Whole genome duplication: challenges and considerations associated with sequence orthology assignment in Salmoninae.

Abstract:

:To illustrate some of the challenges and considerations in assigning correct orthology necessary for any comparative genomic investigation among salmonids, sequence data from the non-coding regions of different chromosomes in three members of the subfamily Salmoninae, rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar and Arctic charr Salvelinus alpinus, were compared. By analysing c. 55 distinct loci, corresponding to c. 142 kbp sequence information per species, 18 duplicated patterns representative of the two sequential rounds of teleost-specific whole genome duplications (i.e. 3R and 4R WGD) were identified. Sequence similarities between the 4R paralogues were c. 90%, which was slightly lower than those of the 4R orthologues and c. 60% for the 3R products. Through careful examination of the sequence data, however, only 14 loci could reliably be assigned as true orthologues. Locus-specific trees were constructed through maximum parsimony, maximum likelihood and neighbour-joining methods and were rooted using the information from a close relative, lake whitefish Coregonus clupeaformis. All approaches generated congruent trees supporting the {Coregonus [Salmo (Oncorhynchus, Salvelinus)]} topology. The general phenotypic characteristics of sequences, however, were highly suggestive of the basal position of Oncorhynchus, raising the hypothesis of an accelerated rate of nucleotide evolution in this species.

journal_name

J Fish Biol

journal_title

Journal of fish biology

authors

Moghadam HK,Ferguson MM,Danzmann RG

doi

10.1111/j.1095-8649.2011.03030.x

subject

Has Abstract

pub_date

2011-09-01 00:00:00

pages

561-74

issue

3

eissn

0022-1112

issn

1095-8649

journal_volume

79

pub_type

杂志文章
  • The vertical distributions and spawning site choices of red and yellow bluefin killifish Lucania goodei colour morphs.

    abstract::A genetic colour polymorphism is present in bluefin killifish Lucania goodei, where red and yellow anal-fin morphs coexist in clear springs, but the source of balancing selection is unknown. In a field study, vertical distributions did not differ between the morphs and there was little evidence that light environments...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.13661

    authors: Chang CH,Schult JE,Sanders J,Liu SH,Fuller RC

    更新日期:2018-08-01 00:00:00

  • A new rheophilic South American darter (Crenuchidae: Characidium) from the rio Juruena basin, Brazil, with comments on morphological adaptations to life in fast-flowing waters.

    abstract::Characidium iaquira, a new species from the upper rio Juruena, rio Tapajós basin, Brazil, is described. The new species can be promptly distinguished from all congeners by having a unique v-shaped dark mark lying along the caudal-fin extension, in medium- and large-sized specimens, and a remarkable iridescent green co...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.14485

    authors: Zanata AM,Ohara WM,Oyakawa OT,Dagosta FCP

    更新日期:2020-11-01 00:00:00

  • Population demographics of American eels Anguilla rostrata in two Arkansas, U.S.A., catchments that drain into the Gulf of Mexico.

    abstract::The goal of this study was to compare American eel Anguilla rostrata life history in two inland river systems in Arkansas, U.S.A., that ultimately discharge into the Gulf of Mexico via the Mississippi River and the Red-Atchafalaya catchments. From 21 June 2011 to 24 April 2014, 238 yellow-phase A. rostrata were captur...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.12888

    authors: Cox CA,Quinn JW,Lewis LC,Adams SR,Adams GL

    更新日期:2016-03-01 00:00:00

  • Temporal dynamics in growth and white skeletal muscle composition of the mummichog Fundulus heteroclitus during chronic hypoxia and hyperoxia.

    abstract::Specific growth rate (G(S) ) and white skeletal muscle composition were measured in the mummichog Fundulus heteroclitus over a period of 28 days at four levels of dissolved oxygen (DO): severe hypoxia (c. 1.2 mg O(2) l(-1) ), moderate hypoxia (3.0 mg O(2) l(-1) ), normoxia (7.1 mg O(2) l(-1) ) and hyperoxia (10.6 mg O...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2012.03319.x

    authors: Rees BB,Targett TE,Ciotti BJ,Tolman CA,Akkina SS,Gallaty AM

    更新日期:2012-07-01 00:00:00

  • Effects of global warming on sex ratios in fishes.

    abstract::In fishes, sex is determined by genetics, the environment or an interaction of both. Temperature is among the most important environmental factors that can affect sex determination. As a consequence, changes in temperature at critical developmental stages can induce biases in primary sex ratios in some species. Howeve...

