■♥tr♦❞✉❝t✐♦♥ t♦ ♣❤②❧♦❣❡♥❡t✐❝s ❚❤✐❜❛✉t ❏♦♠❜❛rt ✶✺ ❉❡❝❡♠❜❡r ✷✵✶✼ ▼❘❈ ❈❡♥tr❡ ❢♦r ❖✉t❜r❡❛❦ ❆♥❛❧②s✐s ❛♥❞ ▼♦❞❡❧❧✐♥❣ ■♠♣❡r✐❛❧ ❈♦❧❧❡❣❡ ▲♦♥❞♦♥
❖✉t❧✐♥❡ P❤②❧♦❣❡♥✐❡s✳✳✳ ❉✐st❛♥❝❡ tr❡❡s P❛rs✐♠♦♥② ▲✐❦❡❧✐❤♦♦❞✴❇❛②❡s✐❛♥ ❯♥❝❡rt❛✐♥t② P✐t❢❛❧❧s ✫ ❜❡st ♣r❛❝t✐❝❡s ✶ ❆♥❞ ♠♦r❡✳✳✳
P❤②❧♦❣❡♥❡t✐❝s✿ ❢r♦♠ t❤❡ ♦r✐❣✐♥s✳✳✳ ✬❋r♦♠ t❤❡ ✜rst ❣r♦✇t❤ ♦❢ t❤❡ tr❡❡✱ ♠❛♥② ❛ ❧✐♠❜ ❛♥❞ ❜r❛♥❝❤ ❤❛s ❞❡❝❛②❡❞ ❛♥❞ ❞r♦♣♣❡❞ ♦✛❀ ❛♥❞ t❤❡s❡ ❢❛❧❧❡♥ ❜r❛♥❝❤❡s ♦❢ ✈❛r✐♦✉s s✐③❡s ♠❛② r❡♣r❡s❡♥t t❤♦s❡ ✇❤♦❧❡ ♦r❞❡rs✱ ❢❛♠✐❧✐❡s✱ ❛♥❞ ❣❡♥❡r❛ ✇❤✐❝❤ ❤❛✈❡ ♥♦✇ ♥♦ ❧✐✈✐♥❣ r❡♣r❡s❡♥t❛t✐✈❡s✱ ❛♥❞ ✇❤✐❝❤ ❛r❡ ❦♥♦✇♥ t♦ ✉s ♦♥❧② ✐♥ ❛ ❢♦ss✐❧ st❛t❡✳✬ ❈✳ ❉❛r✇✐♥✱ ◆♦t❡❜♦♦❦✱ ✶✽✸✼✳ ✷
P❤②❧♦❣❡♥❡t✐❝s✿ ✳✳✳t♦ t❤❡ ♣r❡s❡♥t • ♣❤②❧♦❣❡♥❡t✐❝ tr❡❡s ❛r❡ ♣❛rt ♦❢ t❤❡ st❛♥❞❛r❞ t♦♦❧❜♦① ♦❢ ❣❡♥❡t✐❝ ❞❛t❛ ❛♥❛❧②s✐s • r❡♣r❡s❡♥t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ♦❢ ❛ s❡t ♦❢ ✭s❛♠♣❧❡❞✮ t❛①❛ ❇✐♥✐♥❞❛✲❊♠♦♥❞s ❡t ❛❧✳ ✱ ✷✵✵✼✱ ◆❛t✉r❡✳ ✸
❈✉rr❡♥t tr❡❡s ❧♦♦❦ ❜❡tt❡r✦ ✭❛♥❞ s♦♠❡ ♦t❤❡r ♠✐♥♦r ❞✐✛❡r❡♥❝❡s✮ ❆♥❞ t❤❡ ♠❛✐♥ ❞✐✛❡r❡♥❝❡ ✐s✳✳✳ ✹
✭❛♥❞ s♦♠❡ ♦t❤❡r ♠✐♥♦r ❞✐✛❡r❡♥❝❡s✮ ❆♥❞ t❤❡ ♠❛✐♥ ❞✐✛❡r❡♥❝❡ ✐s✳✳✳ ❈✉rr❡♥t tr❡❡s ❧♦♦❦ ❜❡tt❡r✦ ✹
❆♥❞ t❤❡ ♠❛✐♥ ❞✐✛❡r❡♥❝❡ ✐s✳✳✳ ❈✉rr❡♥t tr❡❡s ❧♦♦❦ ❜❡tt❡r✦ ✭❛♥❞ s♦♠❡ ♦t❤❡r ♠✐♥♦r ❞✐✛❡r❡♥❝❡s✮ ✹
❉✐✛❡r❡♥t ✇❛②s t♦ ❡①♣❧♦✐t t❤✐s ✐♥❢♦r♠❛t✐♦♥✳ ❆❜♦✉t t❤❡ ♠✐♥♦r ❞✐✛❡r❡♥❝❡s✳✳✳ • ❉◆❆ s❡q✉❡♥❝✐♥❣ r❡✈♦❧✉t✐♦♥ • ❤✉❣❡ ❞❛t❛ ❜❛♥❦s ❢r❡❡❧② ❛✈❛✐❧❛❜❧❡ ✭❡✳❣✳ ●❡♥❇❛♥❦✮ • ❡❛s✐❡r✱ ❝❤❡❛♣❡r✱ ❢❛st❡r t♦ ♦❜t❛✐♥ ❉◆❆ s❡q✉❡♥❝❡s • ✐♥❝r❡❛s✐♥❣ ♥✉♠❜❡r ♦❢ ❢✉❧❧ ❣❡♥♦♠❡s ❛✈❛✐❧❛❜❧❡ ✺
❆❜♦✉t t❤❡ ♠✐♥♦r ❞✐✛❡r❡♥❝❡s✳✳✳ • ❉◆❆ s❡q✉❡♥❝✐♥❣ r❡✈♦❧✉t✐♦♥ • ❤✉❣❡ ❞❛t❛ ❜❛♥❦s ❢r❡❡❧② ❛✈❛✐❧❛❜❧❡ ✭❡✳❣✳ ●❡♥❇❛♥❦✮ • ❡❛s✐❡r✱ ❝❤❡❛♣❡r✱ ❢❛st❡r t♦ ♦❜t❛✐♥ ❉◆❆ s❡q✉❡♥❝❡s • ✐♥❝r❡❛s✐♥❣ ♥✉♠❜❡r ♦❢ ❢✉❧❧ ❣❡♥♦♠❡s ❛✈❛✐❧❛❜❧❡ ❉✐✛❡r❡♥t ✇❛②s t♦ ❡①♣❧♦✐t t❤✐s ✐♥❢♦r♠❛t✐♦♥✳ ✺
❖✉t❧✐♥❡ P❤②❧♦❣❡♥✐❡s✳✳✳ ❉✐st❛♥❝❡ tr❡❡s P❛rs✐♠♦♥② ▲✐❦❡❧✐❤♦♦❞✴❇❛②❡s✐❛♥ ❯♥❝❡rt❛✐♥t② P✐t❢❛❧❧s ✫ ❜❡st ♣r❛❝t✐❝❡s ✻ ❆♥❞ ♠♦r❡✳✳✳
