SINE insertions: powerful tools for molecular systematics

Shedlock, Andrew M.; Okada, Norihiro

doi:10.1002/(sici)1521-1878(200002)22:2<148::aid-bies6>3.0.co;2-z

Cited by 347 publications

(233 citation statements)

References 90 publications

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“…Because there are billions of potential insertion sites in any primate genome, the probability of a SINE inserting precisely in the same locus in two separate evolutionary lineages is "exceedingly minute, and for all practical purposes, can be ignored" (p. 151, ref. 3). Five SINEs support haplorhine monophyly to the exclusion of strepsirrhines and eight are shared among strepsirrhines (4).…”

Section: Phylogenetics Of Crown Primatesmentioning

confidence: 95%

New perspectives on anthropoid origins

Williams

Kay

Kirk

2010

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

117

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Adaptive shifts associated with human origins are brought to light as we examine the human fossil record and study our own genome and that of our closest ape relatives. However, the more ancient roots of many human characteristics are revealed through the study of a broader array of living anthropoids and the increasingly dense fossil record of the earliest anthropoid radiations. Genomic data and fossils of early primates in Asia and Africa clarify relationships among the major clades of primates. Progress in comparative anatomy, genomics, and molecular biology point to key changes in sensory ecology and brain organization that ultimately set the stage for the emergence of the human lineage.primate | Haplorhini | Strepsirrhini | human evolution | phylogeny

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Section: Phylogenetics Of Crown Primatesmentioning

confidence: 95%

New perspectives on anthropoid origins

Williams

Kay

Kirk

2010

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

117

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“…Accordingly, 35% divergence in the coelacanth genome may correspond to an insertion event that occurred over 400 Ma. This suggests the very interesting possibility that we can elucidate phylogenetic relationships among tetrapods, coelacanths, and lungfish using the retroposon method (Shedlock and Okada 2000). Because the divergence time among tetrapods, coelacanths, and lungfish is assumed to be around 400 Ma, these times fall within the scope of the estimation determined by the retroposon method.…”

Section: Comparison Of Tes Among Vertebratesmentioning

confidence: 99%

Coelacanth genomes reveal signatures for evolutionary transition from water to land

et al. 2013

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Coelacanths are known as ''living fossils,'' as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish to tetrapods. Here, we report the genome sequences of five coelacanths, including four Latimeria chalumnae individuals (three specimens from Tanzania and one from Comoros) and one L. menadoensis individual from Indonesia. These sequences cover two African breeding populations and two known extant coelacanth species. The genome is~2.74 Gbp and contains a high proportion (~60%) of repetitive elements. The genetic diversity among the individuals was extremely low, suggesting a small population size and/or a slow rate of evolution. We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands. We also found that limb enhancers of bmp7 and gli3, both of which are essential for limb formation, are conserved between coelacanth and tetrapods, but not ray-finned fishes. We expect that some tetrapod-like genes may have existed early in the evolution of primitive Sarcopterygii and were later co-opted to adapt to terrestrial environments. These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals.

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“…Retroelements have strong potential to resolve difficult nodes of a phylogeny (Shedlock and Okada 2000;Springer et al 2004;Bashir et al 2005;Kriegs et al 2006;Nishihara et al 2006;Rokas and Carroll 2006). Their advantages are immunity to later identical events and probably a higher event (insertion) rate than coding indels.…”

Section: Evaluation Of Kriegs Et Al's Two Insertions Supporting Epitmentioning

confidence: 99%

Using genomic data to unravel the root of the placental mammal phylogeny

Murphy¹,

Pringle²,

Crider³

et al. 2007

Genome Res.

405

342

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The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals ∼103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.

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SINE insertions: powerful tools for molecular systematics

Cited by 347 publications

References 90 publications

New perspectives on anthropoid origins

New perspectives on anthropoid origins

Coelacanth genomes reveal signatures for evolutionary transition from water to land

Using genomic data to unravel the root of the placental mammal phylogeny

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