vol 120 (2) ◽  
pp. 485-494
Author(s):  
A F MacRae ◽  
W W Anderson
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Genome ◽  
Drosophila Pseudoobscura ◽  
Initial Population ◽  
Mitochondrial Haplotypes ◽  
Mtdna Haplotypes ◽  
Selective Neutrality ◽  
Frequency Changes ◽  
Apparent Equilibrium ◽  
Neutral Markers

Abstract Mitochondrial DNA (mtDNA) haplotypes usually are assumed to be neutral, unselected markers of evolving female lineages. This assumption was tested by monitoring haplotype frequencies in 12 experimental populations of Drosophila pseudoobscura which were polymorphic for mtDNA haplotypes. Populations were maintained for at least 10 generations, and in one case for 32 generations, while tests of mtDNA selective neutrality were conducted. In an initial population, formed from a mixture of two strains with different mitochondrial haplotypes, the frequency of the Bogota haplotype increased 46% in 3 generations, reaching an apparent equilibrium frequency of 82% after 32 generations. Perturbation of this equilibrium by addition of the less common haplotype resulted in a rapid, dramatic increase in frequency of the second haplotype, and a return to essentially the same equilibrium frequency as before perturbation. This behavior is not consistent with mtDNA neutrality, nor is the equilibrium consistent with a simple model of constant selection on the haploid mtDNAs. Replicate cage experiments with mtDNA haplotypes did not always generate the same result as the initial cage. Several lines of evidence, including manipulations of the nuclear genome, support the idea that both nuclear and mitochondrial genomes are involved in the dramatic mtDNA frequency changes. In another experiment, strong female viability selection was implicated via mtDNA frequency changes. Although the causes of the dramatic mtDNA frequency changes in our populations are not obvious, it is clear that Drosophila mitochondrial haplotypes are not always simply neutral markers. Our findings are relevant to the introduction of a novel mtDNA variant from one species or one population into another. Such introductions could be strongly favored by selection, even if it is sporadic.

scholarly journals 331 Efficient quality control methods for genomic and pedigree data used in routine genomic evaluation

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 50-51
Author(s):  
Yutaka Masuda ◽  
Andres Legarra ◽  
Ignacio Aguilar ◽  
Ignacy Misztal
Keyword(s):  
Quality Control ◽  
Large Scale ◽  
Computing Time ◽  
Academic Research ◽  
Snp Markers ◽  
Pedigree Information ◽  
Memory Usage ◽  
Pedigree Data ◽  
Genomic Evaluation ◽  
Data Set

Abstract Quality control and consistency tests on genotypes and historical pedigree data are applied in a routine genomic evaluation and academic research. The quality control takes more time to finish as more genotypes become available, and this step is a bottleneck in a pipeline of routine evaluation. For the efficient quality control, we have developed several algorithms and a computer program to support for large-scale, biallelic, single nucleotide polymorphisms (SNPs). The program is designed to detect unsatisfactory genomic markers and individuals in terms of call rate, marker allele frequencies, duplicate samples, and Mendelian inconsistency in the large genomic data with the pedigree including millions of individuals. Duplicated genotypes can be detected using a set of markers. An SNP genotype is packed into a 2-bit representation in memory that enables bitwise operations with parallel computing to efficiently perform the quality control. The software optionally checks the inconsistency of pedigree information. We compared QCF90 with preGSf90, a preceding program, in terms of memory usage and computing time using a data set including 200,000 genotyped individuals, 50,000 SNP markers per individual, and 216,500 pedigree individuals. In total running time, QCF90 was approximately 6 times faster than PREGSF90 (307 s vs 2075 s) while the memory usage was 30 times less (2 GB vs 75 GB) using only 1 thread. The QCF90 program performed better in speed as more threads were used. A check for genomic duplications took 159 s with 16 threads when 5,000 genotypes were compared with 200,000 genotypes using 2500 SNP markers. The new tool is useful in the routine genomic evaluation and the academic research in which both the genotypes and the pedigree information are used. The QCF90 executable is available at http://nce.ads.uga.edu with a user manual.

