206 L13 phylogenetics MattHerron 2005 - UA Site...
Transcript of 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