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The tree fern Culcita macrocarpa, a threatened Iberian–Macaronesian endemism, represents the sole European species of the order Cyatheales. Considered a Tertiary relict of European Palaeotropical flora, its evolutionary history and genetic diversity, potentially influenced by presumed high clonal propagation, remain largely unknown. This study elucidates the phylogeographic history of C. macrocarpa, assessing the impact of vegetative reproduction on population dynamics and genetic variability. We provide genetic data from eight newly identified nuclear microsatellite loci and one plastid DNA region for 17 populations spanning the species' range, together with species distribution modeling data. Microsatellites reveal pervasive clonality in C. macrocarpa, which has varied among populations. We assess the impact of clonality on genetic diversity and evaluate how estimates of intra-population genetic diversity indices and genetic structuring are affected by the chosen definition of "individual" (focusing exclusively on genetically distinct individuals, genets, as opposed to considering all independent clonal replicates, ramets). We identify two main population groups, one in the northern Iberian Peninsula and the other in the Macaronesian archipelagos and southern Iberian Peninsula. Within each group, we found relict populations (in the Azores and the Cantabrian Cornice) as well as recent originated populations. This population structure suggests colonization dynamics in which recent populations originated from one or a few genets of relict populations and became established through intra-gametophytic self-fertilization and vegetative expansion. DAPC analysis facilitated the identification of alleles that most significantly contributed to the observed population structure. The current Andalusian populations appear to have originated from colonization events from the Azores and the Cantabrian Cornice. Our findings suggest that C. macrocarpa persisted through the Last Glacial Maximum in two refugia: the Azores and the Cantabrian Cornice. Colonization into new areas occurred presumably from these refuges, generating two large population groups with structured genetic diversity. This study underscores the significance of clonality in establishing new populations and shaping genetic structure. [ABSTRACT FROM AUTHOR]

Abstract Background Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA. Results Here, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms. Conclusions Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.

Background: Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA. Results: Here, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms. Conclusions: Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes. [ABSTRACT FROM AUTHOR]

Genome skimming (shallow whole‐genome sequencing) offers time‐ and cost‐efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter‐plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnSGGA – rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade. [ABSTRACT FROM AUTHOR]

Although genome sequences of lichenized fungi are increasingly becoming available, genome sequences of microalgae involved in the lichen symbiosis are still scarce. For lichenized eukaryotic algae, genome sequencing has focused mostly on Trebouxia and Asterochloris, with little genomic data available for Stichococcus-like algae, such as Diplosphaera. The genus Diplosphaera is a common component of biological soil crusts, and often occurs associated with lichens of the family Verrucariaceae. It is characterized by cylindrical to spherical cells containing a plate-like chloroplast, and more specifically by a vegetative cell division that leads to the formation of typical two- to four-celled clusters. Here, we present a draft genome sequence for the algal partner of an Australian lichen specimen of Endocarpon pusillum. The genome was sequenced with Pac Bio long read and Illumina short read technologies, and transcriptome data were generated to inform the structural annotations. This algal strain is here identified as Diplosphaera chodatii based on nuSSU and ITS data. Compared with closely related lichenized and non-lichenized algae, the genome of D. chodatii stands out for its large size (85.6 Mb) and gene content (21,261 protein-encoding regions), as well as its high rate of duplicated genes (60% of the BUSCO genes are duplicated). These results suggest that whole genome duplication or large-scale segmental duplications may have occurred in the evolutionary history of this algal species. Little genome data are available for lichenized algae. We generated the first genome for a lichenized Diplosphaera chodatii. Results suggest a possible whole genome duplication in this species. [ABSTRACT FROM AUTHOR]

Wild grapevine - Vitis vinifera subsp. sylvestris - ancestors of cultivated grapevines are the main players in understanding the molecular bases of the grapevine domestication process. The goal of the presented research was to assess the genetic diversity of wild grapevine samples from several regions encompassing Europe (Spain, France, Germany, Hungary, Greece), the Mediterranean basin (Algeria, Tunisia, Morocco), and South Caucasus (Georgia), using a complete chloroplast DNA sequencing. The results suggest the existence of three different chloroplast DNA haplotypes reflecting the geographical distribution of the analyzed samples. This study represents the first report focused on analysis of a wide range of wild grapevine samples (Vitis vinifera subsp. sylvestris), applying next-generation technologies, and tracing the grapevine ancestry. [ABSTRACT FROM AUTHOR]

Sequences derived from circular DNA molecules (i.e. most bacterial, viral and plastid genomes) are expected to be linearised and rotated to a common start position for most downstream analyses including alignment. Despite this being a common and straightforward task, available software is either limited to a small number of input sequences, lacks the option to specify a custom anchor string, or requires a commercial license. Here, we present rotate, a simple, open source command line program written in C with no external dependencies, which can rotate a set of input sequences to a custom anchor string (allowing for a specified number of mismatches), or offset the input sequences to the desired position. The combination of both functionalities allows the rotation of all input sequences to any desired starting position, enabling downstream analysis. rotate is extremely fast and scales linearly with the number of input sequences, taking only seconds to rotate over a thousand mitochondrial sequences.

In this study, we explore the relationships among taxa of Prunus subgenus Cerasus in Turkey using a combination of macromorphology, micromorphology and molecular techniques. We recorded qualitative and quantitative characteristics of flowers, leaves, seeds and endocarp for 96 populations representing 14 taxa of Prunus subgenus Cerasus. ITS, matK , ycf1 , trnL - trnF DNA sequence data were used to reconstruct phylogenetic trees for this group. Haplotype analyses results found 11 haplotypes among the samples used in this study. We also note that the infraspecific taxa of Cerasus angustifolia (= P. albicaulis), P. mahaleb , P. microcarpa and P. prostrata , as described by previous authors, do not exhibit significant differences even among the features of foliar morphology that are so often used to distinguish them from one another. As a general rule, our analyses indicate that the highly variable features of leaf micromorphology and endocarp and seed micromorphology are not taxonomically significant. In contrast, although floral morphology is often overlooked in systematic studies of Prunus subgenus Cerasus , we found several taxonomically useful flower characters, including sepal indumentum, hypanthium shape and indumentum and petal shape. This work clarifies the infraspecific relationships of members of Prunus subgenus Cerasus in Turkey and solves some taxonomic problems. [ABSTRACT FROM AUTHOR]

The tree flora of the Mediterranean Basin contains an outstanding taxonomic richness and a high proportion of endemic taxa. Contrary to other regions of the Mediterranean biome, a comprehensive phylogenetic analysis of the relationship between phylogenetic diversity, trait diversity and environmental factors in a spatial ecological context is lacking.We inferred the first calibrated phylogeny of 203 native tree species occurring in the European Mediterranean Basin based on 12 DNA regions. Using a set of four functional traits, we computed phylogenetic diversity for all 10,042 grid cells of 10 × 10 km spatial resolution to completely cover Mediterranean Europe. Then, we tested the spatial influence of environmental factors on tree diversity.Our results suggest that the nature of the relationship between traits and phylogeny varies among the different studied traits and according to the evolutionary distance considered. Phylogenetic diversity and functional diversity of European Mediterranean trees correlated strongly with species richness. High values of these diversity indices were located in the north of the study area, at high altitude, and minimum temperature of the coldest month. In contrast, the two phylogenetic indices that were not correlated with species richness (Mean Phylogenetic Distance, Phylogenetic Species Variability) were located in the south of the study area and were positively correlated with high altitude, soil organic carbon stock and sand soil texture.Our study provides support for the use of phylogenies in conservation biology to assess ecosystem functioning, and provides insights for the implementation of sustainable forest ecosystem management. [ABSTRACT FROM AUTHOR]