Population dynamics of the 2 major mitochondrial DNA haplotypes in experimental populations of Drosophila subobscura

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1010-1018 ◽  
Author(s):  
Pedro Oliver ◽  
Joan Balanyà ◽  
Maria Misericòrdia Ramon ◽  
Antònia Picornell ◽  
Lluis Serra ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Natural Population ◽  
Linear Trend ◽  
Natural Populations ◽  
Drosophila Subobscura ◽  
Random Drift ◽  
Significant Linear Trend ◽  
Low Frequencies ◽  
Mitochondrial Haplotypes ◽  
Experimental Populations

The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Calvià (Majorca, Balearic Islands, Spain). This population, like others founded in Europe, is characterized by the presence of 2 very common (>95%) mitochondrial haplotypes (named I and II) and rare and endemic haplotypes that appear at very low frequencies. Four experimental populations were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. The populations were started with haplotypes I and II at an initial frequency of 50% each. After 33 generations, the 2 haplotypes coexisted. Random drift could be rejected as the only force responsible for the observed changes in haplotype frequencies. A slight but significant linear trend favouring a mtDNA (haploid) fitness effect has been detected, with a nonlinear deviation that could be due to a nuclear component. An analysis of chromosomal arrangements was made before the foundations of the cages and at generation 23. Our results indicated that the hypothesis that the maintenance of the frequencies of haplotypes I and II in natural populations could be due to their association with chromosomal arrangements remains controversial.Key words: natural selection, random drift, cytonuclear interactions, chromosomal arrangements, mtDNA haplotypes, Drosophila subobscura.

scholarly journals Phylogeography and Phylogenetic Evolution in Tibetan Sheep Based on MT-CYB Sequences

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1177
Author(s):  
Jianbin Liu ◽  
Zengkui Lu ◽  
Chao Yuan ◽  
Fan Wang ◽  
Bohui Yang
Keyword(s):  
Mitochondrial Dna ◽  
Tibetan Plateau ◽  
Clustering Analysis ◽  
Genetic Resource ◽  
Population Studies ◽  
Ovis Aries ◽  
Base Pairs ◽  
Branching Order ◽  
Tibetan Sheep ◽  
Phylogenetic Evolution

To date, molecular genetics and population studies in Tibetan sheep (Ovis aries) have been limited, and little is known about the phylogenetic evolution and phylogeography of Tibetan sheep populations. The aim of the present research was to explore phylogeography and phylogenetic evolution of Tibetan sheep populations, on the basis of mitochondrial DNA (mtDNA) gene MT-CYB (1140 base pairs). Our dataset consisted of 641 MT-CYB sequences from the same amount of animals belonging to 15 populations of Tibetan sheep living in the Qinghai–Tibetan Plateau, China. Haplotype and nucleotide diversities were 0.748 ± 0.010 and 0.003 ± 0.001, respectively. The analysis of phylogeography revealed the presence of two formerly described haplogroups in 15 populations of Tibetan sheep, however only one haplogroup was present in Awang sheep. Moreover, 641 Tibetan sheep were distributed into a minimum of two clusters by clustering analysis. The 15 Tibetan sheep populations and 19 reference populations of 878 individuals were separated into six main groups based on their substitutions per site, from which we constructed a phylogenetic tree. Minor differences in branching order of various taxa between trees acquired from either gene were observed. This study provides insights on the origins and phylogenetic evolution of populations residing in the Qinghai–Tibetan Plateau, which will aid information of future conservation programs aimed at conserving this valuable genetic resource.

Genetic relationships among North American bison populations

1996 ◽  
Vol 74 (4) ◽  
pp. 738-749 ◽  
Author(s):  
Renee O. Polziehn ◽  
Curtis Strobeck ◽  
Robin Beech ◽  
Jane Sheraton
Keyword(s):  
Mitochondrial Dna ◽  
North American ◽  
Sequence Data ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Bison Bison ◽  
Mitochondrial Haplotypes ◽  
Length Polymorphisms ◽  
Wood Bison ◽  
Paraphyletic Group

North American bison are presently divided into two subspecies: wood bison (Bison bison athabascae) and plains bison (B. b. bison). A survey was undertaken to determine the distribution of mitochondrial DNA haplotypes among subspecies and populations. Twelve haplotypes were identified with sequence data from the control region of mitochondrial DNA from 32 bison. Mitochondrial haplotypes for 269 bison from nine populations were then determined using the polymerase chain reaction and analyzed for restriction fragment length polymorphisms. Haplotype frequencies suggest genetic distances among bison populations from 0.0715 to 0.362. The extent of differentiation varies considerably. Based on the composition and phylogeny of haplotypes in the bison herds, plains bison form a paraphyletic group and wood bison form a polyphyletic group. Because neither subspecies of bison is derived from one lineage, neither is a well-defined taxon.

scholarly journals Wolbachia-Mitochondrial DNA Associations in Transitional Populations of Rhagoletis cerasi

Insects ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 675
Author(s):  
Vid Bakovic ◽  
Martin Schebeck ◽  
Christian Stauffer ◽  
Hannes Schuler
Keyword(s):  
Mitochondrial Dna ◽  
Selective Sweep ◽  
Fruit Fly ◽  
Mitochondrial Haplotype ◽  
Significant Information ◽  
The Czech Republic ◽  
Transition Zones ◽  
Mitochondrial Haplotypes ◽  
The Relationship ◽  
Rhagoletis Cerasi

