Nuclear DNA-based markers for plant evolutionary biology

Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids

Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an "expanded" malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.

Phylogeography of Himalrandia lichiangensis from the dry-hot valleys in Southwest China

Both changing tectonics and climate may shape the phylogeographic patterns of plant species. The dry-hot valleys in southwestern China harbor a high number of endemic plants. In this study, we investigated the evolutionary history and potential distribution of an endemic shrub Himalrandia lichiangensis (Rubiaceae), to evaluate the effects of tectonic and climatic processes on this thermophilic plant species from the dry-hot valleys. By sequencing DNA from four plastid non-coding regions (psbM-trnD, trnD-trnT, atpB-rbcL and accD-psaI) and the CAMX1F-CAMX2R region and ITS for 423 individuals from 23 populations, we investigated the genetic diversity, phylogeographical pattern and population dynamics of H. lichiangensis. We found a high degree of differentiation in H. lichiangensis during the middle Miocene (15-13 Myr), possibly triggered by the rapid tectonic uplift event in this period area. accompanied by frequent orogeneses in this period. This hypothesis is also supported by the association between genetic differentiation and altitudinal gradients among populations. The middle reach of the Jinsha River, which harbors the greatest genetic diversity, is most likely to have been a refugia for H. lichiangensis during Quaternary. We also detected a strong barrier effect between the Nanpan River and Jinsha River, suggesting the river system may play a role in geographical isolation between clades on both sides of the barrier. The Maximum Entropy Model (MaxEnt) results showed that future climate warming will lead to the niche expansion in some areas for H. lichiangensis but will also cause a scattered and fragmented distribution. Given the high among-population differentiation and no recent expansion detected in H. lichiangensis, its current phylogeographical pattern is possibly due to a long-term geographical barrier caused by uplifting mountains since the Miocene, as well as Quaternary climate refugia isolated also by high mountains. This study illustrated tectonic and climatic processes may have a continuous effect on plant phylogeography and offers insights into the origin of biodiversity and endemism in the dry-hot valleys of southwestern China.

Phytohormone signaling and crosstalk in regulating drought stress response in plants

Phytohormones are ubiquitously involved in plant biological processes and regulate cellular signaling pertaining to unheralded environmental cues, such as salinity, drought, extreme temperature and nutrient deprivation. The association of phytohormones to nearly all the fundamental biological processes epitomizes the phytohormone syndicate as a candidate target for consideration during engineering stress endurance in agronomically important crops. The drought stress response is essentially driven by phytohormones and their intricate network of crosstalk, which leads to transcriptional reprogramming. This review is focused on the pivotal role of phytohormones in water deficit responses, including their manipulation for mitigating the effect of the stressor. We have also discussed the inherent complexity of existing crosstalk accrued among them during the progression of drought stress, which instigates the tolerance response. Therefore, in this review, we have highlighted the role and regulatory aspects of various phytohormones, namely abscisic acid, auxin, gibberellic acid, cytokinin, brassinosteroid, jasmonic acid, salicylic acid, ethylene and strigolactone, with emphasis on drought stress tolerance.

Global phylogeography of a pantropical mangrove genus Rhizophora

Rhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.

Genetic insights into the evolution of genera with the eastern Asia-eastern North America floristic disjunction: a transcriptomics analysis

PREMISE

Large disjunctions in species distributions provide excellent opportunities to study processes that shape biogeographic patterns. One such disjunction is the eastern Asia-eastern North America (EA-ENA) floristic disjunction. For many genera with this disjunction, species richness is greater in EA than in ENA; this pattern has been attributed, in part, to higher rates of molecular evolution and speciation in EA. Longer branch lengths have been found in some EA clades, relative to their ENA sister clades, suggesting that the EA lineages have evolved at a higher rate, possibly due to environmental heterogeneity, potentially contributing to the species richness anomaly.

METHODS

To evaluate whether rates of molecular evolution are elevated in EA relative to ENA, we used transcriptomes from species in 11 genera displaying this disjunction. Rates of molecular evolution were estimated for up to 385 orthologous nuclear loci per genus.

RESULTS

No statistically significant differences were identified in pairwise comparisons between EA and ENA sister species, suggesting equal rates of molecular evolution for both species; the data also suggest similar selection pressures in both regions. For larger genera, evidence likewise argues against more species-rich clades having higher molecular evolutionary rates, regardless of region. Our results suggest that genes across multiple gene ontology categories are evolving at similar rates under purifying selection in species in both regions.

CONCLUSIONS

Our data support the hypothesis that greater species richness in EA than ENA is due to factors other than an overall increase in rates of molecular evolution in EA.

Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus)

BACKGROUND

Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China.

RESULTS

Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations.

CONCLUSIONS

Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.

Low-copy nuclear markers in Isoëtes (Isoëtaceae) identified with transcriptomes

PREMISE OF THE STUDY

Few genetic markers provide phylogenetic information in closely related species of Isoëtes (Isoëtaceae). We describe the development of primers for several putative low-copy nuclear markers to resolve the phylogeny of Isoëtes, particularly in the southeastern United States.

METHODS AND RESULTS

We identified regions of interest in Isoëtes transcriptomes based on low-copy genes in other plants. Primers were designed for these regions and tested with 16 taxa of Isoëtes and one species of Lycopodium. Parts of the pgiC, gapC, and IBR3 gene regions show phylogenetic signal within the North American and Mediterranean clades of Isoëtes.

CONCLUSIONS

Transcriptome data prove useful for identification and primer design of low-copy genes. Three new markers show potential for inferring phylogenies in regional clades of Isoëtes, and possibly across the entire genus.

