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Why Do We Study Phylogeny? Mobile! a Tree Is Like a Mobile! “Tree of Life” (Klimt, Austria) “Tree of Life” Project PHYLOGENETICS

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Why Do We Study Phylogeny? Mobile! a Tree Is Like a Mobile! “Tree of Life” (Klimt, Austria) “Tree of Life” Project PHYLOGENETICS Why do we study phylogeny? Mobile! A tree is like a mobile! “Tree of Life” (Klimt, Austria) “Tree of Life” project http://tolweb.org/tree/ PHYLOGENETICS In biology, phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species or populations), which is discovered through molecular sequencing data and morphological data matrices. The term phylogenetics is of Greek origin from the terms phyle/phylon (φυλή/φῦλον), meaning "tribe, race," and genetikos (γενετικός), meaning "relative to birth" from genesis (γένεσις, "birth"). Taxonomy, the classification, identification, and naming of organisms, has been richly informed by phylogenetics but remains methodologically and logically distinct.[1] The fields overlap however in the science of phylogenetic systematics –often called "cladism" or "cladistics" –, where only phylogenetic trees are used to delimit taxa, which represent groups of lineage-connected individuals.[2] In biological systematics as a whole, phylogenetic analyses have become essential in researching the evolutionary tree of life. • It is a genome world! - The first genome data: Haemophilus influenzae (1995) about 1.8M bp. - Homo sapiens (begun in 1990 and completed in 2001) about 3.0G bp. <$400,000,000 - in 2011, more than 30 plant genomes are determined. In 2013, 40 angiosperm genomes have been sequenced. • Two examples for the effect of phylogeny in the text book: 1) the phylogeny transformed to systematics (classifications) 16S rDNA phylogeny: suggested three domains in the life. (c.f.: Svedverg value) 2) the phylogeny showed evolutionary information HIV gene (env) phylogeny: gave evidence of infection pathway. HIV genome stored evolutionary information recount the very recent history of its spread. ► Not only just pure application to the systematics but also the tracing evolutionary history. Other examples of interesting phylogenetic studies giving great impacts to the classification • Soltis et al. (1999): - Dicots are NOT monophyletic group - Amborella is the basal-most angiosperm • Manatee: a sister to elephant • Whale: a sister to hippo • white stork (황새): a sister to condor And minor impact my studies on Magnoliaceae ;-) Summarized angiosperm phylogeny Asterales 국화, 초롱꽃 Dipsacales 인동, 산토끼꽃 Apiales 당귀, 인삼 Aquifoliales 감탕나무 Campanulids Garryales 두충 Asterids Gentianales 용담, 꼭두서니 Laminales 꿀풀, 금어초 Solanales 토마토, 메꽃 Lamiids Ericales 진달래, 앵초 Cornales 층층나무, 수국 Sapindales 귤, 단풍나무 Malvales 무궁화 Core- Brassicales 애기장대, 무우 Malvids Fagales 자작나무, 참나무 eudicots Cucurbitales 박, 베고니아 Rosales 장미, 느릅나무 Rosids Traditional 콩, 자귀나무 Fabales Dicots part I Zygophyllales 남가새 Celestrales 노박덩굴 Fabids Oxalidales 굉이밥 Malpighiales 버드나무, 제비꽃 Geraniales 쥐손이풀 Myrtales 바늘꽃 Saxifragales 범의귀, 돌나물 Caryphyllales 카네이션, 선인장 Santalales 단향, 겨우살이 Beberidopsidales 매발톱나무 Gunnerales Buxaceae 회양목 Trochodendraceae Proteales 연꽃, 버즘나무 Sabiaceae 나도밤나무 Basal EUDICOTS eudicots 미나리아재비 양귀비 Ranunculales Euptelea