Plastid Lineages Research Articles

Phylogeographic pattern of range expansion provides evidence for cryptic species lineages in Silene nutans in Western Europe.

As a result of recent or past evolutionary processes, a single species might consist of distinct Evolutionary Significant Units (ESUs), even corresponding to cryptic species. Determining the underlying mechanisms of range shifts and the processes at work in the build-up of divergent ESUs requires elucidating the factors that contribute to population genetic divergence across a species' range. We investigated the large-scale patterns of genetic structure in the perennial herbaceous plant species Silene nutans (Caryophyllaceae) in Western Europe. We sampled and genotyped 111 populations using 13 nuclear microsatellite loci and 6 plastid single-nucleotide polymorphisms. Broad-scale spatial population genetic structure was examined using Bayesian clustering, spatial multivariate analyses and measures of hierarchical genetic differentiation. The genotypic structure of S. nutans was typical of a predominantly allogamous mating system. We also identified plastid lineages with no intra-population polymorphism, mirroring two genetically differentiated nuclear lineages. No evidence of admixture was found. Spatial trends in genetic diversity further suggested independent leading-edge expansion associated with founding events and subsequent genetic erosion. Overall, our findings suggested speciation processes in S. nutans and highlighted striking patterns of distinct stepwise recolonisation of Western Europe shaped by Quaternary climate oscillations. Two main potential ESUs can be defined in Western Europe, corresponding to Eastern and Western nuclear-plastid lineages. In situ preservation of populations and genetic rescue implying ex situ conservation techniques should take the lineage identity into account. This is particularly true in Great Britain, northern France and Belgium, where S. nutans is rare and where distinct lineages co-occur in close contact.

PHOTOSYSTEM II PROTEIN33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem II supercomplexes in Arabidopsis.

Photosystem II (PSII) is a multiprotein complex that catalyzes the light-driven water-splitting reactions of oxygenic photosynthesis. Light absorption by PSII leads to the production of excited states and reactive oxygen species that can cause damage to this complex. Here, we describe Arabidopsis (Arabidopsis thaliana) At1g71500, which encodes a previously uncharacterized protein that is a PSII auxiliary core protein and hence is named PHOTOSYSTEM II PROTEIN33 (PSB33). We present evidence that PSB33 functions in the maintenance of PSII-light-harvesting complex II (LHCII) supercomplex organization. PSB33 encodes a protein with a chloroplast transit peptide and one transmembrane segment. In silico analysis of PSB33 revealed a light-harvesting complex-binding motif within the transmembrane segment and a large surface-exposed head domain. Biochemical analysis of PSII complexes further indicates that PSB33 is an integral membrane protein located in the vicinity of LHCII and the PSII CP43 reaction center protein. Phenotypic characterization of mutants lacking PSB33 revealed reduced amounts of PSII-LHCII supercomplexes, very low state transition, and a lower capacity for nonphotochemical quenching, leading to increased photosensitivity in the mutant plants under light stress. Taken together, these results suggest a role for PSB33 in regulating and optimizing photosynthesis in response to changing light levels.

The plastid ancestor originated among one of the major cyanobacterial lineages.

The primary endosymbiotic origin of chloroplasts is now well established but the identification of the present cyanobacteria most closely related to the plastid ancestor remains debated. We analyse the evolutionary trajectory of a subset of highly conserved cyanobacterial proteins (core) along the plastid lineage, those which were not lost after the endosymbiosis. We concatenate the sequences of 33 cyanobacterial core proteins that share a congruent evolutionary history, with their eukaryotic counterparts to reconstruct their phylogeny using sophisticated evolutionary models. We perform an independent reconstruction using concatenated 16S and 23S rRNA sequences. These complementary approaches converge to a plastid origin occurring during the divergence of one of the major cyanobacterial lineages that include N2-fixing filamentous cyanobacteria and species able to differentiate heterocysts.

Genome-wide transcript profiling reveals the coevolution of plastid gene sequences and transcript processing pathways in the fucoxanthin dinoflagellate Karlodinium veneficum.

