如何理解性狀演化完整版

如何理解性狀演化？

123456Contents什么是性狀？性狀的類型性狀與自然分類系統(tǒng)的關(guān)系如何利用性狀進(jìn)行系統(tǒng)發(fā)育研究？性狀和對(duì)類群演化速率的影響?

討論Key

points

性狀的本質(zhì)

性狀對(duì)比的原則

性狀在系統(tǒng)學(xué)中分析的基本方法

分支樹(shù)的意義Most

important

thing:

批判性1.

什么是性狀?定義：性狀

(character/trait):

生物的形態(tài)結(jié)構(gòu)，生理特征，行為

習(xí)慣等具有的各種特征。性狀的劃分與分類的目標(biāo)密切相關(guān)性狀是無(wú)窮無(wú)盡的………………..2.

性狀的類型?

性狀的劃分方式–用途和功能性：

---------------人為分類系統(tǒng)–形態(tài)，生理等的總體相似性：-----自然分類系統(tǒng)

根據(jù)性狀的來(lái)源：?

宏觀性狀微觀性狀生理生化性狀分子性狀……….2

性狀的類型---性狀的來(lái)源性狀的范疇：

宏觀：重要形態(tài)特征

花果葉片莖…..2.

性狀的類型—性狀來(lái)源

微觀

比較形態(tài)解剖學(xué)

細(xì)胞學(xué)

分子序列：

DNA，

RNA，

蛋白質(zhì)

代謝產(chǎn)物….

生理特征

行為

……2

性狀的類型---性狀的狀態(tài)?

質(zhì)量性狀

vs.

數(shù)量性狀：–

e.g.

present

vs.

absent

(disjunction

between

datasets);

–

e.g.

a

variation

range.–

如何對(duì)性狀進(jìn)行描述？！?

單態(tài)性狀

vs.

多態(tài)性狀–

e.g.

Glandular

trichome

vs.

no-glandular

trichome;

–

e.g.

petal

colour:

white

vs.

red

vs.

purple………2

性狀的類型---性狀的狀態(tài)質(zhì)量性狀

(qualitative

trait)表現(xiàn)型和基因型的變異不連續(xù)

(discontinuous)；

在雜交后代的分離群體中可采用經(jīng)典遺傳學(xué)分析方法；2

性狀的類型---性狀的狀態(tài)數(shù)量性狀

quantitative

trait

表現(xiàn)型變異是連續(xù)(continuous)果實(shí)大小，葉片長(zhǎng)度，植株的生育期，產(chǎn)量高低。。。。。–

表現(xiàn)型變異分析

推斷群體的遺傳變異

借助數(shù)量統(tǒng)計(jì)的分析方法

分析數(shù)量性狀的遺傳規(guī)律劃分：

嚴(yán)格連續(xù)變異

(continuous

variation)

準(zhǔn)連續(xù)變異

(Quasi

continuous

variation)注：有的性狀有質(zhì)量亦有數(shù)量性狀的特點(diǎn)：

質(zhì)量—數(shù)量性狀From

Mendel

to

Molecules………What

does

the

“R”

allele

do?How

does

the

SBEI

protein

lead

to

round

seeds?

It

gives

rise

to

highly

branched

starch(amylopectin).Highly

branched

starch

in

the

seeds

leads

to

seeds

with

low

water

content.

When

the

seeds

dry,

they

stay

round.What

does

the

“R”

allele

represent?3500NucleotidesWhat

does

the

“r”

allele

do?How

does

the

altered

SBE1

protein

lead

to

wrinkled

seeds?

It

gives

rise

to

unbranched

starch

only

(amylose).Unbranched

starch

in

the

seeds

leads

to

seeds

with

high

water

content.

They

are

sweet,

but

when

the

seeds

dry,

they

wrinkle.Theoriginal3550nucleotides

plusanadditional800nucleotidesWhat

does

the

“r”

allele

represent?The

R

allele

and

the

r

Allele:R

allele

genetic

coder

allele

genetic

code800

bp

fragment

of

DNA

inserted2

性狀的類型---性狀的本質(zhì)Phenotype

=

Genome

type

+

Enviromental

factorsThe

phenotype

of

an

organism

is

determined

by

the

genes,

the

environment

and

stochastic

developmental

events.Questions:The

same

genotype

produce

different

phenotype?The

different

genotypes

produce

the

same

phenotype

?3.