❙✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s r❡✢❡❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ●❡♥❡t✐❝ ❝❤❛♥❣❡s ✭s✉❜st✐t✉t✐♦♥✮ ❛❝❝✉♠✉❧❛t❡ ♦✈❡r t✐♠❡ ❙✉❜st✐t✉t✐♦♥ ✿ r❡♣❧❛❝❡♠❡♥t ♦❢ ❛ ♥✉❝❧❡♦t✐❞❡ ✭❡✳❣✳ ❛ → t✮ ...attgtacgtaggatctagg... ...attgaacgtaggatctagg... ...attgtacgtaccatctagg... Time ...atcgtacgtaccatctggg... ...attgaacgtagttgctagg... ✼
❙✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s r❡✢❡❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ●❡♥❡t✐❝ ❝❤❛♥❣❡s ✭s✉❜st✐t✉t✐♦♥✮ ❛❝❝✉♠✉❧❛t❡ ♦✈❡r t✐♠❡ ❙✉❜st✐t✉t✐♦♥ ✿ r❡♣❧❛❝❡♠❡♥t ♦❢ ❛ ♥✉❝❧❡♦t✐❞❡ ✭❡✳❣✳ ❛ → t✮ ...attgtacgtaggatctagg... ...attgaacgtaggatctagg... ...attgtacgtaccatctagg... Time ...atcgtacgtaccatctggg... ...attgaacgtagttgctagg... ✼
❙✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s r❡✢❡❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ●❡♥❡t✐❝ ❝❤❛♥❣❡s ✭s✉❜st✐t✉t✐♦♥✮ ❛❝❝✉♠✉❧❛t❡ ♦✈❡r t✐♠❡ ❙✉❜st✐t✉t✐♦♥ ✿ r❡♣❧❛❝❡♠❡♥t ♦❢ ❛ ♥✉❝❧❡♦t✐❞❡ ✭❡✳❣✳ ❛ → t✮ ...attgtacgtaggatctagg... ...attgaacgtaggatctagg... ...attgtacgtaccatctagg... Time ...atcgtacgtaccatctggg... ...attgaacgtagttgctagg... ✼
❙✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s r❡✢❡❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ●❡♥❡t✐❝ ❝❤❛♥❣❡s ✭s✉❜st✐t✉t✐♦♥✮ ❛❝❝✉♠✉❧❛t❡ ♦✈❡r t✐♠❡ ❙✉❜st✐t✉t✐♦♥ ✿ r❡♣❧❛❝❡♠❡♥t ♦❢ ❛ ♥✉❝❧❡♦t✐❞❡ ✭❡✳❣✳ ❛ → t✮ ...attgtacgtaggatctagg... ...attgaacgtaggatctagg... ...attgtacgtaccatctagg... Time ...atcgtacgtaccatctggg... ...attgaacgtagttgctagg... ✼
❙✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s r❡✢❡❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ●❡♥❡t✐❝ ❝❤❛♥❣❡s ✭s✉❜st✐t✉t✐♦♥✮ ❛❝❝✉♠✉❧❛t❡ ♦✈❡r t✐♠❡ ❙✉❜st✐t✉t✐♦♥ ✿ r❡♣❧❛❝❡♠❡♥t ♦❢ ❛ ♥✉❝❧❡♦t✐❞❡ ✭❡✳❣✳ ❛ → t✮ ...attgtacgtaggatctagg... ...attgaacgtaggatctagg... ...attgtacgtaccatctagg... Time ...atcgtacgtaccatctggg... ...attgaacgtagttgctagg... ✼
