Phylogeography: from database to genomics to discovery

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Phylogeography:

from database to genomics to discovery

OEB275br Scott Edwards, OEB5 February 2013

Systematics -- revealing the sequenceof ancestry and descent

common ancestors

Taxonomy -- howwe organize life’s

diversity

Biogeography --the distribution of life

on earth

Process: what are the rules of biodiversification?

Phylogenetic tree

Two types of molecular tools forphylogenetic studies

Mitochondria

Cell Nucleus

Mitochondrial DNA• Small & circular molecule• Maternally inherited• Fast-changing• No recombination

Nuclear DNA• Large & linear molecule• Biparentally inherited• Slower evolution• No recombination

Phe 12s rRNAVal

16s rRNA

LeuIle

Gln

Met

Trp

Ala

Asn

Cys

Tyr

COI

SerAspCOII

LysATP8

ATP6COIII

GlyNADH3

Arg

NADH4L

NADH4

His

Ser

Leu

NADH5

Cyt b

Thr

Control Region

Pro

NADH6

Glu

noncoding

Overview of a birdmitochondrial genome (~17,000 bp)

rRNA genes

tRNA genes

ATP synthase genes

Cytochrome bc1 complex

Cytochrome Oxidase

NADH:Ubiquinone Oxidoreductase

NADH1

NADH2

Case studies

Grassfinches (Poephila)W. Bryan Jennings

Red-backed Wren (Malurus melanocephalus)

June Lee

Gray-crowned Babblers(Pomatostomus temporalis)

Zebra Finches (Taenopygia guttata)Chris Balakrishnan

Life in the Outback

Edwards, S. V. (1993) Proc. R. Soc. Lond. B 252, 177-185.

temporalis rubeculus

Mitochondrial gene tree for grey-crowned babblers

Central East Top End Pilbara

Carpentarian barrier

Sampling localities for grey-crowned babblers

New GuineaCape YorkSoutheast

Examples of large mtDNA breaks within species

Gene flow erodes population monophyly

Migration eventreconstructed byparsimony

Counting the number of interpopulation coalescent events

Examples of discordance between gene and species trees

Hawaiian Honeycreepers (Drepanididae)

Museum collections are archives ofenvironmental history

Traditional specimens

Genetic Resources

Drawings, photographs, field notes

Database search for availablegenetic resources for….

Malurus melanocephalus, the Red-backed Fairy Wren

Striated Grasswren (Amytornis) Southern Emu-wren (Stipiturus)

Superb Fairywren (Malurus)

Diversity of Australo-Papuan Fairy Wrens - Maluridae

Splendid Fairywren (Malurus)

Lee, Joseph, & Edwards 2012. Syst. Biol. 61:253-271.

Multiple genes resolve the phylogenetic tree for Fairy Wrens

Red-backed Fairy wren - discordant subspecies boundaries

B

A

B E

D

Modified from Cracraft Evolution 40: 977-996

Kimberley Plateau(KP)

Arnheim Land(AL)

Cape York(CY)Atherton Plateau

(AP)

Eastern Forests(EF)

Genetic Diversity among loci - A

nony

mou

s lo

ciIn

tron

s

Estimating genetic diversity ( within populations

= a function of the number of polymorphic sites in a population (S)

“Watterson’s theta”

Allele 1: ACTGGCTGAACTT

Allele 2: ACTGGTTGAACTT

Allele 3: GCTGGTTGAACCT * * * S=3

n = number of alleles€

=Sn

1

ii=1

n−1

∑

A second estimate of 4NAllele 1: ACTGGCTGAACTT

Allele 2: ACTGGTTGAACTT

Allele 3: GCTGGTTGAACCT

€

π =k12 + k 23 + k13

3

2

⎛

⎝ ⎜

⎞

⎠ ⎟

=k12 + k 23 + k13

3

k = number of differences between pairs of alleles i and jn = number of alleles

€

π = i=1

n

∑ kijj>1

n

∑

n

2

⎛

⎝ ⎜

⎞

⎠ ⎟

Nucleotide diversity in mammals

Determinants of nucleotide diversity in birds

Simple demographic models of Australian birds

Balakrishnan et al. 2010. Pp. 65-88 In: In Search of the Causes of Evolution: From Field Observations to Mechanisms. (Eds., Peter and Rosemary Grant),Princeton University Press, Princeton, NJ.

Testing neutralityTajima’s D statistic proportional to:

€

π −Under neutrality, Tajima’s D ≈ 0

Under directional selection, Tajima’s D < 0

Testing neutrality

Population assignment using ‘Structure’

0.2

0.4

0.6

0.8

1.0

0.0

High-resolution geolocation using human SNPs

Novembre et al. 2008. Nature 456, 98-101

Neutral evolution

Positive Selection

Phylogenetic manifestations of natural selection

Edwards 2009 PNAS 106:8799-8800

Extraordinary Sperm ProductionIn Fairy Wrens

Sampling Gonads from Fairy Wrens

Non-Breeding Season

Breeding Season

10,284 Contigs 2,062 Contigs

All Year Round

5,809 Contigs

Transcriptomics: Higher diversity of genes in breeding vs. non-breeding season testes

Contig Gene Name Function Coverage

722 Kazal-type Serine Proteinase Inhibitor Protection of viable spermatozoa from the proteinase 125.583

5992 Beta Defensis (6e-05) Microbicidal peptides active many bacteria, fungi, viruses 97.053

1948 Proacrosin Mediating binding between acrosomal membrane and IPVL 91.025

1175 Tubulin Polymerization Promoting Protein Promoting tubulin assemblies and cell proliferation 86.585

10816 Outer Dense Fiber Protein Consists of sperm tail 64.102

5083 60.349

7574 Chromosome 10 Open Reading Frame 122 59.409

7761 Heat Shock Protein 40kd 42.143

5235 Creatine Kinase B-Variant Catalyses the conversion of creatine 34.376

2098 Family with Sequence Similarity 46 Member D Cancer/Testis Antigens 32.419

1895 Chromosome 20 Open Reading Frame 85 30.557

6856 Ribonuclease / angiogenin Inhibitor 1 Rnase Inhibitor 29.209

2639 Cytochrome c Oxidase Subunit Vic 24.909

5768 19.38

6676 Myeloid Leukemia Factor 1 18.959

17202 13.465

13352 9.971

5085 9.316

7629 6.759

16688 6.496

20 highly expressed genes specific to breeding season

testis

Red=genes showing dn/ds ratio > 1

Natural selection? examples of genes showing reciprocal monophyly among

Fairy Wren species

Proacrosin Outer Dense Fiber Protein

Gene tree monophyly as an indicator of natural selection

European corn borer