Systematics and Phylogeny

Dr. Topik Hidayat

Biologi-UPI Bandung

Wha

t is

Sys

tem

atic

s?

•Aim

s to

rec

ogni

ze,

desc

ribe

, na

me,

di

stin

guis

h, r

elat

e an

d cl

assi

fy e

arth

’s

orga

nism

s •

Bor

row

s fr

om o

ther

fie

lds-

-ver

y m

uch

a m

ultidi

scip

linar

y, o

r “h

ybrid”

, di

scip

line

•Sup

plie

s ev

iden

ce t

o ev

olut

iona

ry

biol

ogy,

eco

logy

and

oth

er fie

lds

•Fu

ndam

enta

l to

all o

ther

sci

entific

en

deav

ors

(and

man

y no

n-sc

ient

ific

hum

an c

once

rns)

Why

is “

Sys

tem

atic

s”

Fund

amen

tal?

•W

hy d

o w

e gi

ve n

ames

to

entities

?•

Who

car

es if

diff

eren

t la

bs s

tudy

ing

mut

atio

ns in

“Ara

bido

psis

tha

liana

”, o

r in

vest

igat

ing

gene

tic

dise

ase

in

“chi

mpa

nzee

s”,

wor

k w

ith

the

sam

e or

gani

sm a

cros

s la

bs?

How

do

we

know

?•

How

do

we

acce

ss in

form

atio

n in

lib

raries

and

mus

eum

s, in

com

pute

r or

ca

bine

t fil

es,

or o

n th

e in

tern

et?

Wha

t is

Sys

tem

atic

s?

•U

ses

dive

rse

appr

oach

es:

–M

orph

olog

y–

Ana

tom

y–

Paly

nolo

gy–

Mic

rosc

opy

–Bio

chem

istr

y

–M

olec

ular

Bio

logy

–G

enet

ics

–Ph

ysio

logy

–Ec

olog

y–

Evol

utio

n–

Bio

info

rmat

ics

Why

is S

yste

mat

ics

Impo

rtan

t?•

Det

aile

d in

form

atio

n at

all

hier

arch

ical

leve

ls is

key

to

mos

t sc

ient

ific

field

s, m

edic

ine

and

num

erou

s as

pect

s of

hum

an

soci

ety

•N

ames

of

taxa

(e.

g.,

spec

ies)

, or

ev

en in

divi

dual

s, a

re “

tags

” fo

r in

form

atio

n re

trie

val a

nd

know

ledg

e sy

nthe

sis

Why

is S

yste

mat

ics

Impo

rtan

t?•

Mod

ern

syst

emat

ic s

tudi

es p

rovi

de

biol

ogic

al c

onte

xt t

o ev

olut

iona

ry

and

ecol

ogic

al s

tudi

es•

Mod

ern

clas

sific

atio

ns a

re

pred

ictive

, ca

n gu

ide

biop

rosp

ecting

for

med

icin

es,

food

s, e

tc.

•Spe

cies

-lev

el in

form

atio

n ca

n gu

ide

cons

erva

tion

Syst

emat

ics

is th

e sc

ienc

e of

the

rela

tions

hips

of o

rgan

ism

s

Sys

tem

atic

s is

the

scie

nce

of h

ow o

rgan

ism

s ar

e re

late

d an

d th

e ev

iden

ce fo

r tho

se re

latio

nshi

ps

Sys

tem

atic

s is

div

ided

prim

arily

into

phy

loge

netic

s an

d ta

xono

my

Spe

ciat

ion

-- th

e or

igin

of n

ew s

peci

es fr

om p

revi

ousl

y ex

istin

g on

es

-

ana

gene

sis

- one

spe

cies

cha

nges

into

ano

ther

ove

r tim

e

- c

lado

gene

sis

- one

spe

cies

spl

its to

mak

e tw

o

Clas

sify

ing

Org

anisms

Rec

onst

ruct

evo

lutio

nary

his

tory

Phy

loge

ny

Phylog

enet

ics

Evo

lutio

nary

theo

ry s

tate

s th

at g

roup

s of

sim

ilar o

rgan

ism

s ar

e de

scen

ded

from

a c

omm

on a

nces

tor.

