Gene$csofFishes

Genetics of fishes

1. C values

2. Genome organization

3. Genomes

4. Approahes to Molecular Ecology

5. Speciation

1. C- value

Fugu: 0.4 pg

Protopterus: 72pg

Hinegardner and Rosen, 1972

2. Genome Organization

Isochores

(low GC)

LCold-blooded vertebrates

L L L H3H2H1

(low GC) (high GC)

Warm-blooded vertebrates

(Mb)

GC, %

Black Surfperch

Human

Cyprinid

Human

Danakilia dinicolai

Alcolapia alcalicus Cyprinodon salinus

Warm fishes

3. Genomes

Pufferfish- Takifugu rubripes

Pufferfish – Tetraodon nigroviridis

Zebrafish – Brachydanio rerio

Three spine stickleback – Gasterosteus aculeatus

Black surfperch– Embiotoca jacksoni

Adaptation

Adaptation

D Brawand et al. Nature 000, 1-7 (2014) doi:10.1038/nature13726

Gene duplication in the ancestry of East African lake cichlids.

4. Approaches to Molecular Ecology

1. Allozymes

2. mtDNA RFLP

3. Sanger Sequencing

4. Microsatellites

5. Next generation sequencing

4. Approaches to Molecular Ecology

2.1 Allozymes

2.2 mtDNA RFLP

Mitofish – 16,000 bp

2.3 Sanger Sequencing

2.4 Microsatellites

2.4 Microsatellites

2.5 Next Generation Sequencing

Specia(on Spa(alcomponent

Ecologicalcomponent

Sexualcomponent

Genomics

1.Spa$alcomponent

No Gene flow

Population 1 becomes monophyletic

Population 2 becomes monophyletic

Sorting time for NemtDNA: Ne generationsnuc.DNA: 4Ne generations

Speciation

Time

ESP 01 LFR 02 SCR 01

ACA 01 SCR 02

LFR 01 APA 01

CLI 137 CLI 138 CLI 139 CLI 200 CLI 142 CLI 201

MKF 01 MKF 02 MKF 03

BEL 02 BEL 01

CBR 02 (Blue Morph) CBR 01 (Regular Morph) CBR 03 (Yellow Morph)

H. passer

H. clarionensis

H. limbaughi

H. bernudensis

H. ciliaris

1% seq divergence

54/53/61 100/100/100

62/70/69

-/58/72 100/100/100

-/56/60

100/99/100

100/100/100

86/98/100 90/96/96

51/55/85 66/59/60

TEP

TWA

Tidewater Goby (Eucyclogobius newberryi)

(Dawson et al. 2001)

LAR

Burundi

CongoTanzania

Zambia

100km

AFLP1AFLP2AFLP3AFLP4

GenusTropheusLakeTanganyka

Eggeretal.2007

Dascyllustrimaculatus

0°

2000 Km

D. auripinnis D. albisella

D. strasburgi D. trimaculatus

Distribution range of the Dascyllus trimaculatus species complex

0°

2000 Km

D. auripinnis D. albisella

D. strasburgi D. trimaculatus

Distribution range of the Dascyllus trimaculatus species complex

Sympatry Cook Is

0°

2000 Km

KIN

ZAN

EIL

MAY

OMA

SEY

CKE

MAN

CAM VIT

JAP

FIJ

WAL

PAL

GBR

MAR

MOO

RM

PAL XMA

BAK

MRQ

JOH HAW FFS

KUR

Sampling sites

D. auripinnis D. albisella

D. strasburgi D. trimaculatus

0°

2000 Km

KIN

ZAN

EIL

MAY

OMA

SEY

CKE

MAN

CAM VIT

JAP

FIJ

WAL

PAL

GBR

MAR

MOO

RM

PAL XMA

BAK

MRQ

JOH HAW FFS

KUR

Mitochondrial analysis - 591 individuals

D. auripinnis D. albisella

D. strasburgi D. trimaculatus

Clade 1 Clade 2

Clade 5

Clade 3

Clade 4

5 genetic partitions

Maximum likelihood tree

Clade 5

n = 142

n = 37

n = 105

n = 37 Clade 1

Clade 2

Clade 4

n = 267 Clade 3

1 change

OC3

mtDNA:

0°

2000 Km

KIN

ZAN

EIL

MAY

OMA

SEY

CKE

MAN

CAM VIT

JAP

FIJ

WAL

PAL

GBR

MAR

MOO

RM

PAL XMA

BAK

MRQ

JOH HAW FFS

KUR

Microsatellite analysis - 13 variable loci - 316 individuals

D. auripinnis D. albisella

D. strasburgi D. trimaculatus

2000 Km

7 genetic partitions Nuclear DNA:

mtDNA

Nuclear DNA

Moorea, French Polynesia

West Opunohu

Crest

Channel

West Opunohu

ReefCrest

FringingReef

Channel

OpenOcean

Pass

Currentflow

CrestRow

ChannelRow

MooreaN!

