Abstract:Short k-mer sequences from DNA are both conserved and diverged across species owing to their functional significance in speciation, which enables their use in many species classification algorithms. In the present study, we developed a methodology to analyze the DNA k-mers of whole genome, 5′ UTR, intron, and 3′ UTR regions from 58 insect species belonging to three genera of Diptera that include Anopheles, Drosophila, and Glossina. We developed an improved algorithm to predict and score k-mers based on a schem… Show more
“…For a lengthy description of the algorithm, the reader is referred to Cserhati et al [ 15 ]. However, a short description is provided here for better understanding.…”
Section: Methodsmentioning
confidence: 99%
“…Since morphology-based classification of A. fulgens is ambiguous, it would be helpful to determine the precise taxonomic status of this species based on a whole genome-based algorithm. To this end, the Whole Genome K-mer Signature (WGKS) algorithm [ 15 ] is used to analyze the genomes of five bear species, eleven cat species and ten species from the family Mustelidae (weasels, otters, martens, and badgers), Spilogala gracilis , a mephitid species, as well as A. fulgens , making 28 species in total.…”
Background
The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement.
Results
A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids and A. fulgens were aligned to draw further phylogenetic inferences.
The results from the whole genome study suggested that A. fulgens is a member of the mustelid clade (p = 9·10− 97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10− 62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study as well as neighbor-joining methods based on the sequence identity matrix suggests that A. fulgens forms a monophyletic group. A Maximum Likelihood tree suggests that A. fulgens and Ursidae form a monophyletic group, although the bootstrap value is weak.
Conclusions
The main conclusion that we can draw from this study is that on a whole genome level A. fulgens possibly belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. However, mitochondrial analyses based on neighbor-joining and maximum likelihood methods suggest otherwise.
“…For a lengthy description of the algorithm, the reader is referred to Cserhati et al [ 15 ]. However, a short description is provided here for better understanding.…”
Section: Methodsmentioning
confidence: 99%
“…Since morphology-based classification of A. fulgens is ambiguous, it would be helpful to determine the precise taxonomic status of this species based on a whole genome-based algorithm. To this end, the Whole Genome K-mer Signature (WGKS) algorithm [ 15 ] is used to analyze the genomes of five bear species, eleven cat species and ten species from the family Mustelidae (weasels, otters, martens, and badgers), Spilogala gracilis , a mephitid species, as well as A. fulgens , making 28 species in total.…”
Background
The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement.
Results
A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids and A. fulgens were aligned to draw further phylogenetic inferences.
The results from the whole genome study suggested that A. fulgens is a member of the mustelid clade (p = 9·10− 97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10− 62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study as well as neighbor-joining methods based on the sequence identity matrix suggests that A. fulgens forms a monophyletic group. A Maximum Likelihood tree suggests that A. fulgens and Ursidae form a monophyletic group, although the bootstrap value is weak.
Conclusions
The main conclusion that we can draw from this study is that on a whole genome level A. fulgens possibly belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. However, mitochondrial analyses based on neighbor-joining and maximum likelihood methods suggest otherwise.
“…Since morphology-based classification of A. fulgens is ambiguous, it would be helpful to analyze the precise taxonomic status of this species based on a whole genome-based algorithm. To this end, the Whole Genome K-mer Signature (WGKS) algorithm [14] is used to analyze the genomes of five bear species, eleven cat species and ten species from the family Mustelidae (weasels, otters, martens, and badgers), Spilogala gracilis, a mephitid species, as well as A. fulgens, making 28 species in total.…”
Section: Principle Of Analysismentioning
confidence: 99%
“…For a lengthy description of the algorithm, the reader is referred to Cserhati et al, 2019 [14]. However, a short description is provided here for better understanding.…”
Background: The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid or a member of its own family. Previous genetic studies have given contradictory results as to its phylogenetic placement.Results: Therefore, a recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum.The results show that A. fulgens is a member of the mustelid clade (p = 9·10-97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10-62). This could be due to the geographic isolation of A. fulgens from other mustelid species.Conclusions: The main conclusion that we can draw from this study is that on a whole genome level A. fulgens belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. This study is more substantial because it takes the whole genome into account.
“…For a lengthy description of the algorithm, the reader is referred to Cserhati et al, 2019 [15]. However, a short description is provided here for better understanding.…”
Background: The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results: A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids as well as A. fulgens were also aligned to draw further phylogenetic inferences. The results from the whole genome study show that A. fulgens is a member of the mustelid clade (p = 9·10-97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10-62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study based on the sequence identity matrix seem to place A. fulgens into its own group.Conclusions: The main conclusion that we can draw from this study is that on a whole genome level A. fulgens belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. The mitochondrial results could be due to differing mutational pressures compared to the nucleus. It cannot be said for sure, but it is likely that A. fulgens belongs to the mustelid clade.
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