Evaluation of ultrametric phylogenetic tree estimation

Yujin Chung 한국데이터정보과학회 2020 한국데이터정보과학회지 Vol.31 No.3

A phylogenetic tree is a tree-like graphical representation of the evolutionary history of a group of organisms. An ultrametric tree is a phylogenetic tree scaled to time, which is estimated from DNA sequences of the organisms. PAUP* is a popular software used to estimate diverse types of phylogenetic trees including ultrametric trees. An ultrametric tree includes the lengths of edges which are the major parameters of interest, and PAUP* provides three ways to parameterize the edge lengths. In this work, analyses of simulated and real data were conducted to examine the performance of ultrametric tree estimations by PAUP*. The three parameterizations, called relAge, Thorne, and Rambaut, were found to be correctly estimated in most cases, although the relAge parameterization resulted in tree estimation with zero-length branches less often than others. The Rambaut parameterization had higher accuracy in the tree structure estimation in the simulation.

생물 계통수 생성의 사고 과정 모형 개발

조은미,김수일,정진수,권용주 韓國生物敎育學會 2005 생물교육 Vol.33 No.1

The purpose of this study was to develop the thinking process model for the generation of biological phylogenetic-tree. Firstly, this study analyzed several literatures on the process of phylogenetic-tree generation, and developed a tentative model of the phylogenetic-tree generation. To obtain verbal protocols for developing the final model, four tasks were developed. Subjects were 12 college students majoring in biology education. Row protocols were collected by a thinking aloud method and a retrospective interview method. After the protocols were analyzed, the final model was developed by revising the tentative model. The results of this study showed that the phylogenetic-tree was generated through the process of discovering pattern after classifying. Subtypes of classifying thinking process involves inventing, selecting, confirming, and judging the criteria for classifying. Subtypes of pattern-discovery thinking process involves inventing, selecting, confirming, and judging a pattern. This study also discusses the implications of these findings for teaching and evaluating in biology education.

한국산 중고기속(Sarcocheilichthys) 어류의 유전적 다양성과 분자계통학적 유연관계

장지왕,김재구,고재근,윤봉한,배양섭,Ji-Wang Jang,Jae-Goo Kim,Jae-Geun Ko,Bong-Han Yun,Yang-Seop Bae 한국어류학회 2024 韓國魚類學會誌 Vol.36 No.5

한국산 중고기속(genus Sarcocheilichthys)에 속하는 중고기(S. nigripinnis morii) 8개 집단과 참중고기(S. variegatus wakiyae) 5개 집단의 미토콘드리아 DNA의 cytb 유전자를 이용하여 각 집단의 유전적 다양성 및 분자계통학적 유연관계를 검토하였다. 참중고기 집단이 중고기 집단보다 유전적 다양성이 높은 것으로 확인되었다. cytb 유전자를 기반으로 한 한국산 중 고기속 어류의 분자계통도상에서 참중고기의 영산강(YSR) 집단은 중고기의 탐진강(TJR), 영산강(YSR), 섬진강(SJR) 집단과 clade를 이루며 현재의 분류체계와 일치하지 않는 유전적 유역관계가 나타났다. 한편, 핵 DNA 분자계통도상에서는 참중고기와 중고기로 뚜렷하게 구분이 가능하여 미토콘드리아 및 핵 DNA가 분자계통도상에서 상충하는 mitonuclear 불일치 현상이 나타냈다. 중고기의 섬진강(SJR) 집단이 동진강(DJR) 집단에 이입되어 교배가 일어난 것으로 추정되는 유전자형이 확인되었다. 동해로 유입되는 하천 중 유일하게 형산강(HSR)에만 이입되어 서식하는 것으로 알려진 중고기 집단은 한강(HR) 집단으로부터 이입되어 형성된 집단으로 추정되었지만, 고유한 유전적 그룹을 나타내는 유전자형도 확인되었다. 중고기의 한강(HR), 금강(GR), 만경강(MGR) 집단은 압록강 이북에 분포하는 북방중고기(S. czerskii), S. soldatovi와 유전적으로 동일 집단을 형성하였으며, 이에 다양한 표본을 확보하여 형태학적 및 분자계통학적 연구를 통한 분류학적 재검토가 요구되었다. Using the cytb gene region of the mitochondrial DNA of eight populations of Sarcocheilichthys nigripinnis morii and five populations of S. variegatus wakiyae, which belong to the genus Sarcocheilichthys from Korea, the genetic diversity and molecular phylogenetic relationships of each population were examined. As a result of the analysis, it was confirmed that the S. variegatus wakiyae population had higher genetic diversity than the S. nigripinnis morii population. In the phylogenetic tree of genus Sarcocheilichthys fish in Korea based on the cytb gene, the Yeongsan River (YSR) population of S. variegatus wakiyae forms a clade with the Tamjin River (TJR), Yeongsan River (YSR), and Seomjin River (SJR) population of S. nigripinnis morii, and genetic relationships that do not align with the current classification system were observed. Meanwhile, on the nuclear DNA phylogenetic tree, S. variegatus wakiyae and S. nigripinnis morii could be clearly distinguished, showing mitonuclear inconsistency where mitochondrial and nuclear DNA conflicted on the phylogenetic tree. The Seomjin River (SJR) population of S. nigripinnis morii was translocated to the Dongjin River (DJR) population, haplotype from which crossbreeding was presumed to have occurred was confirmed. Among the rivers flowing into the East Sea, the S. nigripinnis morii population is known to have been introduced and inhabit only the Hyeongsan River (HSR), and it is presumed to be a population formed by translocation from the Han River (HR) population, with a haplotype representing a unique genetic group also confirmed. The Han River (HR), Geum River (GR), and Mangyeong River (MGR) populations of S. nigripinnis morii formed a genetically identical population with S. czerskii and S. soldatovi distributed north of the Yalu River, and accordingly, a taxonomic reexamination was required through morphological and molecular phylogenetic studies by securing various specimens.