Polygala fadimeana Dönmez and Çeçen is here described as a new species from the inner part of the Taurus mountain range in Turkey based on morphological data and its phylogenetic position is discussed based on molecular data. This new species is confined to limestone rock walls and is morphologically distinguished from P. kurdica and P. peshmenii by smaller plant size, nearly glabrous leaves, enrolled inner sepals, white colour crest, and other minor diagnostic features. However, a multi‐locus chloroplast phylogeny (trnL‐F and rbcL) including accessions of the new species and related taxa of Turkish Polygala revealed a close relationship to P. pruinosa and P. supina. The taxonomic relationship among the new species and P. kurdica, a poorly known species from Zagros Mountain range, and other closely related species such as P. pruinosa, P. peshmenii and P. supina are discussed. The new species is assessed as critically endangered (CR) based on current knowledge and the distribution of the new species and related taxa is mapped. [ABSTRACT FROM AUTHOR]

Premise: Animal pollinators play an important role in pollen dispersal. Here, we assessed differences in pollen and seed dispersal and the role of pollinator functional groups with different foraging behaviors in generating patterns of genetic diversity over similar geographic ranges for two closely related taxa. We focused on two members of Oenothera section Calylophus (Onagraceae) that co‐occur on gypsum outcrops throughout the northern Chihuahuan Desert but differ in floral phenotype and primary pollinator: Oenothera gayleana (bee) and O. hartwegii subsp. filifolia (hawkmoth). Methods: We measured breeding system and floral traits and studied gene flow and population differentiation at the local (<13 km; four populations) and landscape (60–440 km; five populations) scales using 10–11 nuclear (pollen dispersal) and three plastid (seed dispersal) microsatellite markers. Results: Both taxa were self‐incompatible and floral traits were consistent with expectations for different pollinators. Seed and pollen dispersal patterns were distinctly different for both species. We found no evidence of genetic structure at the local scale but did at the landscape scale; O. gayleana showed greater differentiation and significant isolation by distance than in O. hartwegii subsp. filifolia. The plastid data were consistent with gravity dispersal of seeds and suggest that pollen dispersal is the principal driver of genetic structure in both species. Conclusions: We demonstrated that pollinator functional groups can impact genetic differentiation in different and predictable ways. Hawkmoths, with larger foraging distances, can maintain gene flow across greater spatial scales than bees. [ABSTRACT FROM AUTHOR]

Autophagy is a highly conserved system that delivers cytoplasmic components to lysosomes/vacuoles. Plastids are also degraded through autophagy for nutrient recycling and quality control; however, the involvement of autophagic degradation of plastids in plant cellular differentiation remains unclear. Here, we investigated whether spermiogenesis, the differentiation of spermatids into spermatozoids, in the liverwort Marchantia polymorpha involves autophagic degradation of plastids. Spermatozoids of M. polymorpha possess one cylindrical plastid at the posterior end of the cell body. By fluorescently labeling and visualizing plastids, we detected dynamic morphological changes during spermiogenesis. We found that a portion of the plastid was degraded in the vacuole in an autophagy-dependent manner during spermiogenesis, and impaired autophagy resulted in defective morphological transformation and starch accumulation in the plastid. Furthermore, we found that autophagy was dispensable for the reduction in plastid number and plastid DNA elimination. These results demonstrate a critical but selective role of autophagy in plastid reorganization during spermiogenesis in M. polymorpha. [ABSTRACT FROM AUTHOR]

Genista etnensis is a remarkable and well-known tree endemic to Sicily, Sardinia, and Corsica (Mediterranean Basin). Nevertheless, its morphological variability and its native status throughout its range need to be further investigated. In this study, we aim to clarify some aspects of this infraspecific variability by molecular means. Sequences of one nuclear and five plastid markers were analyzed under maximum parsimony by using TCS software. Plastid data were also time-calibrated under a Bayesian Inference framework. Plastid data revealed strong isolation between the populations from the Cyrno-Sardinian biogeographical province, which are also the most diverse and presumably the most archaic, and those from Sicily and Southern Italy (in this latter area, the species is naturalized). The calibration analysis indicates that the last common ancestor between G. etnensis and its sister group G. fasselata dates back to the middle Pliocene or slightly later, when sclerophyllous Mediterranean vegetation spread, whereas G. etnensis itself might have originated in the middle Pleistocene. The current, rather unusual distribution of G. etnensis could be explained by long-range seed dispersal from the western part of the range or by anthropogenic introduction into Sicily, with extinctions of transported haplotypes in the region of origin. Interestingly, the Vesuvius population, introduced from Sicily in recent times and locally naturalized, shows private genotypes, and was richer in both genotypes and haplotypes than the Sicilian ones. [ABSTRACT FROM AUTHOR]

The delimitation of Limonium taxa is highly complicated due to hybridization, polyploidy, and apomixis. Many "microspecies" were described and aggregated into groups, most of which are still poorly known from both molecular and morphological points of view. The aim of this study is to investigate four endemic species from the Tyrrhenian coast of central Italy and the Ponziane Archipelago belonging to the L. multiforme group (L. amynclaeum, L. circaei, L. pandatariae, and L. pontium) by means of molecular and morphometric analyses. Molecular data by sequencing ITS and three plastid markers and morphometric data highlight new information about the taxonomy of these taxa so as to reduce them into a single specific entity. In fact, the better taxonomic choice is to consider the populations studied as part of a single species, i.e., Limonium pontium. Three subspecies are recognized, i.e., subsp. pontium [= L. circaei = L. amynclaeum; from Circeo to Gianola localities (excluding Terracina) and from islands Ponza, Palmarola, Zannone, and Santo Stefano], subsp. pandatariae comb. et stat. nov. (from island of Ventotene), and subsp. terracinense subsp. nov. (from Terracina). [ABSTRACT FROM AUTHOR]

The aim of DNA barcoding is to enable fast and accurate species identification. However, universal plant DNA barcodes often do not provide species-level discrimination, especially in taxonomically complex groups. Here we use Lauraceae for the design and evaluation of DNA barcoding strategies, considering: (1) the efficacy of taxon-specific DNA barcode regions compared with universal barcodes for species discrimination; and (2) how the extent of intra- and interspecific sampling affects species discrimination rates. To address these areas, we targeted the highly polymorphic, taxon-specific barcode regions ycf1 + ndhH – rps15 + trnL – ycf2 for Lauraceae and compared them against the suite of standard plastid loci used for DNA barcoding (rbcL + matK + trnH – psbA) and the standard nuclear barcode ITS. The highest discrimination success came from nrDNA ITS, whereas the plastid regions (rbcL + matK + trnH – psbA) and the taxon-specific regions (ycf1 + ndhH – rps15 + trnL – ycf2) showed limited and inconsistent resolution. These results highlight that taxon-specific plastid barcodes may provide limited gains in discriminatory power in complex, closely related groups like Lauraceae. Moreover, our study showed that species discrimination greatly depends on the taxon sampling scheme, with relatively lower species discrimination observed where there is more comprehensive intra- and interspecific sampling. The outstanding challenge for plant DNA barcoding is the development of assays that allow routine low-cost access to large numbers of nuclear markers to facilitate the sequencing of large numbers of individuals. [ABSTRACT FROM AUTHOR]

