human-chimp speciation ~

1. inferring the mode of speciation from genomic data: a study of the great apes

2. genetic evidence for complex speciation of humans and chimpanzees

05.dec.06 – frank chan CS374 algorithms in biology

http://www.pbase.com/sheila/

primates: a close family

human and chimps: how long ago have they split?

July 29, 2000 First unambiguous Brennifer anistonii sp. amigos identifiedMalib, CaliforniaJanuary 7, 2005 Allopatry reported for B. anistoniiLos Angeles, CaliforniaMarch 25, 2005 Population crash for B. anistonii (filed for divorce)Los Angeles, CaliforniaJuly 2005, 2005 Printed literature (W magazine) makes mention of Condé Nast Brangelina jolieus sp. cryptovolerusOctober 2, 2005 Extinction (divorce) of B. anistoniiLos Angeles, CaliforniaDecember 2, 2005 Fossil of B. jolieus identifiedSanta Monica, California May 27, 2006 B. jolieus known to be reproductively viableSwakopmund, Namibia

he said, she said… have they, or have they not?

sometimes it is hard to tell exactly when something happens…

Brad Pitt denies relationship with Angelina Jolie “This particular story is completely untrue”

July 2005Circa 2000 Nov 2005

–Pitt, Access Hollywood, 08.apr.05

speciation - terms

Sympatric-Greek sun-, from sun. together, with

AllopatricGreek, from allos, other.

ParapatricGreek, from para, beside.

"Species are groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups."

Mayr, 1942

no gene flow

speciation & divergence - implications

• it all boils down to gene flow

divergence time

X

Our Father, Who art in heaven, Hallowed be Thy Name. Thy Kingdom come.Thy Will be done, on earth as it is in Heaven. Our Father, Who art in heaven, Hallowed be Thy Name. Thy Kingdom come.Thy Will be done, on earth as it is in Heaven.

Notre Père qui es aux cieux, que ton Nom soit sanctifié, que ton règne vienne, que ta volonté soit faite sur la terre comme au ciel. Notre Père qui es aux cieux, que ton Nom soit sanctifié, que ton règne vienne, que ta volonté soit faite sur la terre comme au ciel.

Vater unser im Himmel, geheiligt werde dein Name. Dein Reich komme.Dein Wille geschehe, wie im Himmel so auf Erden.Vater unser im Himmel, geheiligt werde dein Name. Dein Reich komme.Dein Wille geschehe, wie im Himmel so auf Erden.

“speciation” – an example from our daily lives

indo-european

english frenchgerman

Our Father

Vater unser

Notre Père

Es ist unserer Aufmerksamkeit nicht entgangen, dass die speziellen Paarungen...

It has not escaped our notice that the specific pairing…

Il n'a pas échappé à notre attention que l'appariement spécifique des bases…

die wir als gegeben voraussetzen, unmittelbar auf...

we have postulated immediately suggests…

que nous avons proposé suggère immédiatement…

einen möglichen Vervielfältigungsmechanismus für die genetische Erbsubstanz schließen lassen.

a possible copying mechanism for the genetic material.

un mécanisme possible de réplication pour le matériel génétique.

no gene flow

gene flow

but what happens when “species” hybridize?

indo-european

english frenchgerman

X

Osada & Wu

divergence & constraints

That is good!

Il est bon!

Das ist gut!

how constraints may affect rates of hybridization

indo-european

english frenchgerman

Es ist unserer Aufmerksamkeit nicht entgangen...

It has not escaped our notice…

Il n'a pas échappé à notre attention…

vs.

allopatric vs. parapatric speciation revisited

uit uit

τi = 2tui

θi = 4Neui

12

11

2

1

t

eet f

NNf

1tf

tf eN2

11)

2

11( t

e

fN

21 )1(

2

11

2

1uf

NN tee

at equilibrium:

ett fff 1 02 u

14

1

uNf

ee

14

4

1

uN

uNH

fSinceH

e

ee

likelihood calculation

m

iikPL

1

)(ln),(

Defining γ=τ/θ=t/2Ne

testing model

γ1<< γ2

γ1

γ2

testing model

the authors therefore rejected the γCDS = γIGS model

parapatry between chimps and gorilla?

chimps gorilla

http://pin.primate.wisc.edu/factsheets/entry/chimpanzee

divergence (τ)

primate lineage

some ape

chimp gorillahuman organutan macaque

τgenome

τspecies

the model

human chimp

why might there be variations?

human chimp

τgenome

τspecies

primate lineage

some ape

chimp gorillahuman organutan macaque

H

HC

HCG

CG

O

HCGO

M

sometimes local tree disagrees with species tree

some ape

chimpanzee gorillahumanT TA

A

the most parsimonious solution

some ape

chimpanzee gorillahuman

CG

T TA T

A

other scenarios are possible, too

some ape

chimpanzee gorillahuman

HG

TT T

CG

divergences help define relative branch lengths

some ape

chimp gorillahuman organutan macaque

H

HC

HCG

CG

O

HCGO

M

CG

HG

τgenome

can we find these events?

