Inter-and intraspecific variation in fern mating systems after long-distance colonization: the importance of selfing

<p>Abstract</p> <p>Background</p> <p>Previous studies on the reproductive biology of ferns showed that mating strategies vary among species, and that polyploid species often show higher capacity for self-fertilization than diploid species. However, the amount of intraspecific variation in mating strategy and selfing capacity has only been assessed for a few species. Yet, such variation may have important consequences during colonization, as the establishment of any selfing genotypes may be favoured after long-distance dispersal (an idea known as Baker's law).</p> <p>Results</p> <p>We examined intra-and interspecific variation in potential for self-fertilization among four rare fern species, of which two were diploids and two were tetraploids: <it>Asplenium scolopendrium </it>(2n), <it>Asplenium trichomanes </it>subsp. <it>quadrivalens </it>(4n), <it>Polystichum setiferum </it>(2n) and <it>Polystichum aculeatum </it>(4n). Sporophyte production was tested at different levels of inbreeding, by culturing gametophytes in isolation, as well as in paired cultures with a genetically different gametophyte. We tested gametophytes derived from various genetically different sporophytes from populations in a recently planted forest colonized through long-distance dispersal (Kuinderbos, the Netherlands), as well as from older, less disjunct populations.</p> <p>Sporophyte production in isolation was high for Kuinderbos genotypes of all four species. Selfing capacity did not differ significantly between diploids and polyploids, nor between species in general. Rather selfing capacity differed between genotypes within species. Intraspecific variation in mating system was found in all four species. In two species one genotype from the Kuinderbos showed enhanced sporophyte production in paired cultures. For the other species, including a renowned out crosser, selfing capacity was consistently high.</p> <p>Conclusions</p> <p>Our results for four different species suggest that intraspecific variation in mating system may be common, at least among temperate calcicole ferns, and that genotypes with high selfing capacity may be present among polyploid as well as diploid ferns. The surprisingly high selfing capacity of all genotypes obtained from the Kuinderbos populations might be due to the isolated position of these populations. These populations may have established through single-spore colonization, which is only possible for genotypes capable of self-fertilization. Our results therewith support the idea that selection for selfing genotypes may occur during long-distance colonization, even in normally outcrossing, diploid ferns.</p

Classification of a large and widespread genus of Neotropical trees, Guatteria (Annonaceae) and its three satellite genera Guatteriella, Guatteriopsis and Heteropetalum

Guotteria (Annonaceae) is with ca. 265 species one of the largest genera of Neotropical trees together with Inga and 0coteo. Use of Guatterici in evolutionary studies has been hampered by taxonomic problems caused by lack of morphological variability in the genus. This study focuses on molecular phylogenetic relationships within Gucitterici and its satellites Guatteriopsis, Gualleriella and Heteropetalum, and implications of these relationships for classification and character evolution. Results show that Guatteriopsis, Guatteriellci and Heteropetaluin should be merged with Guatteria. Heteropetoluin may be recognized at subgeneric level because of its aberrant morphology and Gucaleriol-)sis and Gualleriella might be given sectional status. Most of the currently recognised sections in Guatteria are probably non-monophyletic. A completely new infrageneric classification of Gacitteria would be premature, however, due to the lack of molecular and morphological synapornorphies to define the sections. Synapomorphies defining Guatteria s.str. probably evolved after divergence of several early branching lineages

Editorial

Several recent studies have suggested that a substantial portion of today’s plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than vicariance, but more data are needed to substantiate this claim. Guatteria (Annonaceae) is, with 265 species, the third largest genus of Neotropical trees after Inga (Fabaceae) and Ocotea (Lauraceae), and its widespread distribution and frequent occurrence makes the genus an excellent model taxon to study diversification patterns. This study reconstructed the phylogeny of Guatteria and inferred three major biogeographical events in the history of the genus: (1) a trans-oceanic Miocene migration from Central into South America before the closing of the Isthmus of Panama; (2) a major diversification of the lineage within South America; and (3) several migrations of South American lineages back into Central America via the closed Panamanian land bridge. Therefore, Guatteria is not an Amazonian centred-genus sensu Gentry but a major Miocene diversification that followed its dispersal into South America. This study provides further evidence that migration into the Neotropics was an important factor in the historical assembly of its biodiversity. Furthermore, it is shown that phylogenetic patterns are comparable to those found in Ocotea and Inga and that a closer comparison of these genera is desirable