Plastids utilize a complex gene expression machinery, which has coevolved with the underlying genome sequence. Relatively, little is known about the genome-wide evolution of transcript processing in algal plastids that have undergone complex endosymbiotic events. We present the first genome-wide study of transcript processing in a plastid acquired through serial endosymbiosis, in the fucoxanthin-containing dinoflagellate Karlodinium veneficum. The fucoxanthin dinoflagellate plastid has an extremely divergent genome and utilizes two unusual transcript processing pathways, 3′-poly(U) tail addition and sequence editing, which were acquired following the serial endosymbiosis event. We demonstrate that poly(U) addition and sequence editing are widespread features across the Karl. veneficum plastid transcriptome, whereas other dinoflagellate plastid lineages that have arisen through independent serial endosymbiosis events do not utilize either RNA processing pathway. These pathways constrain the effects of divergent sequence evolution in fucoxanthin plastids, for example by correcting mutations in the genomic sequence that would otherwise be deleterious, and are specifically associated with transcripts that encode functional plastid proteins over transcripts of recently generated pseudogenes. These pathways may have additionally facilitated divergent evolution within the Karl. veneficum plastid. Transcript editing, for example, has contributed to the evolution of a novel C-terminal sequence extension on the Karl. veneficum AtpA protein. We furthermore provide the first complete sequence of an episomal minicircle in a fucoxanthin dinoflagellate plastid, which contains the dnaK gene, and gives rise to polyuridylylated and edited transcripts. Our results indicate that RNA processing in fucoxanthin dinoflagellate plastids is evolutionarily dynamic, coevolving with the underlying genome sequence.

Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species.

AimTo examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia.LocationNeotropics.MethodsPlastid DNA (trnH–psbA; 410 individuals from 54 populations) and nuclear ribosomal internal transcribed spacer (ITS; 85 individuals from 27 populations) sequences were sampled from Mexico to Bolivia, representing the full extent of the taxon's distribution. Divergence of plastid lineages was dated using a Bayesian coalescent approach. Genetic diversity was assessed with indices of haplotype and nucleotide diversities, and genetic structure was examined using spatial analysis of molecular variance (SAMOVA) and haplotype networks. Population expansion within Amazonia was tested using neutrality and mismatch distribution tests.ResultstrnH–psbA sequences yielded 19 haplotypes restricted to either Mesoamerica or Amazonia; six haplotypes were found among ITS sequences. Diversification of the plastid DNA haplotypes began c. 14.6 Ma. Haplotype diversity for trnH–psbA was higher in Amazonia. Seven genetically differentiated SAMOVA groups were described for trnH–psbA, of which two were also supported by the presence of unique ITS sequences. Population expansion was suggested for both markers for the SAMOVA group that contains most Amazonian populations.Main conclusionsOur results show marked population genetic structure in F. insipida between Mesoamerica and Amazonia, implying that the Andes and seasonally dry areas of northern South America are eco-climatic barriers to its migration. This pattern is shared with other widespread pioneer species affiliated to wet habitats, indicating that the ecological characteristics of species may impact upon large-scale phylogeography. Ficus insipida also shows genetic structure in north-western Amazonia potentially related to pre-Pleistocene historical events. In contrast, evident population expansion elsewhere in Amazonia, in particular the presence of genetically uniform populations across the south-west, indicate recent colonization. Our findings are consistent with palaeoecological data that suggest recent post-glacial expansion of Amazonian forests in the south.

Phylogeography of the Qinghai–Tibet Plateau endemic alpine herb Pomatosace filicula (Primulaceae)

