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Helianthemum is the largest, most widely distributed and most taxonomically complex genus of the Cistaceae. To examine the intrageneric phylogenetic relationships in Helianthemum, we used sequence data from plastid DNA (ndhF, psbA‐trnH, trnL‐trnF) and the nuclear ITS region. The ingroup consisted of 95 species and subspecies (2 subgenera, 10 sections) from throughout the range of Helianthemum, while the outgroup was composed of 30 species representing all the genera in the Cistaceae (Cistus Crocanthemum, Fumana, Halimium, Hudsonia, Lechea, Tuberaria) plus Anisoptera thurifera subsp. polyandra (Dipterocarpaceae). To infer phylogenetic relationships, we analysed three different matrices (cpDNA, nrDNA, cpDNA + nrDNA concatenated) using maximum likelihood and Bayesian inference, and performed molecular dating to estimate the ages of origin of the main clades using a Bayesian approach. The cpDNA + nrDNA concatenated dataset provided the highest Bayesian posterior probabilities and bootstrap support values, and the results supported the monophyly of the genus Helianthemum and its sister relationship to a clade consisting of all species of Cistus, Crocanthemum, Halimium, Hudsonia and Tuberaria. This result means that we did not retrieve the sister relationship between Helianthemum and Crocanthemum (plus Hudsonia) that could be expected according to previous published studies. Despite their different statistical support, the topology of the inner branches of all the consensus trees showed that Helianthemum is characterized by the emergence of three major clades in agreement with above‐species taxonomy, although unresolved polytomies still remain towards the tips of the trees (species and subspecies). Clade I (mainly distributed in Mediterranean and alpine environments in European and western Asiatic mountain chains) fully coincided with subg. Plectolobum, whereas subg. Helianthemum was retrieved in clade II (arid and semi‐arid environments from Macaronesia, the Med, Depto. de Biodiversidad, Ecología y Evolución, Fac. de Ciencias Biológicas, TRUE, pub

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

The Eurasian steppes occupy a significant portion of the worldwide land surface and their biota have been affected by specific past range dynamics driven by ice ages-related climatic fluctuations. The dynamic alterations in conditions during the Pleistocene often triggered reticulate evolution and whole genome duplication events. Employing genomic, genetic and cytogenetic tools as well as morphometry we investigate the intricate evolution of Astragalus onobrychis, a widespread Eurasian steppe plant with diploid, tetraploid and octoploid cytotypes. To analyse the heteroploid RADseq dataset we employ both genotype-based and genotype-free methods that result in highly consistent results, and complement our inference with information from the plastid ycf1 region. We uncover a complex and reticulate evolutionary history, including at least one auto-tetraploidization event and two allo-octoploidization events; one of them involved also genetic contributions from other species, most likely A. goktschaicus. The present genetic structure points to the existence of four main clades within A. onobrychis, which only partly correspond to different ploidies. Time-calibrated diffusion models suggest that diversification within A. onobrychis was associated with ice age-related climatic fluctuations during the last million years. We finally argue for the usefulness of uniparentally inherited plastid markers, even in the genomic era, especially when investigating heteroploid systems.

Artemisia umbelliformis is a herbaceous perennial alpine plant growing in the central and western part of the European Alpine system (Sierra Nevada, Cantabrian Mountains, Pyrenees, Alps and Apennines). We aimed to unravel the large-scale phylogeographic structure across its distribution. To this end, we collected amplified fragment length polymorphism and plastid DNA sequence data for 19 populations covering the distribution of the species. Populations were strongly reciprocally differentiated with 93% of the overall genetic variation partitioned among populations. Bayesian clustering approaches identified two groups: the Alpine group spanning the Alps, the Apennines and the Sierra Nevada and the northern Iberian group including populations from the Pyrenees and the Cantabrian Mountains. The three plastid haplotypes discovered fell into two strongly divergent clades, termed Iberian and Alpine lineages. At the range-wide scale, our results suggest that an early vicariance or, alternatively, an old dispersal event shaped the strong phylogeographic split between Iberian and Alpine populations. Genetic drift caused by highly restricted gene flow between the populations has probably resulted in reduced genetic variability and strong divergence between populations. The Alps, the central Pyrenees, the Cantabrian Mountains and the northern Apennines probably acted as glacial refugia for A. umbelliformis. In contrast, the single population occurring in the Sierra Nevada appears to originate from a fairly recent long-distance dispersal event from the southern central Alps. Altogether, our study shows that the phylogeographic history of A. umbelliformis is complex and has been shaped by processes acting at different time horizons. These processes conferred genetic relationships among disjunct populations, which partly reflected geographical proximity and partly spanned distant mountain ranges such as the Alps and the Sierra Nevada.

