Gene trees, species and species trees in the Ctenosaura palearis clade

Abstract

The growing use of molecular systematics in conservation has increased the importance of accurate resolution of taxonomic units and relationships. DNA data relate most directly to genealogies, which need not have perfect relationships with species limits and phylogenies. We used a multilocus gene tree approach to elucidate the relationships between four endangered Central American iguanas. We found support for the proposition that the described species taxa correspond to distinct evolutionary lineages warranting individual protection. We combined gene trees to estimate a phylogeny using Bayesian Estimation of Species Trees (BEST), minimizing deep coalescence, Species Trees from Average Ranks (STAR), and traditional concatenation. The estimate from concatenation conflicted with the other methods, likely owing to the disproportionate effect of mtDNA on concatenated analyses. This illustrates the importance of appropriate treatment of multilocus sequence data in phylogenetics. Our results indicate that these species have gone through recent and rapid speciation, resulting in four closely related narrowrange endemics.

Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

“…Our partitioned Bayesian analysis generated a concatenated tree for Brachycephalus that is identical in topology and degree of statistical support (posterior probabilities P95%) to the individual mtDNA gene tree. An inherent factor in the concatenation approach is that a high confidence in the concatenated tree can be the outcome of one or a few gene loci that contribute a greater fraction of nucleotides (and possibly variable sites) to the multilocus data set (Mossel and Vigoda, 2005;Pasachnik et al, 2010;Brito and Edwards, 2009). Here, the results show that the concatenated tree is being overridden by the mtDNA loci due to its disproportionate contribution to the data partition relative to the nuclear genes, as has been demonstrated in other studies (e.g., Pasachnik -0.…”

Isolation-driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae)

“…Many recent, empirical studies have inferred species trees with multiple loci, identifying more robust conclusions than from single markers, in spite of incomplete lineage sorting because of recent divergences and prolific gene‐tree heterogeneity (for some recent examples, see: Leache 2009; Li et al. 2010; Pasachnik et al. 2010; Themudo et al.…”

DELIMITING SPECIES USING MULTILOCUS DATA: DIAGNOSING CRYPTIC DIVERSITY IN THE SOUTHERN CAVEFISH,TYPHLICHTHYS SUBTERRANEUS(TELEOSTEI: AMBLYOPSIDAE)

“…The question has no single correct answer, but it remains important because many conservation laws and regulations use taxonomic categories as operational units. Indeed, a pragmatic species definition for conservation is “a distinct group of organisms meriting independent legal status because extinction of such a group would constitute a substantial loss of biological diversity” (Pasachnik et al 2010). In addition, even with an agreed upon definition of “species,” it is not always straightforward to relate this idea to observable patterns in genetic data (Shaffer and Thompson 2007).…”