●❡♥❡t✐❝ ❝❤❛♥❣❡s ✭s✉❜st✐t✉t✐♦♥✮ ❛❝❝✉♠✉❧❛t❡ ♦✈❡r t✐♠❡ ❙✉❜st✐t✉t✐♦♥ ✿ r❡♣❧❛❝❡♠❡♥t ♦❢ ❛ ♥✉❝❧❡♦t✐❞❡ ✭❡✳❣✳ ❛ → t✮ ...attgtacgtaggatctagg... ...attgaacgtaggatctagg... ...attgtacgtaccatctagg... Time ...atcgtacgtaccatctggg... ...attgaacgtagttgctagg... ❙✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s r❡✢❡❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ✼
P❤②❧♦❣❡♥❡t✐❝s ❛✐♠ t♦ r❡❝♦♥str✉❝t ❡✈♦❧✉t✐♦♥❛r② tr❡❡s ✭ ♣❤②❧♦❣❡♥✐❡s ✮ ❢r♦♠ ❣❡♥❡t✐❝ s❡q✉❡♥❝❡ ❞❛t❛✳ ❯s✐♥❣ s✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s t♦ r❡❝♦♥str✉❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ...attaaacgtaggatctagg... ...attaaacgtaggatctagg... ...attcatacgtaggatcagg... ...attgtacgtaggatctttt... ...attgtacgtaggatctttt... Reconstructed phylogeny ...attgcatgtaggatctttt... ✽
P❤②❧♦❣❡♥❡t✐❝s ❛✐♠ t♦ r❡❝♦♥str✉❝t ❡✈♦❧✉t✐♦♥❛r② tr❡❡s ✭ ♣❤②❧♦❣❡♥✐❡s ✮ ❢r♦♠ ❣❡♥❡t✐❝ s❡q✉❡♥❝❡ ❞❛t❛✳ ❯s✐♥❣ s✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s t♦ r❡❝♦♥str✉❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ...attaaacgtaggatctagg... ...attaaacgtaggatctagg... ...attcatacgtaggatcagg... ...attgtacgtaggatctttt... ...attgtacgtaggatctttt... Reconstructed phylogeny ...attgcatgtaggatctttt... ✽
❯s✐♥❣ s✉❜st✐t✉t✐♦♥ ♣❛tt❡r♥s t♦ r❡❝♦♥str✉❝t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ...attaaacgtaggatctagg... ...attaaacgtaggatctagg... ...attcatacgtaggatcagg... ...attgtacgtaggatctttt... ...attgtacgtaggatctttt... Reconstructed phylogeny ...attgcatgtaggatctttt... P❤②❧♦❣❡♥❡t✐❝s ❛✐♠ t♦ r❡❝♦♥str✉❝t ❡✈♦❧✉t✐♦♥❛r② tr❡❡s ✭ ♣❤②❧♦❣❡♥✐❡s ✮ ❢r♦♠ ❣❡♥❡t✐❝ s❡q✉❡♥❝❡ ❞❛t❛✳ ✽
❍♦✇ t♦ ✇❡ ❜✉✐❧❞ t❤❡♠❄ ❯s✐♥❣ tr❡❡s t♦ r❡♣r❡s❡♥t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② ✾
❍♦✇ t♦ ✇❡ ❜✉✐❧❞ t❤❡♠❄ ❯s✐♥❣ tr❡❡s t♦ r❡♣r❡s❡♥t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② - "taxa" - "tips" - "leaves" - "Operational Taxonomic Units (OTUs)" ✾
❍♦✇ t♦ ✇❡ ❜✉✐❧❞ t❤❡♠❄ ❯s✐♥❣ tr❡❡s t♦ r❡♣r❡s❡♥t t❤❡ ❡✈♦❧✉t✐♦♥❛r② ❤✐st♦r② Most Recent Common Ancestors (MRCA) - "nodes" - "Hypothetical Taxonomic Units (HTUs)" ✾
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