Movatterモバイル変換

[0]ホーム
URL:

Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
Thehttps:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

NIH NLM Logo
Log inShow account info
Access keysNCBI HomepageMyNCBI HomepageMain ContentMain Navigation
pubmed logo
Advanced Clipboard
User Guide

Full text links

Elsevier Science full text link Elsevier Science Free PMC article
Full text links

Actions

Share

.2008 Oct;49(1):136-52.
doi: 10.1016/j.ympev.2008.06.008. Epub 2008 Jun 24.

Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes

Affiliations

Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes

Lydia L Smith et al. Mol Phylogenet Evol.2008 Oct.

Abstract

Regulatory genes control the expression of other genes and are key components of developmental processes such as segmentation and embryonic construction of the skull in vertebrates. Here we examine the variability and evolution of three vertebrate regulatory genes, addressing issues of their utility for phylogenetics and comparing the rates of genetic change seen in regulatory loci to the rates seen in other genes in the parrotfishes. The parrotfishes are a diverse group of colorful fishes from coral reefs and seagrasses worldwide and have been placed phylogenetically within the family Labridae. We tested phylogenetic hypotheses among the parrotfishes, with a focus on the genera Chlorurus and Scarus, by analyzing eight gene fragments for 42 parrotfishes and eight outgroup species. We sequenced mitochondrial 12s rRNA (967 bp), 16s rRNA (577 bp), and cytochrome b (477 bp). From the nuclear genome, we sequenced part of the protein-coding genes rag2 (715 bp), tmo4c4 (485 bp), and the developmental regulatory genes otx1 (672 bp), bmp4 (488bp), and dlx2 (522 bp). Bayesian, likelihood, and parsimony analyses of the resulting 4903 bp of DNA sequence produced similar topologies that confirm the monophyly of the scarines and provide a phylogeny at the species level for portions of the genera Scarus and Chlorurus. Four major clades of Scarus were recovered, with three distributed in the Indo-Pacific and one containing Caribbean/Atlantic taxa. Molecular rates suggest a Miocene origin of the parrotfishes (22 mya) and a recent divergence of species within Scarus and Chlorurus, within the past 5 million years. Developmentally important genes made a significant contribution to phylogenetic structure, and rates of genetic evolution were high in bmp4, similar to other coding nuclear genes, but low in otx1 and the dlx2 exons. Synonymous and non-synonymous substitution patterns in developmental regulatory genes support the hypothesis of stabilizing selection during the history of these genes, with several phylogenetic regions of accelerated non-synonymous change detected in the phylogeny.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Phylogenetic hypothesis for the parrotfishes calculated using Bayesian inference. Maximum posterior probability topology resulting from 4 runs of a MCMC analysis each with 6 chains running for 10 million generations. Posterior probabilities are shown for each node (computed from majority rule consensus of post burn-in trees), and the black dots indicate support at the 90% level or greater from a 1000 repetition parsimony bootstrap analysis. The root of the seagrass and reef clades and four clades of the genusScarus are identified. Photos are by John E. Randall (via Fishbase.org) with permission, identified by initials of genus and species.
Figure 2
Figure 2
A comparison of phylogenetic signal in the data partitioned by regulatory (otx1, dlx2, bmp4) and non-regulatory (12s, 16s, cytb, tmo4c4, rag2) genes. Topologies illiustrated are the majority-rule consensus tree of the 95% credible set of trees from 3 runs of a MCMC analysis each with 5 chains running for 10 million generations. Black dots (•) indicate strongly supported nodes at which both partitioned trees agree with each other and with the combined data tree. Strongly supported nodes that agree with the combined data tree but are not strongly supported in the other partition tree (+) are less frequent, and strongly supported nodes that disagree with the combined data tree (*) are rare.
Figure 3
Figure 3
Phylogram of rates of molecular evolution in the (A)12s and (B) cytochrome b data partitions illustrated on the Bayesian consensus tree of all concatenated sequences. Numbers on selected branches indicate that the branchlength is N times the length shown.
Figure 4
Figure 4
Rates of molecular evolution in the (A)rag2 and (B)bmp4 data partitions illustrated on the Bayesian consensus tree of all concatenated sequences. Numbers on selected branches indicate that the branchlength is N times the length shown.
Figure 5
Figure 5
Rates of molecular evolution in the (A)dlx2 exon and (B)dlx2 intron data partitions illustrated on the Bayesian consensus tree of all concatenated sequences. Numbers on selected branches indicate that the branchlength is N times the length shown.
Figure 6
Figure 6
Synonyomus (A) and non-synonymous (B) substitution rate trees for cytochrome b, calculated using the Bayesian consensus topology and the Muse-Gaut (1994) codon substitution model implemented in HyPhy (Kosokovsky Pond et al., 2005).
Figure 7
Figure 7
Synonyomus (A) and non-synonymous (B) substitution rate trees forrag2, calculated using the Bayesian consensus topology and the Muse-Gaut (1994) codon substitution model.
Figure 8
Figure 8
Synonyomus (A) and non-synonymous (B) substitution rate trees forbmp4, calculated using the Bayesian consensus topology and the Muse-Gaut (1994) codon substitution model.
Figure 9
Figure 9
Chronogram illustrating the ages of origin and diversification of parrotfish phylogenetic groups, calculated using the Bayesian inference topology and the Bayesian posterior probability algorithms for mean and variance of nodal ages implemented in CodonRates 1.0 (Seo et al., 2004) assuming a root age of the labrid outgroups of 55 million years ago.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Aagaard JE, Willis JH, Phillips PC. Relaxed selection among duplicate floral regulatory genes in Lamiales. J. Mol. Evol. 2006;63:493–503. - PubMed
    1. Abzhanov A, Protas M, Grant R, Grant PR, Tabin CJ. Bmp4 and morphological variation of beaks in Darwin's finches. Science. 2004;305:1462–1465. - PubMed
    1. Acampora D, Avantaggiato V, Tuorto F, Briata P, Corte G, Simeone A. Visceral endoderm-restricted translation of otx1 mediates recovery of otx2 requirements for specification of anterior neural plate and normal gastrulation. Development. 1998;125:5091–5104. - PubMed
    1. Albertson RC, Streelman JT, Kocher TD. Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes. PNAS. 2003;100:5252–5257. - PMC - PubMed
    1. Albertson RC, Streelman JT, Kocher TD, Yelick PC. Integration and evolution of the cichlid mandible: the molecular basis of alternative feeding strategies. PNAS. 2005;102:16287–16292. - PMC - PubMed

Publication types

MeSH terms

Substances

Related information

Grants and funding

LinkOut - more resources

Full text links
Elsevier Science full text link Elsevier Science Free PMC article
Cite
Send To

NCBI Literature Resources

MeSHPMCBookshelfDisclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

[8]ページ先頭
©2009-2025 Movatter.jp