RESUMEN

AMOVA is a widely used approach that focuses on variance within and among strata to study the hierarchical genetic structure of populations. The recently developed Shannon Informational Diversity Translation Analysis (SIDTA) instead tackles exploration of hierarchical genetic structure using entropic allelic diversity. A mix of artificial and natural population data sets (including allopolyploids) is used to compare the performance of SIDTA (a 'q = 1' diversity measure) vs. AMOVA (a 'q = 2' measure) under different conditions. An additive allelic differentiation index based on entropic allelic diversity measuring the mean difference among populations (ΩAP) was developed to facilitate the comparison of SIDTA with AMOVA. These analyses show that the genetic population structure seen by AMOVA is notably different in many ways from that provided by SIDTA, and the extent of this difference is greatly affected by the stability of the markers employed. Negative among group values are lacking with SIDTA but occur with AMOVA, especially with allopolyploids. To provide more focus on measuring allelic differentiation among populations, additional measures were also tested including Bray-Curtis Genetic Differentiation (BCGD) and several expected heterozygosity-based indices (e.g., GST, G″ST, Jost's D, and DEST). Corrections, such as almost unbiased estimators, that were designed to work with heterozygosity-based fixation indices (e.g., FST, GST) are problematic when applied to differentiation indices (eg., DEST, G″ST, G'STH).

RESUMEN

PREMISE OF THE STUDY: The traditional approach used in analyses of population genetic data for historical inference is to average across multiple marker loci, but averaging conflates the different evolutionary signals provided by stable vs. labile markers. METHODS: We used a battery of microsatellites with a wide range of mutation/substitution rates, grouping them into two sets (stable and hypervariable) to provide a more nuanced reconstruction of the population genetics and evolutionary history of the allotriploid peat moss Sphagnum × falcatulum across three disjunct regions. KEY RESULTS: Shannon diversity translation analyses show that the relative apportionment of total within-species allelic diversity (∆WS ) within and among strata ranges widely, both between the two sets and within and among regions. The majority of diversity in the stable set was inherited directly from the ancestors of this genetically complex allopolyploid, but most of the diversity in the hypervariable set has developed post-hybrid-origin. CONCLUSIONS: It is useful to group markers into sets having similar evolutionary lability, with each set being analyzed separately, particularly for allopolyploids. A methodology for determining how to group markers into such sets is presented, which can be applied to the requirements of other studies. Within-individual allelic diversity (ΔWI ) should be addressed in genetic studies on allopolyploids. Allotriploid haplotypes based on a set of nine highly stable microsatellites appear to serve as a clonal-detection set for S. × falcatulum. An additive "allele-metric" diversity approach is introduced, which facilitates a direct comparison of within- and among-stratum diversity components at all levels of diversity.

Asunto(s)

RESUMEN

Background and Aims: Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations. Methods: Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures. Key Results: The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information. Conclusions: Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation, rather than by subsequent evolutionary radiation. However, some post-hybridization genetic diversification has become fixed in at least one regional population. Methodology allowing statistical analysis of any ploidy level is presented.

Asunto(s)

Asunto(s)

Asunto(s)

RESUMEN

Over the past decade, there have been significant advances in our understanding of the immunopathogenesis and pharmacogenomics of severe immunologically-mediated adverse drug reactions. Such T-cell-mediated adverse drug reactions such as Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN), drug-induced liver disease (DILI) and other drug hypersensitivity syndromes have more recently been shown to be mediated through interactions with various class I and II HLA alleles. Key examples have included the associations of HLA-B*15:02 and carbamazepine induced SJS/TEN in Southeast Asian populations and HLA-B*57:01 and abacavir hypersensitivity. HLA-B*57:01 screening to prevent abacavir hypersensitivity exemplifies a successful translational roadmap from pharmacogenomic discovery through to widespread clinical implementation. Ultimately, our increased understanding of the interaction between drugs and the MHC could be used to inform drug design and drive pre-clinical toxicity programs to improve drug safety.

