Ancestry Relationships Research Articles

Monitoring and Genetic Characterization of Historical Grapevine Varieties (V. vinifera ssp.) from Styria in Slovenia

The aim of this research work was to find historical varieties that existed in this area before phylloxera and to identify them on the basis of historical written sources and genetic analyses. At the beginning of the 19th century, around 300 grape varieties were cultivated in Styria. Between 2020 and 2022, old vineyards were monitored at 115 locations in Styria (between the Mura and Sava rivers) in Slovenia. The directly collected samples (340 grapevine accessions) were determined by molecular analysis with 24 SSR markers. A total of 66 different genotypes were detected. After comparison with the available databases, 29 historical varieties and 37 unknown historical genotypes were identified. Several parameters were calculated to evaluate the usefulness of the selected loci in this work, and a dendrogram representing the genetic similarities between the origins was created using the neighbor-joining method to investigate possible ancestry relationships in the sample set. The most common historical varieties were ‘Belina’ (‘Heunisch weiss’), ‘Vrbovec’ (‘Tantovina Eihenblaetrige’), ‘Ranfol’ (‘Ranfol beli’), and ‘Pelesovna’ (‘Vulpea’). Varieties from the current variety list were also frequently found, such as ‘Frankinja’ (‘Blaufraenkisch’) and ‘Žametovka’ (‘Kavčina črna’). In a few locations, one of the most important red varieties from the beginning of the 20th century was also found in this area (alongside ‘Frankinja’ and ‘Žametovka’), i.e., ‘Vranek’ (‘Zimmettraube balu’). At that time, this variety was planted in multi-variety vineyards and was preserved, but its importance in single-variety vineyards quickly declined due to female flower. In addition, genetic analyses have shown that 37 unknown historical genotypes have been found in this area. These genotypes need to be described ampelographically and technologically evaluated in the future. Most of the vegetative offsprings of these genotypes have already been transferred to the Meranova gene bank, where they can be accurately described ampelographically under the same pedoclimatic conditions.

Quantifying and Understanding the Higher Risk of Atherosclerotic Cardiovascular Disease Among South Asian Individuals: Results From the UK Biobank Prospective Cohort Study.

Individuals of South Asian ancestry represent 23% of the global population, corresponding to 1.8 billion people, and have substantially higher risk of atherosclerotic cardiovascular disease compared with most other ethnicities. US practice guidelines now recognize South Asian ancestry as an important risk-enhancing factor. The magnitude of enhanced risk within the context of contemporary clinical care, the extent to which it is captured by existing risk estimators, and its potential mechanisms warrant additional study. Within the UK Biobank prospective cohort study, 8124 middle-aged participants of South Asian ancestry and 449 349 participants of European ancestry who were free of atherosclerotic cardiovascular disease at the time of enrollment were examined. The relationship of ancestry to risk of incident atherosclerotic cardiovascular disease-defined as myocardial infarction, coronary revascularization, or ischemic stroke-was assessed with Cox proportional hazards regression, along with examination of a broad range of clinical, anthropometric, and lifestyle mediators. The mean age at study enrollment was 57 years, and 202 405 (44%) were male. Over a median follow-up of 11 years, 554 of 8124 (6.8%) individuals of South Asian ancestry experienced an atherosclerotic cardiovascular disease event compared with 19 756 of 449 349 (4.4%) individuals of European ancestry, corresponding to an adjusted hazard ratio of 2.03 (95% CI, 1.86-2.22; P<0.001). This higher relative risk was largely consistent across a range of age, sex, and clinical subgroups. Despite the >2-fold higher observed risk, the predicted 10-year risk of cardiovascular disease according to the American Heart Association/American College of Cardiology Pooled Cohort equations and QRISK3 equations was nearly identical for individuals of South Asian and European ancestry. Adjustment for a broad range of clinical, anthropometric, and lifestyle risk factors led to only modest attenuation of the observed hazard ratio to 1.45 (95% CI, 1.28-1.65, P<0.001). Assessment of variance explained by 18 candidate risk factors suggested greater importance of hypertension, diabetes, and central adiposity in South Asian individuals. Within a large prospective study, South Asian individuals had substantially higher risk of atherosclerotic cardiovascular disease compared with individuals of European ancestry, and this risk was not captured by the Pooled Cohort Equations.

