Mitochondrial genomics of gadine fishes: implications for taxonomy and biogeographic origins from whole-genome data sets

Genome ◽  
2006 ◽  
Vol 49 (9) ◽  
pp. 1115-1130 ◽  
Author(s):  
Mark W. Coulson ◽  
H. Dawn Marshall ◽  
Pierre Pepin ◽  
Steven M. Carr
Keyword(s):  
Atlantic Cod ◽  
Distinct Species ◽  
Walleye Pollock ◽  
Polar Cod ◽  
Data Sets ◽  
Amino Acid Residues ◽  
Bering Strait ◽  
Genome Data ◽  
Gadus Macrocephalus ◽  
Pacific Species

Phylogenetic analysis of 13 substantially complete mitochondrial DNA genome sequences (14 036 bp) from 10 taxa of gadine codfishes and pollock provides highly corroborated resolution of outstanding questions on their biogeographic evolution. Of 6 resolvable nodes among species, 4 were supported by >95% of bootstrap replications in parsimony, distance, likelihood, and similarly high posterior probabilities in bayesian analyses, one by 85%–95% according to the method of analysis, and one by 99% by one method and a majority of the other two. The endemic Pacific species, walleye pollock (Theragra chalcogramma), is more closely related to the endemic Atlantic species, Atlantic cod (Gadus macrocephalus), than either is to a second Pacific endemic, Pacific cod (Gadus macrocephalus). The walleye pollock should thus be referred to the genus Gadus as originally described (Gadus chalcogrammus Pallas 1811). Arcto-Atlantic Greenland cod, previously regarded as a distinct species (G. ogac), are a genomically distinguishable subspecies within pan-Pacific G. macrocephalus. Of the 2 endemic Arctic Ocean genera, Polar cod (Boreogadus) as the outgroup to Arctic cod (Arctogadus) and Gadus sensu lato is more strongly supported than a pairing of Boreogadus and Arctogadus as sister taxa. Taking into consideration historical patterns of hydrogeography, we outline a hypothesis of the origin of the 2 endemic Pacific species as independent but simultaneous invasions through the Bering Strait from an Arcto-Atlantic ancestral lineage. In contrast to the genome data, the complete proteome sequence (3830 amino acids) resolved only 3 nodes with >95% confidence, and placed Alaska pollock outside the Gadus clade owing to reversal mutations in the ND5 locus that restore ancestral, non-Gadus, amino acid residues in that species.

Molecular systematics of gadid fishes: implications for the biogeographic origins of Pacific species

1999 ◽  
Vol 77 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Steven M Carr ◽  
David S Kivlichan ◽  
Pierre Pepin ◽  
Dorothy C Crutcher
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Molecular Data ◽  
Pacific Basin ◽  
Bering Strait ◽  
Pacific Cod ◽  
The Pacific ◽  
Phylogenetic Lineages ◽  
Pacific Species

Phylogenetic relationships among 14 species of gadid fishes were investigated with portions of two mitochondrial DNA (mtDNA) genes, a 401 base pair (bp) segment of the cytochrome b gene, and a 495 bp segment of the cytochrome oxidase I gene. The molecular data indicate that the three species of gadids endemic to the Pacific Basin represent simultaneous invasions by separate phylogenetic lineages. The Alaskan or walleye pollock (Theragra chalcogramma) is about as closely related to the Atlantic cod (Gadus morhua) as is the Pacific cod (Gadus macrocephalus), which suggests that T. chalcogramma and G. macrocephalus represent separate invasions of the Pacific Basin. The Pacific tomcod (Microgadus proximus) is more closely related to the Barents Sea navaga (Eleginus navaga) than to the congeneric Atlantic tomcod (Microgadus tomcod), which suggests that the Pacific species is derived from the Eleginus lineage and that Eleginus should be synonymized with Microgadus. Molecular divergences between each of the three endemic Pacific species and their respective closest relatives are similar and consistent with contemporaneous speciation events following the reopening of the Bering Strait ca. 3.0-3.5 million years BP. In contrast, the Greenland cod (Gadus ogac) and the Pacific cod have essentially identical mtDNA sequences; differences between them are less than those found within G. morhua. The Greenland cod appears to represent a contemporary northward and eastward range extension of the Pacific cod, and should be synonymized with it as G. macrocephalus.

