Genomic study sheds new light on the evolutionary relationship of amphibians

A new genomic study of how the three orders of amphibians evolved and diverged over millions of years provides an updated view of amphibian evolutionary discordances and of the differing explanations of amphibian relationships.

The work was published in the January issue of Systematic Biology by an international group of researchers. 

Using genetic data from existing species and new genomic techniques, the researchers investigated early evolution among the three amphibian orders: frogs and toads, salamanders and newts, and caecilians (limbless amphibians). They sought to estimate a backbone phylogeny for amphibians using genomic data and to shed light on competing hypotheses about the evolutionary relationships among the three amphibian orders.

Current Science Daily interviewed the lead author of the study, Paul Hime, assistant director of bioinformatics and genomics at the Biodiversity Institute and Natural History Museum at the University of Kansas in Lawrence.

"This was one of the first studies to combine large numbers of genetic markers with large numbers of individuals across amphibians," Hime said. "Our study used sequence data from several hundred different genes sampled across representatives from nearly all of the major amphibian lineages to estimate the evolutionary relationships among living amphibians."

Because of recent advances in genomics, Hime said, the researchers were able to "capture many regions of the genome from a wide variety of species in parallel."

Hime then summarized the study's key findings.

"This work," he said, "provides some new perspectives on relationships among amphibians, corroborates results from many previous studies on amphibian relationships, and highlights the importance of combining information from genetic markers across the genome when reconstructing evolutionary histories."

The divergence question

Why is it important to determine when the amphibian orders diverged?

Hime said phylogenetics, the study of the evolutionary history, looks at relationships among species as a "species tree." Species diverge over time, with genetic differences building up across their genomes. Sometimes the evolutionary history of a particular part of the genome, the "gene tree," can be different from the species tree. 

"Before the advent of genomics, when phylogenetics was a largely data-limited field, phylogeneticists sometimes used a gene tree as a proxy for the species tree," Hime said. 

Today genomics can tell us about evolutionary relationships from independent regions of the genome which may involve different topologies, he added.

"Things get complicated when different genetic markers sequenced from the same species yield different topologies, or branching structures," Hime said. "A wealth of recent methods can now account for gene-tree/species-tree discordance and allow phylogeneticists to integrate information from multiple regions of the genome to gain a more complete picture of the species tree."

Competing hypotheses for evolutionary history

Current Science Daily asked Hime to explain the competing hypotheses (known as Batrachia, Procera and Acauda) for the relationships among the amphibian orders. 

The Batrachia hypothesis holds that frogs and salamanders are more closely related to each other than they are to caecilians. The Procera hypothesis is that salamanders and caecilians are more closely related to each other than they are to frogs. The Acauda hypothesis is that frogs and caecilians are more closely related to each other than they are to salamanders. 

The study's findings show how species trees and gene trees can disagree and highlight the importance of sampling many parts of the genome, Hime said. 

"We used two different approaches to quantify how many gene trees supported each of these competing hypotheses and found that even though most gene trees supported the traditional Batrachia hypothesis, a minority supported either Procera or Acauda," he said. "We concluded that although the Batrachia hypothesis is strongly supported, evolutionary processes in the deep evolutionary history of amphibians contributed to the gene-tree/species-tree discordance that we observe today."

The sampling process

What was the process that enabled the researchers come to this conclusion? 

In their genetic analysis, the researchers used tissues and genomic DNA, mostly gathered from natural history museum specimens. Hime noted that they would have preferred to include all the approximately 8,300 species of amphibians but to keep things manageable, "we selected about 300 amphibian species that represent most of the major lineages of amphibians."

The researchers sequenced the same regions of the genome across many divergent species, Hime said, designing "an amphibian-specific targeted gene capture system to sequence hundreds of genomic regions from across amphibians."

"We focused our genomic sequencing on the small fraction of the genome that encodes protein-coding genes," Hime said. "Specifically, we selected a few hundred protein-coding regions of the genome that are variable enough to be phylogenetically informative, but that are conserved enough to be easily sequenced across very divergent species.

"The resulting phylogeny represents a backbone of the amphibian tree of life, and future studies will undoubtedly fill in many of the other branches on this tree as additional species are sampled and sequenced."