Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists

Trends in Ecology & Evolution, Journal Year: 2017, Volume and Issue: 32(4), P. 258 - 267

Published: Feb. 16, 2017

Key research questions are defined to foster closer collaboration between systematists, ecologists, and evolutionary biologists working in tropical forests. Long-term plots proposed as a focus of such collaborative studies. Addressing the will require significant shift how both individuals institutions operate collection curation botanical specimens. Closer among forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With key unifying theme importance vouchered precise identification species, especially rare ones, we identify four priority areas where improving links these communities could achieve progress biodiversity conservation science: (i) increasing pace species discovery; (ii) documenting turnover across space time; (iii) models ecosystem change; (iv) understanding assembly biomes. Systematics (see Glossary) ecology tropics each has distinguished heritage, but there bottlenecks fields: systematics, slow discovery description, difficulty ensuring consistent accurate determinations study sites. These problems prevent addressing some most pressing science, diversity is distributed space, it changes over time, contributes resilience ecosystems global change. Here present question-driven justification bringing together, complement recent work that argued specimen archiving [1Ward D.F. et al.More from ecologists support natural history museums.Trends Ecol. Evol. 2015; 30: 373-374Abstract Full Text PDF PubMed Scopus (15) Google Scholar, 2Schilthuizen M. al.Specimens primary data: museums 'open science'.Trends 237-238Abstract (48) Scholar] or highlighted with identifications existing collections [3Goodwin Z.A. al.Widespread mistaken identity plant collections.Curr. Biol. 25: R1066-R1067Abstract (135) Scholar]. The discuss below fall into two categories. Our first question relates taxonomy: completing formal description tree By contrast, answering final three ecological depends solving issues identification. Achieving consistent, precise, forest sites been greatly facilitated by an number field guides, local floras, annotated checklists, taxonomic revisions, monographs (e.g., [4Ribeiro J.E.L.d.S. al.Flora da Reserva Ducke. INPA-DFID, 1999Google Scholar]). In particular, availability automated online tools standardise spellings catalogue synonyms plants major step forward datasets large comparative analyses [5Boyle B. al.The name resolution service: tool standardization names.BMC Bioinformatic. 2013; 14: 16Crossref (301) However, standardising spelling nomenclature does not address assumption correct Uniform unlikely case many species-rich clades tree, even committed effort community, because identification, sterile vouchers, can challenging (Box 1). This problem limits our capacity make reliable links, based names, phylogenetic, functional trait, inventory required large-scale analyses. Overall, broad aim suggest solution requires individual researchers collections-based operate. We concentrate they have monitoring high richness means conservation. arguments also apply more broadly other biomes taxa, diverse poorly known grass flora savannah ecosystems, taxonomically complex groups temperate evergreen insect diversity.Box 1Evaluating Identification Success Complex Groups Tropical TreesConsistent maintain dispersed networks forests time space. related variation knowledge botanists different regions at times, new taxonomies published concurrently. Abundant, widespread likely identified successfully, particularly if possess distinctive vegetative features facilitate five ten abundant found RAINFOR plot network Amazonia arboreal palms [57Fauset S. al.Hyperdominance Amazonian carbon cycling.Nat. Commun. 6: 6857Crossref (183) Scholar], which readily field). rarer taxa particular challenges, lack diagnostic morphological characters. few examine whether 'difficult' vary determination current appropriately applied [19Dexter K.G. al.Using DNA assess errors identifications: often wrong when matter?.Ecol. Monogr. 2010; 80: 267-286Crossref (70) used image library hosted ForestPlots.net [54Lopez-Gonzalez G. al.ForestPlots.net: web application manage analyse data.J. Veg. Sci. 2011; 22: 610-613Crossref (141) western explore uncertainties eight trees difficulties identification: Andira, Apuleia, Inga, Parkia, Platymiscium, Poeppigia, Protium, Tachigali.Specialists group assessed accuracy had made genera 18 60 during past 30 years. total, 452 were examined species-level incorrect voucher images. originally 77 species. results encouraging: difficult very rare, 75% correctly (Figure I). lineages clearly greater than others: Andira Tachigali, approximately 50% apparently misidentified Successful frequency Rather, achieving levels idiosyncratic. Undoubtedly, groups, material Tachigali). For might reflect all occur extremely low density therefore unfamiliar Andira). cases, relative success depend systematists transfer this Inga). Consistent Tachigali. Specialists It embarrassment estimates rest extrapolations [6ter Steege H. flora.Science. 342: 1243092Crossref (772) Forest inventories contain c. 5000 ≥10 cm diameter total ∼11 600 collected date region [7ter updated checklist taxa.Sci. Rep. 2016; 29549Crossref (102) data 16 000 estimated ∼5000 await discovery. proportion undescribed neotropical rain 20–40% science [8Maas P.J.M. al.Confronting nightmare: revision genus Guatteria (Annonaceae).Blumea. 