Background and Aims: The Labrador Teas (genus Rhododendron, subsection Ledum) are a complex of species widely distributed in the Northern Hemisphere. They occupy cold-resistant plant communities from highlands to forest understory and wetland habitats almost circumboreally and they are especially abundant in Northeast Asia (NE Asia) and northern North America (NN Am), still there are no clear species boundaries in this group. The genetic structure of species of the subsect. Ledum from Eurasia and North America as well as the dispersal history of the group require clarification., Methods: Phylogeny and biogeography of the subsect. Ledum of the genus Rhododendron were assessed using phylogenetic trees constructed based on the analysis of variation in chloroplast petB-petD, trnV-ndhC, trnH-psbA, K2R-K707, atpB oligo2 - rbcL oligo5 and nuclear (ITS1) markers of four Eurasian and one American species (65 populations, 408 individuals). The data were evaluated with Maximum Parsimony and Bayesian analysis. Molecular dating and ancestral areas reconstruction were obtained., Key Results: Dense sampling revealed widespread presence of shared haplotypes and ribotypes among Ledum populations and species. Two American, three Eurasian and one mixed lineage diversified during the Neogene climate cooling and then rapidly dispersed during the Pleistocene. The ability to accumulate high genetic diversity and to preserve it across distribution ranges and generations prevented Ledum from lineage sorting. As a result, a species complex with a reserve of genetic variability appeared., Conclusions: Although no clear phylogenetic inference can be obtained at present, the plastid genealogy is consisted with the nuclear genealogy and demonstrates the processes involved in speciation in the Ledum species complex., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Polymorph Allium pallasii s.l. from monotypic A. sect. Pallasia was studied using a wide spectrum of methods and divided into two clearly morphologically, geographically, cytologically and genetically isolated species: A. pallasii s. str.—North-East Kazakhstan, Western Siberia, and the Altai Mountains; A. caricifolium—Kyrgyzstan, Northwest China, South-East Kazakhstan until Zaysan Lake in the east. Despite serious genetic differences, both species are sisters and are related to species of the A. sect. Codonoprasum (Subg. Allium). Allium caricifolium differs from A. pallasii s. str. by taller stems, dense inflorescence, and with filaments longer than perianth. The possible phylogenetic reasons for the separation of these species are discussed. A nomenclature analysis of synonyms was carried out. [ABSTRACT FROM AUTHOR]

Viola sect. Melanium, the so-called pansy, is an allopolyploid morphologically well-defined lineage of ca. 110 perennial and annual species in the northern hemisphere, characterized by markedly complex genomic configurations. Five annual pansies occur in Italy, four of which are morphologically very similar and belong to the informal 'V. tricolor species complex': V. arvensis (2n = 34), V. hymettia (2n = 16), V. kitaibeliana (2n = 16), and V. tricolor (2n = 26). Their field recognition is difficult and reflects a long-debated taxonomy often resulting in doubtful records in field inventories and across European herbaria. The current lack of comprehensive intra- and interspecific comparative studies and a relative scarcity of appropriate genetic markers coupled with unambiguous cytological descriptions are hindering clear taxa circumscription and phylogenetic inferences within this group. In this work, we tested DNA sequence variation of three highly variable plastid markers and High-Throughput Sequencing (HTS) of the nuclear ribosomal 5S-IGS region in an attempt to decipher species identity within the V. tricolor species complex and to obtain an insight on their genome organization and evolution. Our results document the close relationships within this species group, a reliable molecular resolution for V. tricolor, and the common ancestry of V. arvensis and the poorly differentiated V. kitaibeliana and V. hymettia. Evidence of an important inter-population geographical divergence was recorded in V. tricolor and V. arvensis, pointing at the existence of different eco-cytotypes within these entities. Overall diversity patterns and the occurrence of two to four differently diverging 5S-IGS lineages are discussed in the light of the acknowledged taxonomy and genomic evolutive trajectories of sect. Melanium. [ABSTRACT FROM AUTHOR]

Ranunculus section Batrachium (water crowfoot) ranks among the most taxonomically challenging aquatic plant groups due to morphological reduction, phenotypic plasticity, polyploidy and reticulate evolution. This study, for the first time in this group, linked morphology, genome size and genetic data (two non-coding regions of plastid DNA and the ITS region of nuclear ribosomal DNA). This extensive data set, including 258 central European populations, enables us to recognize widespread lineages from hybrids and to trace the evolutionary processes underlying the observed diversity. Most of the traditionally recognized species are supported. However, the presence of two morphologically cryptic but genetically well-differentiated lineages was detected within Ranunculus trichophyllus , and three separate lineages of different parentage were confirmed in the Ranunculus penicillatus complex. An allopolyploid origin was revealed in Ranunculus aquatilis , Ranunculus baudotii and in both lineages of R. trichophyllus , for which the parentage has not yet been studied, and allopolyploidy is suspected in all other polyploid taxa except for the triploid cytotype of Ranunculus fluitans , which is most likely autopolyploid. We detected putative F1 hybrids of seven different parentage combinations, including two involving Ranunculus rionii , representing the first known hybrids of this species. An additional 13 hybrid cytotypes (backcrosses or entailing additional polyploidization) were revealed; c. 20% of Ranunculus peltatus accessions seem to be influenced by introgression detectable only using sequence data. The Batrachium group is remarkable due to the coexistence of well-defined lineages with recently evolved biotypes arising due to hybridization and polyploidization. [ABSTRACT FROM AUTHOR]

Fern phylogeographic studies have mostly focused on the influence of the Pleistocene climate on fern distributions and the prevalence of long-distance dispersal. The effect of pre-Pleistocene events on the distributions of fern species is largely unexplored. Here, we elucidate a hypothetical scenario for the evolutionary history of Vandenboschia speciosa, hypothesised to be of Tertiary palaeotropical flora with a peculiar perennial gametophyte. We sequenced 40 populations across the species range in one plastid region and two variants of the nuclear gapCp gene and conducted time-calibrated phylogenetic, phylogeographical, and species distribution modelling analyses. Vandenboschia speciosa is an allopolyploid and had a Tertiary origin. Late Miocene aridification possibly caused the long persistence in independent refugia on the Eurosiberian Atlantic and Mediterranean coasts, with the independent evolution of gene pools resulting in two evolutionary units. The Cantabrian Cornice, a major refugium, could also be a secondary contact zone during Quaternary glacial cycles. Central European populations resulted from multiple post-glacial, long-distance dispersals. Vandenboschia speciosa reached Macaronesia during the Pliocene–Pleistocene, with a phylogeographical link between the Canary Islands, Madeira, and southern Iberia, and between the Azores and northwestern Europe. Our results support the idea that the geological and climate events of the Late Miocene/Early Pliocene shifted Tertiary fern distribution patterns in Europe. [ABSTRACT FROM AUTHOR]

