Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae)

BACKGROUND: The temporal origin and diversification of orchids (family Orchidaceae) has been subject to intense debate in the last decade. The description of the first reliable fossil in 2007 enabled a direct calibration of the orchid phylogeny, but little attention has been paid to the potential influence of dating methodology in obtaining reliable age estimates. Moreover, two new orchid fossils described in 2009 have not yet been incorporated in a molecular dating analysis. Here we compare the ages of major orchid clades estimated under two widely used methods, a Bayesian relaxed clock implemented in BEAST and Penalized Likelihood implemented in r8s. We then perform a new family-level analysis by integrating all 3 available fossils and using BEAST. To evaluate how the newly estimated ages may influence the evolutionary interpretation of a species-level phylogeny, we assess divergence times for the South American genus Hoffmannseggella (subfam. Epidendroideae), for which we present an almost complete phylogeny (40 out of 41 species sampled). RESULTS: Our results provide additional support that all extant orchids shared a most recent common ancestor in the Late Cretaceous (approximately 77 million years ago, Ma). However, we estimate the crown age of the five orchid subfamilies to be generally (approximately1-8 Ma) younger than previously calculated under the Penalized Likelihood algorithm and using a single internal fossil calibration. The crown age of Hoffmannseggella is estimated here at approximately 11 Ma, some 3 Ma more recently than estimated under Penalized Likelihood. CONCLUSIONS: Contrary to recent suggestions that orchid diversification began in a period of global warming, our results place the onset of diversification of the largest orchid subfamilies (Orchidoideae and Epidendroideae) in a period of global cooling subsequent to the Early Eocene Climatic Optimum. The diversification of Hoffmannseggella appears even more correlated to late Tertiary climatic fluctuations than previously suggested. With the incorporation of new fossils in the orchid phylogeny and the use of a method that is arguably more adequate given the present data, our results represent the most up-to-date estimate of divergence times in orchids

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies. © Copyright © 2020 Andermann, Torres Jiménez, Matos-Maraví, Batista, Blanco-Pastor, Gustafsson, Kistler, Liberal, Oxelman, Bacon and Antonelli

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies. © Copyright © 2020 Andermann, Torres Jiménez, Matos-Maraví, Batista, Blanco-Pastor, Gustafsson, Kistler, Liberal, Oxelman, Bacon and Antonelli

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies. © Copyright © 2020 Andermann, Torres Jiménez, Matos-Maraví, Batista, Blanco-Pastor, Gustafsson, Kistler, Liberal, Oxelman, Bacon and Antonelli