60: 1-219Crossref (24) 9Pennington R. A monograph (Leguminosae–Papilionoideae).Syst. Bot. 2003; 64: 145Crossref 10Klitgård B.B. Platymiscium (Leguminosae: Dalbergieae): biogeography, morphology, taxonomy uses.Kew Bull. 2005; 321-400Google While surprisingly Drypetes gentryana [11Vasquez Una nueva especia de Vahl (Putranjivaceae) del Perú.Arnoldoa. 2014; 21 (in Spanish): 9-24Google Brownea jaramilloi [12Pérez A.J. al.Brownea Caesalpinioideae), new, over-looked endemic Ecuadorian Amazon.Kew 2012; 68: 157-162Crossref (5) Scholar]; Box 2), cases population sizes small: ter al. estimate 62% collectively comprise only 0.12% Amazon.Box 2Using Networks Long-Term Monitoring Sites Increase Taxonomic KnowledgeThere several examples value closely linking increase example, Jenaro Herrera Research Centre Peru, – one 9-ha arboretum upland 6-ha seasonally flooded established since 1980s. subsequent decades, numerous specimens repeated resulted 26 (Table 1 Figure II) (E. Honorio, MSc thesis, University Edinburgh, 2006). descriptions archived herbaria internationally, them widely accessible community. similar example comes part fragmentation project near Manaus, Brazil, specialist potential Sapotaceae vouchers early 1990s. responsible revisited annually finally flowers fruit decade, resulting publication 10 [58Pennington T.D. Flora Ducke, Amazonas, Brasil: Sapotaceae.Rodriguésia. 2006; 57: 251-366Crossref (26) Scholar].Table 1The New Species Tree Described Using Herbarium Vouchers Collected Herrera, PeruFamilySpeciesType citationAnacardiaceaeThyrsodium herrerense Encarn.60Encarnacion F. Thyrsodium Encarnación, especie Anacardiaceae departamento Loreto, Perú. Contribución al estudio la y vegetación Peruana. VI.Candollea. 1984; 39 1-4Google ScholarAnnonaceaeKlarobelia inundata ChatrouL.W. Chatrou, PhD Utrecht University, 1998AraliaceaeSchefflera megacarpa A.H. Gentry61Gentry combination Palmae, Theaceae, Araliaceae, Apocynaceae, Bignoniaceae Choco Peru.Ann. Mo. Gard. 1981; 112-121Crossref ScholarArecaceaeOenocarpus balickii Kahn62Kahn Las palmeras Arborétum (Provincia Requena, Departamento Perú). Amazonía XVII.Candollea. 1990; 45 341-362Google ScholarCalophyllaceaeHaploclathra cordata Vásquez63Vásquez Haploclathra (Clusiaceae) Peruana.Novon. 1993; 3 499-501Crossref ScholarCaryocaraceaeCaryocar harlingii Prance & Encarn.64Prance G.T. An update distribution Caryocaraceae: actualización sobre taxonomía distribución las Caryocaraceae.Opera 1987; 92: 179-184Google ScholarEbenaceaeDiospyros nanay Walln.65Wallnöfer Neue Diospyros-Arten (Ebenaceae) aus Südamerika.Ann. Nat. Hist. Mus. Wien Ser. B Zool. 1999; 101 German): 565-592Google ScholarHumiriaceaeVantanea spichigeri Gentry66Gentry A. Vantanea (Humiriaceae) Peru. Contribution vegetation Peruvian Amazonia: 20.Candollea. 45: 379-380Google ScholarLauraceaeEndlicheria argentea Chanderb.67Chanderbali A.S. Endlicheria (Lauraceae). Neotropica Monograph 91. York Botanic Garden, 2004Google citriodora van der Werff68van Werff Lauraceae Ecuador 1991; 78: 409-423Crossref ScholarLauraceaeMezilaurus opaca Kubitzki Werff69Van Der Mezilaurus (Lauraceae).Ann. 74: 153-182Crossref ScholarLauraceaeOcotea immersa Werff70van Vicentini central Amazonia, Brazil.Novon. 2000; 10: 264-297Crossref (12) ScholarLauraceaePleurothyrium acuminatum Werff71van Pleurothyrium 39-118Crossref ScholarMagnoliaceaeTalauma rimachiiaThis now basionym Magnolia rimachii (Lozano) Govaerts. Lozano72Lozano Contreras Dugandiodendron Talauma (Magnoliaceae) en el Neotrópico.Academia Colombiana Ciencias Exactas, Físicas, Naturales. 1994; Spanish)Google ScholarMelastomataceaeMiconia Wurdack73Wurdack J.J. Miconia P. (Melastomataceae) Peru.Candollea. 1989; 44: 517-519Google ScholarMelastomataceaeVotomita pubescens Morley74Morley T. Five World Memecyleae (Melastomataceae).Ann. 1985; 72: 548-557Crossref ScholarMeliaceaeCarapa vasquezii Kenfack75Kenfack D. Carapa (Meliaceae), Amazonia.Brittonia. 63: 7-10Crossref (4) ScholarMeliaceaeTrichilia tenuifructa Penn.76Pennington Clarkson American Trichilia (Meliaceae).Phytotaxa. 259: 1-2Crossref ScholarMoraceaeNaucleopsis herrerensis C.C. Berg77Berg Rosselli P.F. combinations Moraceae Cecropiaceae Central South America.Novon. 1996; 230-252Crossref (6) ScholarOchnaceaeFroesia diffusa Gereau Vásquez78Gereau R.E. Vasquez Froesia (Quiinaceae) Amazónia occidental.Novon. 4 246-249Crossref (3) ScholarOchnaceaeQuiina attenuata J.V. Schneid. Zizka79Schneider Zizka novelties Quiina Aubl (Quiinaceae).Candollea. 58: 461-471Google ScholarPrimulaceaeCybianthus Pipoly80Pipoly J. Cybianthus subgenus Conomorpha (Myrsinaceae) 46: 41-45Google ScholarRubiaceaePlatycarpum loretensis N. Dávila Kin.-Gouv.81Dávila Kinoshita L.S. Platycarpum (Rubiaceae, Henriquezieae) Amazon.Phytotaxa. 260: 276-282Crossref ScholarSapotaceaeMicropholis bochidodroma Penn.82Pennington Sapotaceae. 52. 1990Google ScholarSapotaceaePouteria sessilis ScholarUrticaceaePourouma Berg83Berg Pourouma CC Berg, 15.Candollea. 513-516Google Scholara Open table tab Most remain described common. was 2014 Yanachaga Chemillén National Park eastern flank Andes Peru Previously demonstrated aseasonal seasonal spanning >1000 km lowland Amazonia. demonstrate occurs abundances stems per hectare, classify 'oligarchic' taxon: locally common (abundance hectare) [59Pitman N.C. al.Oligarchies communities: ten-year review.Ecography. 36: 114-123Crossref (38) demonstrates benefit taxonomists plots: provide information abundance assessments status. There