Calluna vulgaris (Ericaceae) is the most widespread and prevalent woody species of the European dry heathland, from the African side of the Strait of Gibraltar to northern Europe. However, previous biogeographic analyses of this species have ignored the western Mediterranean region, despite its preponderant role as a major glacial refugium for European biota. Here, we explore the existence of further Pleistocene glacial refugia for C. vulgaris in the Iberian Peninsula and the Strait of Gibraltar area and provide new insights into the post-glacial colonization of Europe by this emblematic heathland species. We carried out phylogeographical analyses of C. vulgaris samples from 44 locations using four plastid markers (matK , trnH - psbA , trnL-F and rpl16). We built palaeodistribution models using MAXENT to identify possible refugia for C. vulgaris during the mid-Pliocene, Last Interglacial (LIG), Last Glacial Maximum (LGM) and mid-Holocene. Our results identified a genetic lineage exclusive to the Strait of Gibraltar area s.l. (south-western Iberian Peninsula and north-western tip of Africa) as the most probable close to the clade of origin of the species. This lineage also had more private haplotypes than more recent, Eurosiberian clades. The obtained data highlighted two main refugia for C. vulgaris during the LGM, one around the Strait of Gibraltar and another in the north-western Iberian Peninsula. The Strait of Gibraltar area is a major centre of origin or glacial refugium for the heather C. vulgaris. However, the north-western Iberian Peninsula seems to have acted as a secondary glacial refugium for the more recent, Eurosiberian lineage of this species. This study stresses the importance of the Strait of Gibraltar area in the biogeographic history and conservation of the heather and, by extension, the European heathland habitat. [ABSTRACT FROM AUTHOR]

The delimitation of Limonium taxa is highly complicated due to hybridization, polyploidy, and apomixis. Many “microspecies” were described and aggregated into groups, most of which are still poorly known from both molecular and morphological points of view. The aim of this study is to investigate four endemic species from the Tyrrhenian coast of central Italy and the Ponziane Archipelago belonging to the L. multiforme group (L. amynclaeum, L. circaei, L. pandatariae, and L. pontium) by means of molecular and morphometric analyses. Molecular data by sequencing ITS and three plastid markers and morphometric data highlight new information about the taxonomy of these taxa so as to reduce them into a single specific entity. In fact, the better taxonomic choice is to consider the populations studied as part of a single species, i.e., Limonium pontium. Three subspecies are recognized, i.e., subsp. pontium [= L. circaei = L. amynclaeum; from Circeo to Gianola localities (excluding Terracina) and from islands Ponza, Palmarola, Zannone, and Santo Stefano], subsp. pandatariae comb. et stat. nov. (from island of Ventotene), and subsp. terracinense subsp. nov. (from Terracina).

Genista etnensis is a remarkable and well-known tree endemic to Sicily, Sardinia, and Corsica (Mediterranean Basin). Nevertheless, its morphological variability and its native status throughout its range need to be further investigated. In this study, we aim to clarify some aspects of this infraspecific variability by molecular means. Sequences of one nuclear and five plastid markers were analyzed under maximum parsimony by using TCS software. Plastid data were also time-calibrated under a Bayesian Inference framework. Plastid data revealed strong isolation between the populations from the Cyrno-Sardinian biogeographical province, which are also the most diverse and presumably the most archaic, and those from Sicily and Southern Italy (in this latter area, the species is naturalized). The calibration analysis indicates that the last common ancestor between G. etnensis and its sister group G. fasselata dates back to the middle Pliocene or slightly later, when sclerophyllous Mediterranean vegetation spread, whereas G. etnensis itself might have originated in the middle Pleistocene. The current, rather unusual distribution of G. etnensis could be explained by long-range seed dispersal from the western part of the range or by anthropogenic introduction into Sicily, with extinctions of transported haplotypes in the region of origin. Interestingly, the Vesuvius population, introduced from Sicily in recent times and locally naturalized, shows private genotypes, and was richer in both genotypes and haplotypes than the Sicilian ones.

Abstract Calibrachoa is a South-American genus comprising 27 species, several considered endemic or rare; few were subjects in genetic studies. We attempted to generate new data about the phylogenetically related and rare species C. eglandulata, C. sendtneriana, C. serrulata, and C. spathulata concerning their genetic diversity and population structure, which, coupled with their known restricted distribution, could help access their conservation status and contribute to the study of the Brazilian biodiversity. We sequenced 88 individuals for plastid intergenic spacers and genotyped 186 individuals for five microsatellite loci. Compared among each other, C. sendtneriana and C. serrulata presented the highest values of genetic diversity [π% (sd) = 0.23 (0.14) and 0.43 (0.25), respectively], followed by C. spathulata [π% (sd) = 0.19 (0.12)] and C. eglandulata [π% (sd) = 0.02 (0.03)]. Population differentiation was evident for these latter species, whereas it was not significant for C. sendtneriana and C. serrulata. Factors such as habitat specificity and fragmentation, pollination syndrome, and life history could explain the observed patterns. Based on the new genetic data and the species’ biology, a conservation status was assigned for C. sendtneriana and the status of the other three species was reviewed.

Viola sect. Melanium, the so-called pansy, is an allopolyploid morphologically well-defined lineage of ca. 110 perennial and annual species in the northern hemisphere, characterized by markedly complex genomic configurations. Five annual pansies occur in Italy, four of which are morphologically very similar and belong to the informal ‘V. tricolor species complex’: V. arvensis (2n = 34), V. hymettia (2n = 16), V. kitaibeliana (2n = 16), and V. tricolor (2n = 26). Their field recognition is difficult and reflects a long-debated taxonomy often resulting in doubtful records in field inventories and across European herbaria. The current lack of comprehensive intra- and interspecific comparative studies and a relative scarcity of appropriate genetic markers coupled with unambiguous cytological descriptions are hindering clear taxa circumscription and phylogenetic inferences within this group. In this work, we tested DNA sequence variation of three highly variable plastid markers and High-Throughput Sequencing (HTS) of the nuclear ribosomal 5S-IGS region in an attempt to decipher species identity within the V. tricolor species complex and to obtain an insight on their genome organization and evolution. Our results document the close relationships within this species group, a reliable molecular resolution for V. tricolor, and the common ancestry of V. arvensis and the poorly differentiated V. kitaibeliana and V. hymettia. Evidence of an important inter-population geographical divergence was recorded in V. tricolor and V. arvensis, pointing at the existence of different eco-cytotypes within these entities. Overall diversity patterns and the occurrence of two to four differently diverging 5S-IGS lineages are discussed in the light of the acknowledged taxonomy and genomic evolutive trajectories of sect. Melanium.

Polymorph Allium pallasii s.l. from monotypic A. sect. Pallasia was studied using a wide spectrum of methods and divided into two clearly morphologically, geographically, cytologically and genetically isolated species: A. pallasii s. str.—North-East Kazakhstan, Western Siberia, and the Altai Mountains; A. caricifolium—Kyrgyzstan, Northwest China, South-East Kazakhstan until Zaysan Lake in the east. Despite serious genetic differences, both species are sisters and are related to species of the A. sect. Codonoprasum (Subg. Allium). Allium caricifolium differs from A. pallasii s. str. by taller stems, dense inflorescence, and with filaments longer than perianth. The possible phylogenetic reasons for the separation of these species are discussed. A nomenclature analysis of synonyms was carried out.

