Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene

In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring the genetic and chromosomal changes involved in the evolution of dioecy, but is mainly based on data from a single locus (ITS). To establish the order of events more clearly, and inform outgroup choice, we therefore carried out (i) multi-nuclear-gene phylogenetic analyses of 14 Silene species (including 7 hermaphrodite or gynodioecious species), representing species from both Silene clades with dioecious members, plus a more distantly related outgroup, and (ii) a BayesTraits character analysis of the evolution of dioecy. We confirm two origins of dioecy within this genus in agreement with recent work on comparing sex chromosomes from both clades with dioecious species. We conclude that sex chromosomes evolved after the origin of Silene and within a clade that includes only S. latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of S. viscosa, the probable closest non-dioecious S. latifolia relative among the species included in our study.     

Experimental taxonomy of Silene section Elisanthe (Caryophyllaceae): crossing experiments

Silene section Elisanthe is a well-defined group containing (in Europe) the following species: S. alba, S. diclinis, S. dioica, S. heuffelii and S. marizii (dioecious perennials or biennials) and S. noctifloara (a self-compatible hermaphrodite annual). Crosses were attempted among these species, and between these species and members of other Silene sections.
Crosses among the first five species revealed partial cross-incompatibility with moderate hybrid fertility. S. alba proved especially incompatible with S. diclinis. S. noctiflora would not cross at all with other members of the section. It is suggested that S. noctiflora evolved from a dioecious precursor of S. alba , the species to which it is most similar in morphology, distribution and habitat; hybrid sterility, even without incompatibility, would have assured mutual isolation.
Crosses with species from other sections of Silene have usually either failed consistently or revealed high cross-incompatibility with hybrid sterility. Those crosses which were successful have all been within the boundaries of the old genus Melandrium , or with Lychnis species.     

Evolutionary history of Silene latifolia sex chromosomes revealed by genetic mapping of four genes

The sex chromosomes of dioecious white campion, Silene latifolia (Caryophyllaceae), are of relatively recent origin (10-20 million years), providing a unique opportunity to trace the origin and evolution of sex chromosomes in this genus by comparing closely related Silene species with and without sex chromosomes. Here I demonstrate that four genes that are X-linked in S. latifolia are also linked in nondioecious S. vulgaris, which is consistent with Ohno's (1967) hypothesis that sex chromosomes evolve from a single pair of autosomes. I also report a genetic map for four S. latifolia X-linked genes, SlX1, DD44X, SlX4, and a new X-linked gene SlssX, which encodes spermidine synthase. The order of the genes on the S. latifolia X chromosome and divergence between the homologous X- and Y-linked copies of these genes supports the "evolutionary strata" model, with at least three consecutive expansions of the nonrecombining region on the Y chromosome (NRY) in this plant species.     

DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica

The relatively recent origin of sex chromosomes in the plant genus Silene provides an opportunity to study the early stages of sex chromosome evolution and, potentially, to test between the different population genetic processes likely to operate in nonrecombining chromosomes such as Y chromosomes. We previously reported much lower nucleotide polymorphism in a Y-linked gene (SlY1) of the plant Silene latifolia than in the homologous X-linked gene (SlX1). Here, we report a more extensive study of nucleotide diversity in these sex-linked genes, including a larger S. latifolia sample and a sample from the closely related species Silene dioica, and we also study the diversity of an autosomal gene, CCLS37.1. We demonstrate that nucleotide diversity in the Y-linked genes of both S. latifolia and S. dioica is very low compared with that of the X-linked gene. However, the autosomal gene also has low DNA polymorphism, which may be due to a selective sweep. We use a single individual of the related hermaphrodite species Silene conica, as an outgroup to show that the low SlY1 diversity is not due to a lower mutation rate than that for the X-linked gene. We also investigate several other possibilities for the low SlY1 diversity, including differential gene flow between the two species for Y-linked, X-linked, and autosomal genes. The frequency spectrum of nucleotide polymorphism on the Y chromosome deviates significantly from that expected under a selective-sweep model. However, we detect population subdivision in both S. latifolia and S. dioica, so it is not simple to test for selective sweeps. We also discuss the possibility that Y-linked diversity is reduced due to highly variable male reproductive success, and we conclude that this explanation is unlikely.     

