Trends in Ecology & Evolution
SINEs of speciation: tracking lineages with retroposons
Section snippets
Detecting and characterizing new SINEs
The step-by-step process of isolating and characterizing new SINEs for systematic studies has been reviewed in detail [40]. To discover new elements, we can take advantage of the fact that most SINEs are derived from tRNAs and thus have a tRNA-like secondary structure as well as internal promoters for RNA polymerase III. If we know which family of SINEs to expect in a host genome, we can experimentally screen a genomic library of a species of interest with an oligonucleotide probe that is
Limits to SINE analysis
A debate over the limits to the SINE approach has scrutinized the nature of how these genetic markers evolve and how frequently exceptional patterns occur. Crucial assumptions of the method are based on the absence of any known precise deletions of SINE elements and the rarity of parallel insertion events at the exact same site in the genomes of different taxa. Apparent cases of parallel SINE insertion in different lineages have been investigated 42, 43, 44. This phenomenon is a rare random
Fixation of SINEs
Most SINEs that insert into nonfunctional regions throughout the genome do not impart any obvious advantage or disadvantage to the host and they are generally considered to be neutral genetic markers. Hence, their evolution among species can be modeled with the use of neutral theory 46, 47. The time to fixation of a SINE under neutral conditions is usually far shorter than the length of time between lineage splits. In this case, the SINE method gives a robust evolutionary tree without concern
Assessing human genomic diversity with SINEs
Not surprisingly, the Human Genome Project has had a major influence on the study of SINEs, which are the most abundant elements in the mobile DNA that accounts for ∼45% of the chromosomes of humans. Alu elements are human- and primate-specific SINEs that have proliferated to more than a million copies in the human genome over the past ∼65 Myr. Through this dynamic process, they have generated a substantial amount of genetic diversity in our species 4, 52. Alu insertions continue to fuel the
Conclusions
SINEs continue to provide both insight into the role that mobile DNA has played in shaping genomes and a wealth of neutral genetic markers of identical descent and known ancestral condition. Limits to the use of SINEs include the decay of PCR priming sites after ∼150–200 Myr and the large effort needed to establish an informative multi-locus data set for many taxa. In particular, the fundamental assumptions of SINE insertion analysis, namely the rarity of parallel insertion events and lack of
Acknowledgements
We thank Joe Felsenstein, Scott Edwards, Peter Beerli, Mary Kuhner, Alan Weiner, Leroy Hood, Arian Smit, Bruce Rannala, Hidenori Tachida, Masatoshi Nei and Masami Hasegawa for helpful discussions and critical comments. Three anonymous referees provided valuable suggestions that improved earlier versions of the article. This review was produced with support from NSF-JSPS international fellowship P98881 to A.M.S. and Monbusho grant-in-aid for special research to N.O. Additional collaborative
Glossary
- Ancestral polymorphism:
- a situation in which incomplete sorting of gene copies over generations might lead to fixation of alleles in descendant species whose genealogical structure does not reflect the true species phylogeny.
- Clade:
- a natural taxon originating with a common ancestor and including all descendants; a monophyletic group.
- Coalescence theory:
- numerical framework that enables one to use various population genetic models to calculate probabilities of genealogical structure among copies of
References (66)
Mobile elements inserted in the distant past have taken on important functions
Gene
(1997)SINEs and LINEs: the art of biting the hand that feeds you
Curr. Opin. Cell Biol.
(2002)- et al.
A human-specific (HS) subfamily of Alu sequences
Genomics
(1991) - et al.
A human dimorphism resulting from loss of an Alu
Genomics
(1992) Interspersed repeats and other mementos of transposable elements in mammalian genomes
Curr. Opin. Genet. Dev.
(1999)Non-traditional Alu evolution and primate genomic diversity
J. Mol. Biol.
(2002)- et al.
Rare molecular changes as a tool for phylogenetics
Trends Ecol. Evol.
(2000) Does SINE evolution preclude Alu function?
Nucl. Acids Res.
(1998)Retroposons – seeds of evolution
Science
(1991)- et al.
Alu repeats and human genomic diversity
Nat. Rev. Genet.
(2001)
Potential gene conversion and source genes for recently integrated Alu elements
Genome Res.
The impact of L1 retrotransposons on the human genome
Nat. Genet.
Mobile elements: drivers of genome evolution
Science
Evolution of retroposons
Evol. Biol.
SINE insertions: powerful tools for molecular systematics
Bioessays
African origin of human-specific polymorphic Alu insertions
Proc. Natl. Acad. Sci. U. S. A.
Alu evolution in human populations: using the coalescent to estimate effective population size
Genetics
Genetic traces of ancient demography
Proc. Natl. Acad. Sci. U. S. A.
Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa
Genome Res.
Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms
Genome Res.
Comparative analyses of multi-species sequences from targeted genomic regions
Nature
Initial sequencing and comparative analysis of the mouse genome
Nature
Initial sequencing and analysis of the human genome
Nature
Molecular evidence from retroposons that whales form a clade within even-toed ungulates
Nature
Even-toed fingerprints on whale ancestry
Nature
Phylogenetic relationships among cetartiodactyls based on evidence from insertions of SINEs and LINEs: hippopotamuses are the closest extant relatives of whales
Proc. Natl. Acad. Sci. U. S. A.
SINE evolution, missing data, and the origin of whales
Syst. Biol.
Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins
Proc. Natl. Acad. Sci. U. S. A.
Alu elements and hominid phylogenetics
Proc. Natl. Acad. Sci. U. S. A.
The Colugo (Cynocephalus variegatuus Dermoptera): the primates' gliding sister?
Mol. Biol. Evol.
Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution
Proc. Natl. Acad. Sci., U. S. A.
Detection of the ongoing sorting of ancestrally polymorphic SINEs toward fixation or loss in populations of two species of charr during speciation
Genetics
Cited by (129)
Genetic dissection of five ethnic groups from Punjab, North-West India–A study based on Autosomal Markers
2017, Legal MedicineCitation Excerpt :Alu elements and SNPs showed a moderate degree of discriminating power in presently studied population groups. Although Alu elements do not generate discriminating power as high as multi-allelic markers such as STRs, Alu elements are known for their ability to deduce population origin owing to their identity by descent [48]. Previous reports on Alu insertion elements have shown that they are capable of inferring an origin of population accurately, and the possibility can be extended to the forensic identification and genetic differentiation of samples with mixed ancestry [49,50].
Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)
2016, Molecular Phylogenetics and EvolutionA systemic approach for modeling biological evolution using Parallel DEVS
2015, BioSystemsCitation Excerpt :A summary of these topics is presented next: Reticulated phylogenies are now the norm rather than the exception in the main branches of life; including lateral gene and transposon transfer (Dagan et al., 2008; Schaack et al., 2010; Crisp et al., 2015), hybridization (Arnold, 2008; Amaral et al., 2014), phyletic introgression (Baack and Rieseberg, 2007; Carrión García and Cabezudo, 2003), incomplete lineage sorting (Lönnig and Saedler, 2002; Shedlock et al., 2004), symbiosis (Sapp, 2010; Margulis, 2000; Brucker and Bordenstein, 2012) and viral genomes acquisition (Oliver and Greene, 2012; Mindell et al., 2004; Villarreal, 1999; Hunter, 2010). In a broad scale, the validity of the Darwinian tree of life metaphor is being questioned (Raoult, 2010; O’Malley, 2012; Bapteste et al., 2009; Koonin, 2009).
Reunion of Australasian Possums by Shared SINE Insertions
2022, Systematic Biology