High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants.

For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.

Opposite trends in the genus Monsonia (Geraniaceae): specialization in the African deserts and range expansions throughout eastern Africa.

The African Austro-temperate Flora stands out by its important species richness. A distinctive element of this flora is Monsonia (Geraniaceae), mostly found in the Namib-Karoo but also in the Natal-Drakensberg, the Somalian Zambezian and the Saharo-Arabian regions. Here, we reconstruct the evolution and biogeographic history of Monsonia based on nuclear and plastid markers, and examine the role of morphological and niche evolution in its diversification using species distribution modeling and macroevolutionary models. Our results indicate that Monsonia first diversified in the Early Miocene c.21 Ma, coinciding with the start of desertification in southwestern Africa. An important diversification occurred c. 4-6 Ma, after a general cooling trend in western South Africa and the rising of the Eastern African Mountains. The resulting two main lineages of Monsonia are constituted by: (1) Namib-Karoo succulents, and (2) herbs of the Natal-Drakensberg plus three species that further colonised steppes in north and eastern Africa. The highest diversity of Monsonia is found in the Namib-Karoo coastal belt, within a mosaic-like habitat structure. Diversification was likely driven by biome shifts and key innovations such as water-storing succulent stems and anemochorous fruits. In contrast, and unlike other arid-adapted taxa, all species of Monsonia share a C3 metabolism.

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS: We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS: Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION: We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.

Geraniales flowers revisited: evolutionary trends in floral nectaries.

BACKGROUND AND AIMS: The detailed relationships in Geraniales in their current circumscription have only recently been clarified. The disparate floral morphologies and especially the nectaries of the corresponding group have consequently not previously been studied in a phylogenetic context. METHODS: The present study investigates floral and especially nectary morphology and structure for representatives of 12 of the 13 currently accepted genera in the five families of the Geraniales. Flowers were studied using light microscopy and scanning electron microscopy. KEY RESULTS: The data demonstrate the derivation of even the most disparate floral morphologies from a basic pentamerous and pentacyclic organization, with an obdiplostemonous androecium and receptacular nectaries associated with the antesepalous stamens. Divergent morphologies are explained by modifications of merosity (tetramerous flowers), symmetry (several transitions to zygomorphic flowers) and elaboration of the nectaries into variously shaped outgrowths and appendages, especially in Francoaceae. The divergent development of nectar glands ultimately leads to either a reduction in their number (to one in some Geraniaceae and Melianthaceae) or their total loss (some Vivianiaceae). CONCLUSIONS: Floral morphology of the Geraniales shows a high degree of similarity, despite the variation in overall floral appearance and nectary morphology. A hypothesis on the transformation of the nectaries within the Geraniales is presented.

Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae.

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid-nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits.

Variable presence of the inverted repeat and plastome stability in Erodium.

BACKGROUND AND AIMS: Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. METHODS: We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. KEY RESULTS: Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. CONCLUSIONS: The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity.

Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear-plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems.

Population variation affects interactions between two California salt marsh plant species more than precipitation.

Species that occur along broad environmental gradients often vary in phenotypic traits that make them better adapted to local conditions. Variation in species interactions across gradients could therefore be due to either phenotypic differences among populations or environmental conditions that shift the balance between competition and facilitation. To understand how the environment (precipitation) and variation among populations affect species interactions, we conducted a common garden experiment using two common salt marsh plant species, Salicornia pacifica and Jaumea carnosa, from six salt marshes along the California coast encompassing a large precipitation gradient. Plants were grown alone or with an individual of the opposite species from the same site and exposed to one of three precipitation regimes. J. carnosa was negatively affected in the presence of S. pacifica, while S. pacifica was facilitated by J. carnosa. The strength of these interactions varied by site of origin but not by precipitation treatment. These results suggest that phenotypic variation among populations can affect interaction strength more than environment, despite a threefold difference in precipitation. Geographic intraspecific variation may therefore play an important role in determining the strength of interactions in communities.

Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae.

Carbon allocation from source to sink leaf tissue in relation to flavonoid biosynthesis in variegated Pelargonium zonale under UV-B radiation and high PAR intensity.