Atlantic forests to the all Americas: Biogeographical history and divergence times of Neotropical Ficus (Moraceae)

Ficus (Moraceae) is well diversified in the Neotropics with two lineages inhabiting the wet forests of this region. The hemiepiphytes of section Americanae are the most diversified with c. 120 species, whereas section Pharmacosycea includes about 20 species mostly with a terrestrial habit. To reconstruct the biogeographical history and diversification of Ficus in the Americas, we produced a dated Bayesian phylogenetic hypothesis of Neotropical Ficus including two thirds of the species sequenced for five nuclear regions (At103, ETS, G3pdh, ITS/5.8S and Tpi). Ancestral range was estimated using all models available in Biogeobears and Binary State Speciation and Extinction analysis was used to evaluate the role of the initial habit and propagule size in diversification. The phylogenetic analyses resolved both Neotropical sections as monophyletic but the internal relationships between species in section Americanae remain unclear. Ficus started their diversification in the Neotropics between the Oligocene and Miocene. The genus experienced two bursts of diversification: in the middle Miocene and the Pliocene. Colonization events from the Amazon to adjacent areas coincide with the end of the Pebas system (10 Mya) and the connection of landmasses. Divergence of endemic species in the Atlantic forest is inferred to have happened after its isolation and the opening and consolidation of the Cerrado. Our results suggest a complex diversification in the Atlantic forest differing between postulated refuges and more instable areas in the South distribution of the forest. Finally the selection for initial hemiepiphytic habit and small to medium propagule size influenced the diversification and current distribution of the species at Neotropical forests marked by the historical instability and long-distance dispersal.

The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes

PREMISE OF THE STUDY

The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae.

METHODS

Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes.

RESULTS

Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions.

DISCUSSION

Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.

Hybridization among distantly related species: Examples from the polyploid genus Curcuma (Zingiberaceae)

Discerning relationships among species evolved by reticulate and/or polyploid evolution is not an easy task, although it is widely discussed. The economically important genus Curcuma (ca. 120 spp.; Zingiberaceae), broadly distributed in tropical SE Asia, is a particularly interesting example of a group of palaeopolyploid origin whose evolution is driven mainly by hybridization and polyploidization. Although a phylogeny and a new infrageneric classification of Curcuma, based on commonly used molecular markers (ITS and cpDNA), have recently been proposed, significant evolutionary questions remain unresolved. We applied a multilocus approach and a combination of modern analytical methods to this genus to distinguish causes of gene tree incongruence and to identify hybrids and their parental species. Five independent regions of nuclear DNA (DCS, GAPDH, GLOBOSA3, LEAFY, ITS) and four non-coding cpDNA regions (trnL-trnF, trnT-trnL, psbA-trnH and matK), analysed as a single locus, were employed to construct a species tree and hybrid species trees using (*)BEAST and STEM-hy. Detection of hybridogenous species in the dataset was also conducted using the posterior predictive checking approach as implemented in JML. The resulting species tree outlines the relationships among major evolutionary lineages within Curcuma, which were previously unresolved or which conflicted depending upon whether they were based on ITS or cpDNA markers. Moreover, by using the additional markers in tests of plausible topologies of hybrid species trees for C. vamana, C. candida, C. roscoeana and C. myanmarensis suggested by previous molecular and morphological evidence, we found strong evidence that all the species except C. candida are of subgeneric hybrid origin.

Molecular Evidence for the Hybrid Origin of Ilex dabieshanensis (Aquifoliaceae)

Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I. cornuta and I. latifolia, we proposed it as a natural hybrid between them. In this study, we sequenced one chloroplast intergenic spacer (trnH-psbA) and two nuclear genes (gapC and nepGS) in I. dabieshanensis and its putative parental species to test the hybrid origin hypothesis. Our results showed that there were one to two differentially fixed sequence differences between I. cornuta and I. latifolia at the two nuclear genes. Twelve of the 14 individuals of I. dabieshanensis exhibited additivity in chromatograms on these differentially fixed sites at both nuclear genes, and the remaining two exhibited additivity in chromatograms on the fixed site at only the nepGS gene. Except one haplotype of I. cornuta at the nepGS gene, all of the haplotypes of I. cornuta at the two nuclear genes were well separated from those of I. latifolia, and most haplotypes of I. dabieshanensis were shared with those of I. cornuta and I. latifolia. Phylogenetic analysis of these haplotypes was largely consistent with haplotype network analysis. I. cornuta and I. latifolia differed by two nucleotide substitutions in the chloroplast intergenic spacer, and 12 individuals of I. dabieshanensis had the same sequences as I. latifolia, while the remaining two were identical with I. cornuta. The molecular data provide convincing evidence for the hybrid origin of I. dabieshanensis and asymmetrical direction of hybridization. One haplotype of I. cornuta at the nepGS gene was nested with those of I. latifolia, indicating introgression to I. cornuta.

Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.

A New Classification of Ficus Subsection Urostigma (Moraceae) Based on Four Nuclear DNA Markers (ITS, ETS, G3pdh, and ncpGS), Morphology and Leaf Anatomy

Ficus subsection Urostigma as currently circumscribed contains 27 species, distributed in Africa, Asia, Australia and the Pacific, and is of key importance to understand the origin and evolution of Ficus and the fig-wasp mutualism. The species of subsection Urostigma are very variable in morphological characters and exhibit a wide range of often partly overlapping distributions, which makes identification often difficult. The systematic classification within and between this subsection and others is problematic, e.g., it is still unclear where to classify F. amplissima and F. rumphii. To clarify the circumscription of subsection Urostigma, a phylogenetic reconstruction based on four nuclear DNA markers (ITS, ETS, G3pdh, and ncpGS) combined with morphology and leaf anatomy is conducted. The phylogenetic tree based on the combined datasets shows that F. madagascariensis, a Madagascan species, is sister to the remainder of subsect. Urostigma. Ficus amplissima and F. rumphii, formerly constituting sect. Leucogyne, appear to be imbedded in subsect. Conosycea. The result of the phylogenetic analysis necessitates nomenclatural adjustments. A new classification of Ficus subsection Urostigma is presented along with the morphological and leaf anatomical apomorphies typical for the clades. Two new species are described ─ one in subsect. Urostigma, the other in Conosycea. One variety is raised to species level.

