The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera

BACKGROUND AND AIMS

Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification.

METHODS

Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios.

KEY RESULTS

The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered.

CONCLUSIONS

Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability.

Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region

Polygonatum is the largest genus of tribe Polygonateae (Asparagaceae) and is widely distributed in the temperate Northern Hemisphere, especially well diversified in southwestern China to northeastern Asia. Phylogenetic relationships of many species are still controversial. Hence it is necessary to clarify their phylogenetic relationships and infer possible reticulate relationships for the genus. In this study, genome-wide data of 43 species from Polygonatum and its closely related taxa were obtained by Hyb-Seq sequencing. The phylogenetic trees constructed from genome-wide nuclear and chloroplast sequences strongly supported the monophyly of Polygonatum with division into three major clades. A high level of incongruence was detected between nuclear and chloroplast trees as well as among gene trees within the genus, but all occurred within each major clade. However, introgression tests and reticulate evolution analyses revealed low level of gene flow and weak introgression events in the genus, suggesting hybridization and introgression were not dominant during the evolutionary diversification of Polygonatum in the Northern Hemisphere. This study provides important insights into reconstructing evolutionary relationships and speciation pattern of taxa from the north temperate flora.

Retrieval of long DNA reads from herbarium specimens

High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.

Target capture and genome skimming for plant diversity studies

Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.

Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens

PREMISE

Polyploidy has become a central factor in plant evolutionary biological research in recent decades. Methods such as flow cytometry have revealed the widespread occurrence of polyploidy; however, its inference relies on expensive lab equipment and is largely restricted to fresh or recently dried material.

METHODS

Here, we assess the applicability of infrared spectroscopy to infer ploidy in two related species of Veronica (Plantaginaceae). Infrared spectroscopy relies on differences in the absorbance of tissues, which could be affected by primary and secondary metabolites related to polyploidy. We sampled 33 living plants from the greenhouse and 74 herbarium specimens with ploidy known through flow cytometrical measurements and analyzed the resulting spectra using discriminant analysis of principal components (DAPC) and neural network (NNET) classifiers.

RESULTS

Living material of both species combined was classified with 70% (DAPC) to 75% (NNET) accuracy, whereas herbarium material was classified with 84% (DAPC) to 85% (NNET) accuracy. Analyzing both species separately resulted in less clear results.

DISCUSSION

Infrared spectroscopy is quite reliable but is not a certain method for assessing intraspecific ploidy level differences in two species of Veronica. More accurate inferences rely on large training data sets and herbarium material. This study demonstrates an important way to expand the field of polyploid research to herbaria.

Relevance of DNA preservation for future botany and ecology

The use of molecular methods in plant systematics and taxonomy has increased during the last decades; however, the accessibility of curated genetic samples and their metadata is a bottleneck for DNA-based genetic studies in botany. Plant biodiversity DNA banks and DNA-friendly collections could be critical suppliers of curated genetic material for researchers in the current context of plant biodiversity loss. Here, we aimed to understand the potential of plant DNA banks and DNA-friendly collections to enhance the growth and openness of scientific knowledge. The preservation of genetic material should become part of a natural collection's process for the generation of extended specimens enabling the preservation of both the phenotype and genotype and contributing to the generation of data networks which cross-fertilize other fields. These curated collections are advantageous in endangered species research, detecting processes related to extinction, giving a genetic dimension to IUCN assessments or completing the Leipzig Catalogue of Vascular Plants. Therefore, DNA collections are fundamental in producing FAIR data, responsible research and innovation (RRI) and meeting the goals of international conservation programmes. The completion of natural collections is important for current research efforts and furthermore vital to support future research in an era of ongoing plant biodiversity loss.

Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources

Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.

New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)

Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1-3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.

PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data

PREMISE

The application of high-throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low-coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb, a bioinformatic pipeline to efficiently assemble phylogenomic data sets derived from genome skimming.

METHODS AND RESULTS

PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences from all three genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/.

CONCLUSIONS

We demonstrate that PhyloHerb can accurately identify genes using a published data set from Clusiaceae. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.

Taming the beast: a revised classification of Cortinariaceae based on genomic data

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 complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.

Green plant genomes: What we know in an era of rapidly expanding opportunities

Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.

A customised target capture sequencing tool for molecular identification of Aloe vera and relatives

Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.

Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here, we used an automated approach for orthology inference in a target enrichment data set of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration and inferring orthologs from target enrichment data, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach, we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here, we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic data sets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment data sets.[Alchemilla; allopolyploidy; autopolyploidy; gene tree discordance; orthology inference; paralogs; Rosaceae; target enrichment; whole genome duplication.].

Mining museums for historical DNA: advances and challenges in museomics

Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

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 understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}) and 2333 genera (17\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]

Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species

Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.

New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels

Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.

High-throughput methods for efficiently building massive phylogenies from natural history collections

PREMISE

Large phylogenetic data sets have often been restricted to small numbers of loci from GenBank, and a vetted sampling-to-sequencing phylogenomic protocol scaling to thousands of species is not yet available. Here, we report a high-throughput collections-based approach that empowers researchers to explore more branches of the tree of life with numerous loci.

METHODS

We developed an integrated Specimen-to-Laboratory Information Management System (SLIMS), connecting sampling and wet lab efforts with progress tracking at each stage. Using unique identifiers encoded in QR codes and a taxonomic database, a research team can sample herbarium specimens, efficiently record the sampling event, and capture specimen images. After sampling in herbaria, images are uploaded to a citizen science platform for metadata generation, and tissue samples are moved through a simple, high-throughput, plate-based herbarium DNA extraction and sequencing protocol.

RESULTS

We applied this sampling-to-sequencing workflow to ~15,000 species, producing for the first time a data set with ~50% taxonomic representation of the "nitrogen-fixing clade" of angiosperms.

DISCUSSION

The approach we present is appropriate at any taxonomic scale and is extensible to other collection types. The widespread use of large-scale sampling strategies repositions herbaria as accessible but largely untapped resources for broad taxonomic sampling with thousands of species.

A target enrichment probe set for resolving the flagellate land plant tree of life

PREMISE

New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms.

METHODS

We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages.

RESULTS

Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.

CONCLUSIONS

A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

A target enrichment probe set for resolving the flagellate land plant tree of life

PREMISE

New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms.

METHODS

We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages.

RESULTS

Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.

CONCLUSIONS

A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality ("greenness") as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.

The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes

Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.]

Phylogenomic relationships and character evolution of the grape family (Vitaceae)

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements' variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.

Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants

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 inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low-cost sequencing in non-model plant systems.

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

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, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.

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.