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Matrix of confusion resulted from the species classification analysis applied to the morphological variables 'leaf area', 'number of secondary veins' and 'leaf-shape PCA axis', using a Support Vector Machine (SVM) classifier. P. gui m. tapajoensis refers to P. guianensis m. tapajoensis.
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Species complexes are common in the Neotropical flora, and the Pagamea guianensis complex is one of the most widespread groups of species in the Amazonian white-sand flora. Previous analyses suggested the occurrence of ten species in this group, but species limits remained unclear due to poor sampling, morphological overlap and low molecular variat...
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Context 1
... o n g m o s t s p e c i e s (Fig. 3A). However, we found strong patterns of species clustering in the morphological space when clades were analysed separately ( Fig. 3B-D). Discriminant models correctly predicted 85 and 79% (SVM and NB models, respectively) of the samples into their respective species when analysing all species together (Table 2, Fig. 4). Although, on average, the SVM model performed better, the NB model yielded a considerably high value of species assignment for P. m. daviliana (the only taxon with low prediction in the SVM analysis) when compared to the SVM model (0.84 and 0.48%, respectively). We found even higher values of species assignment when applying the SVM ...
Context 2
... main variables explaining relative habitat suitability for the species were 'precipitation of coldest quarter' (for P. m. angustifolia, P. m. occulta, P. plicatiformis, P. puberula), 'precipitation seasonality' (for P. m. cryptica, P. m. daviliana, P. m. peruviana, P. m. resinosa and P. sessiliflora), 'podzols' (for P. m. solimoensis and P. spruceana), 'slope' (for P. dudleyi), 'precipitation of warmest quarter' (for P. pilosa) and 'count of the number of months with mean temperature > 10 °C' (for P. guianensis) (Table 3; Supporting Information, Fig. S4). Values of niche overlap calculated between species were in general low (< 0.5) and less equivalent/similar than random (P < 0.05; Fig. 6), thus indicating niche divergence. ...
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Antecedentes y Objetivos
En las últimas décadas, se han incrementado los estudios florísticos en las selvas secas, en donde reportan que este tipo de vegetación alberga una alta riqueza y endemismo, siendo a la vez uno de los más amenazados por el cambio de uso de suelo. Este trabajo tiene como objetivo dar a conocer un nuevo registro del género Ch...
Citations
... This is due to the fact that the spectral behavior of a leaf is a function of its chemical composition, morphology and internal structure, data that help in the recognition of species [31][32][33]. Recent studies have shown the effectiveness of Fourier transform near-infrared (FT-NIR) spectroscopy in the identification of botanical species [20,21,30,34,35]. ...
... One of them was already expected for the spectra of leaves, with absorbances ranging from 0.55-0.20 (Behavior A), as described by [19], and another totally different from the one recorded in previous studies, with high absorbance values ranging from 1.0-0.7 (Behavior B). It was found that of the 315 individuals who had spectra collected, 244 showed the behavior A and 71 the behavior B. The difference in spectral behaviors was related to the collection method: spectra collected directly without the use of fisheye lens resulted in behavior A, and those collected using fisheye lens resulted in behavior B. Thus, the use of fisheye lens modifies the visualized spectral behavior, producing different absorbance levels in relation to collections performed without this tool, as shown in previous works [19,20,29,[33][34][35]. However, the use of this spectrophotometer tool is recommended by the manufacturer for materials smaller than the integrating sphere [36]. ...
This work aimed to use near-infrared spectroscopy (NIRS) as a tool to discriminate species of the genus Dimorphandra Schott (Leguminosae, Caesalpinioideae). Spectra were collected from 315 individuals (six readings per individual) distributed in 20 species of Dimorphandra using a Thermo Nicollet spectrophotometer, FT-NIR Antaris II Method Development System (MDS) in the INPA (National Institute of Amazonian Research) Herbarium. Absorbance values comprise the wavenumbers from 4,000 to 10,000 cm-1, corresponding to the near infrared region, recorded for 16 scans at a resolution of 8 cm-1. Principal Component Analysis (PCA) was used to visualize the spectral distribution. Discriminant functions were generated in order to evaluate the potential of the data to correctly distinguish the species and the 70-30 cross-validation technique was used to validate the generated models, with selections randomized 1, 10, 50 and 100 times. Excellent results were obtained in the PCA, with prediction values of 95-92%, using the 70-30 validation test in the linear discriminant analyses (LDA), thus indicating high predictive power in the discrimination of species of the genus Dimorphandra. Thus, it is inferred that NIRS contributes to the discrimination of species of the genus and elucidation of taxonomic problems.
... The widespread Protium heptaphyllum contains 9 lineages with most divergences before 750,000 years ago 10 . Similarly, there is abundant "cryptic" variation within a widespread Pagamea species complex of white-sand soils 11 . Cuatrecasas' 4 subspecific classification of cacao (T. ...
