206 L13 phylogenetics MattHerron 2005 - UA Site...

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Phylogenetics, systematics and conservation

Matthew D. Herron

Darwin’s revolution

• “…probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.”

– C. Darwin, 1859 The Origin of Species

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Darwin’s revolution

• One figure in the Origin – a phylogenetic tree

• “God’s plan” vs. ancestor-descendant relationships

Darwin’s dream

• "The time will come, I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of nature."– C. Darwin, 1857 letter to T.H. Huxley

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Phylogenetics

• Inference of genealogical relationships among species and higher taxa

• Importance:– Classification– Comparison– Biogeography– Conservation

Trees• How to read

• Mono/para/polyphyly

• Clade

• Sister taxa

• How to reconstruct

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Placental mammalsEdentata (anteaters, sloths, armadillos)Philodota (pangolins)

Sirenia (manatees, dugongs, sea cows)Hyracoidea (hyraxes)

Tubulidentata (aardvark)Cetacea (whales, dolphins, porpoises)Artiodactyla (even-toed ungulates)Carnivora (dogs, cats, bears, seals, mustellids)Insectivora (shrews, moles, hedghogs)Dermoptera (colugos or flying lemurs)Chiroptera (bats)Scandentia (tree shrews)PrimatesMacroscelidea (elephant shrews)Rodentia (rodents)Lagomorpha (rabbits, hares, pikas)

Proboscidea (elephants)

Perissodactyla (odd-toed ungulates)

Modified from Tree of Life (http://tolweb.org)

Edentata (anteaters, sloths, armadillos)Philodota (pangolins)

Sirenia (manatees, dugongs, sea cows)Hyracoidea (hyraxes)

Tubulidentata (aardvark)Cetacea (whales, dolphins, porpoises)Artiodactyla (even-toed ungulates)Carnivora (dogs, cats, bears, seals, mustellids)Insectivora (shrews, moles, hedghogs)Dermoptera (colugos or flying lemurs)Chiroptera (bats)Scandentia (tree shrews)PrimatesMacroscelidea (elephant shrews)Rodentia (rodents)Lagomorpha (rabbits, hares, pikas)

Proboscidea (elephants)

Perissodactyla (odd-toed ungulates)

Placental mammals

Modified from Tree of Life (http://tolweb.org)

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Sirenia

Hyracoidea

Proboscidea

Perissodactyla

Sirenia

Hyracoidea

Proboscidea

Perissodactyla

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Sirenia

Hyracoidea

Proboscidea

Perissodactyla

Trees

• Can be reconstructed from several types of data:– Morphological

• Skull• Teeth• Soft tissues

– Molecular• DNA• Protein (amino acid sequence)

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Phylogenetics

• Inference of genealogical relationships among species and higher taxa

• Importance:– Classification

• “King Phillip Came Over For Good…”

Phylogenetics

• Inference of genealogical relationships among species and higher taxa

• Importance:– Classification

• “King Phillip Came Over For Good Soup”

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Hierarchical classification• “King Phillip Came Over For Good Soup”

• Kingdom• Phylum• Class• Order• Family• Genus• Species

• “Natural” classification

Spermophilus mexicanusSpermophilus mexicanusSpermophilus tridecemlineatusSpermophilus frankliniiCynomys ludovicianusCynomys mexicanusCynomys parvidensCynomys gunnisoniCynomys leucurusSpermophilus mohavensisSpermophilus tereticaudusSpermophilus spilosomaSpermophilus perotensisSpermophilus spilosoma

Spermophilus mexicanusSpermophilus mexicanusSpermophilus tridecemlineatusSpermophilus frankliniiCynomys ludovicianusCynomys mexicanusCynomys parvidensCynomys gunnisoniCynomys leucurusSpermophilus mohavensisSpermophilus tereticaudusSpermophilus spilosomaSpermophilus perotensisSpermophilus spilosoma

Monophyly

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Paraphyly

Spermophilus mexicanusSpermophilus mexicanusSpermophilus tridecemlineatusSpermophilus frankliniiCynomys ludovicianusCynomys mexicanusCynomys parvidensCynomys gunnisoniCynomys leucurusSpermophilus mohavensisSpermophilus tereticaudusSpermophilus spilosomaSpermophilus perotensisSpermophilus spilosoma

