Download - “Species Trees”
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“Species Trees”
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What is the “species tree?”
• The true tree (when there is one)• The population tree• The dominant history• ????
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Populations are composed of contemporaneous individuals with a high chance of sharing common descendants
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A population lineage is a time-extended population “worm”
• Defines the limits of gene flow
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Population lineages can split to generate population trees
• The trees define the limits of coalescence/lineage sorting
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Gene trees can disagree within the population tree due to ILS
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If there is a strict population tree, it can be estimated using multilocus sequence data
• Given a set of nodal ages (in units of Ne generations) one can determine the likelihood of a particular gene tree topology (and branch lengths)
• With enough genes, you can find the population tree (and nodal ages) that maximize the likelihood of the gene trees
STEM (Kubatko et al. 2009)
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BEST
• A Bayesian MCMC method• Assumes no recombination within loci, free
recombination between loci, and no gene flow following speciation
• Does not mix well
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But what if the population “tree” is not a tree? What should we estimate?
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The full population history?
• Would need priors on hybridization and related phenomena
• Computationally challenging (but progress being made)
• Assumes that individual gene tree estimates are valid
• A reticulogram is not very useful for classification
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An alternative: the primary concordance tree
• A tree composed of clades that are true for a plurality of the genome
• A first order summary of the distribution of gene genealogies
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Implications for “species”
• If species are taxa, they may be defined as clade on the primary concordance tree
• Are they taxa?• If so, what rank of taxa?
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• Species are units of taxonomy– Part of the hierarchy of named
groups
• Species are units of evolution– Entities that participate in evolution
The dual burden of species
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Three responses
• Species are taxa. Period.
• Species are evolutionary units. Period
• Species are both.
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Species are taxa• All organisms are assigned to species• Subspecific taxa may be raised to species
rank and subgenera may be “demoted” to species
• Species are described and keyed much like taxa at other ranks
• Named species play a role in communication
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Three responses
• Species are taxa. Period.
• Species are evolutionary units. Period
• Species are both.
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Evolutionary units and taxa need not coincide
Reproductive isolation
Sp. 3Sp. 2
Species 1
Niche shiftsMorphology
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A bold claim:
We will never find an evolutionary criterion that will assign all individuals to species and maintain perfect
hierarchical nesting with taxa at other ranks
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Three responses
• Species are taxa. Period.
• Species are evolutionary units. Period
• Species are both.
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SYSTEMATICS
PROPERTY OF
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Monophylyphily
• Taxa are historical entities, hence clades• To form a strict nested hierarchy, we should
only recognize clades that are true for more of the genome than they are false
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• When we name a species we are hypothesizing the existence of a clade (on the true concordance tree)
Species are taxa/clades
1.00.35
1.00.8 0.45
0.95
0.75 0.55 0.4
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1.00.35
1.00.8 0.45
0.95
0.75 0.55 0.4
If species are taxa/cladesthey must be ranked clades
• Ranking criterion?
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..in determining whether a form should be ranked as a species or a variety, the opinion of naturalists having sound judgement and wide experience seems the only guide to follow.
Is there an objective and universal ranking criterion?
Which is to say, “No!”
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1.00.35
1.0CF=1.0 0.45
0.95
0.75 0.55 0.4
• Use assorted subjective ranking principles to select set of clades that approximate evolutionary units
• Judicious compromises to reconcile conflicting criteria
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The phylogenetic concept of “speciation”
• The emergence and persistence of distinct clades
• Differential gene lineage extinction (isolation; selection; drift)
• Ecological divergence/specialization and Reproductive isolation