Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers

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.



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.



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.



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.

Related papers:

title: Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae).
abstract: The phylogenetic position of hexaploid Elymus repens within the tribe Triticeae (Poaceae) was examined using cloned sequences from the low-copy nuclear genes encoding phosphoenolpyruvate carboxylase (pepC) and beta-amylase. A previous analysis of E. repens using data from the nuclear granule-bound starch synthase I (GBSSI) gene had yielded five phylogenetically distinct gene copies, two more than expected from hexaploidy alone. The three gene trees share three distinct E. repens clades, suggesting that E. repens contains three phylogenetically divergent genomes, contributed by Hordeum, Pseudoroegneria, and an unknown donor. The two additional GBSSI sequences, including one that was apparently derived from outside of the tribe, appear to reflect past introgression of GBSSI sequences into the E. repens genome. On all three trees, the Hordeum-like E. repens sequences are polyphyletic within Hordeum, and the trees are in conflict with regard to the placement of these sequences within Hordeum, highlighting multiple contributions from Hordeum to E. repens.

title: Three‐genome mosses: complex double allopolyploid origins for triploid gametophytes in Sphagnum
abstract: 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.

title: Subgenome analysis of two southern hemisphere allotriploid species in Sphagnum (Sphagnaceae)
abstract: Sphagnum ×australe s.l. and S. ×falcatulum s.l. are both cryptic species complexes of gametophytically allodiploid and allotriploid cytotypes, with the allodiploid cytotype being one parent of the respective allotriploid cytotype. Phylogenetic analyses of S. ×australe s.l. and S. ×falcatulum s.l. were undertaken using sequences from two plastid loci and cloned sequences from three nuclear loci. Subgenomes from three subgenera were detected in allotriploid S. ×australe. The haploid parent of allotriploid S. ×australe was S. fimbriatum (subg. Acutifolia). One of the two subgenomes contributed by allodiploid S. australe was associated with S. strictum (subg. Rigida); the parental species associated with the other subgenome could not be identified, either at the species level or in terms of subgenus association. It may represent an early diverging lineage of subg. Sphagnum or a previously undetected subgenus. Allotriploid S. ×falcatulum has subgenomes from two subgenera. This study confirms prior findings that S. cuspidatum (subg. Cuspidata) was the haploid parent of allotriploid S. ×falcatulum. One of the two subgenomes contributed by allodiploid S. ×falcatulum was associated with subg. Cuspidata (species unidentified) and the second was associated with subg. Subsecunda (species unidentified). Recurrent allopolyploidy appears to have been associated with the complex evolutionary processes (inter-subgeneric hybridization, interploidal hybridization, double allopolyploidy) which resulted in each of these two allotriploids. The highest level of divergence detected among the subgenomes in each of these Sphagnum allotriploids is comparable to the average genetic divergence reported for angiosperm allopolyploids.

title: The origin, evolution and proposed stabilization of the terms 'genome size' and 'C-value' to describe nuclear DNA contents.
abstract: Perusing the literature on nuclear 'genome size' shows that the term is not stabilized, but applied with different meanings. It is used for the DNA content of the complete chromosome complement (with chromosome number n), for which others use 'C-value', but also for the DNA content of the monoploid chromosome set only (with chromosome number x). Reconsideration of the terminology is required.



Our purpose is to discuss the currently unstable usage of the terms 'genome size' and 'C-value', and to propose a new unified terminology which can describe nuclear DNA contents with ease and without ambiguity.



