Stuart F. McDaniel

Are all sex chromosomes created equal

Three principal types of chromosomal sex determination are found in nature: male heterogamety (XY systems, as in mammals), female heterogamety (ZW systems, as in birds), and haploid phase determination (UV systems, as in some algae and bryophytes). Although these systems share many common features, there are important biological differences between them that have broad evolutionary and genomic implications. Here we combine theoretical predictions with empirical observations to discuss how differences in selection, genetic properties and transmission uniquely shape each system. We elucidate how the differences among these systems can be exploited to gain insights about general evolutionary processes, genome structure, and gene expression. We suggest directions for research that will greatly increase our general understanding of the forces driving sex-chromosome evolution in diverse organisms.

PHYLOGEOGRAPHIC STRUCTURE AND CRYPTIC SPECIATION IN THE TRANS-ANTARCTIC MOSS PYRRHOBRYUM MNIOIDES

Abstract Many bryophyte species have distributions that span multiple continents. The hypotheses historically advanced to explain such distributions rely on either long-distance spore dispersal or slow rates of morphological evolution following ancient continental vicariance events. We use phylogenetic analyses of DNA sequence variation at three chloroplast loci (atpB-rbcL spacer, rps4 gene, and trnL intron and 3′ spacer) to examine these two hypotheses in the trans-Antarctic moss Pyrrhobryum mnioides. We find: (1) reciprocal monophyly of Australasian and South American populations, indicating a lack of intercontinental dispersal; (2) shared haplotypes between Australia and New Zealand, suggesting recent or ongoing migration across the Tasman Sea; and (3) reciprocal monophyly among Patagonian and neotropical populations, suggesting no recent migration along the Andes. These results corroborate experimental work suggesting that spore features may be critical determinants of species range. We use the mid-Miocene development of the Atacama Desert, 14 million years ago, to calibrate a molecular clock for the tree. The age of the trans-Antarctic disjunction is estimated to be 80 million years ago, consistent with Gondwanan vicariance, making it among the most ancient documented cases of cryptic speciation. These data are in accord with niche conservatism, but whether the morphological stasis is a product of stabilizing selection or phylogenetic constraint is unknown.

A Linkage Map Reveals a Complex Basis for Segregation Distortion in an Interpopulation Cross in the Moss Ceratodon purpureus

We report the construction of a linkage map for the moss Ceratodon purpureus (n = 13), based on a cross between geographically distant populations, and provide the first experimental confirmation of maternal chloroplast inheritance in bryophytes. From a mapping population of 288 recombinant haploid gametophytes, genotyped at 121 polymorphic AFLP loci, three gene-based nuclear loci, one chloroplast marker, and sex, we resolved 15 linkage groups resulting in a map length of ∼730 cM. We estimate that the map covers more than three-quarters of the C. purpureus genome. Approximately 35% of the loci were sex linked, not including those in recombining pseudoautosomal regions. Nearly 45% of the loci exhibited significant segregation distortion (α = 0.05). Several pairs of unlinked distorted loci showed significant deviations from multiplicative genotypic frequencies, suggesting that distortion arises from genetic interactions among loci. The distorted autosomal loci all exhibited an excess of the maternal allele, suggesting that these interactions may involve nuclear–cytoplasmic factors. The sex ratio of the progeny was significantly male biased, and the pattern of nonrandom associations among loci indicates that this results from interactions between the sex chromosomes. These results suggest that even in interpopulation crosses, multiple mechanisms act to influence segregation ratios.

Selective sweeps and intercontinental migration in the cosmopolitan moss Ceratodon purpureus (Hedw.) Brid.

The moss Ceratodon purpureus has long been used as a model system in plant development and physiology. However, the molecular population genetics of the species remains virtually unexplored. In this study, we used population genetic analyses of DNA sequence data from three unlinked loci (atpB‐rbcL spacer, adk, and phy2) to examine biogeographical patterns in a global sample of this species. The three loci differed significantly in mutation frequency spectra and implied population structure. Pairs of haplotypes from single populations were frequently more divergent than haplotypes sampled from widely disjunct populations. In the atpB‐rbcL spacer and adk samples, Australasian haplotypes were more closely related to Northern Hemisphere haplotypes than to haplotypes found in the equatorial regions. In contrast, the phy2 sample showed that the north and south temperate regions were genetically divergent, with the equatorial regions intermediate. Maximum‐likelihood estimates (MLE) of the rates of migration between the two hemispheres were significantly different for the two nuclear genes. The frequency spectra of mutations indicated that differences in implied population structure among the three loci resulted from directional selection on the chloroplast genome and on the chromosomal segment containing adk. Collectively, these data suggest that long‐distance migration within the Northern Hemisphere and Australasian regions is common (relative to the mutation rate) and that migration between these two regions, potentially via equatorial populations, is more frequent than migration among equatorial populations.

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts

Unraveling the macroevolutionary history of bryophytes, which arose soon after the origin of land plants but exhibit substantially lower species richness than the more recently derived angiosperms, has been challenged by the scarce fossil record. Here we demonstrate that overall estimates of net species diversification are approximately half those reported in ferns and ∼30% those described for angiosperms. Nevertheless, statistical rate analyses on time-calibrated large-scale phylogenies reveal that mosses and liverworts underwent bursts of diversification since the mid-Mesozoic. The diversification rates further increase in specific lineages towards the Cenozoic to reach, in the most recently derived lineages, values that are comparable to those reported in angiosperms. This suggests that low diversification rates do not fully account for current patterns of bryophyte species richness, and we hypothesize that, as in gymnosperms, the low extant bryophyte species richness also results from massive extinctions.