Orchids differ from other plants in their extremely small and partly air‐filled seeds that can be transported long distances by wind. Seed dispersal in orchids is expected to contribute strongly to overall gene flow, and orchids generally express low levels of genetic differentiation between populations and low pollen to seed flow ratios. However, studies in orchids distributed in northern Europe have often found a poor geographic structuring of genetic variation. Here, we studied geographic differentiation in the marsh orchid Dactylorhiza umbrosa, which is widely distributed in upland regions from Asia Minor to Central Asia. These areas were less affected by Pleistocene ice ages than northern Europe and the orchid should have been able to survive the last ice age in local refugia. In the plastid genome, which is dispersed by seeds, populations at close distance were clearly divergent, but the differentiation still increased with geographic distance, and a significant phylogeographic structure had developed. In the nuclear genome, which is dispersed by both seeds and pollen, populations showed an even stronger correlation between genetic and geographic distance, but average levels of differentiation were lower than in the plastid genome, and no phylogeographic structure was evident. Combining plastid and nuclear data, we found that the ratio of pollen to seed dispersal (mp/ms) decreases with physical distance. Comparison with orchids that grow in parts of Europe that were glaciated during the last ice suggests that a balanced structure of genetic diversity develops only slowly in many terrestrial orchids, despite efficient seed dispersal. [ABSTRACT FROM AUTHOR]

Artemisia herba-alba is an important component of Mediterranean dry steppe floras, being widely distributed in arid areas of the Iberian Peninsula and North-West Africa. In this study, we use genetic, cytogenetic and niche modelling tools to investigate the natural history of the species, focusing particularly on the role played by polyploidization to explain current diversity patterns throughout the main distribution range of the plant. Our sequencing data indicate a complex phylogeographical structure showing similar haplotype diversity patterns on both sides of the Strait of Gibraltar and no clear signals of genetic refugia. According to our cytogeographical results, we inferred multiple polyploidization events, which probably took place on the Iberian Peninsula and in North Africa independently. Environmental niche modelling suggested stable potential distributions of A. herba-alba on both sides of the Mediterranean Sea under present and past Last Glacial Maximum conditions, which could be related to the intricate spatial genetic and cytogenetic patterns shown by the species. Finally, environmental modelling comparison among cytotypes revealed that the niche of tetraploids is narrower and nested in that of diploids, a result that could indicate environmental specialization and could potentially explain recurrent establishment success of tetraploids. [ABSTRACT FROM AUTHOR]

Fern phylogeographic studies have mostly focused on the influence of the Pleistocene climate on fern distributions and the prevalence of long-distance dispersal. The effect of pre-Pleistocene events on the distributions of fern species is largely unexplored. Here, we elucidate a hypothetical scenario for the evolutionary history of Vandenboschia speciosa, hypothesised to be of Tertiary palaeotropical flora with a peculiar perennial gametophyte. We sequenced 40 populations across the species range in one plastid region and two variants of the nuclear gapCp gene and conducted time-calibrated phylogenetic, phylogeographical, and species distribution modelling analyses. Vandenboschia speciosa is an allopolyploid and had a Tertiary origin. Late Miocene aridification possibly caused the long persistence in independent refugia on the Eurosiberian Atlantic and Mediterranean coasts, with the independent evolution of gene pools resulting in two evolutionary units. The Cantabrian Cornice, a major refugium, could also be a secondary contact zone during Quaternary glacial cycles. Central European populations resulted from multiple post-glacial, long-distance dispersals. Vandenboschia speciosa reached Macaronesia during the Pliocene–Pleistocene, with a phylogeographical link between the Canary Islands, Madeira, and southern Iberia, and between the Azores and northwestern Europe. Our results support the idea that the geological and climate events of the Late Miocene/Early Pliocene shifted Tertiary fern distribution patterns in Europe.

Merostachys is a Neotropical woody bamboo genus that occurs in the understory and along forest borders. Our taxonomic studies of its species and morphological analyses have allowed us to recognize morphological groups in the genus. Previous molecular analyses, which included relatively few species, supported Merostachys as monophyletic and sister to Actinocladum or Athroostachys. We here provide a phylogenetic estimation for Merostachys based on a broader taxon sampling and seven plastid markers (one coding: ndhF 3′ end; four intergenic spacers: rps16-trnQ , trnC-rpoB , trnD-trnT and trnT-trnL ; and two introns: rpl16 and rps16). We aimed to test the monophyly of the genus, to verify its relationship with other genera of Arthrostylidiinae, mainly Athroostachys and Actinocladum , and to test whether the previously identified morphological groups were congruent with the molecular data. The monophyly of the genus was confirmed, as was its sister relationship with Athroostachys , although alternate hypothesis testing could not reject a sister relationship with Actinocladum. Two well-supported clades in Merostachys were recovered, one of which encompasses a polytomy. These clades did not exhibit consistent morphological synapomorphies and were not congruent with the morphological groups; however, floret surface (shiny vs. dull) was correlated with the two clades. The lack of resolution in Merostachys , as exemplified by the polytomy, can be attributed mainly to incomplete lineage sorting, suggesting a recent radiation in this group. [ABSTRACT FROM AUTHOR]

Gastridium P. Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, whose species number and diversity are still imperfectly known. We examined patterns of DNA diversity at two plastid (trnH-psbA, trnL-F) and one nuclear (ITS) DNA markers in 44 individuals of the four taxa (Gastridium lainzii, G. phleoides, G. scabrum, G. ventricosum) recently recognised by different authors, based on morpho-ecological descriptors. Diversity data were explored with multiple statistical and phylogenetic tools, and integrated with available GenBank sequences of Gastridium and closely related genera. Despite the limited variability detected, evidence of within-taxon genetic cohesion and estimates of molecular divergence comparable with those of species in the same subtribal lineage (Agrostidinae) were recovered. The identified plastid genealogies are congruent with a subdivision of the genus into four distinct species, coherently with collected morphological descriptors. Phylogenetic reconstructions with ITS were less corresponding to the four taxa, possibly due to reticulation and polyploidization. The broader plastid and nuclear tree topologies were consistent with previous assessments, highlighting the overall little resolution of species and genera within Agrostidinae, and the close relationships shared by Gastridium and Triplachne. The hypothesis of closely related, but separately evolving, lineages within Gastridium is discussed, suggesting a re-evaluation of its current taxonomy. [ABSTRACT FROM AUTHOR]

The Hepatica section Angulosa consists of mainly tetraploid (2n = 28) species that are distributed disjunctly throughout Eurasia. Karyological evidence proves the hybrid origin of the polyploid species of this section. Hepatica transsilvanica is a member of this species group with a conspicuous distribution restricted to the Eastern Carpathians. Based on genome size and cytotypes, the paternal parent of H. transsilvanica is described to be the only diploid species in section Angulosa, H. falconeri. The maternal species is hypothesized to be H. nobilis, a European species with entirely lobed leaves and a wider distribution area. Although the hybrid origin of H. transsilvanica is well documented by karyological evidence, the time of hybridization has never been studied. By using sequences of both the nuclear and plastid genome, we reconstructed the phylogenetic relationships and divergence times of H. transsilvanica and its parental species. The identity of the parental species is corroborated by discordant gene tree topologies of the nrITS and plastid sequences. Moreover, both gene copies of the parental species could be identified with the low-copy nuclear gene, MLH1. Divergence dating analysis using Bayesian phylogenetic methods strongly supported the long-term survival of H. transsilvanica in the Southeastern Carpathians, as the most recent common ancestor of the hybrid and parent species existed not later than the beginning of the Pleistocene, ca. 3 million years ago. These results not only highlight the biogeographic importance of the Southeastern Carpathians in the Quaternary glaciation periods, but also emphasize that Tertiary lineages could have survived in a Central European cryptic refugium.