The contribution of the International Rice Genebank to varietal improvement and crop productivity in Eastern India

Using survey dataset collected from nearly 9000 farmers along with pedigree and evaluation data, this study measures the contribution of the International Rice Genebank (IRG) to varietal improvement and rice productivity of farmers in Eastern India. We empirically test the relationship of ancestry to productivity changes while controlling for the effects of other farm inputs and environmental factors. Estimated coefficients indicate that a 10% increase in the genetic contribution of IRG accessions to an improved rice variety is associated with a yield increase of 27%. Through pedigree analysis, we also confirm that 45 to 77% of the genetic composition of improved rice varieties is derived from the genes of IRG accessions. Peta, Dee Geo Woo Gen, and Fortuna are the three most popular progenitors with definite IRG contribution. High genealogical diversity likely results from the crossing of germplasm received from multiple countries of origin, which also confer multiple, functional trait combinations in a released variety. Further, our calculations reveal that the average coefficient of parentage of all pairwise combinations among the 10 most adopted rice varieties is 0.0973, indicating a high degree of latent genetic diversity. Findings demonstrate the valuable contribution of the genetic resources conserved and distributed by IRG to the development of improved rice varieties.

Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.

RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking pseudoknots. We report 56 subgraph blocks up to nine vertices; among them, 22 are frequently occurring, 15 of which contain pseudoknots. We then catalog atomic fragments corresponding to the subgraph blocks to define a library of building blocks that can be used for RNA design, which we call RAG-3Dual, as we have done for tree graphs. As an application, we analyze the distribution of these subgraph blocks within ribosomal RNAs of various prokaryotic and eukaryotic species to identify common subgraphs and possible ancestry relationships. Other applications of dual graph partitioning and motif library can be envisioned for RNA structure analysis and design.

PHYLOGENETIC ANALYSIS ON FOUR SPECIES OF TILAPIA (Oreochromis niloticus, Tilapia zilli, Sarotherodon galilaeus, Sarotherodon melanotheron) IN NIGERIA

An investigation into evolutionary history of four species of Tilapia species was carried out as a taxonomy tool to relate most tilapia species found within the Nigerian waters. These species are (Oreochromis niloticus, Tilapia zilli, Sarotherodon galilaeus, Sarotherodon melanotheron). Blood samples from the four species of tilapia were collected and preserved on Fast Technology for Analysis (FTA) cards for DNA extraction and PCR amplification. The various nucleotide sequences of the four Tilapia species found in the Mitochondria D-loop region were copied and aligned with the use of BioEdit and Mega 6.0 softwares. Three phylogenetic trees were drawn to show the evolutionary relationship amongst the four species of tilapia. The results indicated that Sarotherodon galilaeus and Sarotherodon melanotheron are sister texa and share a common ancestor with Oreochromis niloticus. Tilapia zilli is an out group which is the most distantly related to the three species (Oreochromis niloticus, Sarotherodon galilaeus Sarotherodon melanotheron). Tilapia zilli (Israel) and Tilapia zilli are sister texa and share a common ancestor in Tilapia sparmanii. The study also revealed ancestry relationship among other species of fish Cyprinus caprio and Clarias gariepinus formed a clade with the three tilapia species (Tilapia zilli, Tilapia zilli (Israel) and Tilapia sparmanii), which share an unknown but common ancestor.

Abstract C56: Relationship of ancestry and breast cancer subtypes in Hispanic women from New Mexico and Washington State