We studied the specific effects of high photosynthetically active radiation (PAR, 400-700 nm) and ecologically relevant UV-B radiation (0.90 W m(-2)) on antioxidative and phenolic metabolism by exploiting the green-white leaf variegation of Pelargonium zonale plants. This is a suitable model system for examining "source-sink" interactions within the same leaf. High PAR intensity (1350 µmol m(-2) s(-1)) and UV-B radiation induced different responses in green and white leaf sectors. High PAR intensity had a greater influence on green tissue, triggering the accumulation of phenylpropanoids and flavonoids with strong antioxidative function. Induced phenolics, together with ascorbate, ascorbate peroxidase (APX, EC 1.11.1.11) and catalase (CAT, EC 1.11.1.6) provided efficient defense against potential oxidative pressure. UV-B-induced up-regulation of non-phenolic H2O2 scavengers in green leaf sectors was greater than high PAR-induced changes, indicating a UV-B role in antioxidative defense under light excess; on the contrary, minimal effects were observed in white tissue. However, UV-B radiation had greater influence on phenolics in white leaf sections compared to green ones, inducing accumulation of phenolic glycosides whose function was UV-B screening rather than antioxidative. By stimulation of starch and sucrose breakdown and carbon allocation in the form of soluble sugars from "source" (green) tissue to "sink" (white) tissue, UV-B radiation compensated the absence of photosynthetic activity and phenylpropanoid and flavonoid biosynthesis in white sectors.

Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates.

Geraniaceae plastid genomes are highly rearranged, and each of the four genera already sequenced in the family has a distinct genome organization. This study reports plastid genome sequences of six additional species, Francoa sonchifolia, Melianthus villosus, and Viviania marifolia from Geraniales, and Pelargonium alternans, California macrophylla, and Hypseocharis bilobata from Geraniaceae. These genome sequences, combined with previously published species, provide sufficient taxon sampling to reconstruct the ancestral plastid genome organization of Geraniaceae and the rearrangements unique to each genus. The ancestral plastid genome of Geraniaceae has a 4 kb inversion and a reduced, Pelargonium-like small single copy region. Our ancestral genome reconstruction suggests that a few minor rearrangements occurred in the stem branch of Geraniaceae followed by independent rearrangements in each genus. The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the family. The distribution of repeats is strongly associated with breakpoints in the rearranged genomes, and the proportion and the number of large repeats (>20 bp and >60 bp) are significantly correlated with the degree of genome rearrangements. Increases in the degree of plastid genome rearrangements are correlated with the acceleration in nonsynonymous substitution rates (dN) but not with synonymous substitution rates (dS). Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed.

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.

BACKGROUND: Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. RESULTS: Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. CONCLUSIONS: The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition, results indicated no major improvements in breadth of coverage with data sets larger than six billion nucleotides or when sampling RNA from four tissue types rather than from a single tissue. Finally, this work demonstrates the power of cross-compartmental genomic analyses to deepen our understanding of the correlated evolution of the nuclear, plastid, and mitochondrial genomes in plants.

Volatiles of Geranium purpureum Vill. and Geranium phaeum L.: chemotaxonomy of balkan Geranium and Erodium species (Geraniaceae).

The essential oils obtained by hydrodistillation of Geranium purpureum and G. phaeum were characterized by GC-FID and GC/MS analyses (the former for the first time in general). In total, 154 constituents were identified, accounting for 89.0-95.8% of the detected GC peak areas. The investigated essential oils consisted mainly of fatty acids and fatty-acid-derived compounds (45.4-81.3%), with hexadecanoic acid and (E)-phytol as the major components. The chemotaxonomic significance of the variations in the essential-oil composition/production of the presently and previously investigated Geranium and highly related Erodium taxa from Serbia and Macedonia was assessed by multivariate statistical analyses. The main conclusions drawn from the high chemical similarity of the two genera, visible from the obtained dendrograms and biplots, confirm the close phylogenetic relationship between the investigated Geranium and Erodium taxa, i.e., that there is no great intergeneric oil-composition variability. Changes in the composition and production of essential oils of the herein investigated taxa and 60 other randomly chosen species belonging to different plant genera were also statistically analyzed. The results put forward pro arguments for the oil-yield-oil-composition correlation hypothesis.

Erodium maritimum (Geraniaceae), a species with an uneven and fragmented distribution along the Western Mediterranean and European Atlantic coasts, has a weak genetic structure.

Erodium maritimum L. is an annual species presenting heterogeneous, sometimes very small, and distant populations, distributed along a discontinuous coastal strip of the European Atlantic and the central and western Mediterranean basin. The aim of this study is to investigate genetic variation and geographic structure changes across its large distribution. Fourteen populations of E. maritimum were studied using AFLP fingerprints, together with their population sizes, reproductive systems and flower visitors. AFLP markers revealed the genetic structure of the species to be weak. Many individuals from one population clustered together with those of other populations, showing a high degree of genetic admixture. Despite having a self-compatible reproductive system, populations (especially the largest ones) showed high levels of genetic polymorphism, and the majority of genetic variation was contained within populations. The low genetic structure suggests high levels of gene flow, which might be explained through the dispersability of the species' fruits. Finally, recommendations are provided for management strategies to facilitate the conservation of this endangered species.

