Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

American Journal of Botany, Год журнала: 2021, Номер 108(7), С. 1059 - 1065

Опубликована: Июль 1, 2021

Язык: Английский

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A New Pipeline for Removing Paralogs in Target Enrichment Data

Systematic Biology, Год журнала: 2021, Номер 71(2), С. 410 - 425

Опубликована: Июнь 13, 2021

Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely pipelines analysis of target data do not have vigorous procedure to remove paralogs in data. In this study, we develop pipeline call Putative Paralogs Detection (PPD) better address putative from The new an add-on the existing HybPiper pipeline, and entire applies criteria both sequence similarity heterozygous sites at each locus identification paralogs. Users may adjust thresholds identity identify according level phylogenetic divergence their group interest. also removes highly polymorphic attributed errors assembly gappy regions alignment. We demonstrated value using empirical generated Hyb-Seq Angiosperms353 kit two woody genera Castanea (Fagaceae, Fagales) Hamamelis (Hamamelidaceae, Saxifragales). Comparisons sets showed PPD identified many more than popular HybPiper. tree topologies times evident differences between our pipeline. further evaluated accuracy error rates by BLAST mapping paralogous orthologous sequences reference genome mollissima. Compared alone, substantially gene mapped multiple (31 genes compared with 4 alone). conjunction HybPiper, can be removed resulting construction robust time analyses. Our study demonstrates derived probe set elucidating species relationships within genus, argues importance additional steps filter poorly aligned (e.g., occur through errors), such described study. [Angiosperms353; Castanea; time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.].

Язык: Английский

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Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae)

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 199, С. 108138 - 108138

Опубликована: Июль 6, 2024

Язык: Английский

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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

Frontiers in Plant Science, Год журнала: 2021, Номер 12

Опубликована: Июнь 23, 2021

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

Язык: Английский

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Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data

Applications in Plant Sciences, Год журнала: 2024, Номер 12(2)

Опубликована: Март 1, 2024

Abstract Premise Digitized biodiversity data offer extensive information; however, obtaining and processing can be daunting. Complexities arise during cleaning, such as identifying removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R‐based Scrubbing (gatoRs). Methods Results The gatoRs workflow includes functions that streamline downloading records from Global Biodiversity Information Facility (GBIF) Integrated Biocollections (iDigBio). We also to clean downloaded specimen Unlike previous packages, accounts for differences in download structure between GBIF iDigBio allows user control via interactive cleaning steps. Conclusions Our pipeline enables scientific community process efficiently is accessible coding novice. anticipate will useful both established beginning users. Furthermore, expect our facilitate introduction of biodiversity‐related concepts into classroom use herbarium specimens.

Язык: Английский

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Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

Applications in Plant Sciences, Год журнала: 2021, Номер 9(7)

Опубликована: Июль 1, 2021

Premise Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm set Angiosperms353 may be the solution. Here, we test relative performance of on Rosaceae subtribe Malinae comparison with custom probes that specifically designed this clade. We then address impact bioinformatically altering by replacing original sequences orthologs extracted from Malus domestica genome. Methods To evaluate these sets, compared efficiency, locus recovery, alignment length, proportion parsimony‐informative sites, potential paralogs, topology support resulting species trees, gene tree discordance. Results Locus recovery was highest our set, a representative improved to Angiosperms353. sites similar between all while discordance lower case probes. Discussion A benefits data completeness can tailored toward specificities project choice; however, equally as phylogenetically informative therefore recommend using both facilitate large‐scale systematic studies, where financially possible.

Язык: Английский

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Phylogeny and Biogeography of Morus (Moraceae)

Agronomy, Год журнала: 2023, Номер 13(8), С. 2021 - 2021

Опубликована: Июль 30, 2023

The mulberry genus, Morus L. (Moraceae), has long been taxonomically difficult, and its species circumscription only defined recently. This genus comprises ca. 16 distributed across Asia the Americas, yet biogeographic history remains poorly understood. In this study, we reconstructed phylogeny explored of using a combination newly generated previously published Hyb-Seq data. Our nuclear recovered three well-supported geographic clades showed that M. notabilis (China) is sister to American clade plus Asian clade. Multiple reticulation events among extensive incomplete lineage sorting (ILS) likely explain difficulties in inferring phylogenetic relationships within genus. Divergence time estimation indicated originated at Eocene–Oligocene boundary, current lineages started diverge during early Miocene, there ambiguity surrounding ancestral area with two most regions being Sino-Himalaya or Americas. Biogeographic inference fossil record suggest might have experienced local extinction Tertiary. expanded distributional range through dispersals from Sino-Himalayan Sino-Japanese Southeast Asia. summary, our new scheme presented here provide an essential foundation for understanding evolutionary Morus.