Natural hybridization and asymmetric introgression at the distribution margin of two Buddleja species with a large overlap

BACKGROUND

Natural hybridization in plants is universal and plays an important role in evolution. Based on morphology it has been presumed that hybridization occurred in the genus Buddleja, though genetic studies confirming this assumption have not been conducted to date. The two species B. crispa and B. officinalis overlap in their distributions over a wide range in South-West China, and we aimed to provide genetic evidence for ongoing hybridization in this study.

RESULTS

We investigated the occurrence of hybrids between the two species at the southern-most edge of the distribution of B. crispa using five nuclear loci and pollination experiments. The genetic data suggest substantial differentiation between the two species as species-specific alleles are separated by at least 7-28 mutations. The natural hybrids found were nearly all F1s (21 of 23), but backcrosses were detected, and some individuals, morphologically indistinguishable from the parental species, showed introgression. Pollen viability test shows that the percentage of viable pollen grains was 50 ± 4% for B. crispa, and 81 ± 2% for B. officinalis. This difference is highly significant (t = 7.382, p < 0.0001). Hand cross-pollination experiments showed that B. crispa is not successful as pollen-parent, but B. officinalis is able to pollinate B. crispa to produce viable hybrid seed. Inter-specific seed-set is low (8 seeds per fruit, as opposed to about 65 for intra-specific pollinations), suggesting post-zygotic reproductive barriers. In addition, one of the reference populations also suggests a history of introgression at other localities.

CONCLUSIONS

The occurrence of morphologically intermediate individuals between B. crispa and B. officinalis at Xishan Mountain is unequivocally linked to hybridization and almost all examined individuals of the putative hybrids were likely F1s. Despite pollination experiments indicating higher chances for introgression into B. officinalis (hybrids only produced viable seed when crossed with B. officinalis), observed introgression was asymmetrical into B. crispa. This could be due to seeds produced by hybrids not contributing to seedlings, or other factors favoring the establishment of backcrosses towards B. crispa. However, further research will be needed to confirm these observations, as the small number of plants used for the pollination experiments could have introduced an artifact, for example if used individuals were more or less compatible than the species average, and also the small number of loci used could convey a picture of introgression that is not representative for the whole genome.

Apparent similarity, underlying homoplasy: Morphology and molecular phylogeny of the North American clade of Manihot

PREMISE OF THE STUDY

Morphologically diverse clades are useful for detecting adaptive morphological evolution. Each of their variants may have evolved once or several times, suggesting that their repeated appearance may be due to environmental pressures. The North American Manihot species are an excellent system to detect possible adaptations and to assess the effect of mono- or polyphyly on classification. With 20 species, this group includes growth forms from tuberous herbs to trees. The monophyly of this group and its relationship with the economically important M. esculenta were tested for the first time with complete sampling of North American species.

METHODS

We carried out maximum likelihood and Bayesian phylogenetic analyses on a matrix of 3662 bp from chloroplast (psbA-trnH, trnL-trnF) and nuclear loci (PEPC and two paralogous copies of G3pdh). We included all North American Manihot species, Manihotoides pauciflora, and published sequences from 34 South American species.

KEY RESULTS

Our results support monophyly of the North American Manihot group. Its taxonomic sections are paraphyletic, and three to four growth forms evolved repeatedly. Manihotoides pauciflora is nested within North American Manihot species. Some PEPC and G3pdh clones grouped with clones of other species and not with clones from their own species.

CONCLUSIONS

North and South American Manihot species are sister clades. Paraphyly of North American sections suggests that taxonomic revision is warranted. The position of Manihotoides pauciflora confirms that Manihotoides should remain subsumed within Manihot. Most growth forms likely evolved repeatedly in this group. The behavior of PEPC and G3pdhNA clones is probably due to incomplete lineage sorting.

Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers

Rosa sections Chinenses and Synstylae contain approximately 39 wild species mainly distributed in East Asia and are closely related according to previous studies. But the specific relationships within these two sections were still obscure due to limited sampling, low genetic variation of molecular markers, and complex evolutionary histories. In this study, we used four chloroplast (ndhC-trnV, ndhF-rpl32, ndhJ-trnF and psbJ-petA) and two nuclear (ribosomal ITS and GAPDH) markers with an extensive geographic and taxonomic sampling to explore their evolutionary history. Our phylogenetic analyses suggested that Rosa sections Chinenses and Synstylae defined in traditional taxonomic system are not monophyletic and close to sections Caninae and Gallicanae. Additionally, our results showed incongruence between chloroplast and nuclear markers, and the patterns of incongruence might be due to ancient hybridization (genetic introgression). One putative hybrid species and three samples identified as interspecific hybrids are further discussed in terms of topological incongruence, biological characters and distribution patterns.

Phylogeny and biogeography of wild roses with specific attention to polyploids

BACKGROUND AND AIMS

The genus Rosa (150-200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus.

METHODS

Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas.

KEY RESULTS

Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa.

CONCLUSIONS

The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.

