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Fish Phylogeny Fleshed Out With New Computational Approach

NEW YORK (GenomeWeb) – A fish-focused phylogenetic analysis claims to clarify some vertebrate positions in the tree of life, using a gene genealogy interrogation (GGI) approach that teases phylogenetic relationships from short coalescent genes, applying constraints to the potential topology of a given tree to dial down its complexity.

"This method is similar to others that place priors on gene tree topologies, but is unique in that priors are set to test specific hypotheses directly," senior author Ricardo Betancur-R., a vertebrate zoology and biology researcher affiliated with the Smithsonian Museum's National Museum of Natural History and the University of Puerto Rico, and his co-authors wrote.

Researchers from the US and Puerto Rico did targeted sequencing at more than 1,000 loci apiece in samples representing 225 species in the otophysan fish clade, which spans four orders and dozens of freshwater fish families. As they reported online today in Nature Ecology & Evolution, the GGI method clarified some murky fish relationships in a manner that coincided with morphological analyses of the fish, prompting the investigators to take a similar tack in analyzing relationships from other branches of the tree of life with available genome and variant datasets.

"[T]he coalescent analyses using GGI trees resolve with high confidence the branching order of major otophysan groups, a result that is fully congruent with the morphological hypothesis, thereby reconciling a long history of molecular and morphological conflict," the authors wrote.

Following from a pilot experiment that involved sequencing nearly 4,000 exons, the team used Illumina sequencing to scrutinize sequences from 1,062 exon sequences or markers captured with RNA tiling baits from 11 characiform, 79 siluriform, 13 gymnotiform, and 23 cypriniform fish species, representing the four orders of otophysan fish.

After developing a topology test-based analytical method "that gauges the strength of phylogenetic signal contained in each gene alignment in favor of alternative hypotheses," the study's authors used DNA and protein sequences gleaned from these data to do dozens of concatenation- or coalescent-based phylogenetic analyses, looking at whether these analyses supported the 15 topologies that came out of the constrained gene tree model.

From there, the researchers incorporated their GGI method in an effort to curb possible gene tree errors, producing a phylogenetic tree that represented a preferred topology for the otophysan fish.

Along with their subsequent analyses of this tree and its reliability, the team applied its GGI strategy to other portions of the animal family tree — from the basal position of sponges and comb jellies relative to other animals, to yeast phylogenetic relationships — using existing sequence data.

Based on their findings so far, the authors argued that "gene genealogy interrogation is a useful tool to distinguish between estimation error and actual biological conflict in explaining gene tree discordance, ultimately improving phylogenetic reconstructions of complex events such as the early diversification of otophysan fishes."