Clownfish recruitment

Loca$onofallAmphiprionchrysopteruscollectedaroundMoorea(FrenchPolynesia)

1-1011-20>21

individuals

2007 2008

2010

Oceanographiccharacteris$cs

Largescaleforcing

Smallscalecircula$on

Coron, Philippines

Altrichthys

clutches n average families average %extra extra sp. AAZ 21 414 19.7 54 2.6 19.2 20

clutches n average families average %extra extra sp. ACU 19 305 16.1 52 2.7 22.5 6

Requirements for sympatric speciation

1. Sympatric distribution

3. Monophyletic sister taxa

4. Reproductive isolation

2. History of allopatry is unlikely

5. Pre-zygotic isolation

Barluenga et al. Nature 439, 719

Nicaragua Cichlids

Barluenga et al. Nature 439, 719

Nicaragua Cichlids

Reproductive Biology

Parental feeding

Multiple paternity and sperm competition

Global change

Invasion genetics Ocean acidification

Suez Canal Ferdinand de Lesseps

Opening 1869

Lessepsian migrants

Nile river outflow

Bitter Lakes

>300 species, >90 fish species

Lessepsian migrants

Introduc$on

1. Invasion of an open niche

2. Low competition

3. Low predation

A. Ecological expectations

Biological Invasions

4. Escape diseaseB. Genetic expectations

3. Large population growth

1. Genetic diversity is related to success

4. Strong acting selection

2. Bottlenecks

Introduc$on

Bluespotted cornetfish, Fistularia commersonii

Introduc$on

1Azzurro et al. 2012 Biol. Inv.

Fistularia commersonii

Introduc$on

N"50""

45"

"40"

35"

30"

25"

10" 20" 30" 40"E"

Longitu

de"

La4tude"

B"S"

Sampling

MaterialsandMethods

Red Sea : 40 Med: 31 Rad: Sbf1, ~ 13,000 loci

Red Sea Mediterranean

12599 loci Neutral Loci

Expected Bottleneck

Results

Polymorphic loci: 8580 8431

Heterogosity: 0.132 0.143

14421

544051676

5295749458 33548425645579

20760

14421

−0.045 −0.050 −0.055 −0.060 −0.065

0.00

200.

0022

0.00

240.

0026

0.00

280.

0030

0.00

32

log10(q value)

fst

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45579

51676

42565440

3354852957

2076049458

Figure3

Heterozygosity0.0 0.1 0.2 0.3 0.4 0.5

0.00

0.05

0.10

0.15

Fst

Fst

p>5%p<=5%p<=1%

50%quanAle10%"5%"5%"

ArlequinArlequin Bayescan

a b

Evidence of selection

Results

25 3317

4767

69Bayescan Arlequin

Stacks

25 3317

4767

69Bayescan Arlequin

Stacks

Figure'S3'

Outlier loci

Results

Red Sea Mediterranean

12599 loci Neutral Loci

Red Sea Mediterranean

47 loci Outlier Loci

Results

Metabolism 7%

Genetic Information Processing 4%

Environmental Information Processing 11%Cellular Processes 21%

Organismal Systems 14%

Diseases 43%

Outlier Loci

Figure'S4'

Outlier loci

Results

Immune response

Osmoregulation

Background

•  AnthropogenicburningoffossilfuelshasincreasedatmosphericCO2to400ppm

•  AtmosphericCO2isakeycontributorto

climatechange– Trapssolarradia$on– Dissolvesintoocean

Photo courtesy of Tenera Environmental

http://theotherco2problem.wordpress.com

•  30% of atmospheric CO2 emissions are absorbed by the oceans (Feely et al. 2004)

•  Ocean surface waters have decreased by 0.1 pH units since 1750

OceanAcidifica$on

EffectsofOAonMarineOrganisms

•  Biologicaleffectsaregenerallylargeandnega$ve(Kroekeretal.,2010)– Decreasedreproduc$on–  Decreasedgrowth– Decreasedcalcifica$on– Decreasedsurvival

•  Fishexpectedtobemoretolerantthaninvertebrates(Portner,2005)

EffectsofElevatedpCO2onFish

•  SeawaterwithCO2hadhighertoxicitythanseawateracidifiedwithHCl

•  Lethalforadultsatextremevalues30,000+ppm(Ishimatsuetal.,2004)

•  Mosteffectswillbesub-lethal