Early evolutionary history of the flowering plant family Annonaceae : steady diversification and boreotropical geodispersal

Aim : Rain forest-restricted plant families show disjunct distributions between the three major tropical regions: South America, Africa and Asia. Explaining these disjunctions has become an important challenge in biogeography. The pantropical plant family Annonaceae is used to test hypotheses that might explain diversification and distribution patterns in tropical biota: the museum hypothesis (low extinction leading to steady accumulation of species); and dispersal between Africa and Asia via Indian rafting versus boreotropical geodispersal. Location : Tropics and boreotropics. Methods : Molecular age estimates were calculated using a Bayesian approach based on 83% generic sampling representing all major lineages within the family, seven chloroplast markers and two fossil calibrations. An analysis of diversification was carried out, which included lineage-through-time (LTT) plots and the calculation of diversification rates for genera and major clades. Ancestral areas were reconstructed using a maximum likelihood approach that implements the dispersal-extinction-cladogenesis model. Results : The LTT plots indicated a constant overall rate of diversification with low extinction rates for the family during the first 80 Ma of its existence. The highest diversification rates were inferred for several young genera such as Desmopsis, Uvariopsis and Unonopsis. A boreotropical migration route was supported over Indian rafting as the best fitting hypothesis to explain present-day distribution patterns within the family. Main conclusions : Early diversification within Annonaceae fits the hypothesis of a museum model of tropical diversification, with an overall steady increase in lineages possibly due to low extinction rates. The present-day distribution of species within the two largest clades of Annonaceae is the result of two contrasting biogeographic histories. The 'long-branch clade' has been diversifying since the beginning of the Cenozoic and underwent numerous geodispersals via the boreotropics and several more recent long-distance dispersal events. In contrast, the 'short-branch clade' dispersed once into Asia via the boreotropics during the Early Miocene and further dispersal was limited

Los tesoros genómicos: secuenciación completa del genoma de especímenes de herbario e insectos del museo

Desbloquear la vasta diversidad genómica almacenada en las colecciones de historia natural crearía oportunidades sin precedentes para estudios evolutivos, filogenéticos, de domesticación y genómicos de poblaciones a escala genómica. Se ha desalentado a muchos investigadores de utilizar muestras históricas en estudios moleculares debido tanto al éxito generalmente limitado de la extracción de ADN como a los desafíos asociados con la amplificación por PCR de ADN altamente degradado. En el mundo actual de la secuenciación de próxima generación (NGS), las oportunidades y las perspectivas del ADN histórico han cambiado drásticamente, ya que la mayoría de los métodos NGS están diseñados para tomar moléculas de ADN fragmentadas cortas como plantillas. Aquí mostramos que utilizando un enfoque de secuenciación de Illumina multiplex estándar y de extremo emparejado, los datos de secuencia a escala del genoma se pueden generar de manera confiable a partir de una planta preservada en seco, especímenes de hongos e insectos recolectados hasta hace 115 años, y con un mínimo de muestreo destructivo. Usando un enfoque de ensamblaje basado en referencias, pudimos producir el genoma nuclear completo de una persona de 43 añosEspécimen de herbario de Arabidopsis thaliana (Brassicaceae) con cobertura de secuencia alta y uniforme. Se generaron secuencias del genoma nuclear de tres especímenes de hongos de 22 a 82 años de edad ( Agaricus bisporus , Laccaria bicolor , Pleurotus ostreatus ) con una cobertura del exoma del 81,4 al 97,9%. Se ensamblaron secuencias genómicas orgánicas completas para todas las muestras. Utilizando el ensamblaje de novo , recuperamos entre el 16,2% y el 71,0% de las regiones de secuencia de codificación y, por tanto, permanecemos algo cautelosos sobre las perspectivas de de novoensamblaje del genoma a partir de especímenes históricos. Se observaron contaminaciones de secuencias no objetivo en 2 de nuestras muestras de insectos del museo. Anticipamos que los proyectos futuros de genómica de museos quizás no generarán secuencias genómicas completas en todos los casos (nuestros especímenes contenían genomas relativamente pequeños y de baja complejidad), pero al menos generarán datos genómicos comparativos vitales para probar (filo) hipótesis genéticas, demográficas y genéticas, que se vuelven cada vez más horizontales. Además, la NGS de ADN histórico permite recuperar información genética crucial de especímenes de tipo antiguo que hasta la fecha no se han utilizado en su mayoría y, por lo tanto, también abre una nueva frontera para la investigación taxonómica.Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today’s next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well