Ceratophyllales 붕어마름 벼, 백합 옥수수 MONOCOTS Acorus 창포 Chloranthales 홀아비꽃대 Basal Canellales Angiosperms Piperales 후추, 족도리풀 Magnoliales 목련, 튜립나무 magnoliids Laurales 녹나무, 아보카도 Traditional Austrobailales 붓순나무, 오미자 Dicots part II Nymphaeaceae 수련 Hydatellaceae Amborella EXTENT GYMNOSPERMS Amborella is a sister to all other angiosperms! Amborella trichopoda KIM, et al., (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. American Journal of Botany 21: 2102-2118. Journal cover http://www.amborella.org/ Manatee (and Dugong) is a sister to elephant! Whales are sister to hippos! 9 66 d1 Mich. cavaleriei Phylogeny of Magnoliaceae 1 8 68 d1 M. pealiana Mi 2 3 Mich. baillonii Michelia Terminal flower 72 d1 5 2 Mich. champaca Elmerrillia 11 4 3 Mich. odora sect. Maingola 2 98 d4 91 d3 Mich. figo sect. Alcimandra A 12 9 E. ovalis sect. Aromadendron 86 d4 6 3 M. cathcartii Al 64 d1 16 M. elegans Ar 5 8 M. biondii Bu 3 100 d8 M. kobus Bu 5 77 d2 M. dawsoniana Yu 3 8 14 3 100 d8 100 d13 M. campbellii Yu subgen. Yulania 2 B 11 M. denudata Yu Base changes 7 95 d5 2 100 d6 M. cylindrica Cy 29 M. acuminataTu 80 d1 5 Bootstrap /Decay value 2 M. sinica Mt sect. Manglietiastrum 20 d0 3 1 C 18 P. praecalva Pachylarnax 100 d15 1 M. nitida Gy sect. Gynopodium 3 D 28 K. duperreana 100 d26 2 K. septentrionalis Kmeria 12 1 66 d2 M. panamensis Th 2 9 20 d0 M. virginiana Ma 2 E 15 M. tamaulipana Th sect. Theorhodon s.s. 100 d14 3 sect. Magnolia 1 M. grandiflora Th 6 Axillary flower 48 d1 M.guatemalensis Th 31 d1 70 d1 5 Gw 3 2 M. coco 7 M. gigantifolia Bl sect. Gwillimia F 17 4 1 M. henryi Gw sect. Lirianthe 100 d16 6 64 d1 M. pterocarpa Li sect. Blumiana 3 6 M. liliifera Bl 7 45 d1 M. mexicana Ta G 9 4 100 d8 17 M. dodecapetala Ta sect. Talauma 82 d3 13 M. splendens Sp sect. Splendentes 33 d1 1 1 86 d2 Mang. grandis 2 H 4 Mang. aroma 17 Mang. conifera Manglietia 100 d13 6 Mang. glauca 7 4 M. officinalis Ry 9 143 I 5 98 d4 M. tripetala Ry sect. Rytidospermum s.s. 21 100 d137 92 d3 6 M. sieboldii Oy sect. Oyama 14 98 d6 M. wilsonii Oy 1 J 17 M. fraseri var. fraseri Ry 1 M. fraseri 100 d17 M. fraseri var. pyramidata Ry 5 K 19 M. macrophylla Ry M. macrophylla 4 100 d17 M. dealbata Ry M. dealbata 52 L. chinense 27 L. tulipifera Phylogeny of Magnoliaceae changes the classification of the family. • Two examples for the effect of phylogeny in the text book: 1) the phylogeny transformed to systematics (classifications) 16S rDNA phylogeny: suggested three domains in the life. 2) the phylogeny showed evolutionary information HIV gene (env) phylogeny: gave evidence of infection pathway. HIV genome stored evolutionary information recount the very recent history of its spread. ► Not only just pure application to the systematics but also the tracing evolutionary history. Phylogeny of HIV: provide an evidence of infection pathway Another example: 3) Phylogenetic tree based on DNA sequences provide the identification of unknown biological samples! - DNA barcoding: Molecular identification method of species name based on the sequences of standard gene(s). - An example of my study: “DNA barcoding study of Korean Lamiaceae” based on three chloroplast DNA regions Two-dimensional barcode QR code barcode DNA-barcoding Lamiaceae (꿀풀과) Immature plants Molecular identifications of biological samples are possible EVEN with chopped or grounded samples. 