Phylogenetic analysis of Lamiaceae based on transcriptome data

김혜원,강유나,주원균,김창수 한국식물생명공학회 2023 Plant biotechnology reports Vol.17 No.6

The Lamiaceae family is included in the angiosperms and comprises over 7000 species, many of which are of considerable ecological, economic, and cultural importance. We seek to establish a taxonomic basis by examining the speciation timeline in Lamiaceae using phylogenetics and publicly available transcriptome data. Since Ks is steadily accumulated over time in plants for environmental adaptation until speciation occurs, the timing of speciation can be estimated from examination of Ks values. A total of 24 species included in the Lamiaceae family used in our analysis belongs to four subfamilies. We performed transcriptome assembly for each of the 24 species using trimmed data collected from public databases. We compiled groups of gene families in which at least one copy of the gene is present in each species from orthologous groups among unigenes. From these groups, we obtained a total of 450,014 single nucleotide polymorphisms (SNPs) across 27 species, incorporating three additional outgroup species. Subsequently, a tree was created using these SNPs. In our tree, the outgroup species were clearly located externally, confirming the proximity of species within the same subfamily. The Ks peak corroborated the outcomes observed in the phylogenetic tree. We estimated the rate of sequence evolution and divergence time for each species on the phylogenetic tree by referencing the time of divergence among the Lamiaceae family. In particular, Clinopodium serpyllifolium, Lavandula × intermedia, Phlomis fruticosa, and Volkameria inermis were analyzed for the first time. Our study helps with the understanding of the function of plants included in the Lamiaceae family and is expected to provide a fundamental resource that can be used to pinpoint the molecular and genomic evolution of the Lamiaceae family.