Язык: Английский

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Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics

Applications in Plant Sciences, Год журнала: 2021, Номер 9(7)

Опубликована: Июль 1, 2021

Target enrichment represents a useful, cost-effective method for researchers working on the phylogenomics of non-model organisms (e.g., Cronn et al., 2012; Hale 2020). The ability to sequence customizable predefined genomic subset several dozens or even hundreds taxa allows in-depth analyses and testing phylogenetic hypotheses in ways that were not previously possible (reviewed McKain 2018). most popular methods targeted sequencing loci include (long-)amplicon (Rothfels 2017) hybridization capture (Mandel 2014; Weitemier 2014). Targeted amplicon is based single-fragment PCR amplification by using multiplexing such as microfluidic PCR-based multiple pre-selected regions Zhang Ozdemir, 2009; Ho 2014), which can then be pooled sequenced. Massively parallel was first used medical diagnostics (Turner 2009) later applied metazoan phylogenetics (Bybee 2011; O'Neill 2013). Microfluidic long-amplicon subsequently plant systematics (Uribe-Convers 2014, 2016; Gostel 2015). Amplicon-based time consuming they require careful optimization validation primers. These are also susceptible many common problems (such nonspecific products, inability amplify large their entirety, simply no products). Recently, approaches have been largely supplanted hybridization-based enrichment, relatively rapid probe design with reference few related transcriptomes genomes, simultaneous efficient recovery genes. via use customized universal probes (short nucleotide fragments between 80 120 bp length, called baits). This versatile powerful approach relies complementary sets targets from whole genome DNA cDNA samples solid-phase in-solution (Gnirke Mamanova 2010; 2012). To account frequent (ancient) duplication events, systematists identify consistently low-to-single-copy markers balance two issues: ensuring across broad range taxa, while containing sufficient informativeness. address specific research questions, including targeting genes metabolic pathway (Gardner Folk 2021) agronomic interest (Witek Soto Gomez 2019). often complete exonic sequences, but non-coding introns untranslated enriched. In-solution depends thermodynamics hybridization. process governed, part, complexity bait length. Longer tolerate more mismatches, making them suitable different species. Higher tiling density (the degree overlap, e.g., 75%) compensate failures hybridize low-quality input material, those stemming historical herbarium specimens, so-called herbariomic (Brewer While overlapping increase chance capturing target neighboring probes, there trade-off, higher tends reduce number examined per kit. nuclear overcomes potential drawbacks estimating phylogenies organelle data alone. single-locus behavior organellar DNAs means only single history provided: entire plastid expected function linkage group (Birky, 2001; see Organellar prone high rates genetic drift small population sizes, could lead less accurate estimate lineage differentiation, compared Wicke Schneeweiss, Although provide gene histories, analysis these requires bioinformatic approaches, assembly sequences without references detection local events violate assumptions orthology. In this regard, community has innovative addressing computational challenges, resulting wide adoption recent years. Angiosperms353 tool enabling phylogenomic-level any angiosperm at scale; associated (Johnson 2019) developed set low-copy infer phylogeny all green plants (One Thousand Plant Transcriptomes Initiative facilitate collection phylogenomic repeatable way. When considering Angiosperms353, it important distinguish orthologous found angiosperms 120-bp enrich libraries. selected copy (ideally, than 1400 available transcriptomes) contain useful signal deep scales. designed ~600 maximize similarity other angiosperms, minimizing design. Distinguishing when advantages, limitations, future directions systematics, discussed below. initial reports utility promising (Dodsworth 2019), key questions remain: (1) Can truly reliably recover groups flowering plants?; (2) Is an angiosperm-wide projects?; (3) What new bioinformatics tools needed apply intractable questions?; (4) Are variable enough within species extend studies? special issue its companion American Journal Botany (Baker 2021b), papers collected demonstrate employing will benefit studies. Applications Sciences focused variety methodological issues, comparisons taxon-specific sets, development lineages, lab technique libraries simultaneously, obtained Low-to-single-copy evolutionary studies Small 2004; Wu 2006; Duarte 2010). identification shared facilitated subsequent high-throughput issue, three application expansion loci. build existing resources lineage-specific (Eserman 2021; Ufimov 2021), generate performance (Siniscalchi investigate efficacy reaction (Hendriks 2021). Eserman al. (2021) describe Orchidaceae963, incorporates 254 loci, tested members subfamilies Orchidaceae. resource systematic work family conservation incorporation along custom marker becoming (Yardeni 2019; Jantzen 2020; Christe Ogutcen allow collaboration teams foster sharing Comparative naturally follow Larridon Shah For example, similar amount parsimony informative sites study Rosaceae subtribe Malinae. They showed allowed improved locus lower levels tree discordance (but Yardeni Siniscalchi Compositae1061 eight sunflower family. able average paralogy trees may simplify downstream latter versus former. Hendriks performed test case combining both (i.e., Brassicaceae) simultaneously 26 Brassicaceae included 16 tribe 10 reflecting broader sampling Their shows little extra cost sample. Taken together, highlight options choosing plants. ready low recovered orthologs taxa. feasibility during suggests additional flexibility. There designs per-sample costs focal group. However, far fewer design, allowing given probes. Whichever choice made, project, meta-analysis parallels single-gene past decades. into molecular genetics paralleled need analytical workflows. One active areas extensions data. specifically tie HybPiper 2016), flanking target-capture reads. A identified assembled Gaynor 2020), unclear whether lies poor DNA) tools). this, McLay files improve mapping frequency reads genes, result independently confirmed Slimp Lee (2021). workflow uses hidden Markov model choose clade-specific database sequences. results indicate divergence nucleic acid forgiving effect same analysis. struggling efficiency solution re-enrich file selecting appropriate Nauheimer HybPhaser, detecting hybrid assemblies. Using Nepenthes, employ two-step strategy representatives clades heterozygosity (and thus presumably hybrids). second step, putative hybrids mapped chosen clade representatives. Differential information phase placed multiply-labeled origins. HybPhaser promise phylogenetics: paralogous builds upon previous paralogs generalizable unsure about target-captured output, calculation within-species demographic parameters. adapts described workflows (Kates 2018) "supercontigs" (targeted coding regions) Within-species variants assessed jointly standard genomics programs (also Beck 2021 Wenzell further populations species, genome-scale estimation parameters now feasible develop methods. Since publication, substantial uptake questions. illustrate generated through extends beyond phylogenomics, applications genomics. Of course, adaptability comes requirement flexible analyze novel already emerging, we recognize some challenges improvements lie ahead. evaluate recovering vitro silico, reflected highlighting distinction them. presented here evidence diversity strong scales ranging level. Several innovations how recovered. Custom still resolution inclusion enable meta-analyses compare enhanced offers enriched illustrates newly complement original set. availability ever-increasing transcriptome massive should refinement better represent length extremely altered lifestyles affect rate evolution, heterotrophic Lam data, accessibility resources. Currently, central repository tailored access way taxon specific. Kew Tree Life Explorer (https://treeoflife.kew.org/) recently launched 2021a) make freely pre- post-publication thousands continued accessible store distribute accelerate progress made far. download repository, rather having filter publication-specific repositories, would significantly incorporate Similarly, centralized uploading annotated life facilitates standardization accessibility. streamlined identifying homologs building collection, much like MarkerMiner (Chamala 2015) provides starting generally cultivate growth methods, seen issue. As people opportunities positive developments further, create solutions paralogs, establishment databases likely addressed head-on embraced community. We thank authors reviewers valuable contributions Sciences. acknowledge tireless APPS publications team, especially Managing Editor Beth Parada Editor-in-Chief Theresa Culley.