AbstractIn order to trace the response of alpine plants on the Qinghai–Tibet Plateau (QTP) to the Quaternary climate oscillations, the phylogeographic history of Pomatosace filicula Maxim. was investigated in the present study. Based on sequence variations of two maternally inherited plastid markers, matK and trnH‐psbA, and the biparentally inherited nuclear ribosomal internal transcribed spacer (nrITS), we estimated the population genetic structure, lineage divergence timescale, and population dynamics of P. filicula. Seven plastid haplotypes and two nrITS genotypes were identified across the range‐wide sampling of 200 individuals from 24 populations. Although AMOVA revealed a high level of differentiation among populations (FST = 0.560), no significant phylogeographic structure was detected (NST = 0.503, GST = 0.518, P > 0.05). Molecular dating suggested that the divergences between major plastid lineages and nrITS genotypes occurred during the early and middle Pleistocene, and the middle Pleistocene, respectively. This species most likely survived at multiple unglaciated sites on the QTP during the Last Glacial Maximum, with most of these sites located above 4000 m a.s.l. The species probably experienced range expansion at its distribution fringe, but demographic tests did not suggest significant population size changes. We proposed that pronounced effective gene flow (Nem = 0.393) and short generation time may have obscured the phylogeographic and demographic patterns of this species. Our findings will shed new light on the Quaternary evolutionary history of the alpine flora of the QTP.

Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.

Brassica species (tribe Brassiceae) belonging to U's triangle—B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC)—originated via two polyploidization rounds: a U event producing the three allopolyploids, and a more ancient b genome-triplication event giving rise to the A-, B-, and C-genome diploid species. Molecular mapping studies, in situ hybridization, and genome sequencing of B. rapa support the genome triplication origin of tribe Brassiceae, and suggest that these three diploid species diversified from a common hexaploid ancestor. Analysis of plastid DNA has revealed two distinct lineages—Rapa/Oleracea and Nigra—that conflict with hexaploidization as a single event defining the tribe Brassiceae. We analysed an R-block region of A. thaliana present in six copies in B. juncea (AABB), three copies each on A- and B-genomes to study gene fractionation pattern and synonymous base substitution rates (Ks values). Divergence time of paralogues within the A and B genomes and homoeologues between the A and B genomes was estimated. Homoeologous R blocks of the A and B genomes exhibited high gene collinearity and a conserved gene fractionation pattern. The three progenitors of diploid Brassicas were estimated to have diverged approximately 12 mya. Divergence of B. rapa and B. nigra, calculated from plastid gene sequences, was estimated to have occurred approximately 12 mya, coinciding with the divergence of the three genomes participating in the b event. Divergence of B. juncea A and B genome homoeologues was estimated to have taken place around 7 mya. Based on divergence time estimates and the presence of distinct plastid lineages in tribe Brassiceae, it is concluded that at least two independent triplication events involving reciprocal crosses at the time of the b event have given rise to Rapa/Oleracea and Nigra lineages.

Plastid origin: who, when and why?

The origin of plastids is best explained by endosymbiotic theory, which dates back to the early 1900s. Three lines of evidence based on protein import machineries and molecular phylogenies of eukaryote (host) and cyanobacterial (endosymbiont) genes point to a single origin of primary plastids, a unique and important event that successfully transferred two photosystems and oxygenic photosynthesis from prokaryotes to eukaryotes. The nature of the cyanobacterial lineage from which plastids originated has been a topic of investigation. Recent studies have focused on the branching position of the plastid lineage in the phylogeny based on cyanobacterial core genes, that is, genes shared by all cyanobacteria and plastids. These studies have delivered conflicting results, however. In addition, the core genes represent only a very small portion of cyanobacterial genomes and may not be a good proxy for the rest of the ancestral plastid genome. Information in plant nuclear genomes, where most genes that entered the eukaryotic lineage through acquisition from the plastid ancestor reside, suggests that heterocyst-forming cyanobacteria in Stanier’s sections IV and V are most similar to the plastid ancestor in terms of gene complement and sequence conservation, which is in agreement with models suggesting an important role of nitrogen fixation in symbioses involving cyanobacteria. Plastid origin is an ancient event that involved a prokaryotic symbiont and a eukaryotic host, organisms with different histories and genome evolutionary processes. The different modes of genome evolution in prokaryotes and eukaryotes bear upon our interpretations of plastid phylogeny.