Speciation within Columnea section Angustiflora (Gesneriaceae): islands, pollinators and climate

Despite many advances in evolutionary biology, understanding the proximate mechanisms that lead to speciation for many taxonomic groups remains elusive. Phylogenetic analyses provide a means to generate well-supported estimates of species relationships. Understanding how genetic isolation (restricted gene flow) occurred in the past requires not only a well-supported molecular phylogenetic analysis, but also an understanding of when character states that define species may have changed. In this study, phylogenetic trees resolve species level relationships for fourteen of the fifteen species within Columnea section Angustiflorae (Gesneriaceae). The distributions of sister species pairs are compared and ancestral character states are reconstructed using Bayesian stochastic mapping. Climate variables were also assessed and shifts in ancestral climate conditions were mapped using SEEVA. The relationships between morphological character states and climate variables were assessed with correlation analyses. These results indicate that species in section Angustiflorae have likely diverged as a result of allopatric, parapatric, and sympatric speciation, with both biotic and abiotic forces driving morphological and phenological divergence.

Molecular and morphological data reveal hybrid origin of wild Prunus yedoensis (Rosaceae) from Jeju Island, Korea: implications for the origin of the flowering cherry

PREMISE OF THE STUDY

The subgenus Cerasus of the genus Prunus includes several popular ornamental flowering cherries. Of the hundreds of cultivars, P. ×yedoensis ('Somei-yoshino') is the most popular and familiar cultivar in Korea and Japan and is considered to be of hybrid origin. However, the hybrid origin of P. ×yedoensis and its relationship to wild P. yedoensis, naturally occurring on Jeju Island, Korea, are highly controversial.

METHODS

We extensively sampled wild P. yedoensis, cultivated P. ×yedoensis, and numerous individuals from other species belonging to subgenus Cerasus on Jeju Island. Samples from 71 accessions, representing 13 species and one cultivar (P. ×yedoensis), were sequenced for nrDNA ITS/ETS (952 characters) and seven noncoding cpDNA regions (5421 characters) and subjected to maximum parsimony and maximum likelihood analysis. Additive polymorphisms in the ITS/ETS regions were confirmed by cloning amplicons from representative species.

KEY RESULTS

The nuclear (ITS/ETS and G3pdh) and cpDNA data, along with several morphological characteristics, provide the first convincing evidence for the hybrid origin of wild P. yedoensis. The maternal parent was determined to be P. spachiana f. ascendens, while the paternal parent was unresolved from the taxonomically complex P. serrulata/P. sargentii clade. The presence of two kinds of ribotypes was confirmed by cloning, and the possible origin of cultivated P. ×yedoensis from wild populations on Jeju Island was also suggested.

CONCLUSIONS

Bidirectional and multiple hybridization events were responsible for the origin of wild P. yedoensis. Extensive gene flow was documented in this study, suggesting an important role of reticulate evolution in subgenus Cerasus.

Comparative transcriptome resources of eleven Primulina species, a group of 'stone plants' from a biodiversity hot spot

The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an N50 value of 2191 bp after pooling and reassembling twelve individual pre-assembled unigene sets. Of these unigenes, 249 973 (70%) were successfully annotated and 256 601 (72%) were identified as coding sequences (CDSs). We identified a total of 38 279 simple sequence repeats (SSRs) and 367 123 single nucleotide polymorphisms (SNPs). Marker validation assay revealed that 354 (27.3%) of the 1296 SSR and 795 (39.6%) of the 2008 SNP loci showed successful genotyping performance and exhibited expected polymorphism profiles. We screened 834 putative single-copy nuclear genes and proved their high effectiveness in phylogeny construction and estimation of ancestral population parameters. We identified a total of 85 candidate orthologs under positive selection for 46 of the 66 species pairs. This study provided an efficient application of RNA-seq in development of genomic resources for a group of 'stone plants' from south China Karst regions, a biodiversity hot spot of the World. The assembled unigenes with annotations and the massive gene-associated molecular markers would help guide further molecular systematic, population genetic and ecological genomics studies in Primulina and its relatives.

Genetic variability and population structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae) based on AFLP analysis

Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP) fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and "excess flowers production, but little fruit set". It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible.

Long-distance dispersal by sea-drifted seeds has maintained the global distribution of Ipomoea pes-caprae subsp. brasiliensis (Convolvulaceae)

Ipomoea pes-caprae (Convolvulaceae), a pantropical plant with sea-drifted seeds, is found globally in the littoral areas of tropical and subtropical regions. Unusual long-distance seed dispersal has been believed to be responsible for its extraordinarily wide distribution; however, the actual level of inter-population migration has never been studied. To clarify the level of migration among populations of I. pes-caprae across its range, we investigated nucleotide sequence variations by using seven low-copy nuclear markers and 272 samples collected from 34 populations that cover the range of the species. We applied coalescent-based approaches using Bayesian and maximum likelihood methods to assess migration rates, direction of migration, and genetic diversity among five regional populations. Our results showed a high number of migrants among the regional populations of I. pes-caprae subsp. brasiliensis, which suggests that migration among distant populations was maintained by long-distance seed dispersal across its global range. These results also provide strong evidence for recent trans-oceanic seed dispersal by ocean currents in all three oceanic regions. We also found migration crossing the American continents. Although this is an apparent land barrier for sea-dispersal, migration between populations of the East Pacific and West Atlantic regions was high, perhaps because of trans-isthmus migration via pollen dispersal. Therefore, the migration and gene flow among populations across the vast range of I. pes-caprae is maintained not only by seed dispersal by sea-drifted seeds, but also by pollen flow over the American continents. On the other hand, populations of subsp. pes-caprae that are restricted to only the northern part of the Indian Ocean region were highly differentiated from subsp. brasiliensis. Cryptic barriers that prevented migration by sea dispersal between the ranges of the two subspecies and/or historical differentiation that caused local adaptation to different environmental factors in each region could explain the genetic differentiation between the subspecies.