性狀與自然分類系統(tǒng)的關(guān)系自然分類系統(tǒng)

vs.

人為分類系統(tǒng)應(yīng)用方便，并根據(jù)一定實(shí)

用目進(jìn)行分類3.

性狀與自然分類系統(tǒng)的關(guān)系1.

林奈前分類學(xué)時(shí)期：古代分類學(xué)時(shí)期2.

林奈后分類學(xué)時(shí)期：

現(xiàn)代分類學(xué)時(shí)期

《Species

Plantarum》1.

人為分類系統(tǒng)時(shí)期——人為分類法2.

進(jìn)化論前的自然系統(tǒng)時(shí)期

3.

系統(tǒng)發(fā)育系統(tǒng)時(shí)期

systematics核心：

物種可變

共同祖先

自然選擇自然分類法

漸變《The

Origin

of

Species》3.

性狀與自然分類系統(tǒng)的關(guān)系現(xiàn)代分類學(xué)是如何對(duì)生物進(jìn)行歸類和劃分的？?

表型分類：Phenetic

classification

–

總體相似性

(overall

similarity)–

傳統(tǒng)分類學(xué)對(duì)于各種分類階元和親緣關(guān)系的劃分

Those

organisms

most

similar

are

classified

more“closely”

together.3.

性狀與自然分類系統(tǒng)的關(guān)系Systematics

-

field

of

biology

dealing

with

diversity

and

evolutionary

history

of

lifeGoal:

Determine

Evolutionary

History

(Phylogeny)

of

LifePhylogeneticclassification

Based

on

known(inferred)

evolutionaryhistory.3.

性狀與自然分類系統(tǒng)的關(guān)系Description=

assign

featuresCharacter

=

a

feature

(e.g.,

“petal

color”)Character

states

=

two

or

more

forms

of

a

character

(e.g.,

“red,”

“white”).對(duì)性狀的認(rèn)識(shí)3.

性狀與自然分類系統(tǒng)的關(guān)系Identification=

associate

an

unknown

with

a

known

How?

One

way:TaxonomicKey,

e.g.,TreeLeaves

simple

…….…………………………

Species

A

Leaves

pinnate

…….………..…..…..………

Species

BHerbFlowers

red

…….……………………………

Species

C

Flowers

white

…….…………………..………Species

D總體相似性比較、性狀狀態(tài)的比較2.

性狀與自然分類系統(tǒng)的關(guān)系NomenclatureNaming,

according

to

a

formal

system.Binomial:

Species

are

two

names

(Linnaeus):

E.g.,

Homo

sapiensHomo

=

genus

namesapiens

=

specific

epithet

Homo

sapiens

=

species

name對(duì)性狀狀態(tài)賦值,

根據(jù)性狀對(duì)類群進(jìn)行歸類3.

性狀與自然分類系統(tǒng)的關(guān)系Classification

Placing

objects,

e.g.,

life,

into

some

type

of

order.

Taxon

=

a

taxonomic

group

(plural

=

taxa).基于形態(tài)總體相似性的比較，確定生物與其它物種的親緣關(guān)系遠(yuǎn)近3.

性狀與自然分類系統(tǒng)的關(guān)系-----分類與系統(tǒng)發(fā)育的關(guān)系Linking

Classification

and

Phylogeny?

Systematists

depict

evolutionary

relationships

in

branching

phylogenetic

trees?

The

branching

of

the

tree

reflects

the

hierarchical

classification

of

groups

nested

within

more

inclusive

groups.?

Each

branch

point

represents

the

divergence

of

two

species?

“Deeper”

branch

points

represent

progressively

greater

amounts

of

divergence3.

性狀與自然分類系統(tǒng)的關(guān)系Phylogenetic

classification

系統(tǒng)發(fā)育的分類法?

