Biased gene introgression and adaptation in the face of chloroplast capture in Aquilegia amurensis.

Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, is frequently invoked to explain cytonuclear discordance in plants. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential for driving species differentiation and possible functional differences in the context of chloroplast capture. To address this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among species, and inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between the two species. We focused on the introgression region and its differentiation from corresponding regions in closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes (CECs; i.e., organelle-targeted genes) of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast-receiving species due to cytonuclear interactions during introgression. Notably, the intrinsic correlation of CEC introgression was a greater degree of evolutionary distance for these CECs between A. amurensis and A. parviflora. Terpene synthase activity genes (GO: 0010333) were overrepresented among the introgressed genes, and more than 30% of these genes were CEC genes. These findings support our observations that floral terpene release pattern is similar between A. amurensis and A. parviflora compared with A. japonica. Our study clarifies the mechanisms of cytonuclear coevolution, species differentiation and functional differences in the context of chloroplast capture and highlights the potential role of chloroplast capture in adaptation.

Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia.

Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyse the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated twelve new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analysed were of similar size and structure; only N. obliqua of subgenus Lophozonia, used as outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.

Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae).

Obtaining a robust phylogeny proves challenging due to the intricate evolutionary history of species, where processes such as hybridization and incomplete lineage sorting can introduce conflicting signals, thereby complicating phylogenetic inference. In this study, we conducted comprehensive sampling of Elsholtzieae, with a particular focus on its largest genus, Elsholtzia. We utilized 503 nuclear loci and complete plastome sequences obtained from 99 whole-genome sequencing datasets to elucidate the interspecific relationships within the Elsholtzieae. Additionally, we explored various sources of conflicts between gene trees and species trees. Fully supported backbone phylogenies were recovered, and the monophyly of Elsholtzia and Keiskea was not supported. Significant gene tree heterogeneity was observed at numerous nodes, particularly regarding the placement of Vuhuangia and the E. densa clade. Further investigations into potential causes of this discordance revealed that incomplete lineage sorting (ILS), coupled with hybridization events, has given rise to substantial gene tree discordance. Several species, represented by multiple samples, exhibited a closer association with geographical distribution rather than following a strictly monophyletic pattern in plastid trees, suggesting chloroplast capture within Elsholtzieae and providing evidence of hybridization. In conclusion, this study provides phylogenomic insights to untangle taxonomic problems in the tribe Elsholtzieae, especially the genus Elsholtzia.

Generic concepts and species diversity within the Gynoxyoid clade (Senecioneae, Compositae).

The Gynoxyoid clade of the Senecioneae (Asteraceae) until now included the five genera Aequatorium, Gynoxys, Nordenstamia, Paracalia and Paragynoxys as diagnosed using selected morphological characters. In their pre-phylogenetic circumscription, the genera Aequatorium and Paragynoxys were considered to inhabit the northern Andes in contrast to Nordenstamia and Paracalia that occur in the central Andes. The most species-rich genus, Gynoxys, was believed to be distributed throughout the Andes. We use a recently established plastid phylogenomic framework that rendered Gynoxys paraphyletic to further evaluate the delimitation of genera in the Gynoxyoid clade. We examine the morphological variation of all members of the Gynoxyoid to identify characters potentially informative at genus level. This results in a matrix of eleven, mostly multistate characters, including those originally used to diagnose these genera. The ancestral character state inference displays a high level of homoplasy, but nevertheless supports the recognition of four genera. Aequatorium is characterised by white radiate capitula. Paracalia and Paragynoxys share white flowers and floral characteristics, such as flower opening and length of disc flowers lobes, as plesiomorphic states, but differ in habit (scandent shrubs vs. trees). Paracalia also retained white flowers, but its two species are characterised by the absence of outer phyllaries. The genera Gynoxys and Nordenstamia comprise species with yellow capitula which appear to be a derived feature in the Gynoxyoids. The genus Nordenstamia, with eight species, is synonymised under Gynoxys since molecular evidence shows its species nested within various parts of the Gynoxys subclade and the morphological variation of Nordenstamia falls well within that of Gynoxys. With the goal to assign all species to four genera (Aequatorium, Gynoxys, Paracalia and Paragynoxys), we assess the states for the eleven characters for all members of the Gynoxyoids and generate new ETS and ITS sequences for 171 specimens belonging to 49 species to further support their generic placement. We provide a taxonomic treatment for the four genera recognised here including amended diagnoses and morphological descriptions. Furthermore, a species-level taxonomic backbone is elaborated for all genera using electronic tools that list 158 currently accepted names and synonyms (209 names in total) with the respective protologue and type information, as well as notes on the current understanding of species limits. Eleven names are newly synonymised, two are lectotypified and eight are newly transferred to other genera.

Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains.

Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome. Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China, exhibit conflicting phylogenetic relationships between nuclear and chloroplast phylogenies. Here, we use multi-omic data at the population level to investigate their historical speciation processes. Population genomic analysis based on ddRAD-seq data revealed limited contemporary inter-specific gene flow involving only populations located close to another species. In a historical context, chloroplast and nuclear data (transcriptome) consistently showed conflicting phylogenetic relationships for T. florinii and the Emei type lineage. ILS and chloroplast recombination were excluded as possible causes, and transcriptome and ddRAD-seq data revealed an absence of the mosaic nuclear genomes that characterize hybrid origin scenarios. Therefore, T. florinii appears to have originated when a lineage of T. florinii captured the T. chinensis plastid type, whereas plastid introgression in the opposite direction generated the Emei Type. All four species have distinct ecological niche based on community investigations and ecological niche analyses. We propose that the origins of both species represent very rare examples of chloroplast capture events despite the paternal cpDNA inheritance of gymnosperms. Specifically, allopatrically and/or ecologically diverged parental species experienced a rare secondary contact, subsequent hybridization and reciprocal chloroplast capture, generating two new lineages, each of which acquired a unique ecological niche. These events might have been triggered by orogenic activities of the Hengduan Mountains and an intensification of the Asian monsoon in the late Miocene, and may represent a scenario more common in these mountains than presently known.

Rampant chloroplast capture in Sarracenia revealed by plastome phylogeny.

Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genus Sarracenia L. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis of Sarracenia estimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring in Sarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembled de-novo from sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history of Sarracenia.

Reticulate Evolution in AA-Genome Wild Rice in Australia.

The wild rice gene pool, i.e., AA-genome, in Australia is geographically and genetically distinct from that in Asia. Two distinct taxa are found growing together in northern Australia, Oryza meridionalis (including annual and perennial forms) and an Oryza rufipogon like taxa that have been shown to have a chloroplast genome sequence that is closer to that of O. meridionalis than to O. rufipogon from Asia. Rare plants of intermediate morphology have been observed in the wild despite a reported reproductive barrier between these two species. We now report the resequencing of plants from 26 populations including both taxa and putative hybrids. A comparison of chloroplast and nuclear genome sequences indicated re-combinations that demonstrated hybridisation in both directions. Individuals with intermediate morphology had high nuclear genome heterozygosity consistent with a hybrid origin. An examination of specific genes (e.g., starch biosynthesis genes) revealed the presence of heterozygotes with alleles from both parents suggesting that some wild plants were early generation hybrids. These plants may have low cross-fertility preserving the continuation of the two distinct species. Repeated backcrossing of these rare hybrids to one parent would explain the plants exhibiting chloroplast capture. These observations suggest that reticulate evolution is continuing in wild Oryza populations and may have been a key process in rice evolution and domestication.

Hybridization and complex evolution of Barbarea vulgaris and related species (Brassicaceae).

Barbarea, winter-cress, is a genus of 29 species in Brassicaceae, the mustard family, which has emerged as a model for evolution of plant defence and specialised metabolites. Notably, some Barbarea species have evolved the ability to produce triterpenoid saponins as the only ones in Brassicaceae, some of which make plants resistant to important herbivores. Resistance has, however, been lost in a distinct group of plants within B. vulgaris ssp. arcuata, which is genetically strongly diverged from other B. vulgaris plants. This divergence is not reflected present in taxonomy. Thus, a phylogeny is needed to understand evolution and defence in Barbarea. Here, we analysed the nuclear ITS and the plastid matK, ndhF, rps16, and psbA-trnH DNA regions from seven out of 29 Barbarea species, 57 accessions of B. vulgaris, 10 accessions of other Barbarea species, and eight outgroup species, in addition to sequences available from GenBank. All Barbarea species formed a highly supported monophyletic group, separated from sister genera. Several clades seem to have radiated within the genus with no simple branching pattern, and discordant nuclear and plastid DNA phylogenies indicate reticulate evolution and chloroplast capture. One of the complex patterns may have resulted from chloroplast capture of a non-Nordic Barbarea species not included in the study. Two pairs of species were almost identical, B. australis and B. grayi, and B. orthoceras and B. stricta. Despite hybridization, chloroplast capture, and incongruence among the plastid and nuclear DNA data, the high level of intraspecific diversity, coupled with lineage specificity, lead us to recognize three groups of Barbarea vulgaris: G-type (glabrous) and P-type (pubescent) individuals of the current B. vulgaris ssp. arcuata as two distinct groups and the current B. vulgaris ssp. vulgaris as the third. Despite the high molecular diversity below species level, the evolutionary history of the saponin-based resistance remains unsettled due to unresolved basal branching.

When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan-Guizhou Plateau, a tropical-subtropical transition area in China.

Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity for hybridization and diversification of Eriobotrya, especially in the YGP. Our study highlights the significant role that paleoclimate changes probably played in driving hybridization and generating rich species diversity in climate transition zones.

Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture.

Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.

Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion.

Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.

Backbone phylogeny and evolution of Apioideae (Apiaceae): New insights from phylogenomic analyses of plastome data.

Traditional phylogenies inferred from chloroplast DNA fragments have not obtained a well-resolved evolutionary history for the backbone of Apioideae, the largest subfamily of Apiaceae. In this study, we applied the genome skimming approach of next-generation sequencing to address whether the lack of resolution at the tip of the Apioideae phylogenetic tree is due to limited information loci or the footprint of ancient radiation. A total of 90 complete chloroplast genomes (including 23 newly sequenced genomes and covering 20 major clades of Apioideae) were analyzed (RAxML and MrBayes) to provide a phylogenomic reconstruction of Apioideae. Dating analysis was also implemented using BEAST to estimate the origin and divergence time of the major clades. As a result, the early divergences of Apioideae have been clarified but the relationship among its distally branching clades (Group A) was only partially resolved, with short internal branches pointing to an ancient radiation scenario. Four major clades, Tordyliinae I, Pimpinelleae I, Apieae and Coriandreae, were hypothesized to have originated from chloroplast capture events induced by early hybridization according to the incongruence between chloroplast-based and nrDNA-based phylogenetic trees. Furthermore, the variable and nested distribution of junction positions of LSC (Large single copy region) and IRB (inverted repeat region B) in Group A may reflect incomplete lineage sorting within this group, which possibly contributed to the unclear phylogenetic relationships among these clades inferred from plastome data. Molecular clock analysis revealed the chloroplast capture events mainly occurred during the middle to late Miocene, providing a geological and climate context for the evolution of Apioideae.

Phylogenetic relationships and chloroplast capture in the Amelanchier-Malacomeles-Peraphyllum clade (Maleae, Rosaceae): Evidence from chloroplast genome and nuclear ribosomal DNA data using genome skimming.

The Amelanchier-Malacomeles-Peraphyllum (AMP) clade consists of ca. 26 species distributed in North and Central America, Europe, Asia, and northwestern Africa. While molecular and morphological data strongly support this clade, relationships of its genera are uncertain. Support for the monophyly of Amelanchier and for the phylogenetic positions of Malacomeles and Peraphyllum has varied between studies. Our goals were to reconstruct a robust phylogeny of the AMP clade in the framework of Maleae and clarify the phylogenetic placements of Malacomeles and Peraphyllum. This study employs sequences of the whole plastome and nuclear ribosomal DNA (nrDNA) repeats assembled using genome skimming with 131 samples representing 115 species in 31 genera of Rosaceae, especially Maleae. Maximum likelihood (ML) and Bayesian analysis (BI) of whole plastome datasets strongly supported Amelanchier as not monophyletic, with Peraphyllum sister to eastern North American Amelanchier and Malacomeles sister to the western North American-Eurasian Amelanchier. In contrast, nrDNA recovered the monophyly of Amelanchier, with Peraphyllum sister to Amelanchier and Malacomeles sister to the Amelanchier-Peraphyllum clade. The strong topological conflicts between plastome and nrDNA phylogenies of Peraphyllum and of Malacomeles are best explained by ancient chloroplast capture that occurred in SW North America.