Huang-lian (Coptis plants in China) are essential medicinal plants in China, C. chinensis var. chinensis and C. deltoidea have been domesticated and cultivated for 700 years. In this study, the genetic diversity patterns and biogeographical information of cultivated Huang-lian and their wild relatives Coptis species were assessed using three plastids DNA regions. A total of 186 individuals from twenty-seven populations representing two species of cultivated Huang-lian and four species of wild relatives were collected and analyzed. Twenty-four haplotypes of six species were identified when three plastid spacers were combined. Historical biogeography inference revealed multiple dispersal events in the groups of cultivated Huang-lian and C. omeiensis. This evidence can infer that large initial population size and interbreeding with co-existing wild relatives in expanding new planting areas might be the main reason for maintaining the high genetic diversity of cultivated Huang-lian. Nevertheless, the multimodal curve of mismatch analysis and positive or negative differed among species and populations by neutrality tests indicated some groups of cultivated Huang-lian experienced genetic bottlenecks. Phylogeny analysis (NJ, MP, BI) showed that cultivated Huang-lian and C. omeiensis were clustered into a monophyletic group while C. chinensis var. brevisepala was paraphyletic, having earlier divergence time from C. chinensis var. chinensis (7.6 Ma) than C. omeiensis. Parsimony network demonstrated that C. deltoidea had more shared haplotypes with C. omeiensis than C. chinensis var. chinensis, and other haplotypes of C. deltoidea and C. omeiensis had less mutation steps than that of C. chinensis var. chinensis and C. omeiensis. This evidence suggests that C. omeiensis has a closer relationship with cultivated Huang-lian and might be a potential wild relative to C. deltoidea. The results reported here provide the baseline data for preserving genetic resources of Huang-lian and also evaluating the genetic impacts of long-term cultivation on medicinal plants, which could be instructive to future cultivation projects of traditional Chinese medicinal plants.

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae—as well as in the sister family Calyceraceae—lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family’s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

The polypeptides encoded by the chloroplast ndh genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I. Except for Charophyceae (algae related to higher plants) and a few Prasinophyceae, all eukaryotic algae lack ndh genes. Among vascular plants, the ndh genes are absent in epiphytic and in some species scattered among different genera, families, and orders. The recent identification of many plants lacking plastid ndh genes allows comparison on phylogenetic trees and functional investigations of the ndh genes. The ndh genes protect Angiosperms under various terrestrial stresses, maintaining efficient photosynthesis. On the edge of dispensability, ndh genes provide a test for the natural selection of photosynthesis-related genes in evolution. Variable evolutionary environments place Angiosperms without ndh genes at risk of extinction and, probably, most extant ones may have lost ndh genes recently. Therefore, they are evolutionary endpoints in phylogenetic trees. The low number of sequenced plastid DNA and the long lifespan of some Gymnosperms lacking ndh genes challenge models about the role of ndh genes protecting against stress and promoting leaf senescence. Additional DNA sequencing in Gymnosperms and investigations into the molecular mechanisms of their response to stress will provide a unified model of the evolutionary and functional consequences of the lack of ndh genes.

Macaronesia has been considered a refuge region of the formerly widespread subtropical lauroid flora that lived in Southern Europe during the Tertiary. The study of relict angiosperms has shown that Macaronesian relict taxa preserve genetic variation and revealed general patterns of colonization and dispersal. However, information on the conservation of genetic diversity and range dynamics rapidly diminishes when referring to pteridophytes, despite their dominance of the herbaceous stratum in the European tropical palaeoflora. Here we aim to elucidate the pattern of genetic diversity and phylogeography of Diplazium caudatum, a hypothesized species of the Tertiary Palaeotropical flora and currently with its populations restricted across Macaronesia and disjunctly in the Sierras de Algeciras (Andalusia, southern Iberian Peninsula). We analysed 12 populations across the species range using eight microsatellite loci, sequences of a region of plastid DNA, and carry out species-distribution modelling analyses. Our dating results confirm the Tertiary origin of this species. The Macaronesian archipelagos served as a refuge during at least the Quaternary glacial cycles, where populations of D. caudatum preserved higher levels of genetic variation than mainland populations. Our data suggest the disappearance of the species in the continent and the subsequent recolonization from Macaronesia. The results of the AMOVA analysis and the indices of clonal diversity and linkage disequilibrium suggest that D. caudatum is a species in which inter-gametophytic outcrossing predominates, and that in the Andalusian populations there was a shift in mating system toward increased inbreeding and/or clonality. The model that best explains the genetic diversity distribution pattern observed in Macaronesia is, the initial and recurrent colonization between islands and archipelagos and the relatively recent diversification of restricted area lineages, probably due to the decrease of favorable habitats and competition with lineages previously established. This study extends to ferns the concept of Macaronesia archipelagos as refugia for genetic variation.

The Mediterranean Basin can be considered as a natural laboratory with which to study the effects of sea currents in the dispersal of coastal plant species that use hydrochory. Pancratium maritimum is a perennial geophyte, with a wide distribution along Mediterranean coasts. We aim to provide a timeframe for the origin of the diversification of this plant, to clarify its phylogeographical structure and to investigate the role of currents in the Mediterranean Sea in influencing spatial patterns of its genetic distribution. The phylogeographic history was analysed using 50 populations. A genetic structure analysis and divergence time estimation was performed using plastid sequences. Five haplotypes were detected, of which two were the most abundant; a third was observed in the central Mediterranean, and two rare haplotypes were present in the eastern Mediterranean. The genetic breaks were concordant with the direction of the major Mediterranean currents. The divergence time estimation for the origin of P. maritimum was located at the end of the Neogene (mid Pliocene to mid Pleistocene). We showed the importance of sea currents in the Mediterranean in acting both as a means of dispersal and as a barrier to the distribution and evolution of P. maritimum due to the special adaptations of its seeds. [ABSTRACT FROM AUTHOR]

The Hepatica section Angulosa consists of mainly tetraploid (2n = 28) species that are distributed disjunctly throughout Eurasia. Karyological evidence proves the hybrid origin of the polyploid species of this section. Hepatica transsilvanica is a member of this species group with a conspicuous distribution restricted to the Eastern Carpathians. Based on genome size and cytotypes, the paternal parent of H. transsilvanica is described to be the only diploid species in section Angulosa, H. falconeri. The maternal species is hypothesized to be H. nobilis, a European species with entirely lobed leaves and a wider distribution area. Although the hybrid origin of H. transsilvanica is well documented by karyological evidence, the time of hybridization has never been studied. By using sequences of both the nuclear and plastid genome, we reconstructed the phylogenetic relationships and divergence times of H. transsilvanica and its parental species. The identity of the parental species is corroborated by discordant gene tree topologies of the nrITS and plastid sequences. Moreover, both gene copies of the parental species could be identified with the low-copy nuclear gene, MLH1. Divergence dating analysis using Bayesian phylogenetic methods strongly supported the long-term survival of H. transsilvanica in the Southeastern Carpathians, as the most recent common ancestor of the hybrid and parent species existed not later than the beginning of the Pleistocene, ca. 3 million years ago. These results not only highlight the biogeographic importance of the Southeastern Carpathians in the Quaternary glaciation periods, but also emphasize that Tertiary lineages could have survived in a Central European cryptic refugium. [ABSTRACT FROM AUTHOR]