Speciation in arctic and alpine diploid plants

The main objectives of this thesis are to study patterns and processes of plant speciation in arctic and alpine diploid plants. Cryptic species are here referred to as morphologically similar individuals belonging to the same taxonomic species but that are unable to produce fertile offspring (i.e. 'sibling' species). The arctic flora is considered as one of the most species-poor floras of the world, and the latitudinal gradient with decreasing diversity from low to high latitudes is likely the oldest recognised pattern in ecology. However, these estimates are usually based on morphological differentiation into taxonomically recognizable species and may not provide accurate numbers of biological species. Previous intraspecific crossing experiments in three diploid circumpolar species of Draba (Brassicaceae) revealed the presence of numerous cryptic biological species within each taxonomic species. The present study expands the knowledge based on these previously published results and suggests that frequent formation of cryptic biological species may be a general pattern in the arctic flora. Intraspecific crossing experiments including several distantly related circumpolar diploid plant species revealed that intrinsic postzygotic isolation has developed multiple times, even at small geographical scales. This was shown for all five selfing species investigated, whereas crosses within one outcrossing species generated fully fertile F1 hybrids. This suggests that a selfing mating system may accelerate the accumulation of hybrid incompatibilities. The barriers have in addition developed very rapidly, apparently within a few millennia, suggesting that speciation rates are unexpectedly high in the arctic flora. Cryptic biological species, although not yet recognisable morphologically, are thought to represent starting points for new evolutionary lineages that given sufficient time may develop into full-fledged new taxa. Other factors may thus account for the low diversity of the contemporary arctic flora in terms of taxonomic species. It is likely that high extinction rates rather than low speciation rates have played an important role in shaping the extent diversity in the arctic flora, possibly associated with climatic shifts during the Pleistocene glacial cycles. The genetic mechanisms involved in the build-up of reproductive isolation are of central importance in understanding the evolution of new species. This thesis presents further insights into the mechanisms underlying reproductive isolation in Draba nivalis (Brassicaceae) – a small, circumpolar, predominantly selfing diploid herb that demonstrates numerous cryptic biological speciation events. By performing genetic linkage mapping and searching for quantitative trait loci (QTL) associated with reproductive isolation more knowledge about the mechanisms involved in the evolution of intrinsic postzygotic reproduction in this system has been gathered. The linkage map was produced by combining both codominant and dominant markers and resolved eight linkage groups that most likely correspond to the eight chromosomes of D. nivalis. Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes. In particular, all seed set QTLs and one pollen fertility QTL displayed underdominant effects, matching expectations of chromosomal speciation models. Theory struggles to account for the establishment of large and strongly underdominant chromosomal translocations. Draba nivalis may however be an exception as a selfing mating system, is conducive for the establishment of chromosomal rearrangements through genetic drift. Overall this study confirms that multiple genetic mechanisms are involved in the build-up of reproductive isolation in D. nivalis, suggesting the involvement of both nuclear-nuclear interactions and structural chromosomal changes. As plants are sessile organisms, they depend largely on adapting to locally changing climatic conditions such as temperature, aridity, and day length. Natural selection acting on traits that respond to such changes has likely played an important role in the evolution of plants. Climatic cycles of the Pleistocene caused drastic changes to species’ ranges. For example, the Japanese alpine endemic plant Cardamine nipponica (Brassicaceae) probably diverged into northern and central populations during the Pleistocene climatic oscillations. The northern and central populations present highly diverged alleles of a particular photoreceptor gene phytochrome E (PHYE). Phytochromes such as PHYE monitor the surrounding light environment, and likely play an important role in the regulation of plant life cycles. The present study infers the evolutionary history of the PHYE in C. nipponica and its close relatives using maximum likelihood models. The resulting genealogical relationship suggested that standing genetic variation of PHYE, which diverged under positive selection prior to speciation, resulted in the selective differentiation between the northern and central Japanese populations of C. nipponica. This further suggests the importance of standing genetic variation in regard to quick responses to climatic changes. List of papers. The papers are removed from the thesis due to publisher restrictions. I. A. Lovisa S. Gustafsson, Galina Gussarova, Liv Borgen, Hajime Ikeda, Jan Suda, Loren H. Rieseberg, Christian Brochmann. High speciation rates in arctic plants. Manuscript. II. A. Lovisa S. Gustafsson, Inger Skrede, Heather C. Rowe, Galina Gussarova, Liv Borgen, Loren H. Rieseberg, Christian Brochmann, Christian Parisod. Genetics of cryptic speciation within an arctic mustard, Draba nivalis. Submitted. III. Hajime Ikeda, A. Lovisa S. Gustafsson, Christian Brochmann, Hiroaki Setoguchi. Pre-speciation origin of selective divergence and balancing selection in a plant photoreceptor gene, phytochrome E. Submitted

Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae

Abstract Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general

Divergence in red light responses associated with thermal reversion of phytochrome B between high‐ and low‐latitude species

Summary ・Phytochromes play a central role in mediating adaptive responses to light and temperature throughout plant life cycles. Despite evidence for adaptive importance of natural variation in phytochromes, little information is known about molecular mechanisms that modulate physiological responses of phytochromes in nature. ・We show evolutionary divergence in physiological responses relevant to thermal stability of a physiologically active form of phytochrome (Pfr) between two sister species of Brassicaceae growing at different latitudes. The higher latitude species (Cardamine bellidifolia; Cb) responded more strongly to light‐limited conditions compared with its lower latitude sister (C. nipponica; Cn). Moreover, CbPHYB conferred stronger responses to both light‐limited and warm conditions in the phyB‐deficient mutant of Arabidopsis thaliana than CnPHYB: that is Pfr CbphyB was more stable in nuclei than CnphyB. ・Our findings suggest that fine tuning Pfr stability is a fundamental mechanism for plants to optimise phytochrome‐related traits in their evolution and adapt to spatially varying environments, and open a new avenue to understand molecular mechanisms that fine tune phytochrome responses in nature

Genetics of cryptic speciation within an arctic Mustard, Draba nivalis

Crossing experiments indicate that hybrid sterility barriers frequently have developed within diploid, circumpolar plant species of the genus Draba. To gain insight into the rapid evolution of postzygotic reproductive isolation in this system, we augmented the linkage map of one of these species, D. nivalis, and searched for quantitative trait loci (QTLs) associated with reproductive isolation. The map adds 63 new dominant markers to a previously published dataset of 31 co-dominant microsatellites. These markers include 52 amplified fragment length polymorphisms (AFLPs) and 11 sequence-specific amplified polymorphisms (SSAPs) based on retrotransposon sequence. 22 markers displaying transmission ratio distortion were further included in the map. We resolved eight linkage groups with a total map length of 894 cM. Significant genotype-trait associations, or quantitative trait loci (QTL), were detected for reproductive phenotypes including pollen fertility (4 QTLs), seed set (3 QTLs), flowering time (3 QTLs) and number of flowers (4 QTLs). Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes on these traits. All seed set QTLs and one pollen fertility QTL displayed underdominant effects suggestive of the involvement of chromosomal rearrangements in hybrid sterility. Interestingly, D. nivalis is predominantly self-fertilizing, which may facilitate the establishment of underdominant loci and contribute to reproductive isolation