Phy

loge

netic

sys

tem

atic

s is

a m

etho

d of

taxo

nom

ic c

lass

ifica

tion

base

don

thei

r evo

lutio

nary

his

tory

.

It w

as d

evel

oped

by

Hen

nig,

a G

erm

an

ento

mol

ogis

t, in

195

0.

Willi

Hen

nig

(191

3-19

76)

Phylog

enet

ics

Phyl

ogen

etic

s is

the

scie

nce

of th

e pa

ttern

of e

volu

tion

Evo

lutio

nary

bio

logy

ver

sus

phyl

ogen

etic

s

- E

volu

tiona

ry b

iolo

gy is

the

stud

y of

the

proc

esse

s th

at g

ener

ate

dive

rsity

- P

hylo

gene

tics

is th

e st

udy

of th

e pa

ttern

of d

iver

sity

pro

duce

d by

th

ose

proc

esse

s

Phylog

enet

ics

Who

use

s ph

ylog

enet

ics?

Som

e ex

ampl

es:

Evo

lutio

nary

bio

logi

sts

(e.g. r

econ

stru

ctin

g tre

e of

life

)

Sys

tem

atis

ts (e.g. c

lass

ifica

tion

of g

roup

s)

Ant

hrop

olog

ists

(e.g. o

rigin

of h

uman

pop

ulat

ions

)

Fore

nsic

s (e.g. t

rans

mis

sion

of H

IV v

irus

to a

rape

vic

tim)

Par

asito

logi

sts

(e.g. p

hylo

geny

of p

aras

ites,

co-

evol

utio

n)

Epi

dem

iolo

gist

s (e.g

. rec

onst

ruct

ion

of d

isea

se tr

ansm

issi

on)

Gen

omic

s/P

rote

omic

s (e.g. h

omol

ogy

com

paris

on o

f new

pro

tein

s)

Phylog

enet

ic t

rees

The

cent

ral p

robl

em o

f phy

loge

netic

s:ho

w d

o w

e de

term

ine

the

rela

tions

hips

bet

wee

n ta

xa?

in p

hylo

gene

tic s

tudi

es, t

he m

ost c

onve

nien

t way

of p

rese

ntin

g ev

olut

iona

ry

rela

tions

hips

am

ong

a gr

oup

of o

rgan

ism

s is

the

phyl

ogen

etic

tree

Phylog

enet

ic t

rees

Spec

ies

A

Spec

ies

E

Spec

ies

D

Spec

ies

C

Spec

ies

B

Nod

e: a

bra

nchp

oint

in a

tree

(a p

resu

med

anc

estra

l OTU

)B

ranc

h: d

efin

es th

e re

latio

nshi

p be

twee

n th

e ta

xa in

term

s of

des

cent

and

an

cest

ryTo

polo

gy: t

he b

ranc

hing

pat

tern

s of

the

tree

Bra

nch

leng

th (s

cale

d tre

es o

nly)

: rep

rese

nts

the

num

ber o

f cha

nges

that

hav

e oc

curr

ed in

the

bran

chR

oot:

the

com

mon

anc

esto

r of a

ll ta

xaC

lade

: a g

roup

of t

wo

or m

ore

taxa

or D

NA

sequ

ence

s th

at in

clud

es b

oth

thei

r co

mm

on a

nces

tor a

nd a

ll th

eir d

esce

nden

tsO

pera

tiona

l Tax

onom

ic U

nit (

OTU

): ta

xono

mic

leve

l of s

ampl

ing

sele

cted

by

the

user

to b

e us

ed in

a s

tudy

, suc

h as

indi

vidu

als,

pop

ulat

ions

, spe

cies

, gen

era,

or

bac

teria

l stra

ins

Roo

t

Bra

nch

Cla

deN

ode

Phylog

enet

ics

Wha

t are

use

ful c

hara

cter

s?

Use

hom

olog

ies,

not

ana

logi

es!

