Lisa Pokorny

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Verified

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• PhD in Biology
• Ramón y Cajal Researcher at Real Jardín Botánico

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe...

With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia – the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands – represents an ideal natural experiment in plant biogeography. However, scattere...

The reduced cost of high‐throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per‐sample cost, which can be i...

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 foundation...

Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in...

Cannabis has provided important and versatile services to humans for millennia. Domestication and subsequent dispersal have resulted in various landraces and cultivars. Unravelling the phylogeography of this genus poses considerable challenges due to its complex history. We relied on a Hyb-Seq approach (combining target capture with shotgun sequenc...

The daisy tribe Anthemideae Cass. is one of the largest and most diverse tribes within Asteraceae. We analyzed a data set including 61 out of 111 Anthemideae genera, and all but four of the 19 currently recognized subtribes (Inulantherinae, Lapidophorinae, Lonadinae, and Vogtiinae) using a targeted high-throughput sequencing approach, the first foc...

Presentation and update of PHYLOPYR project. More info: https://youtu.be/GUU3kvRFK_w

Poster presentations 630 the endosperm (nourishing tissue in the seeds) often leads to triploid inviability, known as the triploid block, especially in inter-ploidy crosses between diploids and their tetraploid descendants. This phenomenon is frequently observed in mixed-ploidy plants. While the mechanistic basis of the triploid block has been docu...

Vascular plants are exceptional among eukaryotes due to their outstanding genome size diversity which ranges ∼2,400-fold, including the largest genome so far recorded in the angiosperm Paris japonica (148.89 Gbp/1C). Despite available data showing that giant genomes are restricted across the Tree of Life, the biological limits to genome size expans...

Poster presenting the project PHYLOPYR at the 4th Syposium of the Spanish Botanic Society (SEBOT), hosted in León, 2023

PHYLOPYR proiektuak Pirinioetan erregistratutako loredun landare espezie guztien (3600 inguru) Bizi Zuhaitza berreraiki nahi du.

Whole genome duplications (WGD) are frequent in many plant lineages; however, ploidy level variation is unknown in most species. The most widely used methods to estimate ploidy levels in plants are chromosome counts, which require living specimens, and flow cytometry estimates, which necessitate living or relatively recently collected samples. Newl...

Giant genomes are rare across the plant kingdom and their study has focused almost exclusively on angiosperms and gymnosperms. The scarce genetic data that are available for ferns, however, indicate differences in their genome organization and a lower dynamism compared to other plant groups. Tmesipteris is a small genus of mainly epiphytic ferns th...

With c. 24 700 species (10% of all flowering plants), Asteraceae are one of the largest and most phenotypically diverse angiosperm families, with considerable economic and ecological importance. Asteraceae are distributed worldwide, from nearly polar latitudes all the way to the tropics, and occur across a diverse range of habitats from extreme des...

Indigenous peoples are important stewards of biodiversity, often living near and possessing intimate knowledge of ecosystems. As a result, species new to science may be long known to indigenous people. While the scientific endeavor has long benefitted from indigenous knowledge, it has usually not engaged with it on equal footing. While Linnaean tax...

Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its...

Premise To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. Methods We combined high-throug...

In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set, and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.

Premise: Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with othe...

PREMISE: Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several altern...

Premise: Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae an...

PREMISE: Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specifi...

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our under...

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology because of their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including m...

Wide‐range geographically discontinuous distributions have long intrigued scientists. We explore the role of ecology, geology, and dispersal in the formation of these large‐scale disjunctions, using the angiosperm tribe Putorieae (Rubiaceae) as a case study. From DNA sequences of nuclear ITS and six plastid markers, we inferred a phylogeny with 65%...

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our under...

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectie...

Morphological characterizations of genera in Cyperaceae tribe Abildgaardieae have been highly problematic and the subject of much debate. Earlier molecular phylogenetic studies based on Sanger sequencing and a limited sampling have indicated that several generic circumscriptions are not monophyletic. Here, we provide the first phylogenetic hypothes...

Editorial on the Research Topic Phylogenomic Approaches to Deal With Particularly Challenging Plant Lineages

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a...

Premise: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. Method...

Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida),...

The world’s herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of s...

High-throughput DNA sequencing (HTS) presents great opportunities for plant systematics, yet genomic complexity needs to be reduced for HTS to be effectively applied. We highlight Hyb-Seq as a promising approach, especially in light of the recent development of probes enriching 353 low-copy nuclear genes from any flowering plant taxon

Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increas...

Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low‐ to single‐copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and close...

Reconstructing phylogenetic relationships at the micro‐ and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large he...

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost associated with developing targeted sequencing approaches is preliminary data needed for identifying orthologous loci for probe design. In plants, identifying...

Providing science and society with an integrated, up‐to‐date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward du...

The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii t...