Although it has been traditionally accepted that Arenaria balearica (Caryophyllaceae) could be a relict Tertiary plant species, this has never been experimentally tested. Nor have the palaeohistorical reasons underlying the highly fragmented distribution of the species in the Western Mediterranean region been investigated. We have analysed AFLP data (213) and plastid DNA sequences (226) from a total of 250 plants from 29 populations sampled throughout the entire distribution range of the species in Majorca, Corsica, Sardinia, and the Tuscan Archipelago. The AFLP data analyses indicate very low geographic structure and population differentiation. Based on plastid DNA data, six alternative phylogeographic hypotheses were tested using Approximate Bayesian Computation (ABC). These analyses revealed ancient area fragmentation as the most probable scenario, which is in accordance with the star-like topology of the parsimony network that suggests a pattern of long term survival and subsequent in situ differentiation. Overall low levels of genetic diversity and plastid DNA variation were found, reflecting evolutionary stasis of a species preserved in locally long-term stable habitats.

Aim: Island radiations imply the emergence of numerous species in a short period of time. Downscaling at the infraspecific level, considerable differentiation among populations can be a sign of ‘incipient radiation’. However, this process remains largely unexplored. We focus on one of the most outstanding cases of infraspecific morphological variation in the Galápagos flora. Our hypothesis is that the phenotypic variation of Croton scouleri is a sign of incipient radiation, in which a single colonization has generated new lineages with considerable morphological differentiation. Location: The Galápagos Islands and Neotropics. Methods: One hundred and forty-four nuclear ribosomal DNA (ITS) and plastid trnL-F sequences of Croton sect. Adenophylli were used to test the hypothesis of a single ancestry (monophyly) of C. scouleri using a phylogenetic approach. Sequence data were analysed using Bayesian inference (BI) and maximum likelihood (ML). A complementary phylogeographical analysis of C. scouleri and phylogenetically related species was also performed using 123 plastid sequences (trnL-F, petL-psbE, trnH-psbA) in search for common ancestry of Galápagos lineages. Results: The phylogenetic approach revealed that the closest relatives of C. scouleri were C. alnifolius, C. pavonis and C. rivinifolius. However, we failed to support monophyly of C. scouleri populations. Despite finding numerous haplotypes (14 polymorphic sequences/9 substitution-based sequences), their distribution across Croton species prevented us from inferring common ancestry for C. scouleri. The phylogeographical reconstruction revealed multiple lineages related to the origin of C. scouleri. Main conclusions: Lack of monophyly likely indicates that an incipient radiation from a single ancestor does not account for the striking infraspecific phenotypic variation in C. scouleri. This morphological diversity could be explained by recurrent biogeographical connections between Galápagos and the mainland, i

The Global change is the most important threat to global bio-diversity, but an excellent opportunity for researchers to study the mechanisms of evolution and adaptation of the organisms to changing environments. High Mediterranean mountains (e. g. the Pyrenees) are among the most threatened ecosystems, and their study must be prioritized due to the large number of threatened and endemic species that inhabit these mountains. Many of these organisms have survived to past climate changes, so their study may clarify the behavior and the processes developed by the species to adapt and evolve. In this study, we proposed the use of plastid DNA markers with the species Silene ciliata, an alpine survivor of several glacial-interglacial processes. The results confirm the existence of unique haplo-types and the great interest of the conservation and evolution of Silene ciliata populations from the Huesca Pyrenees., El cambio global es una de las principales amenazas para la biodiversidad a nivel mundial, pero una oportunidad para el estudio de los mecanismos de evolución y adaptación de los organismos ante los cambios. La alta montaña mediterránea, como son los Pirineos, se encuentra entre los ecosistemas más amenazados y su estudio debe ser prioritario debido a la gran cantidad de especies amenazadas y endémicas que alberga. Muchos de estos organismos ya han sobrevivido a cambios climáticos pasados, por lo que su estudio puede arrojar luz sobre el comportamiento futuro de las especies y los mecanismos que desarrollen para adaptarse y evolucionar. Los resultados con-firman la existencia de haplotipos únicos y el gran interés en la conservación y la evolución de las poblaciones de Silene ciliata en los Pirineos de Huesca.

