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Abstract Detail


Doyle, Jeff [1].

How many coalescent genes does an organelle genome comprise?

The paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC) that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in a historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. For the last 30 or more years, organelle genomes, particularly those of the animal mitochondrion and the plant plastid, have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Recently it has been suggested that species tree methods should be applied to these genomes, using coalescent methods that treat their genes—over 70 protein-coding genes in the case of most plastid genomes (plastomes)—individually, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. The argument is based on the contention that there are several key misconceptions concerning organelle genome recombination, heteroplasmy, and transmission, and that incongruence found among plastid gene trees could be due to incomplete lineage sorting enabled by historical independence of organelle genes, just as occurs in the nuclear genome. This argument mirrors the so-called “gene tree delusion” criticism of species tree approaches: That the sequences used in many coalescent analyses in fact undergo too much recombination among their exons, comprising multiple c-genes, and thus violate a key assumption of the MSC. This criticism has been rejected by adherents of the species tree approach. Although recombination certainly occurs in the plastome, as has been recognized since the 1970’s, it is rarely, if ever, phylogenetically relevant. The plastome is, in fact, a more canonical c-gene than the average mammalian nuclear gene that featured in the “gene tree delusion” debate. The plastome should thus continue to be considered a single estimate of the underlying species phylogeny, and therefore treated like any single nuclear gene, despite its ability to yield a highly resolved and robustly supported tree.

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1 - Cornell University, School Of Integrative Plant Science, Plant Biology Section, 404 Mann Library Building, Ithaca, NY, 14853, US

plastid genome
coalescent gene
species tree
gene tree

Presentation Type: Oral Paper
Session: SYSTIII, Systematics III: Algae to Lilioid Monocots
Location: Virtual/Virtual
Date: Tuesday, July 20th, 2021
Time: 3:15 PM(EDT)
Number: SYSTIII002
Abstract ID:565
Candidate for Awards:None

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