Varias especies vegetales emparentadas entre sí habitan lados opuestos del continente africano, aisladas unas de otras. El origen de esta distribución peculiar, denominada Rand Flora, intriga desde hace tiempo a los botánicos

Significance Colonization of land by plants was a critical event for the emergence of extant ecosystems. The innovations that allowed the algal ancestor of land plants to succeed in such a transition remain unknown. Beneficial interaction with symbiotic fungi has been proposed as one of these innovations. Here we show that the genes required for th...

• Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern ph...

The Rand Flora is a well-known floristic pattern in which unrelated plant lineages show similar disjunct distributions in the continental margins of Africa and adjacent islands—Macaronesia-northwest Africa, Horn of Africa-Southern Arabia, Eastern Africa, and Southern Africa. These lineages are now separated by environmental barriers such as the ari...

Here, we investigate the evolutionary origin and timing of the Rand Flora pattern —a continent-wide geographic pattern where taxa present extreme disjunctions and are found on, e.g., either side of the Sahara— since the Late Miocene until now. Using phylogenetic inference, we dated the disjunction of major Rand flora lineages and quantified their c...

Transoceanic distributions have attracted the interest of scientists for centuries. Less attention has been paid to the evolutionary origins of "continent-wide" disjunctions, in which related taxa are distributed across isolated regions within the same continent. A prime example is the "Rand Flora" pattern, which shows sister-taxa disjunctly distri...

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances inmolecular systematics, some hypotheses of relationships remain weakly resol...

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how t...

Significance Despite being one of the oldest groups of land plants, the majority of living ferns resulted from a relatively recent diversification following the rise of angiosperms. To exploit fully the new habitats created by angiosperm-dominated ecosystems, ferns had to evolve novel adaptive strategies to cope with the low-light conditions exerte...

The Rand flora is a disjunct floristic pattern relating semiarid and subtropical floras between Macaronesia and East Africa. One of the best examples is the bellflower genus Canarina, comprising one species in the Canary Islands (C. canariensis), and two other species endemic to the Afromontane region of East Africa (C. eminii and C. abyssinica). T...

Phylogenetic relationships in Daltoniaceae (~200 species in 14 genera) are inferred from nucleotide sequences from five genes, representing all genomic compartments, using parsimony, likelihood and Bayesian methods. Alternative classifications for Daltoniaceae have favoured traits from either sporophytes or gametophytes; phylogenetic transitions in...

The Hypnales are the largest order of mosses comprising approximately 4200 species. Phylogenetic reconstruction within the group has proven to be difficult due to rapid radiation at an early stage of evolution and, consequently, relationships among clades have remained poorly resolved. We compiled data from four sequence regions, namely, nuclear IT...

We present a list of ferns, lichens, mosses, and liverworts collected in the eastern UAE and northern Oman in January 2009. Of the seven fern species reported, Cosentinia vellea is confirmed for the UAE and Asplenium ceterach is reported for Oman for the second time. We briefly summarise the taxonomic and nomenclatural reasons for using the names A...

To better understand biogeographic patterns in the Southern Hemisphere, infraspecific molecular patterns were compared in two species of the moss genus Calyptrochaeta with contrasting distributions. One, C. apiculata, has a disjunct distribution encompassing South America and Australasia, and the other, C. asplenioides, occurs from South Africa nor...

Allopolyploidy is probably the most extensively studied mode of plant speciation and allopolyploid species appear to be common in the mosses (Bryophyta). The Sphagnum subsecundum complex includes species known to be gametophytically haploid or diploid, and it has been proposed that the diploids (i.e., with tetraploid sporophytes) are allopolyploids...

129 musgos y 28 hepáticas integran el catálogo resultante de las recolecciones de los miembros de la Sociedad Española de Briología participantes en la XVIII Reunión de Briología efectuada en la Sierra de Gredos. 129 mosses and 28 liverworts were collected in the Sierra de Gredos by members of the Sociedad Española de Briología during the 18th Meet...

Se presenta el catálogo de las hepáticas (Marchantiophyta) de Cantabria, incluyendo información de la bibliografía y adiciones propias. En total, se han registrado 135 taxones. The catalogue of the liverworts of Cantabria (Marchantiophyta) is offered, it includes literature records and new additions. In all, 135 taxa have been recorded.

The bryophyte flora of Trento has been studied based on an extensive sampling. To standardize the harvesting, the city has been divided into 5 zones and 12 habitats, depending on the human impact, the substratum nature and moisture state. At least 10 samples of 20 x 20 cm have been collected in all available habitats in each zone. As a result, 136...

Se aportan 49 primeras citas (1 antocerota, 16 hepáticas y 32 musgos) y 11 segundas citas (1 hepática y 10 musgos) para Toledo, una de las provincias españolas menos conocida desde el punto de vista briológico. De ellas, son destacables Atrichum angustatum, Diplophyllum albicans, Frullania tamarisci, Heterocladium heteropterum, Hookeria lucens, Hyo...