Benthic Habitats and the Effects of Fishing

2005 ◽  
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Fish Habitat ◽  
Weather Conditions ◽  
Data Sets ◽  
Fish Stocks ◽  
Habitat Features ◽  
The Irish Sea ◽  
Belfast Lough ◽  
Existing Data

<strong><em>Abstract. </em><strong>Fishers have often complained that standard United Kingdom groundfish survey data do not adequately reflect the grounds targeted by commercial fishers, and hence, scientists tend to make overcautious estimates of fish abundance. Such criticisms are of particular importance if we are to make a creditable attempt to classify potential essential fish habitat (EFH) using existing data from groundfish surveys. Nevertheless, these data sets provide a powerful tool to examine temporal abundance of fish on a large spatial scale. Here, we report a questionnaire-type survey of fishers (2001–2002) that invited them to plot the location of grounds of key importance in the Irish Sea and to comment on key habitat features that might constitute EFH for Atlantic cod <em>Gadus morhua</em>, haddock <em>Melanogrammus aeglefinus</em>, and European whiting <em>Merlangius merlangus</em>. Plotted grounds were cross-checked using records of vessel sightings by fishery protection aircraft (1985–1999). A comparison of the areas of seabed highlighted by fishers and the observations made on groundfish surveys were broadly compatible for all three species of gadoids examined. Both methods indicated important grounds for cod and European whiting off northern Wales, the Ribble estuary, Solway Firth, north of Dublin, and Belfast Lough. The majority of vessel sightings by aircraft did not match the areas plotted by fishers. However, fishing restrictions, adverse weather conditions, and seasonal variation of fish stocks may have forced fishers to operate outside their favored areas on the (few) occasions that they had been recorded by aircraft. Fishers provided biological observations that were consistent among several independent sources (e.g., the occurrence of haddock over brittle star [ophiuroid] beds). We conclude that fishers’ knowledge is a useful supplement to existing data sets that can better focus more detailed EFH studies.

Laevistrombus Abbott 1960 (Gastropoda: Strombidae): Indian and southwest Pacific species

Zootaxa ◽  
2019 ◽  
Vol 4555 (4) ◽  
pp. 491
Author(s):  
STEPHEN J. MAXWELL ◽  
AART M. DEKKERS ◽  
TASMIN L. RYMER ◽  
BRADLEY C. CONGDON
Keyword(s):  
Distinct Species ◽  
Geographic Range ◽  
Species Level ◽  
Type Material ◽  
Marine Gastropod ◽  
Comparative Analyses ◽  
Southwest Pacific ◽  
Significant Variability ◽  
Extant Species ◽  
Pacific Species

Here we evaluate the taxonomy of the marine gastropod genus Laevistrombus Abbott, 1960 and determine that there are five extant species within this genus, three of which occur in the southwest Pacific. Comparative analyses of this complex have been problematic due to the lack of designated type material. Therefore, we present the type material for L. canarium Linnaeus, 1758; L. taeniatus Quoy & Gaimard, 1834; and L. vanikorensis Quoy & Gaimard, 1834. Current taxonomy has L. vanikorensis absorbed within the L. canarium complex. L. taeniatus is generally held to be a synonym of L. turturella Röding, 1789. We demonstrate that both L. taeniatus and L. vanikorensis are distinct species and reinstate both to species level. Our revision also notes the significant variability in early teleoconch structure within the geographic range of L. vanikorensis, and highlights the need for a greater revision of Laevistrombus, given the diversity in early teleoconch morphology present in southwest Pacific species. 

The Indo-West Pacific Pilumnidae XVIII: On the taxonomy of Pilumnus scabriusculus Adams and White, 1849, and P. sluiteri De Man, 1892, with a note on Cancer incanus Forskål, 1775 (Brachyura: Xanthoidea)

Zootaxa ◽  
2005 ◽  
Vol 841 (1) ◽  
pp. 1 ◽  
Author(s):  
PETER K.L. NG ◽  
PAUL F. CLARK
Keyword(s):  
Distinct Species ◽  
West Pacific ◽  
De Man ◽  
Pacific Species

The taxonomy of two Indo-West Pacific species of pilumnid crabs, Pilumnus scabriusculus Adams & White, 1849, and P. sluiteri De Man, 1892, is clarified. Pilumnus sluiteri has long being synonymised under P. scabriusculus but re-examination of the types and other material shows that there are distinct differences between them, notably in the form of the carapace, mouthparts, chelipeds and male first pleopods. They are here regarded as two distinct species.

scholarly journals Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Felix Grewe ◽  
Claudio Ametrano ◽  
Todd J. Widhelm ◽  
Steven Leavitt ◽  
Isabel Distefano ◽  
...  
Keyword(s):  
Data Sets ◽  
Target Enrichment ◽  
Data Set ◽  
Reduced Genome ◽  
Genome Data ◽  
Worldwide Distribution ◽  
Phylogenetic Studies ◽  
Genome Scale ◽  
Scale Data ◽  
Promising Avenue

AbstractParmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.