We argue that there is a need to maintain the term genome size in a broad sense as a covering term, because it is widely understood, short and phonetically pleasing. Proposals are made for a unified and consensual terminology. In this, 'genome size' should mean the DNA content based on chromosome number x and n, and should be used mainly in a general sense. The necessary distinction of the kinds of genome sizes is made by the adjectives 'monoploid' and the neology 'holoploid'. 'Holoploid genome size' is a shortcut for the DNA content of the whole chromosome complement characteristic for the individual (and by generalization for the population, species, etc.) irrespective of the degree of generative polyploidy, aneuploidies, etc. This term was lacking in the terminology and is for reasons of linguistic consistency indispensable. The abbreviated terms for monoploid and holoploid genome size are, respectively, Cx-value and C-value. Quantitative data on genome size should always indicate the C-level by a numerical prefix, such as 1C, 1Cx, 2C, etc. The proposed conventions cover general fundamental aspects relating to genome size in plants and animals, but do not treat in detail cytogenetic particularities (e.g. haploids, hybrids, etc.) which will need minor extensions of the present scheme in a future paper.

title: Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)
abstract: Polyploidy, or whole genome duplication, has played a major role in the evolution of many eukaryotic lineages. Although the prevalence of polyploidy in plants is well documented, the molecular and cytological consequences are understood largely from newly formed polyploids (neopolyploids) that have been grown experimentally. Classical cytological and molecular cytogenetic studies both have shown that experimental neoallopolyploids often have meiotic irregularities, producing chromosomally variable gametes and progeny; however, little is known about the extent or duration of chromosomal variation in natural neoallopolyploid populations. We report the results of a molecular cytogenetic study on natural populations of a neoallopolyploid, Tragopogon miscellus, which formed multiple times in the past 80 y. Using genomic and fluorescence in situ hybridization, we uncovered massive and repeated patterns of chromosomal variation in all populations. No population was fixed for a particular karyotype; 76% of the individuals showed intergenomic translocations, and 69% were aneuploid for one or more chromosomes. Importantly, 85% of plants exhibiting aneuploidy still had the expected chromosome number, mostly through reciprocal monosomy-trisomy of homeologous chromosomes (1:3 copies) or nullisomy-tetrasomy (0:4 copies). The extensive chromosomal variation still present after ca. 40 generations in this biennial species suggests that substantial and prolonged chromosomal instability might be common in natural populations after whole genome duplication. A protracted period of genome instability in neoallopolyploids may increase opportunities for alterations to genome structure, losses of coding and noncoding DNA, and changes in gene expression.

title: Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae)
abstract: Cytological studies have shown many newly formed allopolyploids (neoallopolyploids) exhibit chromosomal variation as a result of meiotic irregularities, but few naturally occurring neoallopolyploids have been examined. Little is known about how long chromosomal variation may persist and how it might influence the establishment and evolution of allopolyploids in nature. In this study we assess chromosomal composition in a natural neoallotetraploid, Tragopogon mirus, and compare it with T. miscellus, which is an allotetraploid of similar age (~40 generations old). We also assess whether parental gene losses in T. mirus correlate with entire or partial chromosome losses. Of 37 T. mirus individuals that were karyotyped, 23 (62%) were chromosomally additive of the parents, whereas the remaining 14 individuals (38%) had aneuploid compositions. The proportion of additive versus aneuploid individuals differed from that found previously in T. miscellus, in which aneuploidy was more common (69%; Fisher’s exact test, P=0.0033). Deviations from parental chromosome additivity within T. mirus individuals also did not reach the levels observed in T. miscellus, but similar compensated changes were observed. The loss of T. dubius-derived genes in two T. mirus individuals did not correlate with any chromosomal changes, indicating a role for smaller-scale genetic alterations. Overall, these data for T. mirus provide a second example of prolonged chromosomal instability in natural neoallopolyploid populations.