The Global change is the most important threat to global bio-diversity, but an excellent opportunity for researchers to study the mechanisms of evolution and adaptation of the organisms to changing environments. High Mediterranean mountains (e. g. the Pyrenees) are among the most threatened ecosystems, and their study must be prioritized due to the large number of threatened and endemic species that inhabit these mountains. Many of these organisms have survived to past climate changes, so their study may clarify the behavior and the processes developed by the species to adapt and evolve. In this study, we proposed the use of plastid DNA markers with the species Silene ciliata, an alpine survivor of several glacial-interglacial processes. The results confirm the existence of unique haplo-types and the great interest of the conservation and evolution of Silene ciliata populations from the Huesca Pyrenees., El cambio global es una de las principales amenazas para la biodiversidad a nivel mundial, pero una oportunidad para el estudio de los mecanismos de evolución y adaptación de los organismos ante los cambios. La alta montaña mediterránea, como son los Pirineos, se encuentra entre los ecosistemas más amenazados y su estudio debe ser prioritario debido a la gran cantidad de especies amenazadas y endémicas que alberga. Muchos de estos organismos ya han sobrevivido a cambios climáticos pasados, por lo que su estudio puede arrojar luz sobre el comportamiento futuro de las especies y los mecanismos que desarrollen para adaptarse y evolucionar. Los resultados con-firman la existencia de haplotipos únicos y el gran interés en la conservación y la evolución de las poblaciones de Silene ciliata en los Pirineos de Huesca.

The Global change is the most important threat to global bio-diversity, but an excellent opportunity for researchers to study the mechanisms of evolution and adaptation of the organisms to changing environments. High Mediterranean mountains (e. g. the Pyrenees) are among the most threatened ecosystems, and their study must be prioritized due to the large number of threatened and endemic species that inhabit these mountains. Many of these organisms have survived to past climate changes, so their study may clarify the behavior and the processes developed by the species to adapt and evolve. In this study, we proposed the use of plastid DNA markers with the species Silene ciliata, an alpine survivor of several glacial-interglacial processes. The results confirm the existence of unique haplo-types and the great interest of the conservation and evolution of Silene ciliata populations from the Huesca Pyrenees., El cambio global es una de las principales amenazas para la biodiversidad a nivel mundial, pero una oportunidad para el estudio de los mecanismos de evolución y adaptación de los organismos ante los cambios. La alta montaña mediterránea, como son los Pirineos, se encuentra entre los ecosistemas más amenazados y su estudio debe ser prioritario debido a la gran cantidad de especies amenazadas y endémicas que alberga. Muchos de estos organismos ya han sobrevivido a cambios climáticos pasados, por lo que su estudio puede arrojar luz sobre el comportamiento futuro de las especies y los mecanismos que desarrollen para adaptarse y evolucionar. Los resultados con-firman la existencia de haplotipos únicos y el gran interés en la conservación y la evolución de las poblaciones de Silene ciliata en los Pirineos de Huesca.

The Global change is the most important threat to global bio-diversity, but an excellent opportunity for researchers to study the mechanisms of evolution and adaptation of the organisms to changing environments. High Mediterranean mountains (e. g. the Pyrenees) are among the most threatened ecosystems, and their study must be prioritized due to the large number of threatened and endemic species that inhabit these mountains. Many of these organisms have survived to past climate changes, so their study may clarify the behavior and the processes developed by the species to adapt and evolve. In this study, we proposed the use of plastid DNA markers with the species Silene ciliata, an alpine survivor of several glacial-interglacial processes. The results confirm the existence of unique haplo-types and the great interest of the conservation and evolution of Silene ciliata populations from the Huesca Pyrenees., El cambio global es una de las principales amenazas para la biodiversidad a nivel mundial, pero una oportunidad para el estudio de los mecanismos de evolución y adaptación de los organismos ante los cambios. La alta montaña mediterránea, como son los Pirineos, se encuentra entre los ecosistemas más amenazados y su estudio debe ser prioritario debido a la gran cantidad de especies amenazadas y endémicas que alberga. Muchos de estos organismos ya han sobrevivido a cambios climáticos pasados, por lo que su estudio puede arrojar luz sobre el comportamiento futuro de las especies y los mecanismos que desarrollen para adaptarse y evolucionar. Los resultados con-firman la existencia de haplotipos únicos y el gran interés en la conservación y la evolución de las poblaciones de Silene ciliata en los Pirineos de Huesca.