A strong 'filter' effect of the East China Sea land bridge for East Asia's temperate plant species: inferences from molecular phylogeography and ecological niche modelling of Platycrater arguta (Hydrangeaceae)

Background

In East Asia, an increasing number of studies on temperate forest tree species find evidence for migration and gene exchange across the East China Sea (ECS) land bridge up until the last glacial maximum (LGM). However, it is less clear when and how lineages diverged in this region, whether in full isolation or in the face of post-divergence gene flow. Here, we investigate the effects of Quaternary changes in climate and sea level on the evolutionary and demographic history of Platycrater arguta, a rare temperate understorey shrub with disjunct distributions in East China (var. sinensis) and South Japan (var. arguta). Molecular data were obtained from 14 P. arguta populations to infer current patterns of molecular structure and diversity in relation to past (Last Interglacial and Last Glacial Maximum) and present distributions based on ecological niche modelling (ENM). A coalescent-based isolation-with-migration (IM) model was used to estimate lineage divergence times and population demographic parameters.

Results

Combining information from nuclear/chloroplast sequence data with nuclear microsatellites, our IM analyses identify the two varieties as genetically distinct units that evolved in strict allopatry since the mid-Pleistocene, c. 0.89 (0.51–1.2) Ma. Together with Bayesian Skyeline Plots, our data further suggest that both lineages experienced post-divergence demographic growth, followed by refugial isolation, divergence, and in the case of var. arguta post-glacial admixture. However, past species distribution modelling indicates that the species’ overall distribution has not greatly changed over the last glacial cycles.

Conclusions

Our findings highlight the important influence of ancient sea-level changes on the diversification of East Asia’s temperate flora. Implicitly, they challenge the notion of general temperate forest expansion across the ECS land bridge, demonstrating instead its ‘filter’ effect owing to an unsuitable environment for certain species and their biological (e.g., recruitment) properties.

Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects

The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.

Intricate patterns of phylogenetic relationships in the olive family as inferred from multi-locus plastid and nuclear DNA sequence analyses: a close-up on Chionanthus and Noronhia (Oleaceae)

Noronhia represents the most successful radiation of the olive family (Oleaceae) in Madagascar with more than 40 named endemic species distributed in all ecoregions from sea level to high mountains. Its position within the subtribe Oleinae has, however, been largely unresolved and its evolutionary history has remained unexplored. In this study, we generated a dataset of plastid (trnL-F, trnT-L, trnS-G, trnK-matK) and nuclear (internal transcribed spacer [ITS]) DNA sequences to infer phylogenetic relationships within Oleinae and to examine evolutionary patterns within Noronhia. Our sample included most species of Noronhia and representatives of the ten other extant genera within the subtribe with an emphasis on Chionanthus. Bayesian inferences and maximum likelihood analyses of plastid and nuclear data indicated several instances of paraphyly and polyphyly within Oleinae, with some geographic signal. Both plastid and ITS data showed a polyphyletic Noronhia that included Indian Ocean species of Chionanthus. They also found close relationships between Noronhia and African Chionanthus. However, the plastid data showed little clear differentiation between Noronhia and the African Chionanthus whereas relationships suggested by the nuclear ITS data were more consistent with taxonomy and geography. We used molecular dating to discriminate between hybridization and lineage sorting/gene duplication as alternative explanations for these topological discordances and to infer the biogeographic history of Noronhia. Hybridization between African Chionanthus and Noronhia could not be ruled out. However, Noronhia has long been established in Madagascar after a likely Cenozoic dispersal from Africa, suggesting any hybridization between representatives of African and Malagasy taxa was ancient. In any case, the African and Indian Ocean Chionanthus and Noronhia together formed a strongly supported monophyletic clade distinct and distant from other Chionanthus, which calls for a revised and more conservative taxonomy for this group.

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

Organismal phylogeny provides a crucial evolutionary framework for many studies and the angiosperm phylogeny has been greatly improved recently, largely using organellar and rDNA genes. However, low-copy protein-coding nuclear genes have not been widely used on a large scale in spite of the advantages of their biparental inheritance and vast number of choices. Here, we identified 1083 highly conserved low-copy nuclear genes by genome comparison. Furthermore, we demonstrated the use of five nuclear genes in 91 angiosperms representing 46 orders (73% of orders) and three gymnosperms as outgroups for a highly resolved phylogeny. These nuclear genes are easy to clone and align, and more phylogenetically informative than widely used organellar genes. The angiosperm phylogeny reconstructed using these genes was largely congruent with previous ones mainly inferred from organellar genes. Intriguingly, several new placements were uncovered for some groups, including those among the rosids, the asterids, and between the eudicots and several basal angiosperm groups. These conserved universal nuclear genes have several inherent qualities enabling them to be good markers for reconstructing angiosperm phylogeny, even eukaryotic relationships, further providing new insights into the evolutionary history of angiosperms.

Comparative nucleotide diversity across North American and European populus species

Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.

Chasing the hare - evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae)

BACKGROUND

The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, agt1, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose Tildenia, a subgenus of Peperomia (Piperaceae), one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, Tildenia is a perfect test case for applying new phylogenetic tools.

RESULTS

We show that the nuclear marker agt1, and in particular the agt1 introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from agt1 intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (trnK intron, trnK-psbA spacer, ndhF-rpl32 spacer, rpl32-trnL spacer, psbA-trnH spacer) provide less than 10% parsimony informative characters. The agt1 dataset provides a deeper resolution than the chloroplast markers in Tildenia.