title: Genomic Plasticity in Polyploid Wheat
abstract: The importance of hybridization and polyploidization in wheat speciation has been recognized for close to a century (Sakamura 1918; Kihara 1919, 1924, 1954; Percival 1921; Sax 1927). Following these pioneering works, it quickly became apparent that polyploid wheats are not the sum of their constituent genomes. This is not unexpected because the nascent hybrids/polyploids are equipped with a complex set of regulatory elements and of copy number variation that originate from two or more divergent genomes and that generate novel types of interactions and dosage effects. Moreover, they have to adjust at the cytological level, at the level of gene expression, and at the protein level. They also have to maintain genome stability through the regulation of meiotic pairing and recombination, the orchestration of cell division, and the silencing of transposons. The recent studies described here provide an impressive account with regard to the extent and the rapid time course at which a new genetic variant was established upon hybridization and polyploidization. We describe here the current knowledge on the changes that occurred in the wheat genome upon allopolyploidization, starting from the early evolutionary and cytological studies to the recent genomic analyses.

title: DYNAMICS OF POLYPLOID FORMATION IN TRAGOPOGON (ASTERACEAE): RECURRENT FORMATION, GENE FLOW, AND POPULATION STRUCTURE
abstract: Polyploidy is a major feature of angiosperm evolution and diversification. Most polyploid species have formed multiple times, yet we know little about the genetic consequences of recurrent formations. Among the clearest examples of recurrent polyploidy are Tragopogon mirus and T. miscellus (Asteraceae), each of which has formed repeatedly in the last ∼80 years from known diploid progenitors in western North America. Here, we apply progenitor‐specific microsatellite markers to examine the genetic contributions to each tetraploid species and to assess gene flow among populations of independent formation. These data provide fine‐scale resolution of independent origins for both polyploid species. Importantly, multiple origins have resulted in considerable genetic variation within both polyploid species; however, the patterns of variation detected in the polyploids contrast with those observed in extant populations of the diploid progenitors. The genotypes detected in the two polyploid species appear to represent a snapshot of historical population structure in the diploid progenitors, rather than modern diploid genotypes. Our data also indicate a lack of gene flow among polyploid plants of independent origin, even when they co‐occur, suggesting potential reproductive barriers among separate lineages in both polyploid species.

title: Partitioning diversity into independent alpha and beta components.
abstract: Existing general definitions of beta diversity often produce a beta with a hidden dependence on alpha. Such a beta cannot be used to compare regions that differ in alpha diversity. To avoid misinterpretation, existing definitions of alpha and beta must be replaced by a definition that partitions diversity into independent alpha and beta components. Such a unique definition is derived here. When these new alpha and beta components are transformed into their numbers equivalents (effective numbers of elements), Whittaker's multiplicative law (alpha x beta = gamma) is necessarily true for all indices. The new beta gives the effective number of distinct communities. The most popular similarity and overlap measures of ecology (Jaccard, Sorensen, Horn, and Morisita-Horn indices) are monotonic transformations of the new beta diversity. Shannon measures follow deductively from this formalism and do not need to be borrowed from information theory; they are shown to be the only standard diversity measures which can be decomposed into meaningful independent alpha and beta components when community weights are unequal.

title: Measurement of biological information with applications from genes to landscapes
abstract: Biological diversity is quantified for reasons ranging from primer design, to bioprospecting, and community ecology. As a common index for all levels, we suggest Shannon's SH, already used in information theory and biodiversity of ecological communities. Since Lewontin's first use of this index to describe human genetic variation, it has been used for variation of viruses, splice‐junctions, and informativeness of pedigrees. However, until now there has been no theory to predict expected values of this index under given genetic and demographic conditions. We present a new null theory for SH at the genetic level, and show that this index has advantages including (i) independence of measures at each hierarchical level of organization; (ii) robust estimation of genetic exchange over a wide range of conditions; (iii) ability to incorporate information on population size; and (iv) explicit relationship to standard statistical tests. Utilization of this index in conjunction with other existing indices offers powerful insights into genetic processes. Our genetic theory is also extendible to the ecological community level, and thus can aid the comparison and integration of diversity at the genetic and community levels, including the need for measures of community diversity that incorporate the genetic differentiation between species.

title: Entropy and Information Approaches to Genetic Diversity and its Expression: Genomic Geography
abstract: This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon’s entropy-based diversity is the standard for ecological communities. The exponentials of Shannon’s and the related “mutual information” excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy and information allows integrated modeling of diversity along one DNA sequence, and between different sequences within and among populations, species, etc. The aim is to identify the formal connections between genetic diversity and the flow of information to and from the environment.

title: An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation
abstract: Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require ‘common currency’ translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi‐parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum‐spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (Nep < Nen), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation.

title: Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss).
abstract: Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.