H+C+HG+CG

H+C+HG+CG+HC+HCG+M

HCGM HCGOM

HC

HG/CG124%

88%

134%

86%

H+C+HG+CG

H+C+HG+CG+HC+HCG+M

what does it look like near these events?

L = 5000bp

Measuring enrichment of human-chimp b(d) divergence:

Measuring human-chimp divergence: b(d)

Out of total events: n(d)

Ratio: r(d)

Parametric model: s(d)

Quadratic function S over a defined window:

Near sites with 2 HG/CG events within 200bp

Near sites with 2 HC events within 200bp

where we find real incongruence, τ differs

human-chimp/human-macaque (5Mb)human-chimp/human-gorilla (10Mb)

HG and CG sites over the XHCGOM shotgun (10Mb)

human-chimp divergencechromosomal average

even less divergence on the X chromosome

Model by Patterson et al.

controversy? you bet!

but did human and chimp hybridize???

some ape

chimpanzee gorillahuman

H+C+HG+CG+HC+HCG+M

at HG sites [or CG sites]

HCGM HCGOM

HC

HG/CG H+C+HG+CG

some ape

chimpanzee gorillahuman

τspecies

τHG/CG

at HC sites

HCGM HCGOM

HC

HG/CG H+C+HG+CG

H+C+HG+CG+HC+HCG+M

some ape

chimpanzee gorillahuman

τspecies

τHC

H+C+HG+CG

H+C+G+HG+CG+HC+HCG+M

τX chr.

HG and CG sites over the XHCGOM shotgun (10Mb)

is there a way to explain the X data?

human-chimp divergencechromosomal average

some ape

chimpanzeehuman gorilla

what if I do the same for HG sites???

H+G+HC+CG

H+C+G+HG+CG+HC+HCG+M

some ape

chimpanzee gorillahuman

τspecies

τHG

If I build a figure using HG/CG double sites, would I get a similar graph?

Does that mean humans and gorillas have hybridized?

τgenome

τspecies

let’s take a closer look at the model

human chimp

is it possible, that the authors have it backwards???

sympatric speciation!

τgenome

τspecies

allopatric speciation

human chimp

τgenome

τspecies

parapatric speciation

human chimp

τspecies

authors’ conclusion: τgenome < τspecies in some regions

human chimp

• based on problematic branch length extrapolations

• is it such a big deal?

τgenome

HC

HG/CG

call me a skeptic

Curr Biol. 2006 Aug 22;16(16):R647-50.

Such a scenario [that human lineage hybridised withthe chimp lineage]— or a range of kinds of populationsubdivision—can indeed account for diversity among loci indivergence, but Patterson et al. do not test whether their data are consistent with the simple null model of abrupt allopatricspeciation of a single well-mixed population. A simple calculation (H. Innan, personal communication) shows that their data are consistent with an ancestral effective population size of Ne ~45,000, which does not seem unreasonable, and isconsistent with previous studies. Thus, there is no statisticalevidence for hybridisation.

viability of hybrids

tend to be a question…

Leopons

other unfortunate unions…

Jaglion

Tigon

more unfortunate unions…

many of these animals don’t do all that well, let alone reproduce…

grolar bear/pizzly bear

zorse

http://www.pbase.com/sheila/

primates: a close family

danke!thank you!

merci!

Other traits also evolve in parallel

2,3

5,6

7,8,9,10,1112

13 141516

17,18,1920

2122

23 24

2625

4

1

Completes Lows

Colosimo, et al., 2005

Control nuclear phylogeny indicates that local evolution of low populations from

marine ancestors

Low morphComplete morph Colosimo, et al., 2005

Eda tree reveals an ancient allele underlying the low-plated trait in far distant populations

Eda

Low morphComplete morph

Reduced pelvisComplete pelvis

Colosimo, et al., 2005

A similar tree from Pitx1 shows no shared allele, unlike the Eda tree