The Global change is the most important threat to global bio-diversity, but an excellent opportunity for researchers to study the mechanisms of evolution and adaptation of the organisms to changing environments. High Mediterranean mountains (e. g. the Pyrenees) are among the most threatened ecosystems, and their study must be prioritized due to the large number of threatened and endemic species that inhabit these mountains. Many of these organisms have survived to past climate changes, so their study may clarify the behavior and the processes developed by the species to adapt and evolve. In this study, we proposed the use of plastid DNA markers with the species Silene ciliata, an alpine survivor of several glacial-interglacial processes. The results confirm the existence of unique haplo-types and the great interest of the conservation and evolution of Silene ciliata populations from the Huesca Pyrenees., El cambio global es una de las principales amenazas para la biodiversidad a nivel mundial, pero una oportunidad para el estudio de los mecanismos de evolución y adaptación de los organismos ante los cambios. La alta montaña mediterránea, como son los Pirineos, se encuentra entre los ecosistemas más amenazados y su estudio debe ser prioritario debido a la gran cantidad de especies amenazadas y endémicas que alberga. Muchos de estos organismos ya han sobrevivido a cambios climáticos pasados, por lo que su estudio puede arrojar luz sobre el comportamiento futuro de las especies y los mecanismos que desarrollen para adaptarse y evolucionar. Los resultados con-firman la existencia de haplotipos únicos y el gran interés en la conservación y la evolución de las poblaciones de Silene ciliata en los Pirineos de Huesca.

Cycles of Quaternary climatic change are assumed to be major drivers of African rainforest dynamics and evolution. However, most hypotheses on past vegetation dynamics relied on palaeobotanical records, an approach lacking spatial resolution, and on current patterns of species diversity and endemism, an approach confounding history and environmental determinism. In this context, a comparative phylogeographical study of rainforest species represents a complementary approach because Pleistocene climatic fluctuations may have left interpretable signatures in the patterns of genetic diversity within species. Using 1274 plastid DNA sequences from eight tree species (Afrostyrax kamerunensis, A. lepidophyllus, Erythrophleum suaveolens, Greenwayodendron suaveolens, Milicia excelsa, Santiria trimera, Scorodophloeus zenkeri and Symphonia globulifera) sampled in 50 populations of Atlantic Central Africa (ACA), we averaged divergence across species to produce the first map of the region synthesizing genetic distinctiveness and standardized divergence within and among localities. Significant congruence in divergence was detected mostly among five of the eight species and was stronger in the northern ACA. This pattern is compatible with a scenario of past forest fragmentation and recolonization whereby forests from eastern Cameroon and northeastern Gabon would have been more affected by past climatic change than those of western Cameroon (where one or more refugia would have occurred). By contrast, southern ACA (Gabon) displayed low congruence among species that may reflect less drastic past forest fragmentation or a more complex history of vegetation changes. Finally, we also highlight the potential impact of current environmental barriers on spatial genetic structures. © 2014 John Wiley & Sons Ltd., SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