Los tesoros genómicos: secuenciación completa del genoma de especímenes de herbario e insectos del museo

Desbloquear la vasta diversidad genómica almacenada en las colecciones de historia natural crearía oportunidades sin precedentes para estudios evolutivos, filogenéticos, de domesticación y genómicos de poblaciones a escala genómica. Se ha desalentado a muchos investigadores de utilizar muestras históricas en estudios moleculares debido tanto al éxito generalmente limitado de la extracción de ADN como a los desafíos asociados con la amplificación por PCR de ADN altamente degradado. En el mundo actual de la secuenciación de próxima generación (NGS), las oportunidades y las perspectivas del ADN histórico han cambiado drásticamente, ya que la mayoría de los métodos NGS están diseñados para tomar moléculas de ADN fragmentadas cortas como plantillas. Aquí mostramos que utilizando un enfoque de secuenciación de Illumina multiplex estándar y de extremo emparejado, los datos de secuencia a escala del genoma se pueden generar de manera confiable a partir de una planta preservada en seco, especímenes de hongos e insectos recolectados hasta hace 115 años, y con un mínimo de muestreo destructivo. Usando un enfoque de ensamblaje basado en referencias, pudimos producir el genoma nuclear completo de una persona de 43 añosEspécimen de herbario de Arabidopsis thaliana (Brassicaceae) con cobertura de secuencia alta y uniforme. Se generaron secuencias del genoma nuclear de tres especímenes de hongos de 22 a 82 años de edad ( Agaricus bisporus , Laccaria bicolor , Pleurotus ostreatus ) con una cobertura del exoma del 81,4 al 97,9%. Se ensamblaron secuencias genómicas orgánicas completas para todas las muestras. Utilizando el ensamblaje de novo , recuperamos entre el 16,2% y el 71,0% de las regiones de secuencia de codificación y, por tanto, permanecemos algo cautelosos sobre las perspectivas de de novoensamblaje del genoma a partir de especímenes históricos. Se observaron contaminaciones de secuencias no objetivo en 2 de nuestras muestras de insectos del museo. Anticipamos que los proyectos futuros de genómica de museos quizás no generarán secuencias genómicas completas en todos los casos (nuestros especímenes contenían genomas relativamente pequeños y de baja complejidad), pero al menos generarán datos genómicos comparativos vitales para probar (filo) hipótesis genéticas, demográficas y genéticas, que se vuelven cada vez más horizontales. Además, la NGS de ADN histórico permite recuperar información genética crucial de especímenes de tipo antiguo que hasta la fecha no se han utilizado en su mayoría y, por lo tanto, también abre una nueva frontera para la investigación taxonómica.Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today’s next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well

Probing molecular choreography through single-molecule biochemistry

Single-molecule approaches are having a dramatic impact on views of how proteins work. The ability to observe molecular properties at the single-molecule level allows characterization of subpopulations and acquisition of detailed kinetic information that would otherwise be hidden in the averaging over an ensemble of molecules. In this Perspective, we discuss how such approaches have successfully been applied to in vitro-reconstituted systems of increasing complexity

Phylogenomics and the rise of the angiosperms.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade