Sandra B. Boles

Genetics of Drought Adaptation in Arabidopsis thaliana II. Qtl Analysis of a New Mapping Population, Kas-1 × Tsu-1

Abstract Despite compelling evidence that adaptation to local climate is common in plant populations, little is known about the evolutionary genetics of traits that contribute to climatic adaptation. A screen of natural accessions of Arabidopsis thaliana revealed Tsu-1 and Kas-1 to be opposite extremes for water-use efficiency and climate at collection sites for these accessions differs greatly. To provide a tool to understand the genetic basis of this putative adaptation, Kas-1 and Tsu-1 were reciprocally crossed to create a new mapping population. Analysis of F3 families showed segregating variation in both δ13C and transpiration rate, and as expected these traits had a negative genetic correlation (rg=− 0.3). 346 RILs, 148 with Kas-1 cytoplasm and 198 with Tsu-1 cytoplasm, were advanced to the F9 and genotyped using 48 microsatellites and 55 SNPs for a total of 103 markers. This mapping population was used for QTL analysis of δ13C using F9 RIL means. Analysis of this reciprocal cross showed a large effect of cytoplasmic background, as well as two QTL for δ13C. The Kas-1 × Tsu-1 mapping population provides a powerful new resource for mapping QTL underlying natural variation and for dissecting the genetic basis of water-use efficiency differences.

Polarity of peatmoss (Sphagnum) evolution: who says bryophytes have no roots?

The class Sphagnopsida (Bryophyta) includes two genera: Ambuchanania and Sphagnum. Ambuchanania contains just one rare species known from two Tasmanian localities, but Sphagnum comprises a speciose clade of mosses that dominates many wetland ecosystems, especially in the boreal zone of the Northern Hemisphere. Recent phylogenetic analyses have resolved well-supported clades within Sphagnum, but polarizing Sphagnum evolution has been problematic because the genus is so isolated that it is difficult to determine homologies between morphological and/or molecular traits within Sphagnum with those of any potential outgroup. DNA sequences from 16 genomic regions representing the mitochondrial, chloroplast, and nuclear genomes (ca. 16 kilobases) were obtained from 24 species of Sphagnum plus one species each from Takakia and Andreaea in order to resolve a rooted phylogeny. Two tropical species, S. sericeum and S. lapazense, were resolved as sister to the rest of the genus and are extremely divergent from all other sphagna. The main Sphagnum lineage consists of two clades; one includes the sections Sphagnum, Rigida, and Cuspidata, and the other includes Subsecunda, Acutifolia, and Squarrosa. The placement of section Subsecunda is weakly supported, but other nodes are strongly supported by maximum parsimony, maximum likelihood, and Bayesian analyses. In addition to homogeneous Bayesian analyses, heterogeneous models were employed to account for different patterns of nucleotide substitution among genomic regions.

Phylogenetic Relationships among the Mosses Based on Heterogeneous Bayesian Analysis of Multiple Genes from Multiple Genomic Compartments

Abstract Nucleotide sequences from eight nuclear, chloroplast, and mitochondrial genes were obtained from 30 mosses (plus four outgroup liverworts) in order to resolve phylogenetic relationships among the major clades of division Bryophyta. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood (ML), and Bayesian inference. Inferences were compared from Bayesian analyses using homogeneous and several heterogeneous models. Estimates of clade confidence were based on bootstrap analyses, posterior probabilities (in Bayesian analyses) and novel combined approaches. Most ingroup relationships were congruent among analyses, but support for individual clades depended on the analytical approach. Increasingly parameterized models of nucleotide substitution in the likelihood analyses provided significantly higher goodness-of-fit to the data. The results suggest that 1) the Bryophyta, including Sphagnum and Takakia, are monophyletic, 2) Andreaea and Andreaeobryum form a monophyletic group, 3) Oedipodium griffithianum is sister to all other operculate taxa, 4) mosses with nematodontous peristomes are paraphyletic and basal to arthrodontous mosses, 5) Diphyscium is sister to all other arthrodontous mosses, 6) Encalypta is sister to the Funariaceae, and 6) mosses with diplolepideous-alternate peristomes form a monophyletic group. Implications of the phylogenetic hypothesis for morphological evolution in mosses include 1) a pseudopodium has arisen independently in Sphagnum and Andreaea, 2) the mucilage hairs of Andreaeobryum and Takakia are non-homologous, 3) the stomata found in Sphagnum are not homologous to those of other mosses, and 4) that stomata were absent in the ancestor of all mosses.

PHYLOGENETIC EVIDENCE OF A RAPID RADIATION OF PLEUROCARPOUS MOSSES (BRYOPHYTA)

Abstract Pleurocarpous mosses, characterized by lateral female gametangia and highly branched, interwoven stems, comprise three orders and some 5000 species, or almost half of all moss diversity. Recent phylogenetic analyses resolve the Ptychomniales as sister to the Hypnales plus Hookeriales. Species richness is highly asymmetric with approximately 100 Ptychomniales, 750 Hookeriales, and 4400 Hypnales. Chloroplast DNA (cpDNA) sequences were obtained to compare partitioning of molecular diversity among the orders with estimates of species richness, and to test the hypothesis that either the Hookeriales or Hypnales underwent a period (or periods) of exceptionally rapid diversification. Levels of biodiversity were quantified using explicitly historical “phylogenetic diversity” and non‐historical estimates of standing sequence diversity. Diversification rates were visualized using lineage‐through‐time (LTT) plots, and statistical tests of alternative diversification models were performed using the methods of Paradis (1997). The effects of incomplete sampling on the shape of LTT plots and performance of statistical tests were investigated using simulated phylogenies with incomplete sampling. Despite a much larger number of accepted species, the Hypnales contain lower levels of (cpDNA) biodiversity than their sister group, the Hookeriales, based on all molecular measures. Simulations confirm previous results that incomplete sampling yields diversification patterns that appear to reflect a decreasing rate through time, even when the true phylogenies were simulated with constant rates. Comparisons between simulated results and empirical data indicate that a constant rate of diversification cannot be rejected for the Hookeriales. The Hypnales, however, appear to have undergone a period of exceptionally rapid diversification for the earliest 20% of their history.