    journal_title:Journal of fish biology

    pub_type: 杂志文章,评审

    doi:10.1111/jfb.14429

    authors: Geffroy B,Wedekind C

    更新日期:2020-09-01 00:00:00

  • Using hierarchical models to estimate effects of ocean anomalies on north-west Pacific Chinook salmon Oncorhynchus tshawytscha recruitment.

    abstract::The high variability in survival over the past three decades of north-west Pacific Chinook salmon Oncorhynchus tshawytscha is summarized for 24 stocks and analysed using hierarchical Bayesian models. Results from a simple model indicate that recruitment anomalies appear to be correlated in time and space. A simple mod...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2010.02779.x

    authors: Sharma R,Liermann M

    更新日期:2010-11-01 00:00:00

  • The onset of piscivory in a freshwater fish species: analysis of behavioural and physiological traits.

    abstract::The onset of piscivory in fish, resulting in a shift from zooplankton or invertebrate to fish prey, was studied on pikeperch (Sander lucioperca) larvae displaying and not displaying piscivorous behaviour at different ages (23, 30, 37, 44 and 52 days post-hatching) using behavioural (attack, capture and swimming activi...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.14322

    authors: Colchen T,Dias A,Gisbert E,Teletchea F,Fontaine P,Pasquet A

    更新日期:2020-06-01 00:00:00

  • Parasites of native and exotic freshwater fishes in south-western Australia.

    abstract::In this study, 1429 fishes of 18 different species (12 native and six exotic) were sampled from 29 localities to compare the levels of parasitism between native and exotic fish species and to examine the relationship between environmental degradation and parasite diversity. Forty-four putative species of parasites wer...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2010.02615.x

    authors: Lymbery AJ,Hassan M,Morgan DL,Beatty SJ,Doupé RG

    更新日期:2010-05-01 00:00:00

  • Genetic structure and divergence of tench Tinca tinca European populations.

    abstract::The tench Tinca tinca is a freshwater species with human-mediated translocations, aquaculture interest and limited information on its genetic structure. mtDNA sequencing analysis of control region and two genes in 50 individuals from five European populations identified two phylogroups, with greater variability than t...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.14448

    authors: Karaiskou N,Gkagkavouzis K,Minoudi S,Botskaris D,Markou K,Kalafatakis S,Antonopoulou E,Triantafyllidis A

    更新日期:2020-09-01 00:00:00

  • Partial migration in fishes: causes and consequences.

    abstract::Partial migration, where only some individuals from a population migrate, has been widely reported in a diverse range of animals. In this paper, what is known about the causes and consequences of partial migration in fishes is reviewed. Firstly, the ultimate and proximate drivers of partial migration are reflected upo...

    journal_title:Journal of fish biology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1095-8649.2012.03342.x

    authors: Chapman BB,Hulthén K,Brodersen J,Nilsson PA,Skov C,Hansson LA,Brönmark C

    更新日期:2012-07-01 00:00:00

  • An overview on the role of Hexanchiformes in marine ecosystems: biology, ecology and conservation status of a primitive order of modern sharks.

    abstract::The large size, high trophic level and wide distribution of Hexanchiformes (cow and frilled sharks) should position this order as important apex predators in coastal and deep-water ecosystems. This review synthesizes available information on Hexanchiformes, including information not yet published, with the purpose of ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1095-8649.2012.03242.x

    authors: Barnett A,Braccini JM,Awruch CA,Ebert DA

    更新日期:2012-04-01 00:00:00

  • Time and size at seaward migration influence the sea survival of Salmo salar.

    abstract::Whether time of seaward migration of young Atlantic salmon Salmo salar influences their subsequent survival and growth was investigated in the River Imsa, south-western Norway. Salmo salar were tagged when moving downstream through a trap near the outlet between 1976 and 2010 and recaptured on their adult return. Most...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.12370

    authors: Jonsson N,Jonsson B

    更新日期:2014-05-01 00:00:00

  • Population subdivision in Siamese mud carp Henicorhynchus siamensis in the Mekong River basin: implications for management.

    abstract::A molecular approach was employed to investigate stock structure in Siamese mud carp Henicorhynchus siamensis populations collected from 14 sites across mainland south-east Asia, with the major focus being the lower Mekong River basin. Spatial analysis of a mitochondrial DNA fragment (ATPase 6 and 8) identified four s...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2009.02369.x

    authors: Adamson EA,Hurwood DA,Baker AM,Mather PB

    更新日期:2009-10-01 00:00:00

  • Long-term sperm storage in the brownbanded bamboo shark Chiloscyllium punctatum.