- Hom

olog

y: c

omm

on a

nces

try o

f tw

o or

mor

e ch

arac

ter s

tate

s

- Ana

logy

: sim

ilarit

y of

cha

ract

er s

tate

s no

t due

to s

hare

d an

cest

ry

- Hom

opla

sy: a

col

lect

ion

of p

heno

men

a th

at le

ads

to s

imila

ritie

s in

ch

arac

ter s

tate

s f

or re

ason

s ot

her t

han

inhe

ritan

ce fr

om a

com

mon

anc

esto

r (e.g.

con

verg

ence

, par

alle

lism

, rev

ersa

l) H

omop

lasy

is h

uge

prob

lem

in m

orph

olog

y da

ta s

ets!

But

in m

olec

ular

dat

a se

ts, t

oo!

Cac

tace

ae(c

actu

s sp

ines

are

mod

ified

leav

es)

Eup

horb

iace

ae(e

upho

rb s

pine

s ar

e m

odifi

ed s

hoot

s)

Phylog

enet

ics

Mol

ecul

ar d

ata

and

hom

opla

sy

260 * 280 * 300 * 320

0841r : CCTTCAATTTTTATT-----------------------AGAGTTTTAGGAGAAATAAGTATGTG : 272

0992r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 213

3803r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 305

4062r : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGAACAGAGTTTTAGGAGAAATAAGTATGTG : 319

3802r : CCTCCAATTTTTATTAGTTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 282

ph2f : CCTCCAATTTTTATTAGCTTGCCTACTCCTTTGGGCACAGAGTTTTAGGAGAAATAAGTATGTG : 306

CCTcCAATTTTTATTag ttgcctactcctttggg acAGAGTTTTAGGAGAAATAAGTATGTG

gene

seq

uenc

es re

pres

ent c

hara

cter

dat

ach

arac

ters

are

pos

ition

s in

the

sequ

ence

(not

all

wor

kers

ag

ree;

som

e sa

y on

e ge

ne is

one

cha

ract

er)

char

acte

r sta

tes

are

the

nucl

eotid

es in

the

sequ

ence

(or a

min

o ac

ids

in th

e ca

se o

f pro

tein

s)Pr

oble

ms:

the

prob

abilit

y th

at tw

o nu

cleo

tides

are

the

sam

e ju

st b

y ch

ance

m

utat

ion

is 2

5%w

hat t

o do

with

inse

rtion

s or

del

etio

ns (w

hich

may

them

selv

es b

e ch

arac

ters

)ho

mop

lasy

in s

eque

nces

may

cau

se a

lignm

ent e

rrors

Mod

ern

phyl

ogen

etic

sys

tem

atic

s ar

e ba

sed

on

clad

istic

ana

lysi

s

a. A

phy

loge

netic

dia

gram

(tre

e) is

als

o ca

lled

a cl

adog

ram

. b.

Eac

h br

anch

in th

e tr

ee is

cal

led

a cl

ade.

c.

Mon

ophy

letic

per

tain

s to

a ta

xon

that

is d

eriv

ed fr

om a

sin

gle

ance

stra

l sp

ecie

s.

onl

y le

gitim

ate

clad

ogra

m ty

pe!

d. P

olyp

hyle

tic p

erta

ins

to a

taxo

n w

hose

mem

bers

wer

e de

rived

from

two

or

mor

e an

cest

ors

not c

omm

on to

all

mem

bers

. e.

Par

aphy

letic

per

tain

s to

a ta

xon

that

exc

lude

s so

me

mem

bers

that

sha

re a

co

mm

on a

nces

tor w

ith m

embe

rs in

clud

ed in

the

taxo

n.

Con

stru

ctin

g cl

adog

ram

s

Id

entif

y ho

mol

ogie

s

sha

red

char

acte

ristic

s de

rived

from

one

anc

esto

r.

