Limits...
Evolutionary history of LINE-1 in the major clades of placental mammals.

Waters PD, Dobigny G, Waddell PJ, Robinson TJ - PLoS ONE (2007)

Bottom Line: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics.Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up.Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa.

ABSTRACT

Background: LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.

Methodology: To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria) were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed.

Principal findings: Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE) clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE) falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria) hypothesis.

Significance: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

Show MeSH

Related in: MedlinePlus

Phylogenetic tree of LINE-1: longer sequences only. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our long (1050 bp) dataset that included 69 sequences. Posterior probability values ≥95% are shown. Grey branches indicate sequences with >98% homology to other LINE-1 copies in their respective genomes. A species key shows the abbreviated names, scientific names and common names.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC1764860&req=5

pone-0000158-g002: Phylogenetic tree of LINE-1: longer sequences only. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our long (1050 bp) dataset that included 69 sequences. Posterior probability values ≥95% are shown. Grey branches indicate sequences with >98% homology to other LINE-1 copies in their respective genomes. A species key shows the abbreviated names, scientific names and common names.

Mentions: Moreover, our two data sets (longer sequences only vs. combined data) retrieved similar topologies (Figure 1 and Figure 2) with the shorter sequences grouping/falling in expected positions around the corresponding longer sequences. Consequently, the following discussion largely focuses on the outcomes reflected in the combined tree (Figure 1). Although we are aware that our investigations represent gene phylogenies, since most sequences are paralogous many clades of LINE-1 elements were, nonetheless, found to reflect closely what is known about species relationships in mammals. This clearly suggests that for many lineages all LINE-1 active at any one time coalesce to a common and not too distant ancestor. Hence these signatures of ancestral but exclusively shared TE activity can reasonably be used as potential synapomorphies, and are thus useful for inferring phylogenetic relationships between species.


Evolutionary history of LINE-1 in the major clades of placental mammals.

Waters PD, Dobigny G, Waddell PJ, Robinson TJ - PLoS ONE (2007)

Phylogenetic tree of LINE-1: longer sequences only. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our long (1050 bp) dataset that included 69 sequences. Posterior probability values ≥95% are shown. Grey branches indicate sequences with >98% homology to other LINE-1 copies in their respective genomes. A species key shows the abbreviated names, scientific names and common names.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1764860&req=5

pone-0000158-g002: Phylogenetic tree of LINE-1: longer sequences only. Bayesian consensus tree generated by a GTR invariant-sites plus Γ model applied to our long (1050 bp) dataset that included 69 sequences. Posterior probability values ≥95% are shown. Grey branches indicate sequences with >98% homology to other LINE-1 copies in their respective genomes. A species key shows the abbreviated names, scientific names and common names.
Mentions: Moreover, our two data sets (longer sequences only vs. combined data) retrieved similar topologies (Figure 1 and Figure 2) with the shorter sequences grouping/falling in expected positions around the corresponding longer sequences. Consequently, the following discussion largely focuses on the outcomes reflected in the combined tree (Figure 1). Although we are aware that our investigations represent gene phylogenies, since most sequences are paralogous many clades of LINE-1 elements were, nonetheless, found to reflect closely what is known about species relationships in mammals. This clearly suggests that for many lineages all LINE-1 active at any one time coalesce to a common and not too distant ancestor. Hence these signatures of ancestral but exclusively shared TE activity can reasonably be used as potential synapomorphies, and are thus useful for inferring phylogenetic relationships between species.

Bottom Line: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics.Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up.Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa.

ABSTRACT

Background: LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.

Methodology: To examine LINE-1 relationships, sequences from the 3' region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria) were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed.

Principal findings: Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE) clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE) falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria) hypothesis.

Significance: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent.

Show MeSH
Related in: MedlinePlus