Abstract The ancestral makeup of Hispanic women in the United States is complex; they form an admixed population including European (EUR), Amerindian (AI), and African (AFR) ancestry. Studies have demonstrated differences in the distribution of molecular subtypes of breast cancer between non-Hispanic white women and Hispanic women. To better understand the relationship of breast cancer biomarkers/molecular subtypes and ancestry in a U.S. Hispanic population, we assessed histologic characteristics, tumor cell protein expression by immunohistochemistry (IHC), gene expression using the Affymetrix Human HTA 2.0 array, and ancestry by ancestry informative markers (AIMs) in a cohort of 331 Hispanic women diagnosed with breast cancer in either Washington or New Mexico. To assess individual ancestry, we genotyped a panel of 215 AIMs in 260 women with available DNA. We ran ancestry analyses using one to ten populations in the model; three populations gave the lowest cross-validation error (0.53). In this cohort, we observed the largest contribution from EUR ancestry (mean=58.6%; range=8.3-97.6%), followed by AI ancestry (mean=33.6%; range=0-89.5%) and AFR ancestry (mean=7.9%; range=0-83.9%). We did not see significant associations between ancestry proportion and individual IHC markers ER, PR, HER2, CK5/6, EGFR, or tumor grade. However, three markers (tumor lymphocyte response, p53 positivity, high Ki67 positivity) were associated with ancestry: greater AFR ancestry with higher lymphocyte response (OR=1.045 per 1% increase in AFR ancestry, 95% CI: 1.004-1.087, p=0.03) and an increasing AI ancestry with high Ki67 positivity (OR=1.032 per 1% increase in AI ancestry, 95% CI: 1.005-1.061, p=0.02) and high p53 expression (OR=1.035 per 1% increase in AI ancestry, 95% CI: 1.008-1.062, p=0.01). We compared St. Gallen IHC subtypes with ancestry and observed a positive association between the ER-/PR-/HER2+ subtype and AI ancestry. Specifically, for every 1% increase in AI ancestry, we observed a 4.2% (95% CI: 0.2%-8.3%) increased risk for ER-/PR-/HER2+ disease compared to patients with Luminal A (ER+/PR+/HER2-) disease (p=0.04). Gene expression intrinsic subtyping by PAM50 was also suggestive of this association: an increasing proportion of AI ancestry was associated with increased odds of having the HER2-enriched subtype compared with Luminal A subtype (OR=1.030, 95% CI: 0.995-1.067, p=0.09). In conclusion, ancestry in this population of Hispanic women with breast cancer was mixed. Greater AI ancestry was associated with increased odds of ER-/PR-/HER2+ disease and of two markers of aggressive breast cancer, high tumor cell proliferation and p53 expression. There was no association identified between ancestry and triple negative breast cancer. Other studies have identified that HER2+ breast cancer rates in Hispanic women are higher than those in non-Hispanic white women. These data highlight the ancestral heterogeneity of the Hispanic population and the need to fully understand which subgroups of Hispanic women might be at an increased risk for specific breast cancer types, especially those that are aggressive and associated with poor outcomes. Citation Format: Jamie Guenthoer, Xiaoyu Chai, Karen W. Makar, Chris S. Carlson, Rania Bakkar, Irena B. King, Huining Kang, Beti Thompson, Christopher I. Li, Li Hsu, Linda S. Cook, Peggy L. Porter. Relationship of ancestry and breast cancer subtypes in Hispanic women from New Mexico and Washington State. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr C56.

On the complexity of finding a largest common subtree of bounded degree

The largest common subtree problem is to find a bijective mapping between subsets of nodes of two input rooted trees of maximum cardinality or weight that preserves labels and ancestry relationship. The problem is known to be NP-hard for unordered trees. In this paper, we consider a restricted unordered case in which the maximum outdegree of a common subtree is bounded by a constant D. We present an O(nD) time algorithm where n is the maximum size of two input trees, which improves a previous O(n2D) time algorithm. We also present an O((H2⋅22H−1⋅D2H)D−1poly(n)) time algorithm, where H is the maximum height of two input trees.

Efficacy of population structure analysis with breeding populations and inbred lines

The objective was to assess by simulation the efficacy of population structure analysis in plant breeding. Twelve populations and 300 inbred lines were simulated and genotyped using 100 microsatellite loci. The experimental material included populations with and without admixture, ancestry relationship and linkage disequilibrium, and with distinct levels of genetic differentiation and effective sizes. The analyses were performed using Structure software and employed all available models. For all the group number (K) tested, for both populations and inbred lines, the admixture model with correlated allelic frequencies provided the highest value for the logarithm of the marginal likelihood. Fitting appropriate model and using adequate sample size for individuals and markers, Structure was effective in identifying the correct population structure, migrants and individuals with genome from distinct populations. The linkage model did not result in an improvement in clustering relative to the admixture model with correlated allelic frequencies. The inclusion of prior information did not change the results; for some K values the analyses showed slight higher values of the marginal likelihood. The reduction in the number of individuals and markers negatively affected the results. There was a high variation in the most probable K value between the evaluated methods.