NO

TE:

Ana

logo

us s

truc

ture

s m

ay lo

ok s

imila

r to

one

anot

her,

but a

re n

ot

deriv

ed fr

om a

com

mon

anc

esto

r. T

hese

are

in c

ontr

ast t

o ho

mol

ogou

s st

ruct

ures

. Fi

g. b

elow

is a

n ex

ampl

e of

an

anal

ogou

s st

ruct

ure

in tw

o di

stan

tly re

late

d pl

ants

.

Whe

n tw

o or

gani

sms

have

ana

logo

us s

truc

ture

s, th

is is

an

exam

ple

of

conv

erge

nt e

volu

tion

In

depe

nden

t dev

elop

men

t of s

imila

rity

betw

een

spec

ies

due

to s

imila

r sel

ectio

n pr

essu

res.

Exam

ple

of h

ow to

con

stru

ct a

cla

dogr

am:

1. S

elec

t you

r spe

cies

for w

hich

you

wan

t to

mak

e a

clad

ogra

m.

Thes

e ar

e ca

lled

the

ingr

oup.

The

y ha

ve s

hare

d pr

imiti

ve a

nd d

eriv

ed c

hara

cter

s.

2. S

elec

t an

outg

roup

a

spe

cies

that

is c

lose

ly re

late

d to

the

spec

ies

unde

r stu

dy, t

he o

utgr

oup

has

a sh

ared

prim

itive

cha

ract

er th

at is

com

mon

to

all

spec

ies.

3. C

onst

ruct

a c

hara

cter

tabl

e an

d ta

bula

te th

e da

ta.

The

mor

e sh

ared

ch

arac

ters

, the

mor

e cl

osel

y re

late

d ar

e th

e sp

ecie

s.

4. C

onst

ruct

a c

lado

gram

bas

ed o

n th

e nu

mbe

r of s

hare

d c

hara

cter

s. F

or

exam

ple:

Figu

re in

nex

t slid

e –

Con

stru

ctin

g a

clad

ogra

m.

The

outg

roup

her

e, th

e la

ncel

et h

as a

not

ocho

rd, t

he s

hare

d pr

imiti

ve

char

acte

r. T

he in

grou

p is

five

ver

tebr

ates

.

Phyl

ogen

y ca

n be

infe

rred

als

o fr

om

mol

ecul

ar d

ata

DN

A an

d R

NA

sequ

ence

s of

nuc

leic

aci

ds c

an b

e co

mpa

red

to d

eter

min

e ph

ylog

eny.

E

xam

ple

to fo

llow

.

Not

e th

at e

ach

chan

ge in

a n

ucle

ic a

cid

= on

e ev

olut

iona

ry e

vent

! Th

e m

ore

even

ts, t

he m

ore

dist

antly

re

late

d ar

e th

e sp

ecie

s. F

ewer

eve

nts

mea

ns th

at a

sp

ecie

s is

mor

e cl

osel

y re

late

d.

Th

e P

hyl

og

en

eti

c A

pp

roach

in

Pra

ctic

e

Basal Dicots

MagnoliidsMonocots

Eud

icot

s

Judd

et a

l. (2

002)

BA

RC

OD

ING

LIF

E

Bar

codi

ng is

a st

anda

rdiz

ed a

ppro

ach

to

iden

tifyi

ng p

lant

s and

ani

mal

s by

min

imal

se

quen

ces o

f DN

A, c

alle

d D

NA

bar

code

s.

DN

A B

arco

de: A

sho

rt D

NA

sequ

ence

, fro

m

a un

iform

loca

lity

on th

e ge

nom

e, u

sed

for

iden

tifyi

ng s

peci

es.

Why

bar

code

ani

mal

and

pla

nt s

peci

es?

By

harn

essi

ng a

dvan

ces

in e

lect

roni

cs a

nd

gene

tics,

bar

codi

ng w

ill

•he

lp m

any

peop

le q

uick

ly a

nd c

heap

ly

reco

gniz

e kn

own

spec

ies

and

retri

eve

info

rmat

ion

abou

t the

m•

spee

d di

scov

ery

of th

e m

illio

ns o

f spe

cies

ye

t to

be n

amed

•

prov

ide

vita

l new

tool

s fo

r app

reci

atin

g an

d m

anag

ing

the

Ear

th’s

imm

ense

and

ch

angi

ng b

iodi

vers

ity.