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.

Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling

Global climate changes sometimes spark biological radiations that can feed back to effect significant ecological impacts. Northern Hemisphere peatlands dominated by living and dead peatmosses (Sphagnum) harbor almost 30% of the global soil carbon pool and have functioned as a net carbon sink throughout the Holocene, and probably since the late Tertiary. Before that time, northern latitudes were dominated by tropical and temperate plant groups and ecosystems. Phylogenetic analyses of mosses (phylum Bryophyta) based on nucleotide sequences from the plastid, mitochondrial, and nuclear genomes indicate that most species of Sphagnum are of recent origin (ca. <20 Ma). Sphagnum species are not only well-adapted to boreal peatlands, they create the conditions that promote development of peatlands. The recent radiation that gave rise to extant diversity of peatmosses is temporally associated with Miocene climatic cooling in the Northern Hemisphere. The evolution of Sphagnum has had profound influences on global biogeochemistry because of the unique biochemical, physiological, and morphological features of these plants, both while alive and after death.

Phylogeny, Species Delimitation, and Recombination in Sphagnum Section Acutifolia

Abstract Nucleotide sequences for six nuclear loci and one chloroplast region were used to reconstruct phylogenetic relationships in Sphagnum section Acutifolia. The combined data matrix, which includes 136 accessions (129 ingroup taxa and seven outgroups) and 5126 nucleotide sites, was analyzed using Bayesian inference. Most of the individual morphospecies commonly recognized in the section were represented by multiple populations, in some cases by up to 16 accessions from throughout the Northern Hemisphere. Results of the combined seven-locus analysis resolved many of the species as monophyletic, but the deeper nodes were generally without support. Separate analyses of single-locus data sets revealed significant conflicts, indicating gene flow among both closely and more distantly related species within the section. The sequence data allowed likely parentage to be identified for several species of hybrid origin, and identified individual accessions that appear to be genetic admixtures. Taxonomic conclusions that can be made from the analyses include: 1. Sphagnum wulfianum and S. aongstroemii should both be included in section Acutifolia, 2. S. subtile cannot be separated from S. capillifolium, and the two should be synonymized, 3. S. capillifolium and S. rubellum each contain a monophyletic core of populations and should be retained as separate species, but 4. S. rubellum cannot be separated from S. andersonianum and S. bartlettianum and the three should be merged, 5. S. tenerum is highly differentiated from S. capillifolium and should be treated as a separate species, 6. interspecific mixed ancestry is demonstrated for S. russowii (a likely allopolyploid), S. skyense, S. arcticum, and S. olafii. Interspecific recombination appears to be rather common in section Acutifolia, yet species, for the most part, maintain cohesiveness.

A phylogenetic delimitation of the "Sphagnum subsecundum complex" (Sphagnaceae, Bryophyta).

A seemingly obvious but sometimes overlooked premise of any evolutionary analysis is delineating the group of taxa under study. This is especially problematic in some bryophyte groups because of morphological simplicity and convergence. This research applies information from nucleotide sequences for eight plastid and nuclear loci to delineate a group of northern hemisphere peat moss species, the so-called Sphagnum subsecundum complex, which includes species known to be gametophytically haploid or diploid (i.e., sporophytically diploid-tetraploid). Despite the fact that S. subsecundum and several species in the complex have been attributed disjunct ranges that include all major continents, phylogenetic analyses suggest that the group is actually restricted to Europe and eastern North America. Plants from western North America, from California to Alaska, which are morphologically similar to species of the S. subsecundum complex in eastern N. America and Europe, actually belong to a different deep clade within Sphagnum section Subsecunda. One species often considered part of the S. subsecundum complex, S. contortum, likely has a reticulate history involving species in the two deepest clades within section Subsecunda. Nucleotide sequences have a strong geographic structure across the section Subsecunda, but shallow tip clades suggest repeated long-distance dispersal in the section as well.

One haploid parent contributes 100% of the gene pool for a widespread species in northwest North America.

The monoicous peatmoss Sphagnum subnitens has a tripartite distribution that includes disjunct population systems in Europe (including the Azores), northwestern North America and New Zealand. Regional genetic diversity was highest in European S. subnitens but in northwestern North America, a single microsatellite‐based multilocus haploid genotype was detected across 16 sites ranging from Coos County, Oregon, to Kavalga Island in the Western Aleutians (a distance of some 4115 km). Two multilocus haploid genotypes were detected across 14 sites on South Island, New Zealand. The microsatellite‐based regional genetic diversity detected in New Zealand and North American S. subnitens is the lowest reported for any Sphagnum. The low genetic diversity detected in both of these regions most likely resulted from a founder event associated with vegetative propagation and complete selfing, with one founding haploid plant in northwest North America and two in New Zealand. Thus, one plant appears to have contributed 100% of the gene pool for the population systems of S. subnitens occurring in northwest North America, and this is arguably the most genetically uniform group of plants having a widespread distribution yet detected. Although having a distribution spanning 12.5° of latitude and 56° of longitude, there was no evidence of any genetic diversification in S. subnitens in northwest North America. No genetic structure was detected among the three regions, and it appears that European plants of S. subnitens provided the source for New Zealand and northwest North American populations.

Cytotype variation and allopolyploidy in North American species of the Sphagnum subsecundum complex (Sphagnaceae)

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.