Quantifying how fine-grained environmental heterogeneity and genetic variation affect demography in an annual plant population.

The ability of plant species to colonize new habitats and persist in changing environments depends on their ability to respond plastically to environmental variation and on the presence of genetic variation, thus allowing adaptation to new conditions. For invasive species in particular, the relationship between phenotypic trait expression, demography, and the quantitative genetic variation that is available to respond to selection are likely to be important determinants of the successful establishment and persistence of populations. However, the magnitude and sources of individual demographic variation in exotic plant populations remain poorly understood. How important is plasticity versus adaptability in populations of invasive species? Among environmental factors, is temperature, soil nutrients, or competition most influential, and at what scales and life stages do they affect the plants? To investigate these questions we planted seeds of the exotic annual plant Erodium brachycarpum into typical pasture habitat in a spatially nested design. Seeds were drawn from 30 inbred lines to enable quantification of genetic effects. Despite a positive population growth rate, a few plants (0.1 %) produced >50 % of the seeds, suggesting a low effective population size. Emergence and early growth varied by genotype, but as in previous studies on native plants, environmental effects greatly exceeded genetic effects, and survival was unrelated to genotype. Environmental influences shifted from microscale soil compaction and litter depth at emergence through to larger-scale soil nutrient gradients during growth and to competition during later survival and seed production. Temperature had no effect. Most demographic rates were positively correlated, but emergence was negatively correlated with other rates.

Genetic diversity of mountain plants: two migration episodes of Mediterranean Erodium (Geraniaceae).

This paper examines the phylogeny of Erodium subsect. Petraea, a group of six morphologically and genetically very similar species from the mountains of the western Mediterranean. Combined trnL-F-ITS analysis was unable to determine the phylogenetic relationships of these species owing to sequence similarity. AFLP fragment analysis showed different populations to cluster in six closely related phylogroups that partially coincided with morphological species. In the Iberian Peninsula, high temperatures during interstadial periods probably impeded the survival of these species at low altitudes, and their populations may have been forced to migrate northward within Iberia or remain isolated on high mountains. AFLP variation suggests that this might have led to their differentiation into groups and speciation during interglacials, but it probably also provided the basis for recurrent recolonisations and the mixing of neighbouring populations at the last glacial maxima. The genetic diversity of the two Erodium lineages suggests two migration episodes took place from southern Iberia towards the north, with one lineage migrating via western Iberia and the other via eastern Iberia. The patterns of genetic diversity observed in populations of 56 European species (27 genera) leads to the hypothesis that disparate proportions of unique polymorphic fragments are the result of the evolutionary histories of their mountain populations irrespective of the currently recognised species.

Linking the spatial scale of environmental variation and the evolution of phenotypic plasticity: selection favors adaptive plasticity in fine-grained environments.

Adaptive phenotypic plasticity and adaptive genetic differentiation enable plant lineages to maximize their fitness in response to environmental heterogeneity. The spatial scale of environmental variation relative to the average dispersal distance of a species determines whether selection will favor plasticity, local adaptation, or an intermediate strategy. Habitats where the spatial scale of environmental variation is less than the dispersal distance of a species are fine grained and should favor the expression of adaptive plasticity, while coarse-grained habitats, where environmental variation occurs on spatial scales greater than dispersal, should favor adaptive genetic differentiation. However, there is relatively little information available characterizing the link between the spatial scale of environmental variation and patterns of selection on plasticity measured in the field. I examined patterns of spatial environmental variation within a serpentine mosaic grassland and selection on an annual plant (Erodium cicutarium) within that landscape. Results indicate that serpentine soil patches are a significantly finer-grained habitat than non-serpentine patches. Additionally, selection generally favored increased plasticity on serpentine soils and diminished plasticity on non-serpentine soils. This is the first empirical example of differential selection for phenotypic plasticity in the field as a result of strong differences in the grain of environmental heterogeneity within habitats.

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae).