Exploring heuristic and optimum branching algorithms for image phylogeny

Currently, multimedia objects can be easily created, stored, (re)-transmitted, and edited for good or bad. In this sense, there has been an increasing interest in finding the structure of temporal evolution within a set of documents and how documents are related to one another overtime. This process, also known in the literature as Multimedia Phylogeny, aims at finding the phylogeny tree(s) that best explains the creation process of a set of near-duplicate documents (e.g., images/videos) and their ancestry relationships. Solutions to this problem have direct applications in forensics, security, copyright enforcement, news tracking services and other areas. In this paper, we explore one heuristic and one optimum branching algorithm for reconstructing the evolutionary tree associated with a set of image documents. This can be useful for aiding experts to track the source of child pornography image broadcasting or the chain of image distribution in time, for instance. We compare the algorithms with the state-of-the-art solution considering 350,000 test cases and discuss advantages and disadvantages of each one in a real scenario.

Local search for the generalized tree alignment problem.

BackgroundA phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The patterns that can be observed in nature are the product of complex interactions, constrained by the template that our ancestors provide. The problem of simultaneous tree and alignment estimation under Maximum Parsimony is known in combinatorial optimization as the Generalized Tree Alignment Problem (GTAP). The GTAP is the Steiner Tree Problem for the sequence edit distance. Like many biologically interesting problems, the GTAP is NP-Hard. Typically the Steiner Tree is presented under the Manhattan or the Hamming distances.ResultsExperimentally, the accuracy of the GTAP has been subjected to evaluation. Results show that phylogenies selected using the GTAP from unaligned sequences are competitive with the best methods and algorithms available. Here, we implement and explore experimentally existing and new local search heuristics for the GTAP using simulated and real data.ConclusionsThe methods presented here improve by more than three orders of magnitude in execution time the best local search heuristics existing to date when applied to real data.

Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees

Given two rooted, labeled, unordered trees, the common subtree problem is to find a bijective matching between subsets of nodes of the trees of maximum cardinality which preserves labels and ancestry relationship. The tree edit distance problem is to determine the least cost sequence of insertions, deletions and substitutions that converts a tree into another given tree. Both problems are known to be hard to approximate within some constant factor in general.We tackle these problems from two perspectives: giving exact algorithms, either for special cases or in terms of some parameters; and approximation algorithms and hardness of approximation. We present a parameterized algorithm in terms of the number of branching nodes that solves both problems and yields polynomial algorithms for several special classes of trees. This is complemented with a tighter APX-hardness proof that holds when the trees are of height one and two, respectively. Furthermore, we present the first approximation algorithms for both problems. In particular, for the common subtree problem for t trees, we present an algorithm achieving a tlog2(bOPT+1) ratio, where bOPT is the number of branching nodes in the optimal solution. We also present constant factor approximation algorithms for both problems in the case of bounded height trees.

Relationships among durum wheat accessions. II. A comparison of molecular and pedigree information

The study of direct ancestry relationships provides information with which to determine essential derivation. SSR profiles were used to determine the pattern of relatedness among 134 durum wheat accessions, representing the most important modern durum wheat gene pools. Simple sequence repeat (SSR)- and amplified fragment length polymorphism (AFLP)-based genetic similarities among cultivars with accurate pedigrees were compared with pedigree-based coefficients of parentage. Sizeable departures of molecular similarities from the expected ones were observed, indicating the unreliability of inferring the pattern of genetic relatedness from the coefficient of parentage. Case studies consisting of parent-progeny cultivar trios and pairs, identified on the basis of their registered pedigree, were studied to evaluate the probability of ancestry of each progeny cultivar, compared with all the remaining accessions. Rare alleles and haplotype sharing were also explored. When the results did not agree with the registered parentages, SSR markers provided information with which to identify the most probable parents (or the corresponding "breeding lineages") in the collection.

