A population genetic study of the evolution of SINEs. I. Polymorphism with regard to the presence or absence of an element

Long-term evolution of transposable elements

Transposable elements are often considered parasitic DNA sequences, able to invade the genome of their host thanks to their self-replicating ability. This colonization process has been extensively studied, both theoretically and experimentally, but their long-term coevolution with the genomes is still poorly understood. In this work, we aim to challenge previous population genetics models by considering features of transposable elements as quantitative, rather than discrete, variables. We also describe more realistic transposable element dynamics by accounting for the variability of the insertion effect, from deleterious to adaptive, as well as mutations leading to a loss of transposition activity and to nonautonomous copies. Individual-based simulations of the behavior of a transposable-element family over several thousand generations show different ways in which active or inactive copies can be maintained for a very long time. Results reveal an unexpected impact of genetic drift on the "junk DNA" content of the genome and strongly question the likelihood of the sustainable long-term stable transposition-selection equilibrium on which numerous previous works were based.

SINEs of speciation: tracking lineages with retroposons

The value of short interspersed elements (SINEs) for diagnosing common ancestry is being expanded to examine the differential sorting of lineages through the course of speciation events. Because most SINEs are neutral markers of identical descent, are not precisely excised from the genome and have a known ancestral condition, they are advantageous for reconciling gene trees and species trees with minimal phylogenetic error. A population perspective on SINE evolution combined with coalescence theory provides a context for investigating the phenomenon of ancestral polymorphism and its role in producing incongruent SINE insertion patterns among multiple loci. Studies of human Alu repeats demonstrate the value of young polymorphic SINEs for assessing human genomic diversity and tracking ancient demographics of human populations, whereas incongruent insertion patterns revealed by older fixed SINE loci, such as those in African cichlid fishes, contain information that might help identify ancient radiations that are otherwise obscured by accumulated mutations in sequence data. Here, we review the utility of retroposons for inferring common ancestry, discuss limits to the method, and clarify confusion by providing examples from the literature that illustrate how discordant multi-locus insertion patterns of retroelements can indicate lineage-sorting events that should not be misinterpreted as phylogenetic noise.

Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons

Lake Tanganyika harbors numerous endemic species of extremely diverse cichlid fish that have been classified into 12 major taxonomic groups known as tribes. Analysis of short interspersed element (SINE) insertion data has been acknowledged to be a powerful tool for the elucidation of phylogenetic relationships, and we applied this method in an attempt to clarify such relationships among these cichlids. We studied insertion patterns of 38 SINEs in total, 24 of which supported the monophyly of three clades. The other 14 loci revealed extensive incongruence in terms of the patterns of SINE insertions. These incongruencies most likely stem from a period of adaptive radiation. One possible explanation for this phenomenon is the extensive incomplete lineage sorting of alleles for the presence or absence of a SINE during successive speciation events which took place about 5-10 MYA. The present study is the first to report the successful application of the SINE method in demonstrating the existence of such possible "ancient" incomplete lineage sorting. We discuss the possibility that it might potentially be very difficult to resolve the species phylogeny of a group that radiated explosively, even by resolving the genealogies of more than 10 nuclear loci, as a consequence of incomplete lineage sorting during speciation.

Molecular systematics: Perfect SINEs of evolutionary history?

Short interspersed repetitive elements - SINEs - are being championed as near-perfect phylogenetic characters; they have recently been used with notable success to resolve some phylogenetic conundrums, but they do have certain limitations that restrict their use as 'perfect' characters for molecular systematics.

Alu evolution in human populations: using the coalescent to estimate effective population size

There are estimated to be approximately 1000 members of the Ya5 Alu subfamily of retroposons in humans. This subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLa-derived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of approximately 18,000 during the last one to two million years.

Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa

Alu insertion polymorphisms (polymorphisms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer several advantages over other nuclear DNA polymorphisms for human evolution studies. First, they are typed by rapid, simple, PCR-based assays; second, they are stable polymorphisms-newly inserted Alu elements rarely undergo deletion; third, the presence of an Alu element represents identity by descent-the probability that different Alu elements would independently insert into the exact same chromosomal location is negligible; and fourth, the ancestral state is known with certainty to be the absence of an Alu element. We report here a study of 8 loci in 1500 individuals from 34 worldwide populations. African populations exhibit the most between-population differentiation, and the population tree is rooted in Africa; moreover, the estimated effective time of separation of African versus non-African populations is 137,000 +/- 15,000 years ago, in accordance with other genetic data. However, a principal coordinates analysis indicates that populations from Sahul (Australia and New Guinea) are nearly as close to the hypothetical ancestor as are African populations, suggesting that there was an early expansion of tropical populations of our species. An analysis of heterozygosity versus genetic distance suggests that African populations have had a larger effective population size than non-African populations. Overall, these results support the African origin of modern humans in that an earlier expansion of the ancestors of African populations is indicated.

Details of retropositional genome dynamics that provide a rationale for a generic division: the distinct branching of all the pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo)

Salmonid species contain numerous short interspersed repetitive elements (SINEs), known collectively as the HpaI family, in their genomes. Amplification and successive integration of individual SINEs into the genomes have occurred during the evolution of salmonids. We reported previously a strategy for determining the phylogenetic relationships among the Pacific salmonids in which these SINEs were used as temporal landmarks of evolution. Here, we provide evidence for extensive genomic rearrangements that involved retropositions and deletions in a common ancestor of all the Pacific salmon and trout. Our results provide genetic support for the recent phylogenetic reassignment of steelhead and related species from the genus Salmo to the genus Oncorhynchus. Several other informative loci identified by insertions of HpaI SINEs have been isolated, and previously proposed branching orders of the Oncorhynchus species have been confirmed. The authenticity of our phylogenetic tree is supported both by the isolation of more than two informative loci per branching point and by the congruence of all our data, which suggest that the period between successive speciations was sufficiently long for each SINE that had been amplified in the original species to become fixed in all individuals of that species.

The evolutionary dynamics of repetitive DNA in eukaryotes

Repetitive DNA sequences form a large portion of the genomes of eukaryotes. The 'selfish DNA' hypothesis proposes that they are maintained by their ability to replicate within the genome. The behaviour of repetitive sequences can result in mutations that cause genetic diseases, and confer significant fitness losses on the organism. Features of the organization of repetitive sequences in eukaryotic genomes, and their distribution in natural populations, reflect the evolutionary forces acting on selfish DNA.

Evolution of repeated sequences in non-coding regions of the genome

Repeated sequences are found ubiquitously in the eukaryotic genome. Population genetic studies on the evolution of such repeated sequences are reviewed while paying special attention to those sequences found in the non-coding regions of the genome. Specifically, the evolution of dispersed repeated sequences by the transposition as well as the evolution of short tandemly repeated sequences due to either replication slippage or unequal sister chromatid exchange are considered. The approach of combining both model and data analyses which has been successfully employed in the development of the neutral theory is also considered to be useful in better understanding the evolution and biological meaning of these sequences.