Complete Mitogenomes of Two Aragoa Species and Phylogeny of Plantagineae (Plantaginaceae, Lamiales) Using Mitochondrial Genes and the Nuclear Ribosomal RNA Repeat.

Aragoa, comprising 19 high-altitude North Andean species, is one of three genera in the Plantagineae (Plantaginaceae, Lamiales), along with Littorella and Plantago. Based primarily on plastid data and nuclear ITS, Aragoa is sister to a clade of Littorella + Plantago, but Plantagineae relationships have yet to be assessed using multigene datasets from the nuclear and mitochondrial genomes. Here, complete mitogenomes were assembled for two species of Aragoa (A. abietina and A. cleefii). The mitogenomes of both species have a typical suite of genes for 34 proteins, 17 tRNAs, and three rRNAs. The A. abietina mitogenome assembled into a simple circular map, with no large repeats capable of producing alternative isoforms. The A. cleefii mitogenomic map was more complex, involving two circular maps bridged by a substoichiometric linear fragment. Phylogenetics of three mitochondrial genes or the nuclear rRNA repeat placed Aragoa as sister to Littorella + Plantago, consistent with previous studies. However, P. nubicola, the sole representative of subg. Bougueria, was nested within subg. Psyllium based on the mitochondrial and nuclear data, conflicting with plastid-based analyses. Phylogenetics of the nuclear rRNA repeat provided better resolution overall, whereas relationships from mitochondrial data were hindered by extensive substitution rate variation among lineages.

Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella.

Tribe Plantagineae (Plantaginaceae) comprises ~ 270 species in three currently recognized genera (Aragoa, Littorella, Plantago), of which Plantago is most speciose. Plantago plastomes exhibit several atypical features including large inversions, expansions of the inverted repeat, increased repetitiveness, intron losses, and gene-specific increases in substitution rate, but the prevalence of these plastid features among species and subgenera is unknown. To assess phylogenetic relationships and plastomic evolutionary dynamics among Plantagineae genera and Plantago subgenera, we generated 25 complete plastome sequences and compared them with existing plastome sequences from Plantaginaceae. Using whole plastome and partitioned alignments, our phylogenomic analyses provided strong support for relationships among major Plantagineae lineages. General plastid features-including size, GC content, intron content, and indels-provided additional support that reinforced major Plantagineae subdivisions. Plastomes from Plantago subgenera Plantago and Coronopus have synapomorphic expansions and inversions affecting the size and gene order of the inverted repeats, and particular genes near the inversion breakpoints exhibit accelerated nucleotide substitution rates, suggesting localized hypermutation associated with rearrangements. The Littorella plastome lacks functional copies of ndh genes, which may be related to an amphibious lifestyle and partial reliance on CAM photosynthesis.

Arms races with mitochondrial genome soft sweeps in a gynodioecious plant, Plantago lanceolata.

Biological situations involving conflict can create arms race situations with repeated fixations of different functional variants, producing selective sweeps and lowering neutral diversity in genome regions linked to the functional locus. However, they can sometimes lead to balancing selection, potentially creating long coalescent times for sites with functionally different variants, and, if recombination occurs rarely, for extended haplotypes carrying such variants. We tested between these possibilities in a gynodioecious plant, Plantago lanceolata, in which cytoplasmic male-sterility factors conflict with nuclear restorers of male fertility. We find low mitochondrial diversity, which does not support very long-term coexistence of highly diverged mitochondrial haplotypes. Interestingly, however, we found a derived haplotype that is associated with male fertility in a restricted geographic region, and that has fixed differences from the ancestral sequence in several genes, suggesting that it did not arise very recently. Taken together, the results suggest arms race events that involved "soft" selective sweeps involving a moderately old-established haplotype, consistent with the frequency fluctuations predicted by theoretical models of gynodioecy.

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

Different outcomes for the MYB floral symmetry genes DIVARICATA and RADIALIS during the evolution of derived actinomorphy in Plantago.