The endosymbiont Wolbachia can manipulate arthropod host reproduction by inducing cytoplasmic incompatibility (CI), which results in embryonic mortality when infected males mate with uninfected females. A CI-driven invasion of Wolbachia can result in a selective sweep of associated mitochondrial haplotype. The co-inheritance of Wolbachia and host mitochondrial DNA can therefore provide significant information on the dynamics of an ongoing Wolbachia invasion. Therefore, transition zones (i.e., regions where a Wolbachia strain is currently spreading from infected to uninfected populations) represent an ideal area to investigate the relationship between Wolbachia and host mitochondrial haplotype. Here, we studied Wolbachia-mitochondrial haplotype associations in the European cherry fruit fly, Rhagoletis cerasi, in two transition zones in the Czech Republic and Hungary, where the CI-inducing strain wCer2 is currently spreading. The wCer2-infection status of 881 individuals was compared with the two known R. cerasi mitochondrial haplotypes, HT1 and HT2. In accordance with previous studies, wCer2-uninfected individuals were associated with HT1, and wCer2-infected individuals were mainly associated with HT2. We found misassociations only within the transition zones, where HT2 flies were wCer2-uninfected, suggesting the occurrence of imperfect maternal transmission. We did not find any HT1 flies that were wCer2-infected, suggesting that Wolbachia was not acquired horizontally. Our study provides new insights into the dynamics of the early phase of a Wolbachia invasion.

scholarly journals Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1310
Author(s):  
Enrico Mancin ◽  
Michela Ablondi ◽  
Roberto Mantovani ◽  
Giuseppe Pigozzi ◽  
Alberto Sabbioni ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genomic Structure ◽  
Population Level ◽  
Snp Markers ◽  
Pedigree Information ◽  
Pedigree Data ◽  
Selection Signatures ◽  
Effective Population ◽  
Genomic Inbreeding ◽  
Inbreeding Level

This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.

scholarly journals Introgression of mitochondrial DNA among lineages in a hybridogenetic ant

2015 ◽  
Vol 11 (2) ◽  
pp. 20140971 ◽  
Author(s):  
Hugo Darras ◽  
Serge Aron
Keyword(s):  
Mitochondrial Dna ◽  
Social Insect ◽  
Nuclear Dna ◽  
Geographical Origin ◽  
Nuclear Markers ◽  
Genetic Analyses ◽  
Genetic Lineages ◽  
Desert Ant ◽  
Mitochondrial Haplotypes

We report a remarkable pattern of incongruence between nuclear and mitochondrial variations in a social insect, the desert ant Cataglyphis hispanica . This species reproduces by social hybridogenesis. In all populations, two distinct genetic lineages coexist; non-reproductive workers develop from hybrid crosses between the lineages, whereas reproductive offspring (males and new queens) are typically produced asexually by parthenogenesis. Genetic analyses based on nuclear markers revealed that the two lineages remain highly differentiated despite constant hybridization for worker production. Here, we show that, in contrast with nuclear DNA, mitochondrial DNA (mtDNA) does not recover the two lineages as monophyletic. Rather, mitochondrial haplotypes cluster according to their geographical origin. We argue that this cytonuclear incongruence stems from introgression of mtDNA among lineages, and review the mechanisms likely to explain this pattern under social hybridogenesis.

scholarly journals Mitochondrial DNA Haplotype Frequencies in Natural and Experimental Populations of Drosophila subobscura

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1377-1382 ◽  
Author(s):  
José García-Martínez ◽  
José Aurelio Castro ◽  
Misericordia Ramón ◽  
Amparo Latorre ◽  
Andrés Moya
Keyword(s):  
Mitochondrial Dna ◽  
Natural Population ◽  
Linear Trend ◽  
Statistical Evidence ◽  
Drosophila Subobscura ◽  
Random Drift ◽  
Low Frequencies ◽  
Mitochondrial Haplotypes ◽  
Haplotype Frequencies ◽  
Experimental Populations

Abstract The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Esporles (Majorca, Balearic Islands, Spain). This population, like other European ones, is characterized by the presence of two very common (>96%) mitochondrial haplotypes (called I and II) and rare and endemic haplotypes that appear at very low frequencies. There is no statistical evidence of positive Darwinian selection acting on the mitochondrial DNA variants according to Tajima's neutrality test. Two experimental populations, with one replicate each, were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. Both populations were started with the two most frequent mitochondrial haplotypes, but at different initial frequencies. After 13 to 16 generations, haplotype II reached fixation in three cages and its frequency was 0.89 by generation 25 in the fourth cage. Random drift can be rejected as the force responsible for the observed changes in haplotype frequencies. There is not only statistical evidence of a linear trend favoring a mtDNA (haploid) fitness effect, but also of a significant nonlinear deviation that could be due to a nuclear component.

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