황금 곽향 Scutellaria baicalensis 1 (황금) Scutellaria baicalensis 2 (황금) Scutellaria indica var. coccinea (연지골무꽃) Scutellaria indica var. tsusimensis 1 (떡잎골무꽃) Scutellaria indica var. tsusimensis 2 (떡잎골무꽃) Scutellaria insignis 1 (광릉골무꽃) Scutellaria insignis 2 (광릉골무꽃) Anaysis of three DNA Scutellaria moniliorrhiza (구슬골무꽃) Scutellaria regeliana 2 (가는골무꽃) Scutellaria strigillosa (참골무꽃) Scutellaria regeliana 1 (가는골무꽃) regions in chloroplast: Scutellaria pekinensis var. alpina 1 (수골무꽃) Scutellaria pekinensis var. alpina 2 (수골무꽃) Scutellaria Scutellaria pekinensis var. maxima 4 (왕골무꽃) trnH~psbA Scutellaria pekinensis var. ussuriensis 2 (호골무꽃) Scutellaria pekinensis var. ussuriensis 1 (호골무꽃) Scutellaria pekinensis var. maxima 1 (왕골무꽃) atpF~atpH Scutellaria pekinensis var. maxima 2 (왕골무꽃) Scutellaria pekinensis var. maxima 3 (왕골무꽃) Scutellaria pekinensis var. transitra 1 (산골무꽃) Scutellaria pekinensis var. transitra 2 (산골무꽃) psbK~psbI Scutellaria pekinensis var. transitra 3 (산골무꽃) Scutellaria pekinensis var. ussuriensis 3 (호골무꽃) Lamium album var. barbatum 1 (광대수염) Lamium album var. barbatum 2 (광대수염) Lamium album var. album 1 (왜광대수염) Lamium takesimense 1 (섬광대수염) Lamium takesimense 2 (섬광대수염) Lamium Lamium album var. album 2 (왜광대수염) Stachys japonica 1 (석잠풀) Stachys japonica 3 (석잠풀) Stachys japonica 2 (석잠풀) Stachys Lamium amplexicaule 1 (광대나물) Lamium amplexicaule 2 (광대나물) Lamium amplexicaule 3 (광대나물) Leonurus japonicus 1 (익모초) Lamium Leonurus japonicus 2 (익모초) Leonurus macranthus 1 (송장풀) Neighbor joining Leonurus macranthus 2 (송장풀) Leonurus Phlomis umbrosa (속단) Dysophylla stellata (물꼬리풀) Phlomis tree Dysophylla yatabeana (전주물꼬리풀) Ajuga decumbens 1 (금창초) Dysophylla Ajuga decumbens 2 (금창초) Ajuga decumbens 3 (금창초) Ajuga spectabilis (자란초) Ajuga multiflora 1 (조개나물) Ajuga Ajuga multiflora 2 (조개나물) Teucrium japonicum (개곽향) Teucrium veronicoides 1 (곽향) Teucrium veronicoides 2 (곽향) Teucrium viscidum (덩굴곽향) Teucrium Clinopodium chinense (층층이꽃) Clinopodium micranthum (두메층층이) Clinopodium gracile (애기탑꽃) Clinopodium Agastache rugosa 1 (배초향) Agastache rugosa 2 (배초향) Dracocephalum rupestreAgastache 1 (벌깨풀) Dracocephalum rupestre 2 (벌깨풀) Meehania urticifolia 1 (벌깨덩굴) Dracocephalum Meehania urticifolia 2 (벌깨덩굴) Lycopus maackianus 1 (애기쉽싸리) Meehania Lycopus maackianus 2 (애기쉽싸리) Lycopus maackianus 3 (애기쉽싸리) Lycopus ramosissimus (개쉽싸리) Lycopus Prunella asiatica (꿀풀) Salvia chanroenica (참배암차즈기) Prunella Salvia plebeia (배암차즈기) Perilla frutescens var. frutescens 1 (들깨) Salvia Perilla frutescens var. frutescens 2 (들깨) Mosla chinensis (가는잎산들깨) Perilla Mosla dianthera (쥐깨풀) Elsholtzia minima (좀향유) Mosla Elsholtzia splendens 1 (꽃향유) Elsholtzia splendens 2 (꽃향유) Elsholtzia Isodon inflexus (산박하) Isodon japonicus (방아풀) Isodon 0.005 substitutions/site Q1 Scutellaria pekinensis var. transitra 2 (산골무꽃) Scutellaria pekinensis var. transitra 3 (산골무꽃) Scutellaria pekinensis var. ussuriensis 3 (호골무꽃) Q2 Q3 Scutellaria pekinensis var. alpina 2 (수골무꽃) Scutellaria pekinensis var. maxima 1 (왕골무꽃) Scutellaria pekinensis var. maxima 2 (왕골무꽃) Scutellaria pekinensis var. maxima 3 (왕골무꽃) Identifying unknown samples (Qs) Scutellaria pekinensis var. maxima 4 (왕골무꽃) Scutellaria
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