Ontogeny Discombobulates Phylogeny: Paedomorphosis and Higher-Level Salamander Relationships

Abstract

Evolutionary developmental biology ("evo-devo") has revolutionized evolutionary biology but has had relatively little impact on systematics. We show that similar large-scale developmental changes in distantly related lineages can dramatically mislead phylogenetic analyses based on morphological data. Salamanders are important model systems in many fields of biology and are of special interest in that many species are paedomorphic and thus never complete metamorphosis. A recent study of higher-level salamander phylogeny placed most paedomorphic families in a single clade based on morphological data. Here, we use new molecular and morphological data to show that this result most likely was caused by the misleading effects of paedomorphosis. We also provide a well-supported estimate of higher-level salamander relationships based on combined molecular and morphological data. Many authors have suggested that paedomorphosis may be problematic in studies of salamander phylogeny, but this hypothesis has never been tested with a rigorous phylogenetic analysis. We find that the misleading effects of paedomorphosis on phylogenetic analysis go beyond the sharing of homoplastic larval traits by paedomorphic adults, and the problem therefore is not solved by simply excluding suspected paedomorphic characters. Instead, two additional factors are critically important in causing paedomorphic species to be phylogenetically "misplaced": (1) the absence of clade-specific synapomorphies that develop during metamorphosis in nonpaedomorphic taxa and allow their "correct" placement and (2) parallel adaptive changes associated with the aquatic habitat of the larval stage. Our results suggest that the effects of paedomorphosis on phylogenetic analyses may be complex, difficult to detect, and can lead to results that are both wrong and statistically well supported by parsimony and Bayesian analyses.

Biogeography and body size shuffling of aquatic salamander communities on a shifting refuge

“…Our sampling of 27 taxa included all the recognized species (and most subspecies) of amphiumid, proteid and sirenid salamanders, as well as representatives of the other seven extant salamander families, three divergent frogs and one caecilian. We sequenced nearly all of the proteids, sirenids and several outgroups, but most amphiumid and other outgroup sequences were taken from Genbank [22,[28][29][30][31] (see the electronic supplementary material, methods S1, tables S1 and S2). MRMODELTEST v. 2.2 [32] was used to determine the best model of nucleotide substitution for each codon position of each gene (see the electronic supplementary material, table S3).…”

Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa

“…Paedomorphic species have been notoriously difficult for phylogenetic analyses based on morphology (Wiens et al, 2005) and molecular data can be particularly important for such cases. Our analyses consistently place Halammohydra within Trachylina (Figures 4-8) and confirm earlier suggestions that actinulids are related to Narco-and Trachymedusae.…”

Cytogenetic analysis of the Asian Plethodontid salamander, Karsenia koreana: Evidence for karyotypic conservation, chromosome repatterning, and genome size evolution

“…The recent discovery of an Asian plethodontid from South Korea, Karsenia koreana (Min et al 2005), has helped to clarify the phylogenetic relationships and historical biogeography of Holarctic plethodontids. Molecular phylogenetic studies of these species have led to a reassessment of their taxonomy and phylogenetic relationships (Mueller et al 2004, Wiens et al 2005Vieites et al 2007). In conflict with traditional taxonomy (Wake 1966), molecular evidence from complete mitochondrial genomes and multiple nuclear loci identifies two distinct subfamilies: Plethodontinae and Hemidactyliinae ( Figure 1) (Vieites et al 2007).…”