Spermophilus mexicanusSpermophilus mexicanusSpermophilus tridecemlineatusSpermophilus frankliniiCynomys ludovicianusCynomys mexicanusCynomys parvidensCynomys gunnisoniCynomys leucurusSpermophilus mohavensisSpermophilus tereticaudusSpermophilus spilosomaSpermophilus perotensisSpermophilus spilosoma

SpermophilusAmmospermophilusSpermophilusSpermophilusSpermophilusCynomysSpermophilusSpermophilusSpermophilusMarmota

SpermophilusAmmospermophilusSpermophilusSpermophilusSpermophilusCynomysSpermophilusSpermophilusSpermophilusMarmota

Paraphyly

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A: Chlamydomonas reinhardtii

B: Gonium pectorale

C: Eudorina elegans

D: Pleodorina californica

E: Volvox carteri

F: Volvox rousseletii

Polyphyly

5%

Chlamydomonas reinhardtii (1)

Gonium pectorale (16)Platydorina caudata (32)

Volvox globator (16,000)Volvox barberi (32,000)

Volvox rousselettii (32,000)Volvulina steinii (16)

Volvulina compacta (16)Volvulina pringsheimii (16)

Pandorina morum A (16)Pandorina colemaniae (16)

Pandorina morum B (16)Pandorina morum C (16)

Volvulina boldii (16)Yamagishiella unicocca (32)

Eudorina elegans A (32)Eudorina minodii (32)

Eudorina elegans B (32)Eudorina unicocca (32)

Volvox gigas (2000)Eudorina elegans C (32)

Pleodorina indica (64)Pleodorina illinoisensis A (32)Eudorina elegans D (32)

Pleodorina illinoisensis B (32)Eudorina cylindrica (16)

Pleodorina californica (128)

Volvox aureus (2000)Volvox africanus (8000)

Volvox dissipatrix (16,000)Volvox tertius (1000)

Volvox obversus (2000)Volvox carteri f. nagariensis (4000)

Volvox carteri f. kawasakiensis (2000)Volvox carteri f.weismannia (2000)

Pleodorina japonica (128)

Volvocaceae

5%

Chlamydomonas reinhardtii (1)

Gonium pectorale (16)Platydorina caudata (32)

Volvox globator (16,000)Volvox barberi (32,000)

Volvox rousselettii (32,000)Volvulina steinii (16)

Volvulina compacta (16)Volvulina pringsheimii (16)

Pandorina morum A (16)Pandorina colemaniae (16)

Pandorina morum B (16)Pandorina morum C (16)

Volvulina boldii (16)Yamagishiella unicocca (32)

Eudorina elegans A (32)Eudorina minodii (32)

Eudorina elegans B (32)Eudorina unicocca (32)

Volvox gigas (2000)Eudorina elegans C (32)

Pleodorina indica (64)Pleodorina illinoisensis A (32)Eudorina elegans D (32)

Pleodorina illinoisensis B (32)Eudorina cylindrica (16)

Pleodorina californica (128)

Volvox aureus (2000)Volvox africanus (8000)

Volvox dissipatrix (16,000)Volvox tertius (1000)

Volvox obversus (2000)Volvox carteri f. nagariensis (4000)

Volvox carteri f. kawasakiensis (2000)Volvox carteri f.weismannia (2000)

Pleodorina japonica (128)

Volvocaceae

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Phylogenetics

• Inference of genealogical relationships among species and higher taxa

• Importance:– Classification– Comparison

• Reconstruction of ancestral characters

5%

Chlamydomonas reinhardtii (1)

Gonium pectorale (16)Platydorina caudata (32)

Volvox globator (16,000)Volvox barberi (32,000)

Volvox rousselettii (32,000)Volvulina steinii (16)

Volvulina compacta (16)Volvulina pringsheimii (16)

Pandorina morum A (16)Pandorina colemaniae (16)

Pandorina morum B (16)Pandorina morum C (16)