The gene network that specifies flower shape in Antirrhinum majus (bilateral floral symmetry or zygomorphy) includes two MYB-class genes - RADIALIS (RAD) and DIVARICATA (DIV). RAD is involved in establishing the dorsal identity program and its role is to regulate the domain of activity of DIV (the ventral identity program) by restricting it to ventral regions of the flower. Plantago is in the same family as Antirrhinum but has small, radially symmetrical (actinomorphic) flowers derived from a zygomorphic ancestral state. Here we investigate the MYB-class floral symmetry genes and the role they have played in the evolution of derived actinomorphy in Plantago lanceolata. A DIV ortholog (PlDIV) but no RAD ortholog was identified in P. lanceolata. PlDIV is expressed across all petals and stamens later in flower development, which is consistent with the loss of RAD gene function. PlDIV expression in anther sporogenous tissue also suggests that PlDIV was co-opted to regulate cell proliferation during the early stages of pollen development. These results indicate that evolution of derived actinomorphy in Plantago involved complete loss of dorsal gene function, resulting in expansion of the domain of expression of the ventral class of floral symmetry genes.

Characterization of microsatellite loci in Tilia platyphyllos (Malvaceae) and cross-amplification in related species.

PREMISE OF THE STUDY: Microsatellite markers in the genus Tilia were developed to investigate the genetic variation in T. platyphyllos and its relationship with T. cordata. • METHODS AND RESULTS: Fifteen microsatellite markers were developed using a microsatellite enrichment protocol. Most loci show a high level of polymorphism in two T. platyphyllos populations from France. The number of alleles ranged from one to 15, with a mean of 8.96. The mean observed and expected heterozygosities were 0.71 and 0.70, respectively. Cross-amplification results indicated that 12 out of 15 loci amplified polymorphic loci in 23 species in the genus. • CONCLUSIONS: These markers will be useful tools for investigating the phylogeography and hybridization of Tilia species.

Genetic population structure of the ground beetle, Pterostichus oblongopunctatus, inhabiting a fragmented and polluted landscape: evidence for sex-biased dispersal.

Ground beetles are an integral and functionally important part of many terrestrial ecosystems. Habitat change often influences population genetic structure of carabid beetles. In this study, genetic variation, population differentiation, and sex-specific dispersal patterns were studied in the forest ground beetle, Pterostichus oblongopunctatus F. (Coleoptera: Carabidae), in a fragmented and metal-polluted landscape to assess the consequences of human-induced changes on the population genetic structure. Genotypic variation at five microsatellite loci was screened in 309 beetles from 21 sample locations around zinc-and-lead smelter in southern Poland. Low levels of genetic differentiation among sampling sites were observed, suggesting high gene flow among populations. A negative correlation was found between levels of genetic differentiation and habitat patch size. No significant effects of metal pollution, in terms of genetic bottlenecks and genetic differentiation, were observed. Analyses revealed weak genetic clustering that is loosely tied to the geographic position of the sampled populations. Several tests of sex-biased dispersal were conducted. Most of them indicated male-biased dispersal. Differing levels of dispersal between females and males resulted in sex-specific spatial genetic patterns. Genetic differentiation was significantly correlated with geographical distance for males, but not for females, who were more diverged locally. Also, the effect of habitat patch size was sex-dependent, supporting the finding of different dispersal patterns between the sexes. This study demonstrated the application of microsatellite markers to answer questions regarding complex interactions between population structure and physical properties of the landscape. In the study system, migration appears to be sufficient to override potential effects of environmental pollution as well as habitat fragmentation. This investigation of population genetic structure indicated, for the first time, male-biased dispersal in carabid beetles.

The effect of surface colour on the adhesion strength of Elminius modestus Darwin on a commercial non-biocidal antifouling coating at two locations in the UK.

