Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences

Miya, Masaki; Takeshima, Hirohiko; Endo, Hiromitsu; Ishiguro, Nozomu; Inoue, Jun; Mukai, T.; Satoh, Taku; Yamaguchi, Motoomi; Kawaguchi, Akira; Mabuchi, Kohji; Shirai, Shigeru; Nishida, Mutsumi

doi:10.1016/s1055-7903(02)00332-9

Cited by 682 publications

(616 citation statements)

References 42 publications

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“…Sequences from the following taxa were used as out‐groups: Atherinomorus lacunosus (GenBank #KJ667868; Stelbrink, Stöger, Hadiaty, Schliewen, & Herder, 2014) and Hypoatherina tsurugae (GenBank #AP004420.1; Miya et al., 2003). The curated sequences were deposited in GenBank under accession numbers MF924405–MF924566.…”

Section: Methodsmentioning

confidence: 99%

Insight into the population structure of hardhead silverside,Atherinomorus stipes(Teleostei: Atherinidae), in Belize and the Florida Keys usingnd2

Nash

Kraczkowski

Chernoff

2017

Ecology and Evolution

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Little is known about the natural history, biology, and population genetic structure of the Hardhead Silverside, Atherinomorus stipes, a small schooling fish found around islands throughout the Caribbean. Our field observations of A. stipes in the cays of Belize and the Florida Keys found that populations tend to be in close association with the shoreline in mangrove habitats. Due to this potential island‐based population structuring, A. stipes represents an ideal system to examine questions about gene flow and isolation by distance at different geographic scales. For this study, the mitochondrial gene nd2 was amplified from 394 individuals collected from seven different Belizean Cays (N = 175) and eight different Floridian Keys (N = 219). Results show surprisingly high haplotype diversity both within and between island‐groups, as well as a high prevalence of unique haplotypes within each island population. The results are consistent with models that require gene flow among populations as well as in situ evolution of rare haplotypes. There was no evidence for an isolation by distance model. The nd2 gene tree consists of two well‐supported monophyletic groups: a Belizean‐type clade and a Floridian‐type clade, indicating potential species‐level differentiation.

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Section: Methodsmentioning

confidence: 99%

Insight into the population structure of hardhead silverside,Atherinomorus stipes(Teleostei: Atherinidae), in Belize and the Florida Keys usingnd2

Nash

Kraczkowski

Chernoff

2017

Ecology and Evolution

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“…Recently, complete mitochondrial genome sequences (usually 16–17 kbp among vertebrate species) have proven useful in clarifying phylogenetic relationships among species (Arnason et al., 2008; Cooper et al., 2001; Coulson, Marshall, Pepin, & Carr, 2006; Horai, Hayasaka, Kondo, Tsugane, & Takahata, 1995; Inoue, Miya, Tsukamoto, & Nishida, 2001; Miya, Kawaguchi, & Nishida, 2001; Miya et al., 2003). Following extensive use in human population and evolutionary genetics (Horai et al., 1995; Ingman, Kaessmann, Pääbo, & Gyllensten, 2000; Mishmar et al., 2003; Pope, Carr, Smith, & Marshall, 2011; Tanaka et al., 2004), increasing use has been made in intraspecific studies of fish (Carr & Marshall, 2008a; Feutry et al., 2014; Teacher, André, Merilä, & Wheat, 2012) and other mammals (Carr et al., 2015; Knaus, Cronn, Liston, Pilgrim, & Schwartz, 2011; Stone et al., 2010).…”

Section: Introductionmentioning

confidence: 99%

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Lait

Marshall

Carr

2018

Ecology and Evolution

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The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

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“…The tree is adapted from a recent extensive survey of mitochondrial genomes [22,42,60,23]. In particular, protacanthopterygii [25] and perciformes [42] seem to be polyphyletic; see also [7] about ambiguities in teleost phylogeny. All investigated clupeocephala have duplicated Hox clusters (see text for references), while the bichir Polypterus senegalus did not share the duplication event(s).…”

Section: Introductionmentioning

confidence: 99%

The duplication of the Hox gene clusters in teleost fishes*1

Prohaska

Stadler

2004

Theory in Biosciences

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Higher teleost fishes, including zebrafish and fugu, have duplicated their Hox genes relative to the gene inventory of other gnathostome lineages. The most widely accepted theory contends that the duplicate Hox clusters orginated synchronously during a single genome duplication event in the early history of ray-finned fishes. In this contribution we collect and re-evaluate all publicly available sequence information. In particular, we show that the short Hox gene fragments from published PCR surveys of the killifish Fundulus heteroclitus, the medaka Oryzias latipes and the goldfish Carassius auratus can used to determine with little ambiguity not only their paralog group but also their membership in a particular cluster. Together with a survey of the genomic sequence data from the pufferfish Tetraodon nigroviridis we show that at least percomorpha, and possibly all eutelosts, share a system of seven orthologous Hox gene clusters, while at least the HoxC and HoxD clusters in ostariophysian (zebrafish) lineage might have arisen independently. There is little doubt about the orthology of the two teleost duplicates of the HoxA and HoxB clusters. A careful analysis of both the coding sequence of Hox genes and of conserved noncoding sequences provides additional support for the "duplication early" hypothesis that the Hox clusters in teleosts are derived by subsequent gene loss from an eight-cluster situation, although the data remain ambiguous in particular for the HoxC clusters. Assuming the "duplication early" hypothesis we use the new evidence on the Hox gene complements to determine the phylogenetic positions of gene-loss events in the wake of the cluster duplication. Surprisingly, we find that the resolution of redundancy seems to be a slow process that ist still-ongoing. A few suggestion on which additional sequence data would be most informative for resolving the history of the teleostean Hox genes are discussed.

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Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences

Cited by 682 publications

References 42 publications

Insight into the population structure of hardhead silverside,Atherinomorus stipes(Teleostei: Atherinidae), in Belize and the Florida Keys usingnd2

Insight into the population structure of hardhead silverside,Atherinomorus stipes(Teleostei: Atherinidae), in Belize and the Florida Keys usingnd2

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

The duplication of the Hox gene clusters in teleost fishes*1

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