Huang-lian (Coptis plants in China) are essential medicinal plants in China, C. chinensis var. chinensis and C. deltoidea have been domesticated and cultivated for 700 years. In this study, the genetic diversity patterns and biogeographical information of cultivated Huang-lian and their wild relatives Coptis species were assessed using three plastids DNA regions. A total of 186 individuals from twenty-seven populations representing two species of cultivated Huang-lian and four species of wild relatives were collected and analyzed. Twenty-four haplotypes of six species were identified when three plastid spacers were combined. Historical biogeography inference revealed multiple dispersal events in the groups of cultivated Huang-lian and C. omeiensis. This evidence can infer that large initial population size and interbreeding with co-existing wild relatives in expanding new planting areas might be the main reason for maintaining the high genetic diversity of cultivated Huang-lian. Nevertheless, the multimodal curve of mismatch analysis and positive or negative differed among species and populations by neutrality tests indicated some groups of cultivated Huang-lian experienced genetic bottlenecks. Phylogeny analysis (NJ, MP, BI) showed that cultivated Huang-lian and C. omeiensis were clustered into a monophyletic group while C. chinensis var. brevisepala was paraphyletic, having earlier divergence time from C. chinensis var. chinensis (7.6 Ma) than C. omeiensis. Parsimony network demonstrated that C. deltoidea had more shared haplotypes with C. omeiensis than C. chinensis var. chinensis , and other haplotypes of C. deltoidea and C. omeiensis had less mutation steps than that of C. chinensis var. chinensis and C. omeiensis. This evidence suggests that C. omeiensis has a closer relationship with cultivated Huang-lian and might be a potential wild relative to C. deltoidea. The results reported here provide the baseline data for preserving genetic resources of Huang-lian and also evaluating the genetic impacts of long-term cultivation on medicinal plants, which could be instructive to future cultivation projects of traditional Chinese medicinal plants. [ABSTRACT FROM AUTHOR]

Reconstructions of phylogenetic relationships in the flowering plant family Rubiaceae have up until now relied heavily on single‐ or multi‐gene data, primarily from the plastid compartment. With the availability of cost‐ and time‐efficient techniques for generating complete genome sequences, the opportunity arises to resolve some of the relationships that, up until now, have proven problematic. Here, we contribute new data from complete 58 plastid genome sequences, representing 55 of the currently 65 recognized tribes of the Rubiaceae. Also contributed are new data from the nuclear rDNA cistrons for corresponding taxa. Phylogenetic analyses are conducted on two plastid data sets, one including data from the protein coding genes only, and a second where protein coding data are combined with non‐coding regions, and on a nuclear rDNA data set. Our results clearly show that simply adopting a "more characters" approach does not resolve the relationships in the Rubiaceae. More importantly, we identify conflicting phylogenetic signals in the data. Analyses of the same plastid data, treated as nucleotides or as codon‐degenerated data, resolve and support conflicting topologies in the subfamily Cinchonoideae. As these analyses use the same data, we interpret the conflict to result from erroneous assumptions in the models used to reconstruct our phylogenies. Conflicting signals are also identified in the analyses of the plastid versus the nuclear rDNA data sets. These analyses use data from different genomic compartments, with different inheritance patterns, and we interpret the conflicts as representing "real" conflicts, reflecting biological processes of the past. [ABSTRACT FROM AUTHOR]

Leptocereus is an Antillean genus of thin-stemmed cacti with 17 described species. We carried out a phylogenetic reconstruction with plastid DNA sequence data and a combined analysis with a set of 39 morphological characters using Maximum Likelihood and Bayesian inference criteria to explore the monophyly of the genus. We further analyzed the evolution of eight morphological characters to interpret the circumscription of Leptocereus and test for putative synapomorphies for the clade. Five plastid markers (trnL-F, trnQ-rps16, psbA-trnH, petL-psbE, and rpl16) were sequenced for fifteen species of Leptocereus, seven species of the related genera (Armatocereus, Dendrocereus, Strophocactus) and ten species from Hylocereeae, Pachycereinae, Stenocereinae were used as outgroup taxa. Our phylogenetic analyses suggest that Leptocereus is paraphyletic with a clade of the two Dendrocereus species nested within it. All Cuban species constitute a monophyletic group, as do the species of Hispaniola and Puerto Rico, which are sister to the Cuban clade + Dendrocereus clade. No morphological character analyzed here was synapomorphic for the genus, but sunken areoles in the depressions of the ribs were a character present in all subclades of Leptocereus. Based on our molecular data and extensive fieldwork, a new circumscription of Leptocereus is proposed, which includes three new combinations (Leptocereus albellus comb. et stat. nov., L. nudiflorus comb. nov., L. undulosus comb. nov.). [ABSTRACT FROM AUTHOR]

The plant communities associated with iron-rich outcrops are still little known about to their genetic structure and diversity. Outcrops are often considered to be 'terrestrial islands', and gene flow among populations on different outcrops is presumed to be hampered by the isolation effect provided by the surrounding matrix. Here, we studied the genetic diversity and structure of populations of Dyckia excelsa to test the hypothesis that the disjunction of the ironstone outcrops where this species occurs promotes its highly structured genetic variability. Seven nuclear microsatellite markers and two plastid DNA intergenic spacers (rps16-trnK and rpl32-trnL) were used to characterize individuals from seven locations in the region of Urucum Residual Plateau, Mato Grosso do Sul State, Brazil. These markers low haplotype and allelic diversity and high levels of genetic divergence among outcrops, indicating prolonged genetic isolation, with diversification of haplotypes dating from the Pleistocene (1.0 Mya). Pollen movement may occur between neighbouring populations, resulting in a pattern of isolation-by-distance. For conservation purposes, it is recommended that D. excelsa be preserved in situ in each specific location given the low levels of gene flow and the high degree of genetic uniqueness in each group of populations investigated. [ABSTRACT FROM AUTHOR]

Ochagavia (four species) and Fascicularia (one species) form a well-supported clade of the early-diverging Bromelioideae. The two genera are morphologically similar, but they can be easily discerned on the basis of generative characters. Besides the species distributed on the Chilean mainland, the group includes O. elegans , endemic to the Robinson Crusoe Island of the Juan Fernández Islands. In previous molecular phylogenetic studies, O. elegans formed a sister clade to the remainder of Fascicularia and Ochagavia. A phylogenomic approach, including nearly complete and, in five cases, full plastomes (c. 160 kbp) and the nuclear rDNA cistron (c. 6 kbp), and scanning electron microscope (SEM) images of pollen were used to analyse relationships in the Fascicularia-Ochagavia group. Plastome and nuclear trees were largely congruent and supported previous phylogenetic analyses of O. elegans being sister to the remainder of the group. A divergent phylogenetic position was suggested for O. carnea using different organellar trees. SEM analysis of pollen supported the division of Fascicularia and Ochagavia. Evolutionary and taxonomic implications of our results are discussed. [ABSTRACT FROM AUTHOR]