Язык: Английский

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A phylogenomic investigation into the biogeography of the Mexico–eastern U.S. disjunction in Symphyotrichum

American Journal of Botany, Год журнала: 2025, Номер unknown

Опубликована: Март 17, 2025

Abstract Premise Biotic disjunctions have attracted scientific attention for the past 200 years. Despite being represented in many familiar plants (such as bald cypress, flowering dogwood, sweetgum, partridgeberry, etc.), eastern North American (ENA)–Mexican (M) disjunction remains poorly understood. Major outstanding questions include divergence times of taxa exhibiting and environmental/geological processes that may underlie disjunction. Symphyotrichum Nees (Asteraceae), one most diverse genera USA, displays several examples disjunct ENA–M taxa. Methods We generated target capture data using Angiosperms353 baitset first well‐sampled phylogenomic hypothesis its close relatives. Focusing on S . subgenus Virgulus , we used MCMC TREE to perform time estimation R package BioGeoBEARS infer ancestral regions biogeographic transitions between America Mexico. Finally, niche reconstruction method Utremi test a role historical aridification generating Results Our molecular suggest recent radiation at Plio‐Pleistocene boundary (~2.5 mya), with early connections Mexico lineages closed off shortly after were followed by vicariance across this region. Except some present‐day broadly distributed species, there is complete lack movement ENA M ~0.5 mya. Conclusions A reconstructed distribution suitable habitat Pleistocene climatic models corroborates results from modeling confirms glacial cycles are more likely be associated breakup connections.

Язык: Английский

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Phylogenomics and diversification drivers of the Eastern Asian – Eastern North American disjunct Podophylloideae

Molecular Phylogenetics and Evolution, Год журнала: 2022, Номер 169, С. 107427 - 107427

Опубликована: Фев. 4, 2022

Язык: Английский

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