Placing the regionally threatened moss Orthodontium gracile in the big picture - Phylogeny, genome incongruence and anthropogenic dispersal in the order Orthodontiales.

The Orthodontiaceae is a small family of predominantly Southern Hemisphere temperate and South East Asian mosses that has a key phylogenetic position for research into the evolution of pleurocarpy. In the United Kingdom it is represented by the rare conservation priority species Orthodontium gracile and the abundant exotic O. lineare, introduced from the Southern Hemisphere around a century ago. Although the two species are superficially very similar and difficult to tell apart in the field, very little is known about how closely they are related or about the phylogeny, biogeography and evolutionary history of the genus Orthodontium as a whole. Phylogenetic inference and divergence time estimation were used to explore relationships within the genus globally, date major lineage splits, detect reticulate evolutionary processes and test monophyly of taxa. It was shown that Orthodontium gracile belongs to a Holarctic and Asian clade that diverged from the exclusively southern temperate lineage of O. lineare approximately 53 Ma and that it is sister to the Himalayan and South Siberian bispecific genus Orthodontopsis, which we now recognise as a single species within Orthodontium, O. lignicola. Orthodontium lignicola is quite distinct from O. gracile morphologically but may have a closely overlapping centre of extant diversity in the Himalaya, in contrast to O. lineare which is morphologically similar but biogeographically dissimilar. The introduced European populations of Orthodontium lineare were shown to share plastid and nuclear haplotypes with four collections from Tasmania and Southern Chile, but to be distinct from other Chilean and South African haplotypes. Finally, well-supported incongruence between nuclear and plastid sequences in some Western North American populations of Orthodontium gracile strongly implies one or more chloroplast capture or horizontal genome transfer events involving this species and the regionally sympatric O. pellucens. An appeal is made for targeting phylogenetic research at the intersection points of practical conservation, taxonomic uncertainty and wider biological questions and for the factoring of historical evolutionary and phylogenetic diversity into conservation assessments.

Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes.

PREMISE OF THE STUDY: Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers. METHODS: We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation. KEY RESULTS: Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal. CONCLUSIONS: Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.

Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia.

The sweet potato is one of the world's most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our research combined genome skimming and target DNA capture to sequence whole chloroplasts and 605 single-copy nuclear regions from 199 specimens representing the sweet potato and all of its crop wild relatives (CWRs). We present strongly supported nuclear and chloroplast phylogenies demonstrating that the sweet potato had an autopolyploid origin and that Ipomoea trifida is its closest relative, confirming that no other extant species were involved in its origin. Phylogenetic analysis of nuclear and chloroplast genomes shows conflicting topologies regarding the monophyly of the sweet potato. The process of chloroplast capture explains these conflicting patterns, showing that I. trifida had a dual role in the origin of the sweet potato, first as its progenitor and second as the species with which the sweet potato introgressed so one of its lineages could capture an I. trifida chloroplast. In addition, we provide evidence that the sweet potato was present in Polynesia in pre-human times. This, together with several other examples of long-distance dispersal in Ipomoea, negates the need to invoke ancient human-mediated transport as an explanation for its presence in Polynesia. These results have important implications for understanding the origin and evolution of a major global food crop and question the existence of pre-Columbian contacts between Polynesia and the American continent.

Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing.

Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta, A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, A. nipponica and A. stelleri, differ at similar levels to possible maternal donor species A. flagellosa, which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while A. nipponica and A. flagellosa were more similar to each other than to A. hirsuta. This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian Arabis species.