Based

on

known

(inferred)

evolutionary

history.

?

Advantage:–

Classification

reflects

pattern

of

evolution–

Classification

not

ambiguous基于同不性狀標(biāo)記，對(duì)生物系統(tǒng)位置的驗(yàn)證Phylogenetic

systematics

informs

the

construction

of

phylogenetic

trees

based

on

shared

characteristics?

If

shared

characteristics

are

homologous

and,

thus,

explained

by

common

ancestry,

then

the

cladogram

forms

the

basis

of

a

phylogenetic

tree.?

A

cladogram

depicts

patterns

of

shared

characteristics

among

taxa?

A

clade

is

a

group

of

species

that

includes

an

ancestral

species

and

all

its

descendants?

Cladistics

studies

resemblances

among

cladesArchaefructus3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)？Tree

of

lifeor

clade3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)presentlineageTIMECladogram

or

Phylogenetic

Tree=

representation

of

the

history

of

life3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)TAXAA

B

C

D

E

Flineageor

cladeTIMECladogram

or

Phylogenetic

Tree3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)TAXAA

B

C

D

E

FTIMEspeciationCladogram

or

Phylogenetic

Tree3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)4.

研究系統(tǒng)發(fā)育，理解生物的進(jìn)化？Hints:

The

crucial

issue

in

systematics

is

that

there

is

a

history

of

the

organisms

we

wish

to

classify,

but

we

don't

know

that

history.

We

must

infer

the

sequence

of

branches

or

evolutionary

transformations

that

have

taken

place.

There

is

a

true

phylogeny

which

we

may

never

know,

our

task

is

to

collect

and

analyze

data

to

provide

the

best

estimate

of

the

true

phylogeny.Distance

(or

similarity)

matrix

derived

from

morphological

measurements,

genetic

distance

measuresCladistics:

classification

reflects

sequence

of

branching

events,

not

degree

of

difference/similarity.shared

derived

characters

(synapomorphies)

Cladogram:

a

hypothesis

of

relationship.原始

vs.

進(jìn)化特征？Primitive

vs.

derived

(advanced)

Question1:

如何知道哪些性狀或是類群原始或進(jìn)化？原

始

特

征進(jìn)

化

特

征木本草本莖直立

纏繞無(wú)導(dǎo)管只有管胞

有導(dǎo)管具環(huán)紋,

螺紋導(dǎo)管,

梯紋穿孔,

斜端壁具網(wǎng)紋,

孔紋導(dǎo)管,

單穿孔,

平端壁常綠落葉葉單葉全緣,

羽狀脈

葉形復(fù)雜化,

狀脈互生(

螺旋狀排列)

花單生聚傘類花序

兩性花雌雄同株對(duì)生或輪生

花形成花序

總狀類花序

單性花雌雄異株花花部呈螺旋狀排列

花部呈輪狀排列花的各部多數(shù)而不固定

花的各部數(shù)目不多,

有定數(shù)

(3,4

或

5)

花被同形,不分化為萼片和花瓣花被分化為萼片和花瓣,或退化為單被花,無(wú)被花花各部離生

整齊花子房上位花各部合生

不整齊花子房下位

Question2:

如何知道哪些類群原始或進(jìn)化？ExampleArchaefructus3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)Ingroup

–

group

studiedOutgroup

–

group

not

part

of

ingroup,

used

to

“root”

treeOutgroups?

An

outgroup

is

a

species

or

group

of

species

that

is

closely

related

to

the

ingroup,

the

various

species

being

studied?

Systematists

compare

each

ingroup

species

with

the

outgroup

to

differentiate

between

shared

derived

and

shared

primitive

characteristics?

It

enables

us

to

focus

on

characters

derived

at

various

branch

points

in

the

evolution

of

a

clade?

Outgroup

comparison

assumes

that

homologies

shared

by

the

outgroup

and

ingroup

must

be

primitive

characters

that

predate

the

divergence

of

both

groups

from

a

common

ancestor***determine

the

"polarity"

or

direction

of

evolution常見(jiàn)的問(wèn)題：

Outgroup

becomes

ingroup?