The influence of maternal effects in larval survival on fishery harvest reference points for two life-history patterns

2014 ◽  
Vol 71 (1) ◽  
pp. 151-161 ◽  
Author(s):  
Paul D. Spencer ◽  
Sarah B.M. Kraak ◽  
Edward A. Trippel
Keyword(s):  
Life History ◽  
Pacific Ocean ◽  
Maternal Effects ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Larval Survival ◽  
Reference Points ◽  
Life History Pattern ◽  
Gadus Macrocephalus ◽  
Potential Interactions

Increased larval viability with increased spawner age (i.e., maternal effects) have been observed in Atlantic cod (Gadus morhua) and Pacific rockfish (Sebastes spp.) stocks. Analytical results from a Beverton–Holt recruitment model indicate density-independent maternal effects affected the relative stock productivity and fishing rate reference points. We simulated populations based on Pacific cod (Gadus macrocephalus) and Pacific ocean perch (Sebastes alutus) to explore how estimates of reference points Fmsy and Fcrash are affected by maternal effects and potential interactions with life-history pattern, recruitment autocorrelation, and exploitation rate. Estimates of Fmsy and Fcrash were made from populations with maternal effects using either total larvae (proportional to eggs) or viable larvae (incorporating the maternal effect). Maternal effects have the largest impact upon estimated population productivity at high fishing rates. Estimates of Fmsy and Fcrash for cod were also affected by autocorrelated recruitment variability because of their reduced longevity compared with Pacific ocean perch. These results suggest the importance of evaluating the influence of maternal effects on estimated stock productivity on a case-by-case basis, particularly for depleted stocks composed of relatively young spawners.

scholarly journals Growth, mortality, and recruitment signals in age-0 gadids settling in coastal Gulf of Alaska

2016 ◽  
Vol 73 (9) ◽  
pp. 2227-2237 ◽  
Author(s):  
Benjamin J. Laurel ◽  
Brian A. Knoth ◽  
Clifford H. Ryer
Keyword(s):  
Early Life History ◽  
Gulf Of Alaska ◽  
Walleye Pollock ◽  
First Year ◽  
Pacific Cod ◽  
Temperature Dependent ◽  
Gadus Macrocephalus ◽  
Class Strength ◽  
Saffron Cod ◽  
Recruitment Signals

Abstract Age-0 juveniles may be the earliest, reliable indicators of recruitment into commercial marine fisheries, but independent fisheries assessments are usually conducted on older life stages in adult habitats. We used an 8 year juvenile gadid survey along the coast of Kodiak, Alaska to examine annual abundance, growth and mortality in age-0 Pacific cod (Gadus macrocephalus), with comparisons to saffron cod (Eleginus gracilis) and walleye pollock (Gadus chalcogrammus) where possible. Annual abundance of age-0 fish was positively correlated among all three species, suggesting Pacific gadids respond similarly to processes controlling pre-settlement survival and/or delivery to coastal nurseries. In Pacific cod, June temperature was positively correlated with size-at-settlement but post-settlement growth was density- rather than temperature-dependent. Age-0 abundance indices for Pacific and saffron cod predicted the number of age-1 fish the following year (i.e. positive “recruitment signals”), but only in the larger nursery (Anton Larsen Bay) where age-1 gadids were more likely to remain resident after their first year. Recruitment signals for Pacific cod improved with later estimates of age-0 abundance, likely because of high mortality following settlement in July. In contrast, very few age-0 and age-1 walleye pollock were caught across the entire time-series of the survey. Collectively, these data suggest that nearshore surveys may be a tractable means of examining early life history processes and assessing year-class strength in juvenile Pacific and saffron cod, but have relatively low value in understanding the population dynamics of walleye pollock.

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