CONCLUSIONS

Single (or very low) copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of taxonomic levels from family down to population level. As more plant genomes are sequenced, we will obtain increasingly precise information about which genes return to single copy most rapidly following gene duplication and may be most useful across a wide range of plant groups.

Diversification of CYCLOIDEA expression in the evolution of bilateral flower symmetry in Caprifoliaceae and Lonicera (Dipsacales)

BACKGROUND AND AIMS

The expression of floral symmetry genes is examined in the CYCLOIDEA lineage following duplication, and these are linked to changes in flower morphology. The study focuses on Dipsacales, comparing DipsCYC2 gene expression in Viburnum (radially symmetrical Adoxaceae) to members of early-diverging lineages of the bilaterally symmetrical Caprifoliaceae (Diervilla and Lonicera).

METHODS

Floral tissue from six species, which included dorsal, lateral and ventral regions of the corolla, was dissected. RNA was extracted from these tissues and each copy of DipsCYC2 was amplified with reverse transcriptase PCR.

KEY RESULTS

Members of DipsCYC2 were expressed across the corolla in the radially symmetrical Viburnum plicatum. A shift to bilaterally symmetrical flowers at the base of the Caprifoliaceae was accompanied by a duplication of the DipsCYC2 gene, resulting in DipsCYC2A and DipsCYC2B, and by loss of expression of both of these copies in the ventral petal. In Lonicera (Caprifolieae), there is a shift from flowers with two dorsally and three ventrally oriented corolla lobes to a clear differentiation of dorsal, lateral and ventral lobes. This shift entailed a decoupling of expression of DipsCYC2A and DipsCYC2B; DipsCYC2B continues to be expressed in the dorsal and lateral lobes, while DipsCYC2A expression is restricted to just the two dorsal lobes. A reversion to more radially symmetrical flowers within Lonicera was accompanied by a re-expansion of expression of both DipsCYC2A and DipsCYC2B.

CONCLUSIONS

The transition to bilateral symmetry in Caprifoliaceae involved: (a) duplication of an ancestral DipsCYC2 gene; (b) the loss of expression of both of these copies in the ventral petal; and (c) changes in the zone of expression, with one copy continuing to be expressed across the dorsal and lateral petals, and the other copy becoming restricted in expression to the dorsal corolla lobes.

Plant DNA sequencing for phylogenetic analyses: from plants to sequences

DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.

Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehirae Hay. (Lauraceae) in Taiwan inferred from nuclear genes

Background

Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM) is critically important for the conservation of this species.

Results

Populations of C. kanehirae were classified into four geographic regions: northwestern (NW), west-central (WC), southwestern (SW), and southeastern (SE). In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs) intron and leafy (Lfy) intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M) through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP) method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples.

Conclusions

Common haplotype distributions among geographic regions and the relatively shallow genetic structuring displayed are the result of historical gene flows. Southward dispersals in an earlier time frame from the NW region and in a later time frame from the SE region were inferred. The BSP analysis suggested a postglacial expansion event. Recent trends, however, refer to a bottleneck due to human interventions observed for both pooled and regional C. kanehirae samples.

Are spurred cyathia a key innovation? Molecular systematics and trait evolution in the slipper spurges (Pedilanthus clade: Euphorbia, Euphorbiaceae)

The study of traits that play a key role in promoting diversification is central to evolutionary biology. Floral nectar spurs are among the few plant traits that correlate with an enhanced rate of diversification, supporting the claim that they are key innovations. Slight changes in spur morphology could confer some degree of premating isolation, explaining why clades with spurs tend to include more species than their spurless close relatives. We explored whether the cyathial nectar spur of the Pedilanthus clade (Euphorbia) may also function as a key innovation. We estimated the phylogeny of the Pedilanthus clade using one plastid (matK) and three nuclear regions (ITS and two G3pdh loci) and used our results and a Yule model of diversification to test the hypothesis that the cyathial spur correlates with an increased diversification rate. We found a lack of statistical support for the key innovation hypothesis unless specific assumptions regarding the phylogeny apply. However, the young age (hence small size) of the group may limit our ability to detect a significant increase in diversification rate. Additionally, our results confirm previous species designations, indicate higher homoplasy in cyathial than in vegetative features, and suggest a possible Central American origin of the group.

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

BACKGROUND

Although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. Using the gene clustering algorithm MCL-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa. To characterize these genes, we have performed a number of analyses examining GO annotations, coding sequence length, number of exons, number of domains, presence in distant lineages, such as Selaginella and Physcomitrella, and phylogenetic analysis to estimate copy number in other seed plants and to demonstrate their phylogenetic utility. We then provide examples of how these genes may be used in phylogenetic analyses to reconstruct organismal history, both by using extant coverage in EST databases for seed plants and de novo amplification via RT-PCR in the family Brassicaceae.