Language: Английский

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A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 10

Published: July 24, 2019

Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific variation is unknown for most species. Standard methods determination chromosome counting flow cytometry approaches. While approaches typically use fresh tissue, an increasing number studies have shown that recently dried specimens can be used to yield data. Recent started explore whether high-throughput sequencing (HTS) data assess levels by analysing allelic frequencies from single copy nuclear genes. Here we compare different using a range yam (Dioscorea) tissues varying ages, drying quality, including herbarium tissue. Our aims were to: (1) limits estimating level samples, vouchers collected between 1831–2011, (2) optimize HTS-based method estimate considering genes obtained target-capture method. We show that, although up fifteen years ago, success rate low (5.9 %). validated our estimates 260 benchmarking with samples species known (D. alata, D. communis sylvatica). Subsequently, successfully applied 85 analysed cytometry, provided results 91.7% them, comprising across phylogenetic tree Dioscorea. also explored this approach identifying high material effects heterozygosity sequence coverage. Overall, demonstrated diversity within may ascertained historical collections, allowing polyploidization two centuries ago. This has potential provide insights into drivers dynamics changes during evolution crop domestication.

Language: Английский

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

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: March 20, 2020

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

Language: Английский

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

New Phytologist, Journal Year: 2020, Volume and Issue: 230(2), P. 433 - 450

Published: Dec. 6, 2020

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

Language: Английский

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Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1289 - 1306

Published: June 26, 2021

PREMISE Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard markers. Target capture of many independent nuclear loci has the potential improve resolution radiations. METHODS Here we applied target 353 protein‐coding genes (Angiosperms353 bait kit) Veronica sect. Hebe (common name hebe) determine its utility improving section originated 5–10 million years ago in New Zealand, forming monophyletic radiation ca 130 extant species. RESULTS We obtained approximately 150 kbp exons an additional 200 flanking noncoding sequences each 77 hebe two outgroup When comparing coding, noncoding, combined data sets, found that latter provided best overall resolution. While some deep nodes remained unresolved, our phylogeny broad often improved support subclades identified by both morphology markers previous studies. Gene‐tree discordance was nonetheless widespread, indicating methods are needed disentangle fully history radiation. CONCLUSIONS Phylogenomic sets increase signal deliver new insights into complex evolutionary as compared traditional Improving resolve remaining among from is now important facilitate further study

Language: Английский

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