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Martin, Andrew P.

doi:10.1023/a:1013747532647

Cited by 13 publications

(3 citation statements)

References 38 publications

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“…Lungfish and bichir were placed in a basal position on the piscine branch. This topology (Figure 1b) was supported, or at least not refuted, by some other molecular studies [12], [13].…”

Section: Introductionsupporting

confidence: 65%

Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

et al. 2012

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The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p = 0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences.

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“…Lungfish and bichir were placed in a basal position on the piscine branch. This topology (Figure 1b) was supported, or at least not refuted, by some other molecular studies [12], [13].…”

Section: Introductionsupporting

confidence: 65%

Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

et al. 2012

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“…Second, there is a risk that orthology is mistaken in the phylogenetic analysis if some of the existing outparalogues are not detected, or if some of the paralogues are lost in some lineages. The phylogeny will then be influenced by which copy is lost (or not detected) in which lineage [16]. On the other hand, inparalogues (gene copies that are monophyletic within an individual) will not cause such problems (Figure 1a).…”

Section: Discussionmentioning

confidence: 99%

“…Paralogy problems may, however, exist even if entire genome sequences are at hand, if paralogues have gone extinct haphazardly in different lineages [16]. To complicate matters even further, members of a multi-copy gene family, and also alleles of the same gene, may recombine and make phylogenetic analysis difficult [7].…”

Section: Introductionmentioning

confidence: 99%

Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene

et al. 2008

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BackgroundIncreasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe.ResultsWe sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict.ConclusionThe phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.

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Evolution of TLR5

Pinheiro

2021

Encyclopedia of Life Sciences

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TLR5 is an evolutionary conserved protein. Evidence so far shows that it emerged in a vertebrate ancestor and maintained its flagellin recognition function throughout evolution. The single TLR5 gene that was present in the vertebrates' ancestor was duplicated in the Actinopterygii lineage originating a short ECD only TLR5 (TLR5S). The single TLR5 again suffered a duplication in the tetrapoda ancestor originating another short ECD only TLR5 (TLR5L). This TLR5L was then independently lost in the Reptilia Archosauromorpha lineage, which comprises crocodiles and birds, and in the mammals' lineage, and is nowadays present only in Amphibians and most reptiles. TLR5 pseudogenisation events are common, with higher incidence in birds and mammals. These gene gains and losses may reflect species adaptation to particular environments and pathogens. It is also apparent that, in birds and mammals, TLR5 may be functionally redundant and is acquiring new functions beyond flagellin recognition. Key Concepts TLR5 is a vertebrate Toll‐like receptor that binds bacterial flagellin. TLR5 is overall an evolutionary conserved protein being present and maintaining its function from lampreys to mammals. The TLR5 evolution has been punctuated by several independent gene gains and losses, characteristic events of a multigene family evolution. In birds and mammals, the finding of positively selected codons suggests that TLR5 is evolving in response to pathogen pressure. Growing evidence suggests that TLR5 function may be redundant, and hence, the gene has been lost or pseudogenised in many birds and mammals.

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Untitled

Cited by 13 publications

References 38 publications

Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene

Evolution of TLR5

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