Retrieving a mitogenomic mammal tree using composite taxa

Campbell, Véronique; Lapointe, François‐Joseph

doi:10.1016/j.ympev.2010.11.017

Cited by 26 publications

(16 citation statements)

References 87 publications

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“…Tree topology used for ancestor state reconstruction was fixed based on published molecular phylogenetic studies (topology at and above level of order: Alfaro et al . ; Campbell & Lapointe ; turtles: Krenz et al . ; salmonids: Crespi & Fulton ; pinnipeds: Davis et al .…”

Section: Methodsmentioning

confidence: 99%

Mediating free glucocorticoid levels in the blood of vertebrates: are corticosteroid‐binding proteins always necessary?

et al. 2013

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Summary1. Glucocorticoids (GC) are integral to the stress response of vertebrates to environmental challenges. Their impact is immediate and widespread, and prolonged exposure can result in major activational and organizational changes. The vertebrate body has two mechanisms to limit GC impact: first, a rapid negative feedback system to turn off their release, and second, a protein -corticosteroid-binding globulin (CBG) -to prevent them being free in the blood. Species used in biomedical research have CBG levels that normally bind 90-95% of blood GC. This evidence was the basis for the 'Free Hormone Hypothesis,' which posits that only unbound, free hormone is available for use by tissues and is biologically active. High levels of free GC typically occur only under conditions of chronic stress and are associated with major suppression of key body functions. The hypothesis proposes that the primary role of CBG is to render GCs unavailable, thereby preventing tissue exposure. 2. From a field study in southern Ontario on northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels, we found virtually no CBG binding capacity in their plasma, resulting in only about 10% of cortisol being bound throughout the year. However, neither species showed any evidence of being physiologically compromised. This presents a major challenge to the potential consequences of chronically high levels of free GC. 3. To assess the generality of this finding, we carried out a phylogenetic comparison of 91 vertebrate species in which both GC and CBG levels were measured. In 93%, CBG levels were sufficient to bind about 90% of circulating GCs. This evidence is thus concordant with that from biomedical research. However, both flying squirrel species and four species of New World monkeys were extreme outliers. These two groups had the highest GC concentrations, but relatively little binding capacity (10% or less of their GC was bound).4. An ancestor state reconstruction of the proportion of GCs bound indicated that the flying squirrels and New World monkeys evolved this character state from ancestors that followed the common 90% bound pattern. It also indicated that the original vertebrates -the earliest fishes -have most of their GC in the free state and little or no steroid-binding protein.5. We thus demonstrate a dichotomous pattern with respect to CBG: a dominant branch, where high levels of CBG bind most of the GC, applies to the majority of vertebrates; and a secondary branch, where low levels of CBG bind almost none of the GC, applies to a very small subset. For the latter, the critical unknown is how these species mitigate the impact of the high free GC levels and how such a dramatic trait shift could evolve.

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Section: Methodsmentioning

confidence: 99%

Mediating free glucocorticoid levels in the blood of vertebrates: are corticosteroid‐binding proteins always necessary?

et al. 2013

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“…We exhaustively surveyed the available data, so that the species chosen for each terminal were the ones with the greatest number of loci, such that the percentage identity of each terminal was as high as possible. This approach has been shown to be robust under empirical conditions (Campbell and Lapointe 2009, 2010). The final matrix contained sequence data totaling up to 18,924 bp from 29 genes for 41 taxa (terminal taxa, genes, and accession numbers are in Appendix S1; the matrix and trees are available in Dryad repository (doi:10.5061/dryad.63kf4), with an average of 20 genes sampled per taxon.…”

Section: Methodsmentioning

confidence: 99%

Extinction, Ecological Opportunity, and the Origins of Global Snake Diversity

2011

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Snake diversity varies by at least two orders of magnitude among extant lineages, with numerous groups containing only one or two species, and several young clades exhibiting exceptional richness (>700 taxa). With a phylogeny containing all known families and subfamilies, we find that these patterns cannot be explained by background rates of speciation and extinction. The majority of diversity appears to derive from a radiation within the superfamily Colubroidea, potentially stemming from the colonization of new areas and the evolution of advanced venom-delivery systems. In contrast, negative relationships between clade age, clade size, and diversification rate suggest the potential for possible bias in estimated diversification rates, interpreted by some recent authors as support for ecologically mediated limits on diversity. However, evidence from the fossil record indicates that numerous lineages were far more diverse in the past, and that extinction has had an important impact on extant diversity patterns. Thus, failure to adequately account for extinction appears to prevent both rate-and diversity-limited models from fully characterizing richness dynamics in snakes. We suggest that clade-level extinction may provide a key mechanism for explaining negative or hump-shaped relationships between clade age and diversity, and the prevalence of ancient, species-poor lineages in numerous groups.

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“…In recent years, the mitochondrial genome (mitogenome) has been widely used in phylogenetic studies because of its matrilineal inheritance, lack of extensive recombination and accelerated nucleotide substitution rates (Ingman et al , 2000; Zhang et al , 2008). A complete mitogenome contains more information on the evolutionary history of a species than individual genes, and the use of this genome in phylogenetic analyses reduces stochastic errors and minimizes the effect of homoplasy (Campbell and Lapointe, 2011). Mitogenomes can also be used as a source of molecular markers in conservation studies of endangered species (Krajewski et al , 2010; Meyer et al , 2011).…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella)

Huang

Jing

et al. 2012

Genet. Mol. Biol.

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The phylogenetic relationships of primates have been extensively investigated, but key issues remain unresolved. Complete mitochondrial genome (mitogenome) data have many advantages in phylogenetic analyses, but such data are available for only 46 primate species. In this work, we determined the complete mitogenome sequence of the black-capped capuchin (Cebus apella). The genome was 16,538 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other primates. The control region contained several distinct repeat motifs, including a putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB-F, E, D, C, B and 1). Among the protein-coding genes, the COII gene had lower nonsynonymous and synonymous substitutions rates while the ATP8 and ND4 genes had higher rates. A phylogenetic analysis using Maximum likelihood and Bayesian methods and the complete mitogenome data for platyrrhine species confirmed the basal position of the Callicebinae and the sister relationship between Atelinae and Cebidae, as well as the sister relationship between Aotinae (Aotus) and Cebinae (Cebus/Saimiri) in Cebidae. These conclusions agreed with the most recent molecular phylogenetic investigations on primates. This work provides a framework for the use of complete mitogenome information in phylogenetic analyses of the Platyrrhini and primates in general.

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Retrieving a mitogenomic mammal tree using composite taxa

Cited by 26 publications

References 87 publications

Mediating free glucocorticoid levels in the blood of vertebrates: are corticosteroid‐binding proteins always necessary?

Mediating free glucocorticoid levels in the blood of vertebrates: are corticosteroid‐binding proteins always necessary?

Extinction, Ecological Opportunity, and the Origins of Global Snake Diversity

The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella)

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