Cycles of Quaternary climatic change are assumed to be major drivers of African rainforest dynamics and evolution. However, most hypotheses on past vegetation dynamics relied on palaeobotanical records, an approach lacking spatial resolution, and on current patterns of species diversity and endemism, an approach confounding history and environmental determinism. In this context, a comparative phylogeographical study of rainforest species represents a complementary approach because Pleistocene climatic fluctuations may have left interpretable signatures in the patterns of genetic diversity within species. Using 1274 plastid DNA sequences from eight tree species (Afrostyrax kamerunensis, A. lepidophyllus, Erythrophleum suaveolens, Greenwayodendron suaveolens, Milicia excelsa, Santiria trimera, Scorodophloeus zenkeri and Symphonia globulifera) sampled in 50 populations of Atlantic Central Africa (ACA), we averaged divergence across species to produce the first map of the region synthesizing genetic distinctiveness and standardized divergence within and among localities. Significant congruence in divergence was detected mostly among five of the eight species and was stronger in the northern ACA. This pattern is compatible with a scenario of past forest fragmentation and recolonization whereby forests from eastern Cameroon and northeastern Gabon would have been more affected by past climatic change than those of western Cameroon (where one or more refugia would have occurred). By contrast, southern ACA (Gabon) displayed low congruence among species that may reflect less drastic past forest fragmentation or a more complex history of vegetation changes. Finally, we also highlight the potential impact of current environmental barriers on spatial genetic structures. © 2014 John Wiley & Sons Ltd.

Cycles of Quaternary climatic change are assumed to be major drivers of African rainforest dynamics and evolution. However, most hypotheses on past vegetation dynamics relied on palaeobotanical records, an approach lacking spatial resolution, and on current patterns of species diversity and endemism, an approach confounding history and environmental determinism. In this context, a comparative phylogeographical study of rainforest species represents a complementary approach because Pleistocene climatic fluctuations may have left interpretable signatures in the patterns of genetic diversity within species. Using 1274 plastid DNA sequences from eight tree species (Afrostyrax kamerunensis, A. lepidophyllus, Erythrophleum suaveolens, Greenwayodendron suaveolens, Milicia excelsa, Santiria trimera, Scorodophloeus zenkeri and Symphonia globulifera) sampled in 50 populations of Atlantic Central Africa (ACA), we averaged divergence across species to produce the first map of the region synthesizing genetic distinctiveness and standardized divergence within and among localities. Significant congruence in divergence was detected mostly among five of the eight species and was stronger in the northern ACA. This pattern is compatible with a scenario of past forest fragmentation and recolonization whereby forests from eastern Cameroon and northeastern Gabon would have been more affected by past climatic change than those of western Cameroon (where one or more refugia would have occurred). By contrast, southern ACA (Gabon) displayed low congruence among species that may reflect less drastic past forest fragmentation or a more complex history of vegetation changes. Finally, we also highlight the potential impact of current environmental barriers on spatial genetic structures. © 2014 John Wiley & Sons Ltd., SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

The 480 species of leafy spurges, Euphorbia subgenus Esula, represent the main temperate radiation in the large genus Euphorbia. This group is distributed primarily in temperate Eurasia, but with smaller, disjunct centres of diversity in the mountains of the Old World tropics, in temperate southern Africa and in the New World. The majority of New World diversity (32 species) occurs in a single section, section Tithymalus . We analysed sequences of the nrITS and plastid ndhF, trnH-psbA, trnS-trnG and trnD-trnT regions to reconstruct the phylogeny of section Tithymalus and to examine the origins and diversification of the species native to the New World. Our results indicate that the New World species of section Tithymalus form a clade that is sister to the widespread, weedy E. peplus. The New World species fall into two primary groups: a ‘northern annual clade’ from eastern North America and a diverse clade of both annual and perennial species that is divided into three subgroups. Within the second group, there is a small ‘southern annual clade’ from Texas and northern Mexico, a perennial ‘Brachycera clade’ from the western United States and northern Mexico, and a perennial ‘ Esuliformis clade’ from montane areas of Mexico, Guatemala, Honduras and the Caribbean island of Hispaniola. Ancestral state reconstructions indicate that the annual habit probably evolved in the ancestor of E. peplus and the New World clade, with a subsequent reversal to the perennial habit. In conjunction with this phylogenetic framework, the New World species of section Tithymalus are comprehensively reviewed.

Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL–trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. Within Eurystachys, although monophyly is supported by both nuclear and plastid data for several named and unnamed groups, the majority of recognized taxa appear to be para- or polyphyletic. The taxon compositions of most subclades are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic placements are often not. This level of plastid–nuclear incongruence suggests considerable impact of hybridization in the evolution of Stachydeae., Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL-trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. Within Eurystachys, although monophyly is supported by both nuclear and plastid data for several named and unnamed groups, the majority of recognized taxa appear to be para- or polyphyletic. The taxon compositions of most subclades are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic placements are often not. This level of plastid-nuclear incongruence suggests considerable impact of hybridization in the evolution of Stachydeae. (C) 2013 Elsevier Inc. All rights reserved.

Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL–trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. Within Eurystachys, although monophyly is supported by both nuclear and plastid data for several named and unnamed groups, the majority of recognized taxa appear to be para- or polyphyletic. The taxon compositions of most subclades are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic placements are often not. This level of plastid–nuclear incongruence suggests considerable impact of hybridization in the evolution of Stachydeae., Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL-trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. Within Eurystachys, although monophyly is supported by both nuclear and plastid data for several named and unnamed groups, the majority of recognized taxa appear to be para- or polyphyletic. The taxon compositions of most subclades are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic placements are often not. This level of plastid-nuclear incongruence suggests considerable impact of hybridization in the evolution of Stachydeae. (C) 2013 Elsevier Inc. All rights reserved.

Taxonomic complexity may be associated with migration history and polyploidy. We used plastid and nuclear DNA markers to investigate the evolutionary history of the systematically challenging Dactylorhiza maculata polyploid complex. A total of 1833 individuals from 298 populations from throughout Europe were analysed. We found that gene flow was limited between the two major taxa, diploid ssp. fuchsii (including ssp. saccifera) and tetraploid ssp. maculata. A minimum of three autotetraploid lineages were discerned: (1) southern/western ssp. maculata; (2) northern/eastern ssp. maculata; and (3) Central European ssp. fuchsii. The two ssp. maculata lineages, which probably pre-date the last glaciation, form a contact zone with high genetic diversity in central Scandinavia. Intermediate plastid haplotypes in the contact zone hint at recombination. Central Europe may have been a source area for the postglacial migration for the southern/western lineage of ssp. maculata, as well as for ssp. fuchsii. The northern/eastern lineage of ssp. maculata may have survived the LGM in central Russia west of the Urals. The tetraploid lineage of ssp. fuchsii is indistinguishable from diploid ssp. fuchsii, and is probably of postglacial origin. The Mediterranean region and the Caucasus have not contributed to the northward migration of either ssp. fuchsii or ssp. maculata.

In its current circumscription, the herbaceous tribe Spermacoceae s.l. (Rubiaceae, Rubioideae) unites the former tribes Spermacoceae s. str., Manettieae, and the Hedyotis–Oldenlandia group. Within Spermacoceae, and particularly within the Hedyotis–Oldenlandia group, the generic delimitations are problematic. Up until now, molecular studies have focused on specific taxonomic problems within the tribe. This study is the first to address phylogenetic relationships within Spermacoceae from a tribal perspective. Sequences of three plastid markers (atpB-rbcL, rps16, and trnL-trnF) were analyzed separately as well as combined using parsimony and Bayesian approaches. Our results support the expanded tribe Spermacoceae as monophyletic. The former tribe Spermacoceae s. str. forms a monophyletic clade nested within the Hedyotis–Oldenlandia group. Several genera formerly recognized within the Hedyotis–Oldenlandia group are supported as monophyletic (Amphiasma Bremek., Arcytophyllum Willd. ex Schult. & Schult. f., Dentella J. R. Forst. & G. Forst., Kadua Cham. & Schltdl., and Phylohydrax Puff), while others appear to be paraphyletic (e.g., Agathisanthemum Klotzsch), biphyletic (Kohautia Cham. & Schltdl.), or polyphyletic (Hedyotis L. and Oldenlandia L. sensu Bremekamp). Morphological investigations of the taxa are ongoing in order to find support for the many new clades and relationships detected. This study provides a phylogenetic hypothesis with broad sampling across the major lineages of Spermacoceae that can be used to guide future species-level and generic studies.