We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium



Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium



Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.

title: Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses).
abstract: UNLABELLED



PREMISE OF THE STUDY
The Sphagnopsida, an early-diverging lineage of mosses (phylum Bryophyta), are morphologically and ecologically unique and have profound impacts on global climate. The Sphagnopsida are currently classified in two genera, Sphagnum (peat mosses) with some 350-500 species and Ambuchanania with one species. An analysis of phylogenetic relationships among species and genera in the Sphagnopsida were conducted to resolve major lineages and relationships among species within the Sphagnopsida. •



Phylogenetic analyses of nucleotide sequences from the nuclear, plastid, and mitochondrial genomes (11 704 nucleotides total) were conducted and analyzed using maximum likelihood and Bayesian inference employing seven different substitution models of varying complexity. 
Phylogenetic analyses resolved three lineages within the Sphagnopsida: (1) Sphagnum sericeum, (2) S. inretortum plus Ambuchanania leucobryoides, and (3) all remaining species of Sphagnum. Sister group relationships among these three clades could not be resolved, but the phylogenetic results indicate that the highly divergent morphology of A. leucobryoides is derived within the Sphagnopsida rather than plesiomorphic. A new classification is proposed for class Sphagnopsida, with one order (Sphagnales), three families, and four genera. •



The Sphagnopsida are an old lineage within the phylum Bryophyta, but the extant species of Sphagnum represent a relatively recent radiation. It is likely that additional species critical to understanding the evolution of peat mosses await discovery, especially in the southern hemisphere.

title: The Peat Moss Sphagnum cuspidatum in Australia: Microsatellites Provide a Global Perspective
abstract: The distribution of Sphagnum cuspidatum has been subject to controversy. Although historically reported from all continents except Antarctica recent authors consider S. cuspidatum to be endemic to Europe and eastern North America. Microsatellites from Australian plants morphologically identified as S. cuspidatum were compared to microsatellites of plants morphologically identified as S. cuspidatum collected from other regions. The species was found to occur in Australia as well as on every continent except Antarctica. The sample most closely related to the Australian plants was collected in the Philippines, and samples from Australia, the Philippines, Colombia, and Equatorial Guinea formed a subclade within S. cuspidatum. Microsatellites further show that S. cuspidatum is one of the parental species of the double allopolyploid S. falcatulum, a Holantarctic species which is reported from Tasmania, New Zealand, and Chile.

title: The double allopolyploid Sphagnum ×falcatulum (Sphagnaceae) in Tierra del Fuego, a Holantarctic perspective
abstract: A Holantarctic species, the inter-subgeneric allopolyploid Sphagnum ×falcatulum s.l. is a cryptic species complex composed of allodiploid and allotriploid cytotypes. The allotriploid plants are double allopolyploids (one of just two reported for bryophytes), with the allodiploid cytotype being one parent. Using a combination of microsatellites, nucleotide sequences, and morphological characters, allotriploid S. ×falcatulum is shown to be the most widespread Sphagnum species in the Holantarctic, with genetically documented populations in South America (Tierra del Fuego), New Zealand (South Island), and Australia (Macquarie Island, Tasmania). It is further concluded that six Sphagnum species described from the Tierra del Fuego Archipelago (TDF) of South America and a seventh described from South Island, New Zealand are synonymous with the allotriploid cytotype of S. ×falcatulum. The synonymized species include five named by Heikki Roivainen in 1937, S. ×ehyalinum, and S. subditivum. Allotriploid S. ×falcatulum is the predominant, perhaps the only, subgenus Cuspidata species present in TDF and immediate vicinity. The combination of low genetic diversity and an apparent absence of sexual reproduction indicate that the TDF population of the dioicous allotriploid S. ×falcatulum was likely founded by one or a limited number of individuals. The same is apparently the case for Macquarie I. and Tasmanian populations of allotriploid S. ×falcatulum. Several lines of evidence, including high genetic diversity, frequent sporophyte production, and the occurrence of the allodiploid parent, suggest that allotriploid S. ×falcatulum likely evolved in New Zealand.