The

far

relationship

is

the

better

tree

we

can

get?

How

to

choose

outgroup

wisely

?

Other

issue………Answers:

far

away

enough

to

be

a

clear

outgroup

and

near

enough

to

allow

inference

from

the

data.3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)

Cladogram:

分支的關(guān)系，分支樹(shù)的不同表現(xiàn)形式3.

性狀與自然分類系統(tǒng)的關(guān)系-----如何理解系統(tǒng)樹(shù)分支式樣：

cladogram遺傳距離:

phylogram

---the

length

of

a

branch

in

a

cladogram

reflects

the

number

of

genetic

changes

that

have

taken

place

in

a

particular

DNA

or

RNA

sequence

in

that

lineage時(shí)間:

chronogram---

the

branching

of

a

phylogenetic

tree

is

relative

rather

than

absolute

in

representing

timing

of

divergencestimephylogramchronogram4.如何利用性狀進(jìn)行系統(tǒng)發(fā)育研究？性狀是無(wú)窮的………….4.2

系統(tǒng)發(fā)育意義的性狀？

祖征

plesiomorphy

-

a

primitive

character

state(共祖征symplesiomorphy

-

A

character

shared

by

a

number

of

groups,

but

inherited

from

ancestors

older

than

the

last

common

ancestor.)

衍征apomorphy

-

a

derived

or

specialized

character

state.

共衍證synapomorphy

-

An

apomorphy

(derived

or

specialised

character)

shared

by

two

or

more

groups

which

originated

in

their

last

common

ancestor.

自征autopomorphy

-

a

unique

derived

character

state.Hints:

Case

by

case,

不是所有的特征都是祖征或是衍征，以研究對(duì)象不同而不同Apomorphy

(derived

trait)共衍征=

a

new,

derived

featureE.g.,

for

this

evolutionary

transformationscales

-------->

feathers(ancestral

feature)

(derived

feature)

Presence

of

feathers

is

an

apomorphyfor

birds.Taxa

are

grouped

byapomorphiesApomorphies

are

the

result

of

evolution.Taxa

sharing

apomorphiesunderwent

same

evolutionary

historyshould

be

grouped

together.TAXAA

B

C

D

E

Fapomorphy(for

Taxon

D)apomorphies(for

Taxa

B

&

C)TIMEapomorphy(for

Taxa

B,C,D,E,F)Cladogram

or

Phylogenetic

TreeTunaLeopardSequentially

group

taxa

byshared

derived

character

states

(apomorphies)TAXALancelet(outgroup)LampreyVertebral

column(backbone)Hinged

jaws0

10

011111111VertebralcolumnTunaSalamanderHinged

jawsFour

walking

legsAmniotic

(shelled)

egg000

0

10

0

01111Four

walking

legsTurtleHair000

0

0

1Amniotic

eggHairLeopard(a)

Character

table(b)

Phylogenetic

tree4.2

哪些性狀具有系統(tǒng)發(fā)育意義？基于已知系統(tǒng)發(fā)育關(guān)系對(duì)性狀演化研究Question:

Cladistic

analysis

or

Mapping?

And

Which

is

better?Answer:

depends

on

1)Datasets:

How

can

we

obtain

the

best

phylogeny

for

the

taxa

we

studied?2)Purpose:

Infer

phylogeny

?

Evolutionary

pattern?4.

如何對(duì)性狀進(jìn)行比較？----4.3同源性！

?

4.3.

性狀的同源性–

比較的基本原則VSVS2.

性狀與自然分類系統(tǒng)的關(guān)系----存在的問(wèn)題Problem

with

phenetic

classification:?

Can

be

arbitrary,e.g.,

classify

these:DNA

sequence

data

–

most

important

type

of

data

1Deletion2InsertionDNA

sequence

data

-

alignment3Fig.

26-8b4Each

nucleotide

position

=

Character

Character

states

=

specific

nucleotideHomology

(同源）?

Similarity

resulting

from

common

ancestry.–

E.g.,

the

forelimb

bones

of

a

whale,

bat,

and

cat.Homoplasy

(analogy)

趨同

?