    abstract::This study investigated the birth of a brownbanded bamboo shark Chiloscyllium punctatum at the Steinhart Aquarium. Genetic analyses suggest this is the longest documented case of sperm storage for any species of shark (45 months). ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.12606

    authors: Bernal MA,Sinai NL,Rocha C,Gaither MR,Dunker F,Rocha LA

    更新日期:2015-03-01 00:00:00

  • Evaluation of the use of portable ultrasonography to determine pregnancy status and fecundity in bonnethead shark Sphyrna tiburo.

    abstract::This study examined the usefulness of portable ultrasonography in accurately predicting pregnancy and fecundity in the bonnethead shark Sphyrna tiburo by comparing ultrasound-obtained data with those obtained from animal dissection, the gold standard for elasmobranch reproduction studies. Mature female S. tiburo (n = ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.13831

    authors: Anderson B,Belcher C,Slack J,Gelsleichter J

    更新日期:2018-12-01 00:00:00

  • Morphological and histochemical characterisation of the mucosa of the digestive tract in matrinxã Brycon amazonicus (Teleostei: Characiformes).

    abstract::This study describes anatomical, histological and histochemical features of the digestive tract mucosal layer of the matrinxã Brycon amazonicus, an omnivorous freshwater fish endemic from the Amazon basin. This species presents short thick oesophagus with longitudinal folds, that allow the passage of large food items....

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.14217

    authors: Vidal MR,Ruiz TFR,Dos Santos DD,Gardinal MVB,de Jesus FL,Faccioli CK,Vicentini IBF,Vicentini CA

    更新日期:2020-01-01 00:00:00

  • Trophic ecology of northern Australia's terapontids: ontogenetic dietary shifts and feeding classification.

    abstract::The diets of 21 terapontid species from freshwater environments in northern Australia were investigated to determine the similarity and dissimilarity among species and the extent of any ontogenetic shifts. Distinct ontogenetic dietary shifts occurred in all species for which sufficient data were available, with many s...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2010.02862.x

    authors: Davis AM,Pearson RG,Pusey BJ,Perna C,Morgan DL,Burrows D

    更新日期:2011-01-01 00:00:00

  • Diet and trophic plasticity of an herbivorous blenny Scartella cristata of subtropical rocky shores.

    abstract::The goals of the present study were to investigate the feeding rates of Scartella cristata, accounting for different water temperature regimes, and to analyse spatial and seasonal variations in its diet. The feeding rate of S. cristata was higher in warmer waters and was not correlated with season. A typical herbivoro...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2009.02434.x

    authors: Mendes TC,Villaça RC,Ferreira CE

    更新日期:2009-11-01 00:00:00

  • Identification of a novel member in the family Albulidae (bonefishes).

    abstract::A novel Caribbean species Albula sp. cf. vulpes in the family Albulidae (bonefishes) was diagnosed through genetic and morphometric study. Phylogenies derived from 16S rRNA sequences revealed deeply separated lineages among Caribbean bonefishes. Mitochondrial DNA sequence divergences indicated a separation between 3.0...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2010.02639.x

    authors: Wallace EM,Tringali MD

    更新日期:2010-05-01 00:00:00

  • Tetracycline marks visible in Baltic cod Gadus morhua otoliths stored for 40 years.

    abstract::Baltic cod Gadus morhua otoliths marked with oxytetracycline (OTC) in 1974-1975 had been sectioned and the sections stored in paper envelopes at room temperature in dry, dark conditions. After 40 years of storage, the historic OTC marks were still clearly visible showing that OTC is suitable for long-term chemical mar...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.13108

    authors: Krumme U,Bingel F

    更新日期:2016-10-01 00:00:00

  • Exploring factors shaping population genetic structure of the freshwater fish Sinocyclocheilus grahami (Teleostei, Cyprinidae).

    abstract::Phylogeographical analyses on Sinocyclocheilus grahami samples from seven localities within the Lake Dianchi Basin in China were conducted to explore the main factors shaping population structure within this species. Phylogenetic and network analyses revealed two major clades in 24 mtDNA haplotypes. One clade included...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2009.02204.x

    authors: Chen SY,Zhang RD,Feng JG,Xiao H,Li WX,Zan RG,Zhang YP

    更新日期:2009-05-01 00:00:00

  • Development of intestinal ion-transporting mechanisms during smoltification and seawater acclimation in Atlantic salmon Salmo salar.

    abstract::This study investigated the expression of ion transporters involved in intestinal fluid absorption and presents evidence for developmental changes in abundance and tissue distribution of these transporters during smoltification and seawater (SW) acclimation of Atlantic salmon Salmo salar. Emphasis was placed on Na(+) ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.12531

    authors: Sundh H,Nilsen TO,Lindström J,Hasselberg-Frank L,Stefansson SO,McCormick SD,Sundell K