Origin and early evolution of photosynthetic eukaryotes in freshwater environments: reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution

Phylogenetic analyses were performed on concatenated data sets of 31 genes and 11,789 unambiguously alignable characters from 37 cyanobacterial and 35 chloroplast genomes. The plastid lineage emerged somewhat early in the cyanobacterial tree, at a time when Cyanobacteria were likely unicellular and restricted to freshwater ecosystems. Using relaxed molecular clocks and 22 age constraints spanning cyanobacterial and eukaryote nodes, the common ancestor to the photosynthetic eukaryotes was predicted to have also inhabited freshwater environments around the time that oxygen appeared in the atmosphere (2.0-2.3Ga). Early diversifications within each of the three major plastid clades were also inferred to have occurred in freshwater environments, through the late Paleoproterozoic and into the middle Mesoproterozoic. The colonization of marine environments by photosynthetic eukaryotes may not have occurred until after the middle Mesoproterozoic (1.2-1.5Ga). The evolutionary hypotheses proposed here predict that early photosynthetic eukaryotes may have never experienced the widespread anoxia or euxinia suggested to have characterized marine environments in the Paleoproterozoic to early Mesoproterozoic. It also proposes that earliest acritarchs (1.5-1.7Ga) may have been produced by freshwater taxa. This study highlights how the early evolution of habitat preference in photosynthetic eukaryotes, along with Cyanobacteria, could have contributed to changing biogeochemical conditions on the early Earth.

The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers

Arundinarieae is not only a taxonomically difficult group of bamboos, but also a troublesome one in molecular phylogenetics. In this study, the phylogeny of 50 species in Arundinarieae with an emphasis on Chimonocalamus was reconstructed, using four plastid regions (rpl32-trnL, trnT-trnL, rps16-trnQ and trnC-rpoB) and two nuclear genes (GBSSI and LEAFY). The plastid phylogeny was largely consistent with the previous studies, except that Ampelocalamus calcareus was newly recovered as lineage XI. The nuclear phylogeny of LEAFY had better resolution than the one of GBSSI. The close relationships among Ampelocalamus, Drepanostachyum and Himalayacalamus were retrieved by the nuclear datasets. Alpine Bashania, Chimonocalamus, Thamnocalamus, and species currently placed in Fargesia and Yushania formed a clade in the LEAFY and combined nuclear phylogenies. Some of the gene tree disparities revealed in previous studies were reconfirmed. Chimonocalamus was recovered as monophyletic by combining the nuclear genes, but as polyphyletic in plastid analyses. Insufficient informative characters, hybridization, plastid capture or incomplete plastid lineage sorting could be responsible for the incongruent phylogenetic positions of some species of Chimonocalamus.

Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers

Bamboos are large perennial grasses of temperate and tropical forests worldwide. Two general growth forms exist: the economically and ecologically important woody bamboos (tribes Arundinarieae and Bambuseae), and the understory herbaceous bamboos (tribe Olyreae). Evolutionary relationships among the 1400+described species have been difficult to resolve with confidence. Comparative analysis of bamboo plastid (chloroplast) DNA has revealed three to five major lineages that show distinct biogeographic distributions. Taxon sampling across tribes and subtribes has been incomplete and most published data sets include a relatively small number of nucleotide characters. Branching order among lineages is often poorly supported, and in more than one study herbaceous bamboos form a clade within the woody bamboos. In this paper, the Bamboo Phylogeny Group presents the most complete phylogeny estimation to date of bamboo tribes and subtribes using 6.7kb of coding and noncoding sequence data and 37 microstructural characters from the chloroplast genome. Quality of data is assessed, as is the possibility of long branch attraction, the degree of character conflict at key nodes in the tree, and the legitimacy of three alternative hypotheses of relationship. Four major plastid lineages are recognized: temperate woody, paleotropical woody, neotropical woody, and herbaceous bamboos. Woody bamboos are resolved as paraphyletic with respect to Olyreae but SH tests cannot reject monophyly of woody species (Arundinarieae+Bambuseae).