Similarity

not

due

to

common

ancestry?

Reversal

–

loss

of

new

(apomorphic)

feature,

resembles

ancestral

(old)

feature.?

Convergence

(parallelism)

–

gain

of

new,

similar

features

independently.Convergent

evolution:

spines

of

cacti

&

euphorbsCactus

EuphorbRanunculalesProteatalesSabialesBuxalesTrochodendralesGunneralesDillenialesSaxifragalesVitalesZygophyllalesCelastralesMalpighialesOxalidalesFabalesRosalesCucurbitalesFagalesGeranialesMyrtalesCrossosomatalesPicramnialesSapindalesHuertealesBrassicalesMalvalesBerberidopsidalesSantalalesCaryophyllalesCornalesEricalesGarryalesBoraginalesGentianalesLamialesSolanalesAquifolialesEscallonialesAsteralesDipsacalesParacryphialesApialesBrunialesConvergent

evolution:

spines

of

cacti

&

euphorbsEuphorbsCactiEudicotsCore

Eudicots*FabidsRosidsMalvids*AsteridsLamiids

Campanulidseuphorb

spinescactusspinesAngiospermEudicot

Relationships(after

APGIII

2009)Leg-less

lizards

Snake

Both

examples

of

reversal

withinTetrapods:loss

of

a

derived

feature

–

forelimbs.Example

of

convergence

relative

to

one

another!Independently

evolved.snakesleggedlizards*leg-lesslizards**=

loss

oflegsgainof

legs

(Tetrapods)Orthologous

genesGene

Duplicationcan

occur!Ancestral

geneAncestral

speciesSpeciation

withdivergence

of

geneSpecies

A

Species

B(a)

Orthologous

genesSpecies

AGene

duplication

and

divergenceParalogous

genesSpecies

A

after

many

generations(b)

Paralogous

genesFig.

26-18Orthology

–geneshomologousParalogy

–genes

nothomologous課堂練習(xí)1根據(jù)果實(shí)重要分類性狀制作薔薇科4種植物形態(tài)矩陣植物Char1Char2Char3Char4Char5Char6Char7Char8……….蘋(píng)果梨草莓桃子課堂練習(xí)2根據(jù)葉片和枝條形態(tài)列出如下4種裸子植物的形態(tài)矩陣植物Char1Char2Char3Char4Char5Char6Char7Char8……….銀杏蘇鐵松屬冷杉屬Relationship?

=

recency

of

common

ancestryi.e.,

taxa

sharing

a

common

ancestor

more

recent

in

time

are

more

closely

related

than

those

sharing

common

ancestors

more

distant

in

time.Principle

of

ParsimonyThat

cladogram

(tree)

having

the

fewest

number

of

“steps”

(evolutionary

changes)

is

the

one

accepted.Okham’s

razor:

the

simplest

explanation,

with

fewest

number

of

“ad

hoc”

hypotheses,

is

accepted.Other

methods

of

phylogeny

reconstruction:

?

Maximum

Likelihood

or

Bayesian

analysis–

Uses

probabilities–

Advantage:

can

use

evolutionary

models.

Distance

based

methods:

NJ……..Why

I

need

to

believe?

Decay

indices

Bootstrap

percentages

……….Monophyletic

Group

?