RESULTS

There are 959 single copy nuclear genes shared in Arabidopsis, Populus, Vitis and Oryza ["APVO SSC genes"]. The majority of these genes are also present in the Selaginella and Physcomitrella genomes. Public EST sets for 197 species suggest that most of these genes are present across a diverse collection of seed plants, and appear to exist as single or very low copy genes, though exceptions are seen in recently polyploid taxa and in lineages where there is significant evidence for a shared large-scale duplication event. Genes encoding proteins localized in organelles are more commonly single copy than expected by chance, but the evolutionary forces responsible for this bias are unknown.Regardless of the evolutionary mechanisms responsible for the large number of shared single copy genes in diverse flowering plant lineages, these genes are valuable for phylogenetic and comparative analyses. Eighteen of the APVO SSC single copy genes were amplified in the Brassicaceae using RT-PCR and directly sequenced. Alignments of these sequences provide improved resolution of Brassicaceae phylogeny compared to recent studies using plastid and ITS sequences. An analysis of sequences from 13 APVO SSC genes from 69 species of seed plants, derived mainly from public EST databases, yielded a phylogeny that was largely congruent with prior hypotheses based on multiple plastid sequences. Whereas single gene phylogenies that rely on EST sequences have limited bootstrap support as the result of limited sequence information, concatenated alignments result in phylogenetic trees with strong bootstrap support for already established relationships. Overall, these single copy nuclear genes are promising markers for phylogenetics, and contain a greater proportion of phylogenetically-informative sites than commonly used protein-coding sequences from the plastid or mitochondrial genomes.

CONCLUSIONS

Putatively orthologous, shared single copy nuclear genes provide a vast source of new evidence for plant phylogenetics, genome mapping, and other applications, as well as a substantial class of genes for which functional characterization is needed. Preliminary evidence indicates that many of the shared single copy nuclear genes identified in this study may be well suited as markers for addressing phylogenetic hypotheses at a variety of taxonomic levels.

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

Background

Although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. Using the gene clustering algorithm MCL-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa. To characterize these genes, we have performed a number of analyses examining GO annotations, coding sequence length, number of exons, number of domains, presence in distant lineages, such as Selaginella and Physcomitrella, and phylogenetic analysis to estimate copy number in other seed plants and to demonstrate their phylogenetic utility. We then provide examples of how these genes may be used in phylogenetic analyses to reconstruct organismal history, both by using extant coverage in EST databases for seed plants and de novo amplification via RT-PCR in the family Brassicaceae.

Results

There are 959 single copy nuclear genes shared in Arabidopsis, Populus, Vitis and Oryza ["APVO SSC genes"]. The majority of these genes are also present in the Selaginella and Physcomitrella genomes. Public EST sets for 197 species suggest that most of these genes are present across a diverse collection of seed plants, and appear to exist as single or very low copy genes, though exceptions are seen in recently polyploid taxa and in lineages where there is significant evidence for a shared large-scale duplication event. Genes encoding proteins localized in organelles are more commonly single copy than expected by chance, but the evolutionary forces responsible for this bias are unknown.

Regardless of the evolutionary mechanisms responsible for the large number of shared single copy genes in diverse flowering plant lineages, these genes are valuable for phylogenetic and comparative analyses. Eighteen of the APVO SSC single copy genes were amplified in the Brassicaceae using RT-PCR and directly sequenced. Alignments of these sequences provide improved resolution of Brassicaceae phylogeny compared to recent studies using plastid and ITS sequences. An analysis of sequences from 13 APVO SSC genes from 69 species of seed plants, derived mainly from public EST databases, yielded a phylogeny that was largely congruent with prior hypotheses based on multiple plastid sequences. Whereas single gene phylogenies that rely on EST sequences have limited bootstrap support as the result of limited sequence information, concatenated alignments result in phylogenetic trees with strong bootstrap support for already established relationships. Overall, these single copy nuclear genes are promising markers for phylogenetics, and contain a greater proportion of phylogenetically-informative sites than commonly used protein-coding sequences from the plastid or mitochondrial genomes.

Conclusions

Putatively orthologous, shared single copy nuclear genes provide a vast source of new evidence for plant phylogenetics, genome mapping, and other applications, as well as a substantial class of genes for which functional characterization is needed. Preliminary evidence indicates that many of the shared single copy nuclear genes identified in this study may be well suited as markers for addressing phylogenetic hypotheses at a variety of taxonomic levels.

Molecular evidence of hybridization in Florida's sheoak (Casuarina spp.) invasion

The presence of hybrids in plant invasions can indicate a potential for rapid adaptation and an added level of complexity in management of the invasion. Three Casuarina tree species, Casuarina glauca, Casuarina cunninghamiana and Casuarina equisetifolia, native to Australia, are naturalized in Florida, USA. Many Florida Casuarina trees are considered unidentifiable, presumably due to interspecific hybridization. We collected tissue from over 500 trees from Australia and Florida and genotyped these using amplified fragment length polymorphisms. Our goal was to determine the exact identity of the Florida species, including any putative hybrid combinations. In Australia, we found high assignment values to the three parental species, and no evidence of hybridization. In Florida, we found many trees with strong assignment to any one of the three species, as well as 49 trees with assignment values intermediate to C. glauca and C. equisetifolia, suggesting hybridization between these species. One population of 10 trees had assignment values intermediate to C. cunninghamiana and C. glauca, suggesting additional hybridization. For 69 of these putative hybrid and parental types, we sequenced a low-copy intron of nuclear G3pdh, and these sequences indicated that some Florida trees contain heterozygotic combinations of C. glauca and C. equisetifolia haplotypes. The presence of novel hybrids in the Florida invasion may enhance evolution of invasive traits in these species. Novel Casuarina hybrids in Florida have no coevolutionary history with any insects or diseases, which may be problematic for biological control efforts.