title: Update on the Holantarctic Sphagnum ×falcatulum s.l. (Sphagnaceae) complex: S. irritans is associated with the allo-diploid plants
abstract: The Holantarctic Sphagnum ×falcatulum s.l. is a cryptic species complex comprised of the allo-allo-triploid S. ×falcatulum s.s. and its immediate progenitors: the haploid (S. cuspidatum) and an unnamed allo-diploid species. The Holantarctic distributions of the members of this complex are presently unclear. Prior genetic study has shown that (1) amphi-Pacific S. ×falcatulum s.s. is the most widespread Sphagna in the Holantarctic, (2) S. cuspidatum is present in Queensland, Australia, and (3) the allo-diploid plants occur on South Island, New Zealand. Using genetic and morphological analyses, we document the occurrence of S. ×falcatulum s.s. on mainland Australia and on North Island, New Zealand as well as the occurrence of the allo-diploid plants on Chatham Island, New Zealand. The allo-diploid plants on South Island and those on Chatham Island are found to be closely related and the Chatham Island population appears to have been established by long distance dispersal. It is concluded that the type of S. irritans, which was collected on Chatham Island, and the three Chatham Island allo-diploid specimens are the same taxon. Thus the allo-diploid plants are assigned to S. ×irritans. Having a history of inter-subgeneric hybridisation, there is notable morphological variation associated with S. ×irritans. Although several morphotypes occur in the South Island population, just one morphotype was detected among the Chatham Island specimens examined. Further study is required to determine both the genetic divergence between these two island populations as well as the taxonomic status of the various morphotypes associated with S. ×irritans.

title: Invisible in plain sight: recurrent double allopolyploidy in the African Sphagnum ×planifolium (Sphagnaceae)
abstract: Microsatellites, nucleotide sequences, and flow cytometry were used to determine if two sympatricAfrican peat mosses (Sphagnum ×planifolium and S. ×slooveri) had a history of inter-subgeneric hybridization and to assess their phylogenetic relationship. Both species had previously not been considered to be hybrids. Sphagnum ×slooveri was found to be gametophytically allodiploid. Its maternal parent was S. recurvum (or a closely related species) of subg. Cuspidata and its paternal parent was an unidentified species from the S. africanum complex of subg. Subsecunda. Sphagnum ×planifolium was found to be a cryptic species complex of gametophytic allotriploids, with recurrent double allopolyploidy resulting in at least two evolutionarily distinct lineages. The maternal parent of both lineages was S. ×slooveri. The paternal parent of one lineage (S. ×planifolium I) was an unidentified haploid associated with the S. capense complex of subgenus Subsecunda while the paternal parent of the second lineage (S. ×planifolium II) was S. cuspidatum (or a closely related species) of subg. Cuspidata. Four species having a history of double allopolyploidy are now documented in bryophytes; all are gametophytically allotriploid, all are in Sphagnum, and all had an allodiploid parent having a history of inter-subgeneric hybridization. It is postulated that a high genetic divergence between subgenomes may facilitate double allopolyploidy in Sphagnum. Genetic analyses reveal that S. pulchricoma, S. recurvum and S. sancto-josephense form a complex of non-hybrid and hybrid plants in the Neotropics, with the hybrids having a history of hybridization between S. cuspidatum and S. recurvum. Reticulate evolution needs more attention in bryophyte studies and this requires experimental designs sufficiently robust to detect it.