EVOLUTION OF SEX DETERMINATION SYSTEMS WITH HETEROGAMETIC MALES AND FEMALES IN SILENE

The plant genus Silene has become a model for evolutionary studies of sex chromosomes and sex‐determining mechanisms. A recent study performed in Silene colpophylla showed that dioecy and the sex chromosomes in this species evolved independently from those in Silene latifolia, the most widely studied dioecious Silene species. The results of this study show that the sex‐determining system in Silene otites, a species related to S. colpophylla, is based on female heterogamety, a sex determination system that is unique among the Silene species studied to date. Our phylogenetic data support the placing of S. otites and S. colpophylla in the subsection Otites and the analysis of ancestral states suggests that the most recent common ancestor of S. otites and S. colpophylla was most probably dioecious. These observations imply that a switch from XX/XY sex determination to a ZZ/ZW system (or vice versa) occurred in the subsection Otites. This is the first report of two different types of heterogamety within one plant genus of this mostly nondioecious plant family.     

Multiple origins of the ascidian-Prochloron symbiosis: molecular phylogeny of photosymbiotic and non-symbiotic colonial ascidians inferred from 18S rDNA sequences

In the tropics, certain didemnid ascidians harbor the prokaryotic photosymbiont Prochloron. To date, this photosymbiosis has been found in four didemnid genera that include non-symbiotic species. Here, we report the molecular phylogeny of symbiotic and non-symbiotic didemnids based on their 18S rDNA sequences. The data cover all four genera containing symbiotic species and one other genus comprised of only non-symbiotic species. Near-complete nucleotide sequences of 18S rDNAs were determined for four non-didemnid species and 52 didemnid samples (five genera), including 48 photosymbiotic samples collected from the Ryukyu Archipelago, the Great Barrier Reef, Hawaii, and Bali. Our phylogenetic trees indicated a monophyletic origin of the family Didemnidae, as well as each of the didemnid genera. The results strongly support the hypothesis that establishment of the ascidian-Prochloron symbiosis occurred independently in the Didemnidae lineage at least once in each of the genera that possess symbiotic species.     

HOST-PLANT SWITCHES AND THE EVOLUTION OF CHEMICAL DEFENSE AND LIFE HISTORY IN THE LEAF BEETLE GENUS OREINA

Insect-plant interactions have played a prominent role in investigating phylogenetic constraints in the evolution of ecological traits. The patterns of host association among specialized insects have often been described as highly conservative, yet not all specialized herbivorous insect lineages display the same degree of fidelity to their host plants. In this paper, we present an estimate of the evolutionary history of the leaf beetle genus Oreina. This genus displays an amazing flexibility in several aspects of its ecology and life history: (1) host plant switches in Oreina occurred between plant families or distantly related tribes within families and thereby to more distantly related plants than in several model systems that have contributed to the idea of parallel cladogenesis; (2) all species of the genus are chemically defended, but within the genus a transition between autogenous production of defensive toxins and sequestration of secondary plant compounds has occurred; and (3) reproductive strategies in the genus range from oviparity to viviparity including all intermediates that could allow the gradual evolution of viviparity. Cladistic analysis of 18 allozyme loci found two most parsimonious trees that differ only in the branching of one species. According to this phylogeny estimate, Oreina species were originally associated with Asteraceae, with an inclusion of Apiaceae in the diet of one oligophagous species and an independent switch to Apiaceae in a derived clade. The original mode of defense appears to be the autogenous production of cardenolides as previously postulated; the additional sequestration of pyrrolizidine alkaloids could have either originated at the base of the genus or have arisen three times independently in all species that switched to plants containing these compounds. Viviparity apparently evolved twice in the genus, once without matrotrophy, through a retention of the eggs inside the female's oviducts, and once in combination with matrotrophy. We hypothesize that the combination of autogenous defense and a life history that involves mobile externally feeding larvae allowed these beetles to switch host plants more readily than has been reported for highly conservative systems.     

Parallel evolution in Marquesan partulid land snails

Partulid land snails of the genus Samoana inhabiting the Marquesas Islands of French Polynesia exist as two distinct types, the 'thick-shelled' and 'thin-shelled' species. The two types differ in size, shell-thickness, pigmentation of the shell and mantle, stickiness of the mucus, and length of the tentacles. A study of variation in allozymes indicates that the species form a monophyletic group, within which the differences between the two types have twice evolved independendy, once in the northern islands and at least once in the south. In the Society Islands the two suites of characters are found in both Partula and Samoana , where there is evidence of at least four other independent derivations of the two types. The thin-shelled species consistendy tend to occur at the higher altitudes (above 200 m). These cases of parallel evolution argue strongly that the complexes of associated characters have arisen through natural selection.     