    更新日期:2014-10-01 00:00:00

  • Brown trout Salmo trutta express different morphometrics due to divergence in the rearing environment.

    abstract::Variation in the body morphology of juvenile brown trout Salmo trutta was studied for both wild and hatchery-reared individuals from the same gene pool. The thin-plate spline (TPS) method by pointing landmarks was used to characterize juveniles from their natal environment, the River Kuusinkijoki in eastern Finland, a...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2011.03093.x

    authors: Vehanen T,Huusko A

    更新日期:2011-11-01 00:00:00

  • Photoreceptors and eyes of pikeperch Sander lucioperca, pike Esox lucius, perch Perca fluviatilis and roach Rutilus rutilus from a clear and a brown lake.

    abstract::The photoreceptors and eyes of four fish species commonly cohabiting Fennoscandian lakes with different light transmission properties were compared: pikeperch Sander lucioperca, pike Esox lucius, perch Perca fluviatilis and roach Rutilus rutilus. Each species was represented by individuals from a clear (greenish) and ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.13759

    authors: Jokela-Määttä M,Viljanen M,Nevala N,Donner K,Brönmark C

    更新日期:2019-07-01 00:00:00

  • A new species of Chaetostoma (Siluriformes: Loricariidae) from the Orinoco basin with comments on Amazonian species of the genus in Colombia.

    abstract::Chaetostoma chimu sp. nov. is described from 119 specimens collected in the Andean foothills of the Orinoco River in Colombia. The new species can be distinguished from congeners by a combination of characters, including shape of cheek odontodes, presence of a supraoccipital excrescence, sexual dimorphism characters a...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.14640

    authors: Urbano-Bonilla A,Ballen GA

    更新日期:2020-12-05 00:00:00

  • Effect of UV radiation on habitat selection by Girella laevifrons and Graus nigra (Kyphosidae).

    abstract::The effect of UV radiation on habitat use of two species of intertidal fishes that inhabit the same pools but exhibit different activity levels and diets was measured: the highly active omnivorous Girella laevifrons and the cryptic carnivorous Graus nigra. Individuals of each species were acclimated to a tank divided ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.12566

    authors: Pulgar J,Lagos P,Maturana D,Valdés M,Aldana M,Pulgar VM

    更新日期:2015-02-01 00:00:00

  • Fine-scale spatial and temporal variations in diets of the pipefish Stigmatopora nigra within seagrass patches.

    abstract::Diets of the pipefish Stigmatopora nigra were analysed to determine if food availability was causing S. nigra to distribute according to habitat edge effects. Gut analysis found little difference in the diets of S. nigra at the edge and interior of seagrass patches, regardless of time of day or season. Fish diets did,...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2011.02977.x

    authors: Smith TM,Hindell JS,Jenkins GP,Connolly RM,Keough MJ

    更新日期:2011-06-01 00:00:00

  • Mitochondrial DNA differentiation among East and West African Nile tilapia populations

    abstract::Variation of the ND5/6 mtDNA fragment was studied in six Nile tilapia populations using PCR and RFLP analysis. The observed variation allows a strict discrimination between eastern and western African populations. ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.1997.tb02525.x

    authors: Rognon X,Guyomard R

    更新日期:1997-07-01 00:00:00

  • Anadromy and heterogenous population of a tropical shad Tenualosa ilisha in Malaysia, as revealed by otolith microchemistry and molecular evidence.

    abstract::Tenualosa ilisha was found recently in the Perak River in western Peninsular Malaysia. Molecular phylogenetic and haplotype network analyses suggest that T. ilisha has two genetically distinct populations/groups: (i) Peninsular Malaysia (Malaysia population), and (ii) Peninsular Malaysia, Thailand, India and Banglades...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/jfb.14154

    authors: Arai T,Taha H,Amalina R,Iizuka Y,Chang CW

    更新日期:2019-12-01 00:00:00

  • Cloning of arctic lamprey Lethenteron camtschaticum cd9 with roles in the immune response.

    abstract::In this study, the cd9 gene, a member of the tetraspanin superfamily and involved in various cellular processes, was cloned from Lethenteron camtschaticum. Both real-time PCR and immunohistochemical assays showed broad distribution of cd9 in various L. camtschaticum tissues. In addition, expression levels of Cd9 mRNA ...

    journal_title:Journal of fish biology

    pub_type: 杂志文章

    doi:10.1111/j.1095-8649.2012.03299.x

    authors: Wu F,Su P,Chen L,Li M,Liu X,Li Q

    更新日期:2012-09-01 00:00:00