Phylogeny and DNA Barcoding of the Family Sparidae Inferred
from Mitochondrial DNA of the Egyptian Waters

Abbas, Eman M.; Soliman, Taha; El-Magd, Mohammed A.; Farrag, Mahmoud M.S.; Ismail, Rania F.; Kato, Mikio

doi:10.3923/jfas.2017.73.81

Cited by 25 publications

(26 citation statements)

References 19 publications

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“…3) for the five species used. The resulted topology agrees with previous studies (Chiba et al, 2009; Santini et al, 2014; Abbas et al, 2017). Interestingly, the species with the same reproductive mode were grouped together, i.e.…”

Section: Discussionsupporting

confidence: 92%

“…In contrast to the aforementioned findings, two other studies placed common pandora together with the red porgy, leaving common dentex outside; the first study included 66 Sparidae species and 18 mitochondrial loci (Chiba et al, 2009) and the second 91 Sparidae species and five loci (Santini et al, 2014). This relationship is supported also by a recent single-gene approach using mitochondrial COI sequences from sparids inhabiting the Egyptian waters (Abbas et al, 2017). Thus, even though multiple studies have been conducted so far, the evolutionary relationship of Sparidae genera remains unclear.…”

Section: Introductionmentioning

confidence: 54%

See 1 more Smart Citation

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Natsidis

Tsakogiannis

Pavlidis

et al. 2019

Preprint

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19Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 20 species with high popularity and commercial value, such as porgies and seabreams. Although 21 the phylogeny of this family has been investigated multiple times, its position among other 22 teleost groups remains ambiguous. Most studies have used a single or few genes to decipher 23 the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to 24 resolve the position of the family using five recently available Sparidae gene-sets and 26 25 available fish proteomes from species with a sequenced genome, to ensure higher quality of 26 the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes 27 (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding 28 that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the 29 european seabass as closest taxa of sparids. By analytically comparing the methodologies 30 applied in both cases, we show that this discordance is not due to different orthology 31 assignment algorithms; on the contrary, we prove that it is caused by the increased taxon 32 sampling of the present study, outlining the great importance of this aspect in phylogenomic 33 analyses in general. 34 35 Keywords: Sparidae; fish phylogenomics; orthology assignment; jackknife phylogeny test; 36 taxon sampling; 37Teleostei represent the dominant group within ray-finned fish (Actinopterygii), with 39 more than 26,000 extant species. Their evolution has been extensively studied through past 40 decades, using a variety of data including fossil records, morphological characters and 41 molecular data, leading to a gradual resolution of teleost phylogeny (Betancur-R. et al., 2013(Betancur-R. et al., 42 & 2017. 43 With the continuous emergence of new whole-genome sequences, phylogenomic 44 techniques are applied to characterise the evolutionary relationships among species. Whole-45 genome information can help in resolving uncertain nodes, as well as provide stronger evidence 46 on already established relationships. Regarding fish phylogeny, several genome-wide 47 approaches have been implemented so far. One of the first efforts to study ray-finned fish 48 phylogenomics was conducted by (Li et al., 2007). Since then, several studies have been 49 published using not only gene markers, but also noncoding elements such as the work of 50 (Faircloth et al., 2013) who used UCE (ultra-conserved elements) to investigate the 51 diversification of basal clades in ray-finned fish. Most genome papers include a phylogenomic 52 analysis albeit with limited taxon sampling (e.g. Vij et al., 2016 and Xu et al., 2017), while the 53 use of whole-transcriptome data is being employed to uncover phylogenetic relationships of 54 specific taxonomic groups as well (Dai et al., 2018; Rodgers et al., 2018). With the emergence 55 of new genomes and the possibilities of modern sequencing technologies, bigger datasets are ...

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 54%

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Natsidis

Tsakogiannis

Pavlidis

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…In contrast to the aforementioned findings, two other studies placed common pandora together with the red porgy, leaving common dentex outside; the first study included 66 Sparidae species and 18 mitochondrial loci 15 and the second 91 Sparidae species and five loci 16 . This relationship is supported also by a recent single-gene approach using mitochondrial COI sequences from sparids inhabiting the Egyptian waters 17 . Thus, even though multiple studies have been conducted so far, the evolutionary relationship of Sparidae genera remains unclear.…”

Section: Introductionmentioning

confidence: 53%

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

et al. 2019

View full text Add to dashboard Cite

Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.

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“…For fish, the Fish Barcode of life initiative (FISH-BOL) campaign, (Ward et al, 2009) has utilized the sequence of the COI gene "648 bp region" for more than 100,000 specimens representing more than 10,000 species. With these resources, DNA barcoding has embloyed COI to trace fish species in the Egyptian aqua-feed formulations (Galal-Khallaf et al, 2016), differentiate between members of the Sparidae species (Armani et al, 2015;Abbas et al, 2017), and verify the labels on seafood products commercialized in Southern Brazil marketplaces (Carvalho et al, 2015), and other studies on fish in Europe (Di Pinto et al, 2013;Vandamme et al, 2016;Helyar et al, 2014). Cytochrome b (Cyt b) is another mitochondrial gene widely used for animal species differentiation (Tsai et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Comparative Molecular Identification of Genus Dicentrarchus Using Mitochondrial Genes and Internal Transcribed Spacer Region

Ali¹,

Ismail²,

Mamoon³

2019

Egypt. J. of Aquatic Biolo. and Fish.

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DNA barcoding is one of the powerful DNA-based identification tools that are used for accurate identification of a species. Despite several DNA barcodes were used, the accuracy and suitability of these barcodes depend on speciesspecific variations.The current study was conducted to compare the efficiency of two mitochondrial genes to the nuclear Internal Transcribed Spacer (ITS) region in the molecular identification of genus Dicentrarchus. A total of 80 fish samples for Dicentrarchus labrax and Dicentrarchus punctatus were randomly collected from two different locations in Egypt; Alexandria and Bardawil Lagoon. All samples were morphologically characterized. For species barcoding, the ITS region was firstly employed to carry out the PCR amplifications. Additionally, two mitochondrial genes; cytochrome b (Cyt b) and cytochrome oxidase subunit I (COI) were also used for species barcoding. To evaluate the efficiency of each marker, three different approaches were used. Firstly, phylogenetic relationship was constructed between the collected samples and a reference species using each genetic marker. Secondly, Automated Barcode Gap Discovery (ABGD) method was used for each marker in order to assign the samples into presumed species without priori species assumption. Lastly, the Poisson Tree Processes (PTP) model was used which relies on Bayesian support values to delimit species on the input tree. The two species of genus Dicentrarchus exhibited nearly similar ITS sequences, leading to an ambiguous identification of the two species. However, the two mitochondrial COI and Cyt b genes were able to accurately distinguish between the two species. The three approaches, phylogeny, ABGD and PTP presented consistent results. Overall, COI and Cyt b outperformed ITS in assigning species accurately. Mitochondrial barcodes could provide a leading guide for fish species identification. ITS should be abandoned in favor of COI and Cyt b as primary DNA barcode markers for fish species in general and Dicentrarchus genus, in particular.

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Phylogeny and DNA Barcoding of the Family Sparidae Inferred from Mitochondrial DNA of the Egyptian Waters

Cited by 25 publications

References 19 publications

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Comparative Molecular Identification of Genus Dicentrarchus Using Mitochondrial Genes and Internal Transcribed Spacer Region

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