국내 재래종 밀 계통 분리와 농업형질 특성 평가

이유미,오세진,강성욱,최창현,이종태,조성우 한국작물학회 2024 한국작물학회지 Vol.69 No.2

적 요식물유전자원의 중요성이 인식되면서 지속적으로 재배되어 온 재래종에 대한 유전학적 가치가 인정되고 있다. 이 연구에서는 경남에서 수집한 국내 재래종 밀에 대한 염색체와이삭형태 관찰, 종자특성과 농업형질 평가, 및 국내 밀 품종과의 연관관계를 확인하였다. 국내 재래종 밀 4계통의 염색체는 42개로 확인되었으며, 이삭의 형태와 길이는 국내 품종인 금강밀과 차이를 보였다. 국내 재래종 밀 계통의 종실특성은 전반적으로 금강밀의 종실에 비하여 작은 면적, 너비, 및 길이를 보였으나, KWL-3의 배의 길이는 다른 재래종 밀뿐만 아니라 금강밀 종자의 배 길이보다도 길었다. 국내 재래종 밀 계통은 금강밀에 비하여 늦은 출수기와 성숙기를 보였다. 특히, KWL-3는 짧은 간장, KWL-2는 짧은 수장, KWL-1은 적은 분얼수를 보인 반면에 영화수와 일수립수는 금강에 비하여 재래종 밀 모든 계통에서 높았다. 이러한 이유는 금강밀에 비하여 높은 재래종 밀 계통의 임실률이 영향을 미친 것으로 판단된다. 하지만 재래종 밀 계통의종실면적, 너비, 길이, 및 두께가 작아 금강밀보다 낮은 천립중을 보였다. 향후, 종실특성의 향상은 재래종 밀 계통에 필수 조건으로 생각하며, 금강밀에 비하여 높은 영화수와 일수립수 및 임실률은 유용한 유전인자로 활용될 수 있을 것이다. ABSTRACT This study was conducted to evaluate agronomic traits and classify phylogenetic characteristics of Korean wheat landraces (KWLs) collected in Gyeongnam province. We used the squash method for chromosome observation, image analysis to examine seed characteristics, and genotyping using commercial single-nucleotide polymorphism chips to construct a phylogenetic tree. All KWLs contained 42 chromosomes and two pairs of microsatellites as observed in Keumgang, a Korean wheat cultivar. All KWLs showed smaller seed traits compared with those of Keumgang, although KWL-3 had a larger embryo length than that of Keumgang. Among agronomic traits compared with those of Keumgang, all KWLs had a late heading date and ripening period except for KWL-3, which showed the smallest culm and spike length. KWL-1 had the lowest tiller, highest floret, and grain number. All KWLs showed a lower thousand grain weight than that of Keumgang because of their smaller seeds. In the variation of variety and area, the heading date, ripening period, tiller number, and floret number were affected by the cultivation area, whereas the culm length, spike length, and 1000 grain weight were affected by the variety. Correlation distribution analysis showed differences in agronomic traits according to the cultivation area, and the heading date was positively correlated with the culm length and floret number in three cultivation areas. Principal component analysis explained that the heading date had a positive relationship with the ripening period and floret number and a negative relationship with the tiller number. Principal component analysis also revealed that all KWLs had a lower thousand grain weight than that of Keumgang. Phylogenetic tree showed that KWL-1 was near KWL-3, while KWL-2 was near KWL-4. All KWLs were genetically near the Korean wheat cultivars milsung and saeol, whereas they were genetically far from the Korean wheat cultivars goso and olgrue.

ON GENERATING LANGUAGE FAMILY-TREES BASED ON BASIC VOCABULARY

Ren Wu,Yuya Matsuura,Hiroshi Matsuno 대한전자공학회 2015 ITC-CSCC :International Technical Conference on Ci Vol.2015 No.6

This paper discusses generation of language family-trees by using a tool brought from molecular phylogenetics. Focusing on Indo-European languages and Altaic languages, we show the experimental result of generating language family-trees based on basic vocabulary and discuss the topologies of our generated language family-trees for comparison with other researches.

Taxonomic classification on phylogenic information appears a debatable approach: Lessons from the order Cypriniformes

Himanshu Priyadarshi,Rekha Das,Gowrimanohari Rakkannan 국립중앙과학관 2023 Journal of Asia-Pacific Biodiversity Vol.16 No.3

Genes are often selected for molecular taxonomy citing their agreement to taxonomically derived speciestrees. These results are then used to define and edit existing taxonomic hierarchies of species. Wecounter the validity of this practice experimentally using mitochondrial genes routinely employed for thepurpose. We constructed trees from complete mitochondrial DNA sequence (except D-loop) and itsthirteen protein-coding genes namely nd1, nd2, nd3, nd4, nd4L, nd5, nd6, atp6, atp8, COI, COII, COIII, andcytB of 255 species of Cypriniformes fish using the maximum likelihood and Bayesian methods. Whilend4, nd5, COI, COII, COIII, and cytB formed trees at par with the species tree, no gene produced completeconcurrence. Similarly, while few genes formed similar branching patterns at family (COI and COIII) orbroad group (nd1, nd2, and nd3; nd5 and COII) levels, no two gene trees fully agreed with each other. Tajima’s D estimates of all studied genes indicated non-random evolution, violating the basic assumptionof molecular phylogenetics. Bootstrap or Posterior probability values were also poor for several taxaindicating low robustness. Our findings reiterate that tree concurrence noted in studies involving smallersample sizes is not a reflection of the evolutionary signature of the species.