A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations.

Based on sequence data of nuclear ITS and plastid matK, trnL-F and psbA-trnH markers, the phylogeny of the subtribes Caraganinae and Chesneyinae in tribe Caraganeae was inferred. The results support the monophyly of each of the subtribes. Within subtribes Caraganinae, Calophaca and Halimodendron are herein transferred into Caragana to ensure its generic monophyly. The subtribe Chesneyinae is composed of four well-supported genera: Chesneya, Chesniella, Gueldenstaedtia and Tibetia. Based on phylogenetic, morphological, distributional and habitat type evidence, the genus Chesneya was divided into three monophyletic sections: Chesneya sect. Chesneya, Chesneya sect. Pulvinatae and Chesneya sect. Spinosae. Chesneya macrantha is herein transferred into Chesniella. Spongiocarpella is polyphyletic and its generic rank is not maintained. The position of Chesneya was incongruent in the nuclear ITS and the plastid trees. A paternal chloroplast capture event via introgression is hypothesized for the origin of Chesneya, which is postulated to have involved the common ancestor of Chesniella (♂) and that of the Gueldenstaedtia - Tibetia (GUT) clade (♀) as the parents.

Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species.

BACKGROUND: Four plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). To ensure a maximum coverage of intraspecific diversity, and therefore to better evaluate the resolution power of each barcode, we applied a population genetics approach by sampling three to 45 individuals per species over a wide geographical range. RESULTS: All possible combinations between loci were analysed, which showed that using more than one locus does not always improve the resolution power. The trnH-psbA locus was most effective at discriminating among closely related species (Acer, Lonicera, Geranium, and Veronica), singly or in combination. For Salix, Adenostyles, and Gentiana, the best results were obtained with the combination of matK, rpoB, and trnH-psbA. No barcoding gap was found within six genera analysed, excepting Lonicera. This is due to shared polymorphisms among species, combined with very divergent sequences within species. These genetic patterns reflect incomplete lineage sorting and hybridization events followed by chloroplast capture. CONCLUSIONS: Our results strongly suggest that adding trnH-psbA to the two obligate DNA barcodes proposed by the CBOL plant-working group (matK and rbcL) should be mandatory for closely related species. In our sampling, generation time had no influence on DNA barcoding success, as the best and worst identification successes were found for the two tree genera (Acer, 64 % success and Salix, 86 % failure). Evolutionary histories are the main factor influencing DNA barcoding success in the studied genera.

Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host.

Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provide valuable information on evolutionary processes such as chloroplast capture following hybridization, incomplete lineage sorting, and horizontal gene transfer. Statistical tools that to date have been used in cophylogenetic studies only also have the potential to test for the degree of topological congruence between organellar and nuclear data sets and reliably detect outlier associations. Two distance-based methods, namely ParaFit and Procrustean Approach to Cophylogeny (PACo), were used in conjunction to detect those outliers contributing to conflicting phylogenies independently derived from chloroplast and nuclear sequence data. We explored their efficiency of retrieving outlier associations, and the impact of input data (unit branch length and additive trees) between data sets, by using several simulation approaches. To test their performance using real data sets, we additionally inferred the phylogenetic relationships within Neotropical Catasetinae (Epidendroideae, Orchidaceae), which is a suitable group to investigate phylogenetic incongruence because of hybridization processes between some of its constituent species. A comparison between trees derived from chloroplast and nuclear sequence data reflected strong, well-supported incongruence within Catasetum, Cycnoches, and Mormodes. As a result, outliers among chloroplast and nuclear data sets, and in experimental simulations, were successfully detected by PACo when using patristic distance matrices obtained from phylograms, but not from unit branch length trees. The performance of ParaFit was overall inferior compared to PACo, using either phylograms or unit branch lengths as input data. Because workflows for applying cophylogenetic analyses are not standardized yet, we provide a pipeline for executing PACo and ParaFit as well as displaying outlier associations in plots and trees by using the software R. The pipeline renders a method to identify outliers with high reliability and to assess the combinability of the independently derived data sets by means of statistical analyses.