a

group

consisting

of:–

a

common

ancestor

+–

all

descendents

of

that

common

ancestorGrouping

1A

valid

clade

ismonophyletic,

signifying

that

it

consists

of

the

ancestor

species

and

allits

descendantsMonophyleticTAXAA

B

C

D

E

FmonophyleticgroupTIMEcommon

ancestor

(of

taxon

D,

E,

&

F)common

ancestor(of

taxon

A

&

taxa

B-F)Cladogram

or

Phylogenetic

TreeTAXAA

B

C

D

E

FmonophyleticgroupTIMEcommon

ancestor

(of

taxon

D,

E,

&

F)common

ancestor(of

taxon

A

&

taxa

B-F)Cladogram

or

Phylogenetic

TreeTAXAA

B

C

D

E

FmonophyleticgroupTIMEcommon

ancestor

(of

taxon

D,

E,

&

F)common

ancestor(of

taxon

A

&

taxa

B-F)Cladogram

or

Phylogenetic

TreeTAXAA

B

C

D

E

FmonophyleticgroupTIMEcommon

ancestor

(of

taxon

D,

E,

&

F)common

ancestor(of

taxon

A

&

taxa

B-F)Cladogram

or

Phylogenetic

TreeTAXAA

B

C

D

E

FmonophyleticgroupTIMEcommon

ancestor

(of

taxon

D,

E,

&

F)common

ancestor(of

taxon

A

&

taxa

B-F)Cladogram

or

Phylogenetic

TreeParaphyletic

group?

Consist

of

common

ancestor

but

not

all

descendents?

Paraphyletic

groups

are

unnatural,

distort

evolutionary

history,

and

should

not

be

recognized.Grouping

2A

paraphyletic

groupingconsists

of

an

ancestral

species

and

some,

but

not

all,

of

the

descendantsParaphyleticGrouping

3A

polyphyletic

groupingconsists

of

various

speciesthat

lack

a

commonancestorPolyphyleticTAXAA

B

C

D

E

FTIMEspeciationCladogram

or

Phylogenetic

TreeTurtlesLizards

&SnakesLizards

&CrocodylesCrocodilesBirds"Reptilia"TurtlesLizards

&SnakesLizards

&CrocodylesCrocodilesBirds“Reptilia”

hereparaphyletic"Reptilia"TurtlesSnakesCrocodilesBirdsTurtlesSnakesLizards

&CrocodylesBirdsRe-defined

Reptilia

monophyleticReptiliaLizards

&TurtlesSnakes

CrocodilesTurtlesLizards

&Snakes

CrocodylesDinosaursBirdsReptiliaLizards

&???Importance

of

a

name:

Did

humans

evolve

from

apes?Monophyletic

vs.

paraphyleticOrangatanOrangutan

GorillaChimpanzees

HumansChimpanzeesOrangatanOrangutan

Gorilla

Chimpanzees

HumansPongidae“Great

Apes”ChimpanzeesHominidaePongidaeor

“GreatHominidaeApes”O(jiān)rangatanOrangutan

GorillaChimpanzees

HumansChimpanzeesPongidae

orHominidaeOrangatanOrangutan

GorillaChimpanzees

HumansChimpanzeesPongidae

orHominidaeOrangatanOrangutan

GorillaChimpanzees

HumansChimpanzeesWe

are

human,

butwe

are

also

apes.?

We

share

unique

human

features.?

We

also

share

features

with

other

apes(and

with

other

animals,

plants,

fungi,

bacteria,

etc.).?

Humans

didn’t

evolve

from

apes,

humans

are

apes.TAXAA

B

C

D

E

FTIMEspeciationCladogram

or

Phylogenetic

TreeC

B

F

E

D

ATAXAA

B

C

D

E

FTIMEspeciationCladogram

or

Phylogenetic

TreeCladograms

can

be

“flipped”

at

nodes,

show

samerelationshipsOne

can

date

divergence

times

with

molecular

clock

and

fossilsDrosophilaLanceletZebrafishFrogChickenHumanMousePALEOZOICMESOZOICCENOZOIC54225165.5PresentMillions

of

years

agoFish

is

closer

to

Human

or

to

shark?Shark

Fish

HumansTIMEShark

Fish

HumansTIMEcommonancestor

ofFish

and

Humanscommon

ancestor

ofSharks,

Fish,

and

HumansTIMEVertebrataOsteichthyesShark

Fish

Humansmonophyleticgroupcommonancestor

ofFish

and

Humanscommon

ancestor

ofSharks,

Fish,

and

HumansExample:?

Are

crocodiles

more

closely

related

to

lizards

or

to

birds?TurtlesLizards

&SnakesLizards

&CrocodylesCrocodilesBirds"Reptilia"Is

“E”

more

closely

related

to

“D”

or

to

“F”?

Is

“E”

moreclosely

related

to

“B”

or

to

“A”?

Is

“E