Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates)

Singer, Silke S.; Schmitz, Jürgen; Schwiegk, Claudia; Zischler, Hans

doi:10.1016/s1055-7903(02)00312-3

Cited by 68 publications

(55 citation statements)

References 53 publications

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“…These findings support the use of endogenous retroviruses as phylogenetic markers (Shimamura et al 1997;Takahashi et al 2001;Salem et al 2003;Singer et al 2003). One requirement for using endogenous retrovirus sequence for lineage tracing is that many genomic sites must be capable of hosting integration events, so that the observed precise coincidence of integration site locations between taxa can be interpreted as evidence of common descent.…”

Section: Discussionsupporting

confidence: 62%

Integration target site selection by a resurrected human endogenous retrovirus

Brady¹,

Lee²,

Ronen³

et al. 2009

Genes Dev.

103

105

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At least 8% of the human genome was formed by integration of retroviral DNA sequences. Here we analyze the forces directing the accumulation of human endogenous retroviruses (HERVs) by comparing de novo HERV integration targeting with the distribution of fixed HERV elements in the human genome. All known genomic HERVs are inactive due to mutation, but we were able to study integration targeting using a reconstituted consensus HERV-K (designated HERV-K Con ). We found that HERV-K Con integrated preferentially in transcription units, in gene-rich regions, and near features associated with active transcription units and associated regulatory regions. In contrast, genomic HERV-K proviruses are found preferentially outside transcription units. The minority of genomic HERVKs present inside transcription units are in opposite transcriptional orientation relative to the host gene, the orientation predicted to be minimally disruptive to host mRNA synthesis, but de novo HERV-K Con integration within transcription units showed no orientation bias. We also found that the youngest HERV-K elements in the human genome showed a distribution intermediate between de novo HERV-K Con integration sites and older fixed HERV-Ks. These findings indicate that accumulation of HERVs in the human germline is a twostep process: integration targeting biases direct initial accumulation, then purifying selection leads to loss of proviruses disrupting gene function.[Keywords: HERV-K; HML2; genome construction; integration; positive selection] Supplemental material is available at http://www.genesdev.org.

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Section: Discussionsupporting

confidence: 62%

Integration target site selection by a resurrected human endogenous retrovirus

Brady¹,

Lee²,

Ronen³

et al. 2009

Genes Dev.

103

105

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“…The default parameters in the program were go ϭ 10 and ge ϭ 0.2. The phylogeny of the 16 primate species studied here is relatively well established, especially for the major divisions (24)(25)(26)(27), and use of alternative trees does not change our conclusion. We mapped the indels observed in the alignment of the CATSPER1 sequences to this phylogeny by using the parsimony principle and counted the number of indel substitutions in each branch of the tree.…”

Section: Methodsmentioning

confidence: 59%

Positive selection on protein-length in the evolution of a primate sperm ion channel

Podlaha

Zhang

2003

Proc. Natl. Acad. Sci. U.S.A.

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Positive Darwinian selection on advantageous point substitutions has been demonstrated in many genes. We here provide empirical evidence, for the first time, that positive selection can also act on insertion͞deletion (indel) substitutions in the evolution of a protein. CATSPER1 is a voltage-gated calcium channel found exclusively in the plasma membrane of the mammalian sperm tail and it is essential for sperm motility. We determined the DNA sequences of the first exon of the CATSPER1 gene from 15 primates, which encodes the intracellular N terminus region of Ϸ400 aa. These sequences exhibit an excessively high frequency of indels. However, all indels have lengths that are multiples of 3 nt (3n indels) and do not disrupt the ORF. The number of indel substitutions per site per year in CATSPER1 is five to eight times the corresponding rates calculated from two large-scale primate genomic comparisons, which represent the neutral rate of indel substitutions. Moreover, CATSPER1 indels are considerably longer than neutral indels. These observations strongly suggest that positive selection has been promoting the fixation of indel mutations in CATSPER1 exon 1. It has been shown in certain ion channels that the length of the N terminus region affects the rate of channel inactivation. This finding suggests that the selection detected may be related to the regulation of the CATSPER1 channel, which can affect sperm motility, an important determinant in sperm competition.T here have been dozens of reports on detection of positive Darwinian selection at the DNA sequence level (1-3) since the pioneering work by Hughes and Nei (4) on mammalian MHC genes. The majority of the positively selected genes are involved in host-pathogen interactions (4-8) or reproduction (9-18), although a small number of the genes are of other functions (19,20). In all these cases, positive selection has been shown to promote nonsynonymous (amino acid-replacing) nucleotide substitutions that are presumably advantageous. In theory, certain insertion͞deletion (indel) mutations in protein-coding regions may also be advantageous and subject to positive selection. Naturally occurring polymorphisms of indels that alter protein function have been reported (21). However, there has been no evidence for the operation of positive selection promoting fixations of indel mutations. This is probably because a large proportion of indel substitutions would disrupt the reading frame of a gene and thus be subject to strong purifying selection, which makes it difficult to detect positive selection. Nevertheless, here we provide evidence for the operation of positive selection on indel substitutions in the primate CATSPER1 gene, and demonstrate that positive selection plays a role in the evolutionary change of protein length.CATSPER1 is a voltage-gated calcium ion channel that is exclusively found in the plasma membrane of the principal piece of the sperm tail (22). It is necessary for cAMP-induced Ca 2ϩ influx, normal sperm motility, and penetration of the egg (22). Targe...

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“…The placement of tarsiers and the demarcation of the groupings among the hominoidea (including the genus Homo) are two of those exceptions that have been the focus of extensive taxonomic reorganization. Even with the overall structure of primate taxonomy in place there remains much work to be done in understanding the relationships of closely related taxa within many of the major groupings (Ruiz-Garcia & Alvarez 2003;Singer et al 2003).…”

Section: Introductionmentioning

confidence: 99%

The problems and promise of DNA barcodes for species diagnosis of primate biomaterials

Lorenz

Jackson

Beck

et al. 2005

Phil. Trans. R. Soc. B

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The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of 'DNA barcodes' for many species of primates. However, this quality control process is complicated by taxon specific patterns of 'universal primer' failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics.

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Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates)

Cited by 68 publications

References 53 publications

Integration target site selection by a resurrected human endogenous retrovirus

Integration target site selection by a resurrected human endogenous retrovirus

Positive selection on protein-length in the evolution of a primate sperm ion channel

The problems and promise of DNA barcodes for species diagnosis of primate biomaterials

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