title: Systematics of Sphagnum section Sphagnum in New Zealand: A microsatellite‐based analysis
abstract: The systematics of Sphagnum section Sphagnum in New Zealand has been controversial. Two species are currently recognised in the New Zealand flora, S. cristatum and S. perichaetiale, but the presence of the widespread S. magellanicum has been debated. An analysis of 16 microsatellite loci shows that the gametophytes of Sphagnum perichaetiale appear to have one monoploid set of chromosomes (i.e., are haploid). Fixed heterozygosity at 10 loci indicates that S. cristatum is an alloploid. A red morphotype of S. cristatum, similar in macroappearance to S. magellanicum, is not genetically differentiated from the more common brown‐green morphotypes of S. cristatum. Although analysis of the microsatellite data for S. cristatum showed most of the genetic variation to be within populations, significant variation did occur among populations within regions and also between regions.

title: Genetic variation in three Chinese peat mosses (Sphagnum) based on microsatellite markers, with primer information and analysis of ascertainment bias
abstract: Primer sequences are provided for amplification of 21 microsatellite-containing loci in Sphagnum. Although these primers were developed for species in Sphagnum section Subsecunda, they amplify microsatellite loci in most species that have been tested across the genus Sphagnum. Results are described from a survey of genetic variation in three species of Sphagnum collected in China: S. junghuhnianum in section Acutifolia, and S. palustre and S. imbricatum in section Sphagnum. Six and eight multilocus genotypes were detected within one population each of S. junghuhnianum and S. palustre, respectively. Four populations of S. imbricatum were sampled; they vary substantially in allele frequencies and in the amount of genetic diversity detected; overall, approximately 40% of the genetic variation sampled within S. imbricatum could be attributed to differentiation among populations. Microsatellite profiles indicate that S. palustre gametophytes are diploid whereas those of S. junghuhnianum and S. imbricatum are haploid.

title: A comparison of the genetic infrastructure of the Ye'cuana and the Yanomama: a likelihood analysis of genotypic variation among populations.
abstract: A general procedure is described for measuring and testing population differences in gametic frequencies. The total dispersion among populations is subdivided in hierachical fashion. The multiple-locus treatment is simply the sum of the single-locus analyses, provided gametic equilibrium obtains among the loci. In the event that gametic equilibrium does not obtain, correlations among loci need to be dealt with.--The analysis is then used to examine the genetic infrastructure of two Indian tribes from South America, the Ye'cuana (Makiritare) and the Yanomama. From historical evidence, we may identify several "clusters" of villages within each tribe. The demographic and cultural practices affecting village formation and the maintenance of peer integrity are rather different in these tribes, however, and lead us to postulate rather different patterns of genetic variation among villages. Analyses of five codominant two-allele loci, four dominant two-allele loci and two complex loci (with four codominant haplotypes each) demonstrate that Yanomama clusters are more disparate than Ye'cuana clusters, as would have been predicted on sociocultural grounds.

title: Independence of alpha and beta diversities.
abstract: Denny, M., and S. Gaines. 2000. Chance in biology: using probability to explore nature. Princeton University Press, Princeton, New Jersey, USA. Jost, L. 2006. Entropy and diversity. Oikos 113:363-375. Jost, L. 2007. Partitioning diversity into independent alpha and beta components. Ecology 88:2427-2439. Quinn, G. P., and M. J. Keough. 2002. Experimental design and data analysis for biologists.  Ricotta, C. 2005. On hierarchical diversity decomposition.  Computing additive beta-diversity from presence and absence scores: a critique and alternative parameters.  Sokal, R. R., and F.  Third edition. Freeman and Company, New York, New York, USA. Tijms, H. 2004. Understanding probability: chance rules in everyday life.  Measuring beta diversity with presence-absence data.

title: High genetic diversity in a remote island population system: sans sex.
abstract: 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.