Asunto(s)

RESUMEN

It has been proposed that long-distance dispersal of mosses to the Hawaiian Islands rarely occurs and that the Hawaiian population of the allopolyploid peat moss Sphagnum palustre probably resulted from a single dispersal event. Here, we used microsatellites to investigate whether the Hawaiian population of the dioicous S. palustre had a single founder and to compare its genetic diversity to that found in populations of S. palustre in other regions. The genetic diversity of the Hawaiian population is comparable to that of larger population systems. Several lines of evidence, including a lack of sporophytes and an apparently restricted natural distribution, suggest that sexual reproduction is absent in the Hawaiian plants. In addition, all samples of Hawaiian S. palustre share a genetic trait rare in other populations. Time to most recent ancestor (TMRCA) analysis indicates that the Hawaiian population was probably founded 49-51 kyr ago. It appears that all Hawaiian plants of S. palustre descend from a single founder via vegetative propagation. The long-term viability of this clonal population coupled with the development of significant genetic diversity suggests that vegetative propagation in a moss does not necessarily preclude evolutionary success in the long term.

Asunto(s)

RESUMEN

This paper documents the occurrence of allotriploidy (having three differentiated genomes) in gametophytes of two Southern Hemisphere Sphagnum species (S. australe, S. falcatulum). The pattern of microsatellite alleles indicates that both species are composed of a complex of allodiploid and allotriploid gametophytes, with the latter resulting from two allopolyploidization events. No haploid (n = x) gametophytes were found for either species. The ploidal levels suggested by the pattern of microsatellite alleles were confirmed by flow cytometry and Feulgen DNA image densitometry. For both S. australe and S. falcatulum, the respective allodiploid plants (or their ancestors) are one of the parent species of the allotriploid plants. This is the first report of triploidy in Sphagnum gametophytes occurring in nature and also the first report of the presence of three differentiated genomes in any bryophyte. It is also the first report of intersectional allopolyploidy in Sphagnum, with S. australe appearing to have parental species from Sphagnum sections Rigida and Sphagnum, and S. falcatulum having parental species from Sphagnum sections Cuspidata and Subsecunda. In both species, the allotriploid cytotypes were the most prevalent cytotype on the South Island of New Zealand. The pattern of microsatellite alleles shows the presence of two genetically distinct populations of allodiploid S. australe, possibly indicating multiple origins of polyploidy for that allodiploid cytotype. Morphological evidence is also highly indicative of recurrent polyploidy in the allotriploid cytotype of S. falcatulum. Allopolyploidy has clearly played a major evolutionary role in these two Southern Hemisphere taxa. This study, in conjunction with other recent research, indicates that allopolyploidy is a common, if not the predominant, form of polyploidy in Sphagnum.

Asunto(s)

RESUMEN

Allopolyploid speciation is likely the predominant mode of sympatric speciation in plants. The Sphagnum subsecundum complex includes six species in North America. Three have haploid gametophytes, and three are thought to have diploid gametophytes. Microsatellite analyses indicated that some plants of S. inundatum and S. lescurii are heterozygous at most loci, but others have only one allele at each locus. Flow cytometry and Feulgen staining showed that heterozygous plants have twice the genome size as plants with one allele per locus; thus, microsatellite patterns can be used to survey the distribution and abundance of haploid and diploid gametophytes. Microsatellite analyses also revealed that S. carolinianum is consistently diploid, but S. lescurii and S. inundatum include both haploid and diploid populations. The frequency of diploid plants in S. lescurii increases with latitude. In an analysis of one population of S. lescurii, both cytotypes co-occurred but were genetically differentiated with no evidence of interbreeding. The degree of genetic differentiation showed that the diploids were not derived from simple genome duplication of the local haploids. Heterozygosity appears to be fixed or nearly so in diploids, strongly suggesting that although morphologically indistinguishable from the haploids, they are derived by allopolyploidy.