Replacement of an Essentialistic Perspective on Taxonomic Definitions as Exemplified by the Definition of "Mammalia"

?Current controversies about the definitions of taxon names reflect different under? lying philosophical perspectives concerning the nature of definitions. The antithetical perspec? tives, called methodological essentialism and methodological nominalism (Popper, 1966, The open society and its enemies, Princeton Univ. Press, Princeton, NJ), are exemplified by alternative views a controversy surrounding the definition of the name Mammalia. Traditional per? spectives on the definition of Mammalia are essentialistic that the definition takes the form of a description stated terms of the traits of individual organisms, thus implying that taxa are abstract categories, i.e., that taxa have essences. In addition, the extension of the defined term (the set of species or organisms to which the name applies) is logically prior to its intension or defining formula (the property or properties that a species or organism must have to be designated by the name). Consequently, the name is treated as if it had a designation proper to it, which conforms with the essentialistic view that the name is an abbreviated description of the essence. An alternative perspective is manifested the redefinition of Mammalia as the name of the monotreme and therian crown dade. This perspective contrasts with the traditional one that the definition is stated terms of common ancestry relationships rather than organismal traits, thus implying that taxa are concrete composite wholes rather than abstract categories. In addition, the defining formula is logically prior to the extension of the defined term, and thus the name is treated only as a convenient label or shorthand symbol for the defining formula that has no proper designation. The replacement of an essentialistic perspective on the definitions of Mam? malia and other taxon names by a more nominalistic one is associated with the development of a phylogenetic perspective on biological nomenclature and represents an important step the development of a more broadly scientific approach to that subject. [Definition; essentialism; nominalism; Mammalia; nomenclature; philosophy; taxonomy; Karl R. Popper.] It has been said that in no other science is definition as important as it is tax? onomy (Hull, 1965:315). Recently, the im? portance of definitions taxonomy has been highlighted by the realization that explicitly phylogenetic methods for defin? ing the names of taxa are central to the development of a phylogenetic system of biological nomenclature (de Queiroz and Gauthier, 1990, 1992, 1994). But many of the taxon names current use, particu? larly the oldest and most familiar, were coined long before the advent of phylo? genetic definitions. Indeed, many were coined before widespread acceptance of the concept of phylogeny itself. Consequently, it should not be surprising that definitions formulated the context of the phylo? genetic system are coming into conflict with older definitions of the same names. An example of this conflict concerns the name Mammalia, which has been de? f ned phylogenetically as the crown dade stemming from the most recent common ancestor of monotremes and therians (Gau? thier et al., 1988a, 1988b, 1988c, 1989; Rowe, 1988; de Queiroz and Gauthier, 1992). This definition has been contested by system? atists adopting a view that has become tra? ditional among paleontologists, according o which Mammalia designates a taxon including not only the monotreme and therian crown dade but also several of its extinct outgroups (Miao, 1991; Lucas, 1992; for further discussion see Rowe and Gau? thier, 1992; Bryant, 1994). On one level, the disagreement is nothing more than a dif? ference preferences concerning the as? sociation of a taxon name with one dade or another. Here, I argue that it also reflects

Relationships between Australian wheats on the basis of pedigree, grain protein composition, grain quality and morphology

A procedure using numerical analysis has been devised for illustrating ancestry relationships. It has been applied to 60 wheat cultivars recently grown in Australia. The program also permits the grouping of parents to indicate those that are often used in combination. The network illustrating pedigree relationships between these cultivars corresponded closely to a second network which illustrated phenotypic similarities (morphology of plants, heads and grains, agronomic characteristics, grain quality and gluten composition). The specific attributes that most closely followed pedigree relationships were identified in this set of wheats. These procedures thus provide a basis for evaluating the role of pedigree in observed associations between phenotypic characteristics.

Optimal Weighted Ancestry Relationships

A solution method is given for a class of practical optimization problems requiring the determination of a consistent partial ordering for sets of objects, events, preferences, and the like. These problems are characterized by the existence of “noisy” (or contradictory) links of varying strengths. The origin of this class of problems is an anthropological study in which it is desired to specify a global chronological ordering of ancient cemetery data. A mathematical formulation is given which results in a minimum weight feedback model. A heuristic is developed similar to the Greedy algorithm for minimum weight spanning trees which requires only one pass through the network.