Wha

t are

the

bene

fits

of s

tand

ardi

zatio

n?

Why

bar

code

ani

mal

s w

ith m

itoch

ondr

ial

DN

A?

Mito

chon

dria

, ene

rgy-

prod

ucin

g or

gane

lles

in p

lant

an

d an

imal

cel

ls, h

ave

thei

r ow

n ge

nom

e. T

wen

ty

year

s of

rese

arch

hav

e es

tabl

ishe

d th

e ut

ility

of

mito

chon

dria

l DN

A se

quen

ces

in d

iffer

entia

ting

amon

g cl

osel

y-re

late

d an

imal

spe

cies

.

Pla

nt: m

tDN

A no

t sui

tabl

e; lo

w d

iver

sity

Four

pro

perti

es m

ake

mito

chon

dria

l ge

nom

es [C

ytoc

hrom

e c

oxid

ase

I (C

OI)]

es

peci

ally

sui

tabl

e fo

r ide

ntify

ing

spec

ies:

Gre

ater

diff

eren

ces

amon

g sp

ecie

s

Cop

y nu

mbe

r. Th

ere

are

100-

10,0

00 m

ore

copi

es o

f m

itoch

ondr

ial t

han

nucl

ear D

NA

per c

ell

Rel

ativ

ely

few

diff

eren

ces

with

in s

peci

es

Intro

ns, w

hich

are

non

-cod

ing

regi

ons

inte

rspe

rsed

bet

wee

n co

ding

regi

ons

of a

gen

e, a

re a

bsen

t fro

m m

itoch

ondr

ial D

NA

Bar

codi

ng

Nor

th

Am

eric

an

bird

s hi

ghlig

hts

prob

able

cr

yptic

spe

cies

Bar

code

s af

firm

the

unity

of t

he s

peci

es

Hom

o sa

pien

s.

Com

paris

ons

show

we

diffe

r fro

m o

ne a

noth

er

by o

nly

1 or

2

nucl

eotid

es o

ut o

f 648

, w

hile

we

diffe

r fro

m

chim

panz

ees

at 6

0 lo

catio

ns a

nd g

orill

as a

t 70

loca

tions

.

Can

bar

code

s ai

d un

ders

tand

ing

hist

ory

of

anim

al a

nd

plan

t spe

cies

?

Phen

etic

met

hods

con

stru

ct tr

ees

(phe

nogr

ams)

by

cons

ider

ing

the

curr

ent s

tate

s of

cha

ract

ers

with

out r

egar

d to

th

e ev

olut

iona

ry h

isto

ry th

at b

roug

ht th

e sp

ecie

s to

thei

r cur

rent

ph

enot

ypes

;ph

enog

ram

s ar

e ba

sed

on o

vera

ll si

mila

rity

Cla

dist

ic m

etho

ds c

onst

ruct

tree

s (c

lado

gram

s) re

ly o

n as

sum

ptio

ns a

bout

anc

estra

l rel

atio

nshi

ps a

s w

ell a

s on

cur

rent

da

ta; c

lado

gram

s ar

e ba

sed

on c

hara

cter

evo

lutio

n (e.g.

shar

ed d

eriv

ed c

hara

cter

s)

With

in th

e fie

ld o

f tax

onom

y th

ere

are

two

diffe

rent

met

hods

and

phi

loso

phie

s of

bu

ildin

g ph

ylog

enet

ic tr

ees:

cla

dist

ic a

nd

phen

etic

Cla

dist

ics

is b

ecom

ing

the

met

hod

of c

hoic

e; it

is c

onsi

dere

d to

be

mor

e po

wer

ful

and

to p

rovi

de m

ore

real

istic

est

imat

es, h

owev

er, i

t is

slow

er th

an p

hene

tic

algo

rithm

s

Clad

istic

vers

us P

hene

tics

Than

k yo

u fo

r you

r atte

ntio

n