Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts

Kawahara, Ryouka; Miya, Masaki; Mabuchi, Kohji; Lavoué, Sébastien; Inoue, Jun; Satoh, Taku; Kawaguchi, Akira; Nishida, Mutsumi

doi:10.1016/j.ympev.2007.07.009

Cited by 109 publications

(116 citation statements)

References 51 publications

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“…h p = 0.016 in H. kuda; h p = 0.013 in H. spinosissimus, Lourie et al 2005) (Table 1), and consistent with estimates of diversity in cyt b found in this species by Sanders et al (2008). A single insertion was detected at basepair number 207 of this dataset which falls within the control region at basepair 15,787 in the annotated H. kuda mitochondrial genome available on Genbank (NC-010272.1, Kawahara et al 2008). This insertion defines one unique haplotype (named HapA207) with a count of just four.…”

Section: Sequence Variation and Estimates Of Demographic Historysupporting

confidence: 81%

“…A 428 basepair (bp) fragment spanning the last 70 bp of mitochondrial tRNA-Pro and the first 359 bp of the control region was sequenced for all individuals. This region is designated as bp 15,580-16,008 in the annotated H. kuda mitochondrial genome available on Genbank (NC-010272.1, Kawahara et al 2008). The target region was amplified in a 25 ll polymerase chain reaction (PCR) using Taq polymerase (New England Biolabs Inc.) at the recommended final concentration of 25 units per ml.…”

Section: Localities Sampledmentioning

confidence: 99%

“…A burn in of 12,000 generations was excluded from the consensus tree. The corresponding control-region sequence from the H. kuda mitochondrial genome (Genbank NC-010272.1) was used as the outgroup (Kawahara et al 2008;Teske et al 2004). …”

Section: Phylogenetic Analysismentioning

confidence: 99%

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Genetic differentiation across eastern Pacific oceanographic barriers in the threatened seahorse Hippocampus ingens

2010

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Understanding the population structure and evolutionary history of the eastern Pacific seahorse Hippocampus ingens is critical for the effective management of this threatened species. Life history characteristics of H. ingens (site fidelity and brooding of young) may limit gene flow and lead to population differentiation. A recent study analyzing conserved fragments of the mitochondrial cyt b and control region found no population structure. We re-assess this conclusion with a phylogeographic analysis of relationships among 115 individuals of H. ingens over a broader geographic range (San Diego Bay in California, Gulf of California, Central America, Ecuador, and Peru) based on a more variable 428 base pair fragment of the control region. This expanded analysis affirms low overall nucleotide diversity relative to other seahorses (h p = 0.004), and shows evidence of a recent bottleneck and population expansion since the middle Pleistocene. AMOVA analysis shows moderate overall population structure (U ST = 0.10, P val = 0.00), and pairwise U ST estimates indicate structure between the Gulf of California and all Pacific coast localities. Knowledge of population structure in H. ingens may improve conservation efforts by identifying evolutionarily important management units, and could determine source regions in the continuing trade of seahorses for traditional Chinese medicine. The level of genetic divergence observed between the Gulf of California and all other localities sampled may distinguish the Gulf as a separate management unit. Additional phylogeographic research with more quickly evolving genetic markers and targeted sampling at the mouth of the Gulf of California is warranted to inform strategies for conservation of this threatened seahorse.

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Section: Sequence Variation and Estimates Of Demographic Historysupporting

confidence: 81%

Section: Localities Sampledmentioning

confidence: 99%

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Genetic differentiation across eastern Pacific oceanographic barriers in the threatened seahorse Hippocampus ingens

2010

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“…The resulting phylogeny was congruent with previous mitogenome (e.g. Kawahara et al 2008;Setiamarga et al 2008Setiamarga et al , 2009) and nuclear gene marker (e.g. Betancur et al 2013) studies.…”

supporting

confidence: 84%

Complete mitochondrial genome and the phylogenetic position of the Lake Eyre hardyhead (Craterocephalus eyresii), a freshwater atherinid fish endemic to Lake Eyre Basin, South Australia

Setiamarga

2017

Mitochondrial DNA Part B

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The University Museum, The University of Tokyo, Tokyo, Japan ABSTRACTThe Lake Eyre hardyhead (Craterocephalus eyresii) is an endemic freshwater fish living in the Lake Eyre basin in South Australia. Here, I report the full mitogenome description and the phylogenetic position of this species based on the mitogenome phylogenetics. The mitogenome is 16,602 bp-long with the standard 37 genes all included, with a genomic structure typical of a vertebrate mitogenome. A maximum likelihood phylogenetic analysis to confirm this species position was conducted, using a data set including publicly available 28 atherinomorphs, nine percomorphs, and two outgroups. The result confirms C. eyresii position's in Atherinoidei. The complete mitogenome data of C. eyresii reported here would be useful for further genetics, phylogeography, and phylogenetics studies involving this species. ARTICLE HISTORY

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“…Studies using morphological and molecular datasets offer alternative perspectives on the evolutionary relationships of acanthomorphs (6,8,(13)(14)(15). Molecular phylogenies support the monophyly of several traditionally recognized taxonomic groups of percomorphs as well as the resolution of several novel clades (13,14,(16)(17)(18)(19); however, a consistent and well-supported resolution of the phylogenetic relationships among these major groups has eluded the scientific community.…”

mentioning

confidence: 99%

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Near

Dornburg

Eytan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

449

555

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Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the "bush at the top" of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats.

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Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts

Cited by 109 publications

References 51 publications

Genetic differentiation across eastern Pacific oceanographic barriers in the threatened seahorse Hippocampus ingens

Genetic differentiation across eastern Pacific oceanographic barriers in the threatened seahorse Hippocampus ingens

Complete mitochondrial genome and the phylogenetic position of the Lake Eyre hardyhead (Craterocephalus eyresii), a freshwater atherinid fish endemic to Lake Eyre Basin, South Australia

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

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