Lecture 2 Phylogenetics of Fishes

1. Phylogenetic systematics

2. General fish evolution

3. Molecular systematics & Genetic approaches Charles Darwin & Alfred Russel Wallace

All species are related through common descent

1809 - 1882 1823 - 1913 Willi Hennig (1913 – 1976)

• Hennig developed cladistical method to infer relatedness

• Goal is to correctly group ancestors and all their descendants Cladistics (a.k.a Phylogenetic Systematics)

Fundamental approach • divide characters into two groups

• Apomorphies: more recently derived characteristics

• Pleisomorhpies: more ancestral, primitive characteristics

• Identify Synapomorphies (shared derived characteristics)

• group clades by synapomorphies Cladistics (a.k.a Phylogenetic Systematics)

eyes Synapomorphy of rockfish, gills bichir, and sharks? jaws

bony skeleton

swim bladder

Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics)

eyes Sympleisomorphy of gills rockfish, bichir, and sharks? jaws

bony skeleton

swim bladder

Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics)

eyes “Ancestral” and “derived” are gills relative to your focal group jaws

bony skeleton

swim bladder

Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics)

Monophyletic (aka clade): all taxa are descended from a common ancestor that is not the ancestor of any other group (every taxa descended from that ancestor is included)

examples? Cladistics (a.k.a Phylogenetic Systematics)

Paraphyletic: the group does not contain all species descended from the most recent common ancestor of its members

examples? Cladistics (a.k.a Phylogenetic Systematics)

Polyphyletic: taxa are descended from several ancestors that are also the ancestors of taxa classified into other groups

examples? Problems with Traditional Cladistics Homoplasies • traits evolved due to convergence

- keel: stabilizes tail at high speeds Problems with Traditional Cladistics Statistically inconsistent • can lend more support for the wrong answer

Bernal et al. 2001 Problems with Traditional Cladistics Unequal rates • lineages can evolve at different rates

Cyprinidae Molecular Systematics & Genetic Approaches

Compares similarities and differences in DNA sequences • identify informative sequences (aka synapomorphies)

Different parts of the genome evolve at different rates • choose appropriate sequences to compare

Address questions about biogeography & evolutionary history that traditional systematics can not African Cichlids & the Great African Rift Lakes

Lake Victoria ~400-500 spp.

Lake Tanganyika

~180-250 spp.

Lake Malawi ~700-1000 spp. Parallel or Convergent Evolution?

omnivore omnivore

vegetarian vegetarian

piscivorous piscivorous

carnivore carnivore generalist generalist

omnivore omnivore Parallel Evolution Lake Tanganyika Lake Malawi

3 common ancestors Convergent evolution Lake Tanganyika Lake Malawi

1 common ancestor 1 common ancestor Parallel or Convergent Evolution?

Take a few minutes to draw alternative phylogenetic hypotheses for parallel and convergent evolutionary scenarios (talk to your neighbors). Parallel Evolution

Predicted Result Convergent evolution

Predicted Result

Lake Tanganyika

Lake Malawi Molecular tree based on cytochrome b sequences

100 Victoria Haplochromines

100 Malawi Haplochromines Group A

Malawi Haplochromines Group B 100

100 Astatoreochromis Tanganyika Julidochromis Tanganyika Lamprologus

Myrs 6 4 2 0 Molecular Clock Calibration in Sharks • Fossils and geologic events

• Calibrate sequence divergence

• Establish molecular clock

• ~7-8x slower than mammals

Martin et al 1992 Evolution of Endothermy - monophyly or convergence? Molecular Systematics & Genetic Approaches

Gene trees vs. species trees • gene trees don’t necessarily reflect the species tree

The more gene trees you sample, the more likely you converge on the species tree

red = gene tree blue = species tree Surfperches (Embiotocidae)

26 Surfperches (Embiotocidae)

Longo & Bernardi 2015 Longo & Bernardi 2015 Surfperches (Embiotocidae)

Bernardi & Bucciarelli 1999 Surfperches (Embiotocidae)

LongoLongo & &Bernardi Bernardi 2015 2015