Bryophyte dispersal inferred from colonization of an introduced substratum on Whiteface Mountain, New York

A long-standing debate in bryophyte biogeography concerns the frequency of long-distance spore dispersal. The diversity of bryophytes on mortared rock walls along the Veterans Memorial Highway on Whiteface Mountain, New York, USA, was studied to document the recruitment of species over the 65 years since the highway was constructed. The highway is situated in the Adirondack Mountains, a relatively unpopulated region with a largely acidic flora. The introduction of mortar has increased the bryophyte diversity by 50% above that of native lithic substrata on the mountain. The composition of the native and mortar floras differed greatly, suggesting that the walls were not colonized by locally abundant ruderal species. Many of the species sampled on the walls are typically found only in lower elevation forested sites, distant (∼5 km or more) from the highway, and not on anthropogenic calcium carbonate. These results suggest that a bryophyte community consisting of common and uncommon species assembled from distant sites at the rate of at least one species per year in the last 65 years. These data provide the ecological context for experimental and phylogeographic studies and suggest that some bryophytes may be capable of routine dispersal over distances of at least 5 km.

GENETIC CORRELATIONS DO NOT CONSTRAIN THE EVOLUTION OF SEXUAL DIMORPHISM IN THE MOSS CERATODON PURPUREUS

Abstract The trajectory of phenotypic evolution is constrained in the short term by genetic correlations among traits. However, the extent to which genetic correlations impose a lasting constraint is generally unknown. Here, I examine the genetic architecture of life‐history variation in male and female gametophytes from two populations of the moss Ceratodon purpureus, focusing on genetic correlations within and between the sexes. A significant negative correlation between allocation to vegetative and reproductive tissue was evident in males of both populations, but not females. All traits showed between‐sex correlations of significantly less than one, indicating additive genetic variance for sexual dimorphism. The degree of dimorphism for traits was significantly negatively associated with the strength of the between‐sex correlation. The structure of genetic correlations among life‐history traits was more divergent between the two populations in females than in males. Collectively, these results suggest that genetic correlations do not impose a lasting constraint on the evolution of life‐history variation in the species.

The moss Physcomitrella patens: a novel model system for plant development and genomic studies.

The moss Physcomitrella patens has been used as an experimental organism for more than 80 years. Within the last 15 years, its use as a model to explore plant functions has increased enormously. The ability to use gene targeting and RNA interference methods to study gene function, the availability of many tools for comparative and functional genomics (including a sequenced and assembled genome, physical and genetic maps, and >250,000 expressed sequence tags), and a dominant haploid phase that allows direct forward genetic analysis have all led to a surge of new activity. P. patens can be easily cultured and spends the majority of its life cycle in the haploid state, allowing the application of experimental techniques similar to those used in microbes and yeast. Its development is relatively simple, and it generates only a few tissues that contain a limited number of cell types. Although mosses lack vascular tissue, true roots/stems/leaves, and flowers and seeds, many signaling pathways found in angiosperms are intact in moss. For example, the phytohormones auxin, cytokinin, and abscisic acid, as well as the photomorphogenic pigments phytochrome and cryptochrome, are all interwoven into distinct but overlapping pathways and linked to clear developmental phenotypes. In addition, about one quarter of the moss genome contains genes with no known function based on sequence motifs, raising the likelihood of successful discovery efforts to identify new and novel gene functions. The methods outlined in this chapter will enhance the use of the P. patens model system in many laboratories throughout the world. David J. Cove, Pierre-François Perroud, Audra J. Charron, Stuart F. McDaniel, Abha Khandelwal, and Ralph S. Quatrano Department of Biology, Washington University, St. Louis, Missouri 63130 P R O TO CO L S 1 Culturing the Moss Physcomitrella patens, 75 2 Isolation and Regeneration of Protoplasts, 80 3 Somatic Hybridization in P. patens Using PEGinduced Protoplast Fusion, 82 4 Chemical and UV Mutagenesis of Spores and Protonemal Tissue, 84 5 Transformation Using Direct DNA Uptake by Protoplasts, 87 6 Transformation Using T-DNA Mutagenesis, 89 7 Transformation of Gametophytes Using a Biolistic Projectile Delivery System, 91 8 Isolation of DNA, RNA, and Protein from P. patens Gametophytes, 93 This chapter, with full-color images, can be found online at www.cshprotocols.org/emo.

Phylogeography and Phylodemography

Abstract Phylogenetic analyses of infraspecific molecular data in relation to geographic and ecological information has come to be known as phylogeography. Bryophytes offer fertile material for such analyses, which can help clarify long standing biogeographic questions that were intractable before molecular data became available. In particular, molecular data can help distinguish between dispersal and fragmentation explanations for disjunct distributions that characterize many bryophytes at the specific as well as higher levels. Phylodemography is the application of molecular data and phylogenetic analyses to infer past changes in population size within species. Grounded in coalescence theory from population genetics, this new field could be fruitfully applied to bryophytes. Combining phylogeography and phylodemography yields a powerful strategy for elucidating evolutionary processes.

RECURRENT EVOLUTION OF DIOECY IN BRYOPHYTES

The origin and maintenance of separate sexes (dioecy) is an enduring evolutionary puzzle. Although both hermaphroditism and dioecy occur in many diverse clades, we know little about the long‐term evolutionary consequences of changing sexual system. Here we find evidence for at least 133 transitions between sexual systems in mosses, representing an almost unparalleled lability in the evolution of their sexual systems. Furthermore, in contrast to predictions, the transition rate from hermaphroditism to dioecy was approximately twice as high as the reverse transition. Our results also suggest that hermaphrodites may have higher rates of diversification than dioecious mosses. These results illustrate the utility of mosses for understanding the genomic and macroevolutionary consequences of hermaphroditism and dioecy.