The Permian–Triassic mass extinction forces the radiation of the modern marine phytoplankton

Medlin L.K. 2011. The Permian–Triassic mass extinction forces the radiation of the modern marine phytoplankton. Phycologia 50: 684–693. DOI: 10.2216/10-31.1Among modern eukaryotic marine phytoplanktonic lineages possessing red algal plastids are the diatoms, dinoflagellates and haptophytes including coccolithophorids. Although origins of these host lineages and the timing of the endosymbioses leading to their ability to photosynthesize are ancient, their modern radiations are not. Molecular clocks suggest the timing of the origins and the radiations of these host lineages are different among the three groups. Dinoflagellates and haptophytes had class and order level radiations from 500 to 600 megaannum (Ma) and genus-level radiations, especially among the thecate dinoflagellates, about 250 Ma. Pigmented heterokonts, the last divergence in the heterokont tree, originated between 770 and 1000 Ma, but most planktonic unicellular groups diverged at the Permian–Triassic (P/T) boundary (250 Ma) and radiated thereafter based on a clock constrained by both fossil first appearances and biochemical evidence. Recent molecular evidence suggests that heterokont and haptophyte protistan host cells originally possessed both green and red algal plastids with endosymbiosis of the green plastid older than the red one. If one assumes that once the green algal plastid was eliminated, the red algal plastid lineages could then proliferate, then my clocks suggest that this event likely occurred at the P/T extinction. The possession of the red plastid only became advantageous at the P/T extinction when oceanic chemistry changes provided a habitat in which red algal plastids were better adapted and could out-compete green algal plastids. Prior to the P/T, red algal lineages were not dominant as judged by the fossil record, and there is an absence of a dominant green plastid lineage in the modern plankton. Therefore, expulsion of the green algal plastid in favour of a red algal plastid and divergence and subsequent radiation of the planktonic heterokont algae and major orders/families/genera in the haptophytes and the dinoflagellates were likely forced by the Permian–Triassic extinction event.

MONO- AND DIGALACTOSYLDIACYLGLYCEROL COMPOSITION OF RAPHIDOPHYTES (RAPHIDOPHYCEAE): A MODERN INTERPRETATION USING POSITIVE-ION ELECTROSPRAY/MASS SPECTROMETRY/MASS SPECTROMETRY(1).

Raphidophyte algae (Raphidophyceae) can be divided according to pigment composition and plastid ancestry into two categories, brown- and green-pigmented taxa. We sought to examine if there are any biochemical differences in plastid lipid composition between the two groups. To this end, the composition and positional distribution of fatty acids of the chloroplast lipids, mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively), were examined using positive-ion electrospray/mass spectrometry (ESI/MS) and electrospray/mass spectrometry/mass spectrometry (ESI/MS/MS). Brown-pigmented strains from the genera Chattonella, Fibrocapsa, and Heterosigma primarily consisted of 20:5/18:4 (sn-1/sn-2) MGDG and 20:5/18:4 DGDG, while isolates of the green-pigmented raphidophyte Gonyostomum semen (Ehrenb.) Diesing contained these as well as 18:3/18:4 MGDG and DGDG, thus underscoring its green algal plastid lineage. Although previously unseen without the regiochemical information provided by ESI/MS/MS, Chattonella subsalsa Biecheler possessed 20:5/18:3 DGDG as a major form, a potential biosynthetic intermediate in the production of 20:5/18:4 DGDG. These results provide a modern interpretation of the fatty acid regiochemistry of MGDG and DGDG.

Evolutionary inheritance of elemental stoichiometry in phytoplankton

The elemental composition of phytoplankton is a fusion of the evolutionary history of the host and plastid, resulting in differences in genetic constraints and selection pressures associated with environmental conditions. The evolutionary inheritance hypothesis predicts similarities in elemental composition within related taxonomic lineages of phytoplankton. To test this hypothesis, we measured the elemental composition (C, N, P, S, K, Mg, Ca, Sr, Fe, Mn, Zn, Cu, Co, Cd and Mo) of 14 phytoplankton species and combined these with published data from 15 more species from both marine and freshwater environments grown under nutrient-replete conditions. The largest differences in the elemental profiles of the species distinguish between the prokaryotic Cyanophyta and primary endosymbiotic events that resulted in the green and red plastid lineages. Smaller differences in trace element stoichiometry within the red and green plastid lineages are consistent with changes in trace elemental stoichiometry owing to the processes associated with secondary endosymbioses and inheritance by descent with modification.