Volvulina boldii (16)Yamagishiella unicocca (32)

Eudorina elegans A (32)Eudorina minodii (32)

Eudorina elegans B (32)Eudorina unicocca (32)

Volvox gigas (2000)Eudorina elegans C (32)

Pleodorina indica (64)Pleodorina illinoisensis A (32)Eudorina elegans D (32)

Pleodorina illinoisensis B (32)Eudorina cylindrica (16)

Pleodorina californica (128)

Volvox aureus (2000)Volvox africanus (8000)

Volvox dissipatrix (16,000)Volvox tertius (1000)

Volvox obversus (2000)Volvox carteri f. nagariensis (4000)

Volvox carteri f. kawasakiensis (2000)Volvox carteri f.weismannia (2000)

Pleodorina japonica (128)

Volvocaceae

1163264-512>1000

5%

Chlamydomonas reinhardtii (1)

Gonium pectorale (16)Platydorina caudata (32)

Volvox globator (16,000)Volvox barberi (32,000)

Volvox rousselettii (32,000)Volvulina steinii (16)

Volvulina compacta (16)Volvulina pringsheimii (16)

Pandorina morum A (16)Pandorina colemaniae (16)

Pandorina morum B (16)Pandorina morum C (16)

Volvulina boldii (16)Yamagishiella unicocca (32)

Eudorina elegans A (32)Eudorina minodii (32)

Eudorina elegans B (32)Eudorina unicocca (32)

Volvox gigas (2000)Eudorina elegans C (32)

Pleodorina indica (64)Pleodorina illinoisensis A (32)Eudorina elegans D (32)

Pleodorina illinoisensis B (32)Eudorina cylindrica (16)

Pleodorina californica (128)

Volvox aureus (2000)Volvox africanus (8000)

Volvox dissipatrix (16,000)Volvox tertius (1000)

Volvox obversus (2000)Volvox carteri f. nagariensis (4000)

Volvox carteri f. kawasakiensis (2000)Volvox carteri f.weismannia (2000)

Pleodorina japonica (128)

Volvocaceae

1163264-512>1000

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5%

Chlamydomonas reinhardtii (1)

Gonium pectorale (16)Platydorina caudata (32)

Volvox globator (16,000)Volvox barberi (32,000)

Volvox rousselettii (32,000)Volvulina steinii (16)

Volvulina compacta (16)Volvulina pringsheimii (16)

Pandorina morum A (16)Pandorina colemaniae (16)

Pandorina morum B (16)Pandorina morum C (16)

Volvulina boldii (16)Yamagishiella unicocca (32)

Eudorina elegans A (32)Eudorina minodii (32)

Eudorina elegans B (32)Eudorina unicocca (32)

Volvox gigas (2000)Eudorina elegans C (32)

Pleodorina indica (64)Pleodorina illinoisensis A (32)Eudorina elegans D (32)

Pleodorina illinoisensis B (32)Eudorina cylindrica (16)

Pleodorina californica (128)

Volvox aureus (2000)Volvox africanus (8000)

Volvox dissipatrix (16,000)Volvox tertius (1000)

Volvox obversus (2000)Volvox carteri f. nagariensis (4000)

Volvox carteri f. kawasakiensis (2000)Volvox carteri f.weismannia (2000)

Pleodorina japonica (128)

Volvocaceae

UndifferentiatedPartially differentiatedDifferentiatedUnknown

5%

Chlamydomonas reinhardtii (1)

Gonium pectorale (16)Platydorina caudata (32)

Volvox globator (16,000)Volvox barberi (32,000)

Volvox rousselettii (32,000)Volvulina steinii (16)

Volvulina compacta (16)Volvulina pringsheimii (16)

Pandorina morum A (16)Pandorina colemaniae (16)

Pandorina morum B (16)Pandorina morum C (16)

Volvulina boldii (16)Yamagishiella unicocca (32)

Eudorina elegans A (32)Eudorina minodii (32)

Eudorina elegans B (32)Eudorina unicocca (32)

Volvox gigas (2000)Eudorina elegans C (32)

Pleodorina indica (64)Pleodorina illinoisensis A (32)Eudorina elegans D (32)