Plastid genomes in the flowering plant family Geraniaceae are known to be highly rearranged based on complete sequences representing the four major genera Erodium, Geranium, Monsonia, and Pelargonium. In this paper we report on the genome sequence of a second species of Erodium, E. carvifolium, representing the second major clade (clade II) in the phylogeny of this genus. Comparison of this genome sequence to the previously published sequence of E. texanum from clade I demonstrates that the plastid genomes of these two species encode the same number of proteins but differ greatly in their relative degree of rearrangement; 14 kb of additional sequence in E. texanum contains complex repeats associated with rearrangement endpoints, whereas the plastid genome of E. carvifolium is streamlined at 116 kb and displays no unique alterations in gene order. Furthermore, these species from both major clades of Erodium contain intact NADH dehydrogenase (ndh) genes, but the 11 ndh genes are represented as pseudogenes in a small clade of 13 species. It is unclear whether plastid-encoded ndh genes have been lost entirely or functionally transferred to the nucleus. This is the third report of the absence of functional ndh genes, and the current study describes the most recent loss of these genes among photosynthetic seed plants and the second such loss among angiosperms. The other ndh losses from Pinaceae/Gnetales and Orchidaceae are much more ancient. Comparative biochemistry between Erodium species with and without plastid-encoded ndh genes may elucidate changes in photosynthetic function and the role of the Ndh complex.

Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage.

Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be highly variable in size, gene content and order, repetitive DNA, and codon usage. Several unique plastome rearrangements include the disruption of two highly conserved operons (S10 and rps2-atpA), and the inverted repeat (IR) region in M. speciosa does not contain all genes in the ribosomal RNA operon. The sequence of M. speciosa is unusually small (128,787 bp); among angiosperm plastomes sequenced to date, only those of nonphotosynthetic species and those that have lost one IR copy are smaller. In contrast, the plastome of P. hortorum is the largest, at 217,942 bp. These genomes have experienced numerous gene and intron losses and partial and complete gene duplications. Some of the losses are shared throughout the family (e.g., trnT-GGU and the introns of rps16 and rpl16); however, other losses are homoplasious (e.g., trnG-UCC intron in G. palmatum and M. speciosa). IR length is also highly variable. The IR in P. hortorum was previously shown to be greatly expanded to 76 kb, and the IR is lost in E. texanum and reduced in G. palmatum (11 kb) and M. speciosa (7 kb). Geraniaceae plastomes contain a high frequency of large repeats (>100 bp) relative to other rosids. Within each plastome, repeats are often located at rearrangement end points and many repeats shared among the four Geraniaceae flank rearrangement end points. GC content is elevated in the genomes and also in coding regions relative to other rosids. Codon usage per amino acid and GC content at third position sites are significantly different for Geraniaceae protein-coding sequences relative to other rosids. Our findings suggest that relaxed selection and/or mutational biases lead to increased GC content, and this in turn altered codon usage. We propose that increases in genomic rearrangements, repetitive DNA, nucleotide substitutions, and GC content may be caused by relaxed selection resulting from improper DNA repair.

The uneven phylogeny and biogeography of Erodium (Geraniaceae): radiations in the Mediterranean and recent recurrent intercontinental colonization.

BACKGROUND AND AIMS: The genus Erodium is a common feature of Mediterranean-type climates throughout the world, but the Mediterranean Basin has significantly higher diversity than other areas. The aim here is to reveal the biogeographical history of the genus and the causes behind the evolution of the uneven distribution. METHODS: Seventy-eight new nrITS sequences were incorporated with existing plastid data to explore the phylogenetic relationships and biogeography of Erodium using several reconstruction methods. Divergence times for major clades were calculated and contrasted with other previously published information. Furthermore, topological and temporal diversification rate shift analyses were employed using these data. KEY RESULTS: Phylogenetic relationships among species are widely congruent with previous plastid reconstructions, which refute the classical taxonomical classification. Biogeographical reconstructions point to Asia as the ancestral area of Erodium, arising approx. 18 MYA. Four incidences of intercontinental dispersal from the Mediterranean Basin to similar climates are demonstrated. Increases in diversification were present in two independent Erodium lineages concurrently. Two bursts of diversification (3 MYA and 0·69 MYA) were detected only in the Mediterranean flora. CONCLUSIONS: Two lineages diverged early in the evolution of the genus Erodium: (1) subgenus Erodium plus subgenus Barbata subsection Absinthioidea and (2) the remainder of subgenus Barbata. Dispersal across major water bodies, although uncommon, has had a major influence on the distribution of this genus and is likely to have played as significant role as in other, more easily dispersed, genera. Establishment of Mediterranean climates has facilitated the spread of the genus and been crucial in its diversification. Two, independent, rapid radiations in response to the onset of drought and glacial climate change indicate putative adaptive radiations in the genus.