Disentangling phylogeography, polyploid evolution and taxonomy of a woodland herb (Veronica chamaedrys group, Plantaginaceae s.l.) in southeastern Europe

Southeastern Europe is a centre of European biodiversity, but very little is known about factors causing the observed richness. Here, we contribute to fill this gap by reconstructing the spatio-temporal diversification of the cytologically variable and taxonomically intricate complex of Veronica chamaedrys (Plantaginaceae s.l.), growing in open forests, forest edges and grasslands, with flow cytometry, molecular markers (AFLPs, plastid DNA sequences) and morphometry. Our results show that both diploid and tetraploid cytotypes are widespread, but diploids predominate on the southern Balkan Peninsula. Plastid sequences suggest a first split into three main lineages in the mid-Pleistocene and a continuous diversification during the last 0.4my. Two of the identified plastid lineages coincide with geographically distinct AFLP clusters. Altogether, the genetic data suggest forest refugia on the southern-most Balkan Peninsula (Greece), in Bulgaria, Istria (Croatia and Slovenia) and maybe the southeastern Carpathians (Romania). Morphometric and genetic data show little congruence with current taxonomy.

Paradoxically, prior acquisition of antioxidant activity enhances oxidative stress‐induced cell death

Oxidative stress has been implicated in the induction of programmed cell death in a wide variety of organisms. Acquiring antioxidant capacity is thought to enhance the viability of cells challenged by a subsequent oxidative stress. Counter-intuitively, we show that in two phytoplankton species, Chlamydomonas reinhardtii and Peridinium gatunense, representing the green and red plastid lineages, oxidative stress induced cell death in cultures that already possessed high antioxidant activity but not in cells that exhibited low activity. Cell death of low antioxidant possessing cultures was markedly enhanced by the addition of dehydroascorbate, a product of ascorbate peroxidase (APX), but not of ascorbate or reduced glutathione, and was preceded by increased metacaspase expression and activity. These data suggested that the level of APX and its products, strongly upregulated by oxidative stress, serves as a possible surveillance signal, reporting that the cells already experienced an earlier oxidative stress. Our data presents a novel role of APX in antioxidant activity and response to oxidative stress in photosynthetic microorganisms. Elimination of cysts production by phytoplankton cells that were already damaged by oxidative stress (indicated by the rise in oxidized proteins) as the inoculum for the following year's population may be the evolutionary trigger for this phenomenon.

Phylogenetic structure of the grass subfamily Pooideae based on comparison of plastid matK gene–3′trnK exon and nuclear ITS sequences

ABSTRACTThe grass subfamily Pooideae was studied using DNA sequence information from the chloroplast (cp) matK gene–3′trnK exon and the nuclear ribosomal (nr) ITS1–5.8S gene–ITS2 in a sample of 67 taxa covering all of its tribes. Branches with strong bootstrap support are consistently resolved in both datasets, whereas discrepancy is confined to low‐support or unsupported nodes in one of the datasets. The results do not reveal a significant role of past hybridisation, plastid lineage sorting or reticulation in the evolutionary diversification of the major lineages of the subfamily. The combined analysis of the plastid and nuclear datasets results in a largely well‐supported pattern of divergence for the major lineages of the subfamily. Some re‐alignments of tribes and subtribes are proposed and discussed with reference to relevant morphological and structural characters. We propose the recognition of broader tribes Nardeae with subtribes Nardinae and Lygeinae, Meliceae with subtribes Brylkiniinae and Melicinae, Stipeae with subtribes Ampelodesminae and Stipinae, and Triticeae with subtribes Littledaleinae, Brominae and Hordeinae. For the tribe complex of Aveneae and Poeae, the clear‐cut split into two major clades and further resolution into some high‐support lineages depicted by cpDNA is not contradicted by nuclear ITS and their taxonomic treatment as separate tribes or a single tribe remains an unanswered question.