Black cherry (Prunus serotina) is a tree from North America, where it is often used for economical purposes, whereas it is widespread and invasive in Europe. Plastid DNA variation was Wrst investigated in both its native and invasive ranges using microsatellite loci and sequences of three intergenic spacers (trnT-trnL, trnD-trnT and trnS-trnG). This analysis was focused on P. serotina var. serotina, with the inclusion of samples of closely related taxa. Length variation at a microsatellite locus (ccmp5) and a few sequence polymorphisms were identified among P. serotina samples. Four new primer pairs were then designed to specifically amplify variable regions and a combination of five markers was finally proposed for phylogeographic studies in P. serotina. These loci allow identification of six chlorotypes in P. serotina var. serotina, which may be particularly useful to depict the maternal origins of European invasive populations.

Detailed ecological, morphological and molecular analyses were performed in mixed populations of diploid and autotetraploid Dactylorhiza maculata s.l. in Scandinavia. Comparisons were made with pure populations of either diploid ssp. fuchsii or tetraploid ssp. maculata. It was shown that mixed populations are the result of secondary contact between ssp. fuchsii and ssp. maculata. No patterns of recent and local autopolyploidization were found. Morphology and nuclear DNA markers (internal transcribed spacers of nuclear ribosomal DNA) showed that diploids and tetraploids from mixed populations have similar levels of differentiation to diploids and tetraploids from pure populations. Vegetation analyses, as well as analyses of environmental variables, revealed that diploid and tetraploid individuals in mixed populations are ecologically well differentiated on a microhabitat level. Diploids and tetraploids in pure populations have wider ecological amplitudes than they do in mixed populations. Triploid hybrids grew in intermediate microhabitats between diploids and tetraploids in the mixed populations. Plastid DNA markers indicated that both diploids and tetraploids may act as the maternal parent. Based on morphology and nuclear markers triploids are more similar to tetraploids than to diploids. There were indications of introgressive gene flow between ploidy levels. Plastid markers indicated that gene flow from diploid to tetraploid level is most common, but nuclear markers suggested that gene flow in opposite direction also may occur. Similar patterns of differentiation and gene flow appeared in localities that represented contrasting biogeographic regions. Disturbance and topography may explain why hybridization was slightly more common and the differentiation patterns somewhat less clear in the Scandinavian mountains than in the coastal lowland.

Flow cytometry, morphometry and molecular markers [plastid DNA and internal transcribed spacers(ITS) of nuclear ribosomal DNA] were used to determine taxonomic and phylogeographic patterns in Dactylorhiza maculata s.l. from Scandinavia. A total of 238 individuals from 27 populations from throughout all of Scandinavia, including the adjacent Kola Peninsula of Russia, were analyzed. Diploid D. maculata ssp. fuchsii and autotetraploid D. maculata ssp. maculata are morphologically differentiated. Fragment size variants from 10 plastid DNA loci (seven microsatellite loci and three loci with indel variation) were combined to give 43 haplotypes. Three major groups of haplotypes were found. Group I haplotypes were prevalent in the north and the northeast, whereas Group II haplotypes were prevalent in the south and the southwest. Group III was represented by only a single haplotype and appeared to be the result of introgression from D. incarnata s.l. Group I and Group II haplotypes did not correspond with cytologically and morphologically defined D. maculata ssp. fuchsii or D. maculata ssp. maculata. Past introgressive gene flow rather than recent hybridization is envisaged. Intermediate Group I haplotypes between Group II and the rest of Group I were detected in a zone of contact in central Sweden, which may suggest plastid DNA recombination. The six ITS alleles scored showed strong positive correlation with taxonomy. All data sets obtained for ssp. maculata were significantly correlated with geography. Three different autotetraploid lineages are hypothesized. One lineage may represent postglacial immigration from the south and the other two lineages may represent eastern immigration routes. Morphology and ITS data suggested that subarctic populations of ssp. maculata should be recognized as var. kolaensis.