Genetic integrity of sympatric hybridising plant species: the case of Orchis italica and O. anthropophora

Plant species diversification entails the action of reproductive barriers, which are severely challenged when related species grow in contact and form hybrid progeny. Orchis italica and O. anthropophora are two related orchid species that produce a known hybrid form, O. xbivonae. Here, we analysed a hybrid zone of these two orchids using molecular analysis and experimental crosses. As molecular tools, we employed both real-time PCR and PCR amplification of nuclear markers to evaluate the occurrence of backcross recombination. With these approaches, we demonstrated that all examined hybrids belong to the F(1) generation. Chloroplast DNA analysis showed that O. anthropophora was the maternal species of most of hybrid specimens and that cytoplasmic introgression was lacking in both parental species. Pollination experiments showed that the two orchid species were strictly out-crossing, although self-compatible, and have comparable levels of reproductive fitness in all crossing treatments. Conversely, hybrids demonstrated low reproductive success in all intra- and back-crossing treatments. The absence of any backcross generations and plastid introgression suggest that O. xbivonae does not represent a bridge to gene flow between O. italica and O. anthropophora. Indeed, the low hybrid fitness testifies to the effectiveness of late post-zygotic barriers occurring between the parental species.

Reticulate evolution on a mosaic of soils: diversification of the New Caledonian endemic genus Codia (Cunoniaceae)

We reconstructed the evolutionary history of Codia, a plant genus endemic to the New Caledonia biodiversity hotspot in the southwest Pacific, using three single-copy nuclear genes. It seems likely that more than half of Codia species have a hybrid origin, but in the absence of cytological information, it is not known whether polyploids occur. Adaptation to ultramafic soils is possibly a plesiomorphic character for the entire genus. We found that species of hybrid origin can have some morphological characters absent in putative parental species, that is, they exhibit transgressive phenotypes. There is evidence of considerable range alteration post-origin in several species because some likely parental species of hybrid taxa no longer co-occur and are confined to putative rainforest refugia; in some cases, hybrid species do not now co-occur with either of their parental species. These results have implications for the design of conservation strategies, for example, prioritization of parental species for ex-situ conservation and preservation of the contact zones between soil types where hybridization is more likely to occur (i.e. conserving the possibility for the process to continue rather than trying to conserve taxa).

Duplications and expression of DIVARICATA-like genes in dipsacales

The genetics underlying flower symmetry shifts between radial and bilateral symmetry has been intensively studied in the model Antirrhinum majus. Understanding the conservation or diversification of this genetic pathway in other plants is of special interest in understanding angiosperm evolution and ecology. Evidence from Antirrhinum indicates that TCP and MYB transcription factors, especially CYCLOIDEA (CYC), DICHOTOMA (DICH), DIVARICATA (DIV), and RADIALIS (RAD) play a role in specifying dorsal identity (CYC, DICH, and RAD) and ventral identity (DIV) in the corolla and androecium of monosymmetric (bilateral) flowers. Previous data indicate that the ECE clade of TCP genes (including CYC and DICH) underwent two duplication events around the diversification of the core eudicots. In this study, we examined the duplication events within Dipsacales, which contains both radially and bilaterally symmetrical flowered species. Additionally, we report here the phylogenetic relationships of the DIV-like genes across core eudicots. Like TCP genes, we found three core eudicot clades of DIV-like genes, with duplications occurring around the diversification of the core eudicots, which we name DIV1, DIV2, and DIV3. The Antirrhinum genes, DIVARICATA and its sister DVL1, fall into the DIV1 clade. We also found additional duplications within these clades in Dipsacales. Specifically, the Caprifoliaceae (bilaterally symmetrical clade) duplicated independently in each of the three core eudicot DIV clades. Using reverse transcription polymerase chain reaction (rtPCR), we showed that most of these copies are expressed across floral tissues in the Dipsacales species Heptacodium miconioides. One copy, DipsDIV1A (orthologous to DIV and DVL1), was expressed in a dorsal-ventral pattern. DipsDIV1A was expressed only in petal tissue, in both dorsal and ventral regions but was lacking from lateral petals. We argue that this suggests that DipsDIV1A may be expressed in a similar pattern to DIV in Antirrhinum, suggesting a broad conservation of this pathway. Finally, DIV contains a large intron near the beginning of the second MYB domain, which shows promise as a highly variable molecular marker for phylogenetic studies.

Phylogenetic relationships among diploid species of Symphyotrichum (Asteraceae: Astereae) based on two nuclear markers, ITS and GAPDH

The mostly North American subtribe Symphyotrichinae (Asteraceae: Astereae) comprises Canadanthus, Ampelaster, Psilactis, Almutaster, and Symphyotrichum. Intergeneric and interspecific relationships within the subtribe have been investigated in the past, particularly by Nesom [Nesom, G.L., 1994. Review of the taxonomy of Aster sensu lato (Asteraceae: Astereae), emphasizing the new world species, Phytologia 77, 141-297] and Semple [Semple, J.C., 2005. Classification of Symphyotrichum. Available from: <http://www.jcsemple.uwaterloo.ca/Symphyotrichumclassification.htm/>], using morphological and cytological approaches. Symphyotrichum is the largest and most complex genus within the subtribe and includes four subgenera: Symphyotrichum (x=7, 8), Virgulus (x=4, 5), Astropolium (x=5), and Chapmaniani (x=7). In this study we used two nuclear markers, the nrDNA internal transcribed spacer (ITS) and the low-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH), to resolve intergeneric and interspecific relationships within the subtribe at the diploid level, and to determine whether our phylogenies validate the classifications of Nesom or Semple. Our results confirm the distinct generic status of Canadanthus and Ampelaster, whereas Psilactis and Almutaster form a polytomy with Symphyotrichum. Within Symphyotrichum, subg. Virgulus is monophyletic based on ITS and appears polyphyletic based on GAPDH. Neither the ITS nor the GAPDH analyses support a distinct status for subg. Astropolium, which groups within subg. Symphyotrichum. In general, interspecific relationships within Symphyotrichum are unresolved. Lack of resolution may be interpreted as a case of recent and rapid evolutionary radiation.