Sorting wheat from chaff in multi-gene analyses of chlorophyll c-containing plastids

Photosynthetic eukaryotes contain primary, secondary or tertiary plastids, depending on the source of the organelle (a cyanobacterium or a photosynthetic eukaryote). Plastid phylogeny is relatively well investigated, but molecular phylogenies have conflicted as a function of gene choice, taxon-representations, and analytical method. To better understand the influences of these variables, we performed analyses of a multi-gene data set based on 62 plastid-associated genes of 15 taxa representing the major plastid lineages. In an attempt to distinguish phylogenetic signal from non-phylogenetic patterns, we analyzed the data using a wide range of phylogenetic methods and examined the effect of covarion evolution and compositional bias. The data suggest that the chlorophyll c-containing plastids are monophyletic and acquired their plastids from the red algae after the emergence of the Cyanidiales. The relationships among chl c-containing plastids are particularly hard to resolve. This is the largest data set used for this purpose; the analyses show that cryptophyte plastids are sister to other chl c-containing plastids, and haptophyte and peridinin-containing dinoflagellate plastids are closely related.

Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea)

AbstractAim The olive tree is considered one of the best indicators of the Mediterranean climate. The species’ distribution is associated with geographical and bioclimatic factors, as well as being influenced by a long period of cultivation. Despite concerted efforts of different research groups, the origin of the Mediterranean olive tree still remains elusive. In the present study, relationships between taxa and populations covering the entire range of Olea europaea were investigated using both maternal (plastid genome) and biparental (nuclear genome) markers to disclose evolutionary patterns in the olive complex. Phylogenetic and phylogeographical results of the two‐genome analyses were interpreted in a biogeographical context.Location Mediterranean, temperate and subtropical floristic regions of the Old World.Methods Phylogeographical reconstructions of plastid DNA polymorphism were performed using microsatellites, restriction sites and indels on a wide sample of 185 representative trees across the Old World, including 28 herbarium specimens from remote areas. Additionally, the potential utility of one ITS‐1 pseudogene for phylogenetic analyses was explored using Bayesian and maximum parsimony approaches on a subsample of 38 olive trees.Results Forty plastid haplotypes were recognized and split into two lineages and seven sublineages. The analysis of ITS‐1 sequences also allowed the identification of seven well differentiated groups. Distribution of plastid and ribosomal DNA lineages was congruent, but particular cases of phylogenetic incongruence were disclosed (particularly in the Sahara and Madeira). Lastly, two divergent ITS‐1 copies were isolated from the same sample of four individuals of different subspecies.Main conclusions Phylogenetic congruence of both ITS‐1 and plastid lineages suggested an evolutionary scenario of predominant isolation during the Plio‐Pleistocene in Macaronesia, the Mediterranean, southern Africa, eastern Africa and Asia. The Saharan desert appeared to have played an important role of vicariant barrier between southern and northern African populations in early times. Incongruence of some plastid and nuclear results, as well as intermingled ITS‐1 copies of different lineages in single individuals, was interpreted as a result of recurrent reticulation events in the olive complex. We identified an ancient hybrid zone from the Sahara to north‐eastern African mountains, where divergent plastid and nuclear lineages still co‐exist. Results of this paper, and previous studies, suggest that the cultivated olive originated from a pre‐Quaternary Mediterranean ancestor, with no evidence for a recent hybrid origin. In contrast, a continuous process of olive domestication through local hybridization events of cultivated trees with natural populations may have brought about a remarkably high genomic diversity among cultivated trees across the Mediterranean.

Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra

The evolutionary history and relationship between plastids of dinoflagellate algae and apicomplexan parasites have been controversial both because the organelles are unusual and because their genomes contain few comparable genes. However, most plastid proteins are encoded in the host nucleus and targeted to the organelle, and several of these genes have proved to have interesting and informative evolutionary histories. We have used expressed sequence tag (EST) sequencing to generate gene sequence data from the nuclear genome of the dinoflagellate Heterocapsa triquetra and inferred phylogenies for the complete set of identified plastid-targeted proteins. Overall, dinoflagellate plastid proteins are most consistently related to homologues from the red algal plastid lineage (not green) and, in many of the most robust cases, they branch with other chromalveolate algae. In resolved phylogenies where apicomplexan data are available, dinoflagellates and apicomplexans are related. We also identified two cases of apparent lateral, or horizontal, gene transfer, one from the green plastid lineage and one from a bacterial lineage unrelated to plastids or cyanobacteria.