A new nothosubspecies Cirsium × vivantii is described after a molecular and morphological characterization of eight individuals collected in two separate valleys of the French central Pyrenees. Both hypervariable Amplified Fragment Length Polymorphism (AFLP) markers and nuclear rDNA (ITS) and plastid (trnL-F, TRNT-L) DNA sequences were analysed. The profiles of these hybrid samples were compared to those of 43 individuals belonging to their presumed parental taxa C. carniolicum ssp. rufescens and C. palustre. A total of 133 AFLP bands were scored from three primer-pair combinations. All 130 AFLP bands that amplified in the hybrid samples were present in either C. carniolicum ssp. rufescens, C. palustre or both taxa, supporting the participation of these plant genomes in the resulting hybrids. Several Additive Polymorphic Sites (APS) detected in the ITS sequences of the hybrid samples also confirmed their derived origins from ribotypes of the two parental taxa. The lack of exclusive AFLP markers and the nonconcerted evolution of rDNA polymorphisms towards either of the parental ribotypes indicated their recent origin. Plastid trnT-L sequences were used to identify C. palustre as the maternal parent of six of these hybrid individuals; either parent could have acted as the plastid genome donor for the other two individuals. The morphological study revealed that all hybrid individuals were morphologically intermediate between their parents showing largely lobed and less spiny basal leaves as in C. carniolicum ssp. rufescens and decurrent leaf bases and pinkish corollas as in C. palustre.

The aim of this thesis was to investigate and describe different aspects of variation in the Dactylorhiza maculata complex and to relate the variation patterns to underlying biological processes such as Quaternary migration history, hybridization and polyploid evolution. The variation patterns were analysed at various geographic levels using molecular markers (plastid DNA and ITS of nrDNA), cytological data, morphometry and ecological data. A total of c. 2 500 plants from almost 400 populations from throughout Europe were analysed. Dactylorhiza maculata s.l. is the maternal parent of many allotetraploid taxa. It was shown that allotetraploids in Scandinavia belong to several different widespread lineages that probably arose before the last glaciation. A minimum of three autotetraploid lineages were discerned in the D. maculata complex: (i) southern/western ssp. maculata, (ii) northern/eastern ssp. maculata and (iii) Central European ssp. fuchsii. The southern/western and northern/eastern lineages, which probably predate the last glaciation, form a contact zone in central Scandinavia. Measures of genetic diversity therefore reach high values in central Scandinavia. A high frequency of intermediate plastid haplotypes in the contact zone suggests that plastid DNA recombination is occurring there. Source areas for postglacial migration of ssp. maculata may have been Central Europe and parts of central Russia located between the Fennoscandian ice sheet and the Urals. Areas of sheltered topography in Central Europe may have provided suitable habitats for the more thermophilous ssp. fuchsii. A clinal differentiation in genetic markers from the south to the north was observed for ssp. fuchsii (including ssp. saccifera). The tetraploid lineage of ssp. fuchsii is poorly separated from diploid ssp. fuchsii and probably originated during the current postglacial period. The Mediterranean region and the Caucasus have not contributed to northward migration, neither for ssp. fuchsi

Brassica napus complementary deoxyribonucleic acid (cDNA) clones encoding a DNA-binding protein, BnPEND, were isolated by Southwestern screening. A distinctive feature of the protein was a bZIP-like sequence in the amino-terminal portion, which, after expression in Escherichia coli, bound DNA. BnPEND transcripts were present in B. napus roots and flower buds, and to a lesser extent in stems, flowers and young leaves. Treatment in the dark for 72 h markedly increased the amount of BnPEND transcript in leaves of all ages. Sequence comparison showed that BnPEND was similar to a presumed transcription factor from B. napus, GSBF1, a protein deduced from an Arabidopsis thaliana cDNA (BX825084) and the PEND protein from Pisum sativum, believed to anchor the plastid DNA to the envelope early during plastid development. Homology to expressed sequence tag (EST) sequences from additional species suggested that BnPEND homologues are widespread among the angiosperms. Transient expression of BnPEND fused with green fluorescent protein (GFP) in Nicotiana benthamiana epidermal cells showed that BnPEND is a plastid protein, and that the 15 amino acids at the amino-terminal contain information about plastid targeting. Expression of BnPEND in Nicotiana tabacum from the Cauliflower Mosaic Virus 35S promoter gave stable transformants with different extents of white to light-green areas in the leaves, and even albino plants. In the white areas, but not in adjacent green tissue, the development of palisade cells and chloroplasts was disrupted. Our data demonstrate that the BnPEND protein, when over-expressed at an inappropriate stage, functionally blocks the development of plastids and leads to altered leaf anatomy, possibly by preventing the release of plastid DNA from the envelope., QC 20100525