Patterns of reproductive isolation in three angiosperm genera

Analyses among animal species have found that reproductive isolation increases monotonically with genetic distance, evolves more quickly for prezygotic than postzygotic traits, and is stronger among sympatric than allopatric species pairs. The latter pattern is consistent with expectations under the reinforcement hypothesis. To determine whether similar trends are found among plant species, patterns of reproductive isolation (postpollination prezygotic, postzygotic, and "total" isolation) in three plant genera (Glycine, Silene, Streptanthus) were examined using data from previously published artificial hybridization experiments. In Silene, all measures of reproductive isolation were positively correlated with genetic distance. In contrast, in Glycine and Streptanthus, correlations between reproductive isolation and genetic distance were weak or nonsignificant, possibly due to the influence of biologically unusual taxa, variable evolutionary forces acting in different lineages, or insufficient time to accumulate reproductive isolation. There was no evidence that postpollination prezygotic reproductive isolation evolved faster than postzygotic isolation in Glycine or Silene. We also detected no evidence for faster accumulation of postmating prezygotic isolation between sympatric than allopatric species pairs; thus we found no evidence for the operation of speciation via reinforcement. In Silene, which included six polyploid species, results suggest that changes in ploidy disrupt a simple monotonic relationship between isolation and genetic distance.     

TAXONOMY OF THE LENORMANDIA - LENORMANDIOPSIS COMPLEX (RHODOMELACEAE, RHODOPHYTA)

The genus Lenormandia is composed of nine species from Australia and New Zealand. Some of the these are well known, but others are rare, obscure and ill-defined. We have examined material of all described species and found that they fall into two discrete groups that differ in apex morphology and position of reproductive structures. Plants of the first group, containing the type species L. spectabilis , have a cleft apex and reproductive structures produced directly on the blade surface, whereas those of the second group have a strongly inrolled apex and produce reproductive structures dorsally on small branchlets which arise either from the margins or the midrib. The groups were also found to form discrete clades on analysis of 18S rRNA sequences. All the members of the first group are endemic to Australia, whereas the second group, designated by the new genus name Adamsiella , contains two previously described New Zealand species and a single Australian representative. In addition, two new species are described in this group from New Zealand. Members of the closely related genus Lenormandiopsis were also examined and the type species, L. latifolia , was found to conform in apex morphology and position of reproductive structures to the genus Lenormandia. Accordingly Lenormandiopsis has been subsumed within Lenormandia. The remaining three members of the former genus Lenormandiopsis , however, were found to differ from both the type species and the genus Lenormandia and consequently have been transferred to the separate genus Geraldia , along with a new species from Geraldton, Western Australia which is designated as the type.     

The origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)

The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.     

MITOCHONDRIAL DNA SEQUENCE-BASED PHYLOGENY AND THE EVOLUTION OF VIVIPARITY IN THE SCELOPORUS SCALARIS GROUP (REPTILIA,SQUAMATA)

The lizard genus Sceloporus contains both oviparous and viviparous species. The scalaris complex is the only monophyletic group within the genus that includes both reproductive modes, thus it is particularly well suited for studies of the evolution of viviparity. Approximately 874 nucleotides of mtDNA sequence data, collected from 38 specimens, comprising 25 populations of all five recognized species within the group, were used in a phylogenetic analysis of the origin of viviparity. Viviparity appears to have evolved twice in this group: once in S. goldmani, included in a clade formed by a northern group consisting of S. scalaris, S. chaneyi, and S. goldmani, and one more time in S. bicanthalis, included in the southern group formed by S. bicanthalis and S. aeneus. An oviparous population of S. bicanthalis nested within that viviparous clade, indicates that reversal from viviparity to oviparity may be possible. Degree of sequence divergence among several S. bicanthalis individuals pertaining to a population in which both parity modes occur, was no larger between oviparous and viviparous lizards than among viviparous lizards. This suggests that this population is a single species, and it may represent a transition from oviparity to viviparity or vice-versa.     

Karyological analysis of an interspecific hybrid between the dioecious Silene latifolia and the hermaphroditic Silene viscosa.

The genus Silene is a good model for studying evolution of the sex chromosomes, since it includes species that are hermaphroditic and dioecious, while maintain a basic chromosome number of 2n = 24. For some combinations of Silene species it is possible to construct interspecific hybrids. Here, we present a detailed karyological analysis of a hybrid between the dioecious Silene latifolia as the maternal plant and a related species, hermaphroditic Silene viscosa, used as a pollen partner. Using genomic probes (the genomic in situ hybridization (GISH) technique), we were able to clearly discriminate parental genomes and to show that they are largely separated in distinct nuclear domains. Molecular GISH and fluorescence in situ hybridization (FISH) markers document that the hybrid genome of somatic cells was strictly additive and stable, and that it had 12 chromosomes originating from each parent, including the only X chromosome of S. latifolia. Meiotic analysis revealed that, although related, respective parental chromosomes did not pair or paired only partially, which resulted in frequent chromosome abnormalities such as bridges and irregular non-disjunctions. GISH and FISH markers clearly document that the larger genome of S. latifolia and its largest chromosome component, the X chromosome, were mostly employed in chromosome lagging and misdivision.     