SPECTRAL METHOD FOR RECONSTRUCTING PHYLOGENETIC TREE

Paeng, Seong-Hun,Park, Chunjae Korean Mathematical Society 2019 대한수학회논문집 Vol.34 No.3

A new simple method is proposed for reconstructing phylogenetic trees, which we call the spectral method. The most common distance based method is the neighbor-joining method which is based on the minimum evolution principle. The spectral method shows similar performance to the neighbor-joining method for simulated data generated by seq-gen. For real data, the spectral method shows much better performance than the neighbor-joining method. Hence it can be a complementary method for reconstructing phylogenetic trees.

한국산 중고기속 (Sarcocheilichthys) 어류의 유전적 다양성과 분자계통학적 유연관계

장지왕 ( Ji-wang Jang ),김재구 ( Jae-goo Kim ),고재근 ( Jae-geun Ko ),윤봉한 ( Bong-han Yun ),배양섭 ( Yang-seop Bae ) 한국어류학회 2024 韓國魚類學會誌 Vol.36 No.2

Using the cytb gene region of the mitochondrial DNA of eight populations of Sarcocheilichthys nigripinnis morii and five populations of S. variegatus wakiyae, which belong to the genus Sarcocheilichthys from Korea, the genetic diversity and molecular phylogenetic relationships of each population were examined. As a result of the analysis, it was confirmed that the S. variegatus wakiyae population had higher genetic diversity than the S. nigripinnis morii population. In the phylogenetic tree of genus Sarcocheilichthys fish in Korea based on the cytb gene, the Yeongsan River (YSR) population of S. variegatus wakiyae forms a clade with the Tamjin River (TJR), Yeongsan River (YSR), and Seomjin River (SJR) population of S. nigripinnis morii, and genetic relationships that do not align with the current classification system were observed. Meanwhile, on the nuclear DNA phylogenetic tree, S. variegatus wakiyae and S. nigripinnis morii could be clearly distinguished, showing mitonuclear inconsistency where mitochondrial and nuclear DNA conflicted on the phylogenetic tree. The Seomjin River (SJR) population of S. nigripinnis morii was translocated to the Dongjin River (DJR) population, haplotype from which crossbreeding was presumed to have occurred was confirmed. Among the rivers flowing into the East Sea, the S. nigripinnis morii population is known to have been introduced and inhabit only the Hyeongsan River (HSR), and it is presumed to be a population formed by translocation from the Han River (HR) population, with a haplotype representing a unique genetic group also confirmed. The Han River (HR), Geum River (GR), and Mangyeong River (MGR) populations of S. nigripinnis morii formed a genetically identical population with S. czerskii and S. soldatovi distributed north of the Yalu River, and accordingly, a taxonomic reexamination was required through morphological and molecular phylogenetic studies by securing various specimens.

Subgrouping Automata: Automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm

Seo, J.H.,Park, J.,Kim, E.M.,Kim, J.,Joo, K.,Lee, J.,Kim, B.G. Pergamon 2014 Computational biology and chemistry Vol.48 No.-

Sequence subgrouping for a given sequence set can enable various informative tasks such as the functional discrimination of sequence subsets and the functional inference of unknown sequences. Because an identity threshold for sequence subgrouping may vary according to the given sequence set, it is highly desirable to construct a robust subgrouping algorithm which automatically identifies an optimal identity threshold and generates subgroups for a given sequence set. To meet this end, an automatic sequence subgrouping method, named 'Subgrouping Automata' was constructed. Firstly, tree analysis module analyzes the structure of tree and calculates the all possible subgroups in each node. Sequence similarity analysis module calculates average sequence similarity for all subgroups in each node. Representative sequence generation module finds a representative sequence using profile analysis and self-scoring for each subgroup. For all nodes, average sequence similarities are calculated and 'Subgrouping Automata' searches a node showing statistically maximum sequence similarity increase using Student's t-value. A node showing the maximum t-value, which gives the most significant differences in average sequence similarity between two adjacent nodes, is determined as an optimum subgrouping node in the phylogenetic tree. Further analysis showed that the optimum subgrouping node from SA prevents under-subgrouping and over-subgrouping.