Arnica montana (Asteraceae) is a herbaceous species with high interest for pharmaceutical industry due its anti-inflammatory properties. However, commercial collection in wild, habitat loss, abandonment of land, reforestation and the ongoing climate change threaten the conservation of the species throughout its natural distribution. Galicia (north-western Spain) is one of the main flower suppliers, but no legislation on A. montana exploitation is currently applied. In order to assess the genetic status and population structure in this region, 27 locations were genotyped for 14 microsatellite loci and sequenced for 2 plastid DNA (cpDNA) markers. The relationship of environmental, biochemical and morphological variables with genetic differentiation was also evaluated. Two different cpDNA groups previously described were found. One of them was widely distributed while the other was restricted to heathlands of the O Courel Mountains. The percentage of clonality was low (< 10%). Genetic diversity based on microsatellites (He = 0.245) was lower than in Central European populations, with high levels of population differentiation (FST = 0.441), suggesting strong effects of genetic drift. Bayesian clustering methods revealed the presence of four genetically distinct population units, one of them corresponding to the O Courel Mountains group described by cpDNA analysis. Environmental and biochemical factors were related to genetic differentiation, suggesting local adaptation. Necessary conservation measures include the overdue implementation of the Habitats Directive by the Galician Regional Administration, establishing sustainable harvesting regimes, and aim to conserve genetic variation in these endangered populations at the southern range edge. [ABSTRACT FROM AUTHOR]

To what extent Pleistocene sea-level fluctuations have affected the genetic diversity of species is one of the current topics in biogeographical research. Carduncellus dianius is a Mediterranean narrow endemic species, restricted to < 20 populations distributed along coastal areas in Alicante (mainland eastern Iberian Peninsula) and on the island of Ibiza (Balearic Islands). To get insights into its evolutionary history and its genetic diversity and structure, we combined the analysis of molecular markers (three plastid DNA regions and AFLP) with ecological niche modelling. Results from dated phylogeographical analyses revealed that this species might have originated in the continental region during the early Pleistocene. The colonization of Ibiza could have occurred by a single long-distance dispersal event, with a subsequent back-colonization from the island to the same continental area of origin. These results corroborate the role of islands as sources for mainland colonization (biodiversity reservoirs) and as refugia during glacial periods. Notably, we detected that populations located on stable landmasses (i.e. not affected by sea rising during interglacial cycles) harboured significantly higher genetic diversity than those that were periodically submerged during the periods of marine transgressions. Our results point out sea-level fluctuations as a factor to be considered in phylogeographical studies focused on species distributed along coastlines. [ABSTRACT FROM AUTHOR]

The Laperrine’s olive is endemic to the Saharan Mountains. Adapted to arid environments, it may constitute a valuable genetic resource to improve water-stress tolerance in the cultivated olive. However, limited natural regeneration coupled with human pressures make it locally endangered in Central Sahara. Understanding past population dynamics is thus crucial to define management strategies. Nucleotide sequence diversity was first investigated on five nuclear genes and compared to the Mediterranean and African olives. These data confirm that the Laperrine’s olive has a strong affinity with the Mediterranean olive, but it shows lower nucleotide diversity than other continental taxa. To investigate gene flows mediated by seeds and pollen, polymorphisms from nuclear and plastid microsatellites from 383 individuals from four Saharan massifs were analyzed. A higher genetic diversity in Ahaggar (Hoggar, Algeria) suggests that this population has maintained over the long term a larger number of individuals than other massifs. High-to-moderate genetic differentiation between massifs confirms the role of desert barriers in limiting gene flow. Yet contrasting patterns of isolation by distance were observed within massifs, and also between plastid and nuclear markers, stressing the role of local factors (e.g., habitat fragmentation, historical range shift) in seed and pollen dispersal. Implications of these results in the management of the Laperrine’s olive genetic resources are discussed.

Campanula is one of the species-rich genera of the bellflower family (Campanulaceae), in a wider sense with ∼600 species, growing in a wide range of habitats in the northern hemisphere. The Caucasus is one of the areas with especially many endemic Campanula species. The Scapiflorae group comprises alpine and subalpine perennial rocky plants, which develop numerous short single-flowered stems from a basal leaf rosette. In its current circumscription based on the comparative analysis of selected morphological characters, it consists mostly of species endemic to the Caucasus, and some in the Alps and North-East Asia, and it is classified as C. subg. Scapiflorae. We performed a molecular phylogenetic analysis including a dense sampling of C. subg. Scapiflorae and other Caucasian Campanula species and representatives of the large Eurasian Campanula CAM17 clade. Campanula subg. Scapiflorae is non-monophyletic in its current circumscription, but the Caucasian species of this group form a well-supported clade. Ancestral character state reconstruction across the Eurasian CAM17 clade shows that unbranched inflorescences, a basal leaf rosette, calyx appendages and a perennial life form with numerous low stems, which is characteristic for the Scapiflorae group, evolved convergently at least five times in unrelated high mountain species such as C. alpina or C. petrophila. The Caucasian clade comprises four major sublineages in our analyses, suggesting complex biogeographic patterns among the Greater and Lesser Caucasus mountain ranges. [ABSTRACT FROM AUTHOR]

Ficaria is a taxonomically intriguing polyploid complex with high morphological variability. Both hybridization and polyploidization have been suggested as the main evolutionary forces behind the high morphological variability in this genus; however, detailed studies are lacking. In Central Europe, two Ficaria taxa (diploid F. calthifolia and tetraploid F. verna subsp. verna) occasionally co-occur in local sympatry, which might result in hybridization. We investigated sympatric populations of the two Ficaria taxa using flow cytometry, chromosome counts, AFLP analysis and plastid DNA sequencing; we also performed experimental homoploid and heteroploid crosses to determine the frequency and direction of hybrid triploid formation, an alternative route of triploid origin (autopolyploidy) and the possibility of a one-step neoallotetraploid origin. Sympatric populations were composed of three genetic clusters corresponding to diploid F. calthifolia (2 n = 16), tetraploid F. verna subsp. verna (2 n = 32) and triploid plants (2 n = 24). The holoploid genome size and AFLP data suggest a hybrid origin of the triploids, thereby making their formation via autopolyploidization in F. calthifolia unlikely. The triploid populations are monoclonal and of independent origin. In contrast, the parental populations exhibit high genotypic diversity and frequent sexual reproduction, including those of predominantly asexual F. verna subsp. verna. Experimental crossing confirmed that both parental taxa produce fertile seeds via a sexual pathway, but not by apomixis, and that both serve as pollen acceptors in heteroploid crosses, which is consistent with the plastid sequencing. However, hybridization is asymmetric, with maternal-excess crosses being significantly more successful. No signs of neoautotetraploidization or neoallotetraploidization were detected. In summary, recent gene flow between the studied Ficaria taxa is either limited or absent. [ABSTRACT FROM AUTHOR]