A number of factors affect the adhesion strength of organisms to fouling-release coatings, and except for a few studies focussing on black or white surfaces none have dealt specifically with the effect of coating colour. The aim was to test the effect of colour on the adhesion strength of the barnacle Elminius modestus. Panels coated in six commercial colours of Intersleek 700 were submerged at two field sites and barnacles were pushed-off using a standard assay procedure. The strength of adhesion (SOA) varied between and within sites for colour and by barnacle basal area, SOA per unit area being higher for smaller barnacles. Higher SOA with a small basal area may be because of size-specific predation, differential hydrodynamic effects or adhesive failure with age. The complex effect of colour on barnacle adhesion may be because of physico-chemical surface characteristics varying with pigments, and their interactions with local environmental conditions, as well as interactions with the settling barnacle larvae.

Eight polymorphic microsatellite markers for Rhinanthus minor.

Little research has been carried out on the genetics of Rhinanthus minor to date. To enable study of this species, eight polymorphic microsatellite loci were developed, using a genomic library enriched for microsatellites. All loci are polymorphic in the two UK populations tested, Bardister and Oxwich Bay. These microsatellite markers will be useful for studying genetic structure and subspecies differences of R. minor.

Characterization of 38 microsatellite loci in the European blackbird, Turdus merula (Turdidae, AVES).

We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirty-seven loci were identified by testing 242 loci that had been originally isolated in other avian species. One additional locus was isolated from a European blackbird genomic library. All loci were characterized in 20-29 blackbirds from a population in the Czech Republic and displayed between two and 16 alleles, with observed heterozygosity ranging from 0.04 to 1.00. Thirty-seven loci could be assigned a chromosome location in the zebra finch (Taeniopygia guttata) genome based on sequence homology.

Causes of size homoplasy among chloroplast microsatellites in closely related Clusia species.

Chloroplast DNA sequences and microsatellites are useful tools for phylogenetic as well as population genetic analyses of plants. Chloroplast microsatellites tend to be less variable than nuclear microsatellites and therefore they may not be as powerful as nuclear microsatellites for within-species population analysis. However, chloroplast microsatellites may be useful for phylogenetic analysis between closely related taxa when more conventional loci, such as ITS or chloroplast sequence data, are not variable enough to resolve phylogenetic relationships in all clades. To determine the limits of chloroplast microsatellites as tools in phylogenetic analyses, we need to understand their evolution. Thus, we examined and compared phylogenetic relationships of species within the genus Clusia, using both chloroplast sequence data and variation at seven chloroplast microsatellite loci. Neither ITS nor chloroplast sequences were variable enough to resolve relationships within some sections of the genus, yet chloroplast microsatellite loci were too variable to provide any useful phylogenetic information. Size homoplasy was apparent, caused by base substitutions within the microsatellite, base substitutions in the flanking regions, indels in the flanking regions, multiple microsatellites within a fragment, and forward/reverse mutations of repeat length resulting in microsatellites of identical base composition that were not identical by descent.

Interpreting spatial variation in ozone symptoms shown by cutleaf cone flower, Rudbeckia laciniata L.

Visible injury caused by ozone is recorded every year in native plant species growing in Great Smoky Mountains National Park (USA). One of the most sensitive species, cutleaf coneflower (Rudbeckia laciniata L.), shows great variation in symptoms between and within populations but the causes of this variation and its ecological significance are currently unknown. This paper presents data relating to genetic variation, ozone concentrations, stomatal conductance and light (PAR) within populations. The data show that populations differ in genetic diversity, one consisting of only three genets while another was very diverse. In the former population, symptoms varied greatly within a single genet, pointing to a large micro-environmental influence. Measurements of ozone, stomatal conductance and PAR within plant canopies suggest that variation in symptom expression is unlikely to be due to differences in ozone flux and more likely to be due to variation in light. The variation in visible symptoms raises the question of what bioindicators actually indicate, and it suggests that symptoms should be interpreted with great caution until the underlying causes of that variation are fully understood.