A reconsideration of the Lower Guinean species of Sericanthe (Rubiaceae,Coffeeae), with four new species from Cameroon and Gabon

The genus Sericanthe was established and its species were revised 30 years ago by one of the authors. Intensive recent botanical collecting in Lower Guinea (mainly southern Cameroon, Equatorial Guinea and Gabon) has made a reconsideration of species in this area necessary. Revision of the newly collected Lower Guinean herbarium specimens of Sericanthe (twice as many as were available at the time of the first revision) has brought four new species to light, namely S. gabonensis and S. mpassa from Gabon, S. lowryana from Cameroon and S. rabia from Cameroon and Gabon. Distributional data are much augmented, and distributional maps of all species from the area are provided. Four species were reported to be newly recorded for at least one country. The occurrence of the novelties in the main diversity centre of the genus is discussed in the context of the chorology of the entire genus Sericanthe. A first estimation of the conservation status for the new species is given. A synopsis of the genus Sericanthe in Lower Guinea with a taxonomic key is provided. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 530–554.     

A molecular phylogenetic analysis of reproductive trait evolution in the soft coral genus Alcyonium

The soft coral genus Alcyonium is among the most reproductively diverse invertebrate taxa known: The genus includes species that vary both in mode of reproduction (including broadcast spawners, internal brooders, and external brooders) and sexual expression (gonochores, hermaphrodites, and a unisexual parthenogen). Such diversity offers a unique opportunity to examine associations between reproductive and morphological traits in a phylogenetic context. We used an approximately 900-bp sequence of the nuclear ribosomal gene complex spanning the internal transcribed spacer (ITS) regions to construct a molecular phylogeny for 14 European and North American species of Alcyonium onto which we mapped the known distribution of reproductive and morphological traits. The phylogeny suggests that hermaphroditism or parthenogenesis has evolved independently at least twice in this genus, and always in internally brooding species. Broadcast spawning and external brooding only occur in species with large colony size, whereas all species with small colony size brood their larvae internally. Internal brooding and small size appear to be ancestral in this genus; if this is the case, an association between broadcast spawning and large colony size has evolved independently in at least two clades. This tendency of small adults to brood their larvae while large adults broadcast spawn them into the plankton has been observed in a variety of solitary invertebrate taxa, but to date has not been documented in any other colonial invertebrates. Moreoever, it has been suggested that organisms with a colonial growth form should not experience the allometric constraints on brood space that have been proposed to explain the association between adult size and mode of reproduction in solitary organisms. Unlike many other colonial groups, however, module (polyp) size is strongly correlated with colony size in Alcyonium, and constraints on brooding may be imposed by module, rather than colony, allometry. The very close genetic relationship (< 1% sequence divergence) and shared polymorphisms among A. digitatum (a large, gonochoric broadcast spawner), A. siderium, and A. sp. A (intermediate-sized and small hermaphroditic, internal brooders) suggest that evolutionary transitions between broadcast spawning and brooding and between gonochorism and hermaphroditism can occur easily and rapidly in this group.     

The inter-specific hybrid Silene latifolia x S. viscosa reveals early events of sex chromosome evolution

The dioecious plant species Silene latifolia has a sex determination mechanism based on an active Y chromosome. Here, we used inter-specific hybrids in the genus Silene to study the effects of gene complexes on the Y chromosome. If the function of Y-linked genes has been maintained in the same state as in the hermaphrodite progenitor species, it should be possible to substitute such genes by genes coming from a related hermaphrodite species. In the inter-specific hybrid, S. latifolia x S. viscosa, anthers indeed develop far beyond the early bilobal stage characteristic of XX S. latifolia female plants. The S. viscosa genome can thus replace the key sex determination gene whose absence abolishes early stamen development in females (loss of the stamen-promoting function, SPF), so that hybrid plants are morphologically hermaphrodite. However, the hybrids have two anther development defects, loss of adhesion of the tapetum to the endothecium, and precocious endothecium maturation. Both these defects were also found in independent Y-chromosome deletion mutants of S. latifolia. The data support the hypothesis that the evolution of complete gender dimorphism from hermaphroditism involved a major largely recessive male-sterility factor that created females, and the appearance of new, dominant genes on the Y chromosome, including both the well-documented gynoecium-suppressing factor, and two other Y specific genes promoting anther development.