Pleodorina illinoisensis B (32)Eudorina cylindrica (16)

Pleodorina californica (128)

Volvox aureus (2000)Volvox africanus (8000)

Volvox dissipatrix (16,000)Volvox tertius (1000)

Volvox obversus (2000)Volvox carteri f. nagariensis (4000)

Volvox carteri f. kawasakiensis (2000)Volvox carteri f.weismannia (2000)

Pleodorina japonica (128)

Volvocaceae

UndifferentiatedPartially differentiatedDifferentiatedUnknown

Phylogenetics

• Inference of genealogical relationships among species and higher taxa

• Importance:– Classification– Comparison– Biogeography

• History and patterns of species distributions

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X. erythropusX. erythropus

X. princepsX. princeps

X. inaurisX. inauris

SpermophilopsisleptodactylusSpermophilopsisleptodactylus

X. rutilusX. rutilus

Xerine phylogeny – background

• Xerus relationships based on skull and dental morphology

X. rutilusX. rutilus

X. erythropusX. erythropus

X. inaurisX. inauris

X. princepsX. princeps

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Xerus erythropusXerus erythropusX. rutilusX. rutilus

X. inaurisX. inauris

X. princepsX. princeps

Spermophilopsis leptodactylusSpermophilopsis leptodactylus

5 changes5 changes

100100100100 9090

10010075755959

100100100100

100100100100

9999100100

BPPBPPBSBS

Results:

Phylogram based on mitochondrial DNA sequences

Results:

Phylogram based on mitochondrial DNA sequences

X. erythropusX. erythropus

X. princepsX. princeps

X. inaurisX. inauris

SpermophilopsisleptodactylusSpermophilopsisleptodactylus

X. rutilusX. rutilus

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X. erythropusX. erythropus

X. princepsX. princeps

X. inaurisX. inauris

SpermophilopsisleptodactylusSpermophilopsisleptodactylus

X. rutilusX. rutilus

Biogeographic conclusions

• Single invasion of Africa from Eurasia

• Supports “arid corridor” hypothesis

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Phylogenetics

• Inference of genealogical relationships among species and higher taxa

• Importance:– Classification– Comparison– Biogeography– Conservation

• Alpha taxonomy• Genetic diversity

Conservation questions

• “Alpha” taxonomy– Importance of species designations as

units of protection

• Species diversity vs. genetic diversity– Within species– Among higher taxa

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Xerus inaurisXerus inauris Xerus princepsXerus princeps

Are Xerus inauris & X. princepsdistinct species?

Are Xerus inauris & X. princepsdistinct species?

Are Xerus inauris & X. princepsdistinct species?

• Behavioral differences– X. princeps is essentially asocial– X. inauris is highly social

• Both male and female social groups

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Conservation of Xerus princeps

• Endemic to the Western Escarpment of Namibia

• Not listed, but uncommon

• Western Escarpment is high in endemism of plants and birds

Xerus erythropusXerus erythropusX. rutilusX. rutilus

X. inaurisX. inauris

X. princepsX. princeps

Spermophilopsis leptodactylusSpermophilopsis leptodactylus

5 changes5 changes

100100100100 9090

10010075755959

100100100100

100100100100

9999100100

BPPBPPBSBS

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Xerus erythropusXerus erythropusXerus rutilusXerus rutilus

X. inaurisX. inauris

X. princepsX. princeps

Spermophilopsis leptodactylusSpermophilopsis leptodactylus

II

IIII

IIIIIII

IIIII

Genetic structure of X. inauris & X. princeps

Genetic structure of X. inauris & X. princeps

Conservation conclusions• Xerus inauris and X. princeps are

distinct species

• Protection of the Western Escarpment is important for protecting X. princeps

• X. inauris may include cryptic species, one of which may be endemic to the Western Escarpment

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The fifth reasonphylogenetics is important

http://ucjeps.berkeley.edu/TreeofLife/hyperbolic.phphttp://tolweb.org

The fifth reasonphylogenetics is important

• For its own sake: fulfilling Darwin’s dream of understanding the relationships among species and the history of life on Earth