Colli-Silva et al.1 recently proposed that cupuaçu (Theobroma grandiflorum) was domesticated in northwestern Amazonia as a selection from its sister species, cupuí (T. subincanum). This proposal ignores long-term research in taxonomy, botany, biogeography, and genetics about Theobroma, including cupuaçu. Our review of the research that was ignored and of Colli-Silva et al.’s results demonstrates that cupuaçu is a valid species, as they now agree2, but cupuí may be paraphyletic, the distribution of wild cupuaçu was not included in their samples so the origin of domestication continues unknown, precolonial archaeology lacks remains that can be attributed to either species, historical linguistics indicates that the term cupuaçu references the species’ wild distribution and is a recent introduction in northwestern Amazonia, history suggests that cupuaçu started to be domesticated during the last 100-200 years, and the genomics results are not about the domestication of cupuaçu because it is a valid species and its wild distribution was not sampled.
... Morphological traits are often continuous, but their diagnosis is limited by taxonomic thresholds. Additionally, the rapid, repeated evolution of adaptive phenotypes further complicates the situation (Fisěr et al., 2018;Prata et al., 2018;Galtier, 2019). The paucity of reliable molecular markers at lower taxonomic levels further hinders the evolutionary inference within species complexes (Avise, 2012;Galtier, 2019). ...
... This divergence may be attributed to the limits of phylogenetic trees, which are impacted by gene incongruence arising from hybridization, horizontal gene transfer, and gene duplication and loss (Maddison, 1997;Massatti et al., 2016). The influence of phenotypic plasticity (West-Eberhard, 1989;Duminil and Di Michele, 2009;Fujita et al., 2012;Prata et al., 2018) and convergent evolution (Losos, 2011) may also contribute to these complex patterns. ...
The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.
... In the last decade, biologists have increasingly integrated taxonomy with other disciplines, in an attempt to provide a robust framework of independent evidence, aiming to identify, describe, and evaluate the status of several organisms (e.g., Andújar et al., 2014;Prata et al., 2018;Vargheese & Basheer, 2022). Consequentially, some systematists have used the term "integrative taxonomy" to name and differentiate this more inclusive approach when addressing taxonomic questions (e.g., Padial & Riva, 2009;Moraes et al., 2021). ...
The widespread Tantilla melanocephala is a South American snake, which has a convoluted taxonomic history and a
poorly addressed systematics. The taxonomic identity and the phylogenetic affinities of their populations are unclear,
suggesting the existence of a complex of undescribed species. Here, we preliminarily address the morphological
diversity and genetic structure of the T. melanocephala complex through comparative morphological approaches and
phylogenetic analyses using maximum likelihood. Our results confirm the presence of hidden diversity within the T.
melanocephala complex and strongly indicate that the populations of T. melanocephala from southern South America
represent a distinct lineage, which is morphologically diagnosable under a unique combination of character states.
Therefore, we formally describe these populations as a new species and present a comparison among all other South
American species of Tantilla. We also estimate the divergence times of the main clades within the complex through
Bayesian analysis, suggesting a biogeographical scenario of lineage diversification. Finally, our study clarifies aspects
of the intricate taxonomy of the T. melanocephala complex, providing a framework for future studies to avoid the
description of synonyms.
... Regarding taxonomic and systematic studies, SDM has increasingly been applied as a tool to support integrative research aiming to disentangle species complexes, usually with promising outcomes, specially when combined with other lines of evidence such as reconstruction of phylogenetic relationships among species or analyses of morphological variation. Notable examples of applications of SDM in plant taxonomy and systematics include Prata et al. (2018), Viera Barreto et al. (2018), Li et al. (2019), Moroni et al. (2019), Nygaard et al. (2021). ...
Context The Chromolaena congesta complex is an informal group of taxa native to grasslands from south-eastern South America with numerous identification problems, currently under study using an integrative approach. Recent studies with morphological data have aided in defining some taxa, but many questions remain to be assessed, and there is much to gain from combining morphological data with other lines of evidence. Aims We investigated whether the species of the C. congesta complex could be circumscribed and differentiated according to climatic and distributional data and how these results compare to published morphological data. Methods We used a SDM approach and climatic envelope estimates of 12 taxa belonging to the C. congesta complex. To achieve that, we compiled a distributional database from herbarium specimen information and produced distribution models for each taxon by using MaxEnt and 19 bioclimatic variables. Key results We found that many species of the complex share similar predicted suitable distribution and climatic preferences, while also uncovering particular geographic and climatic patterns for C. ascendens and C. caaguazuensis. Our results also contributed with the circumscription of C. squarrulosa and provided data for further recognition of two taxonomic novelties. Conclusions Climatic and distributional data yielded interesting results for the taxonomy of this species complex, particularly when confronted with morphological data. Implications This study provided support for an apparently undescribed Chromolaena that merits recognition at species rank and the treatment of Eupatorium caaguazuense var. nervosum as a separate species from C. squarrulosa, while also supplying further evidence that morphologically diverse populations of C. squarrulosa should be treated as a single taxon.
... While many phylogenetic studies have been performed for different clades in Rubiaceae (Löfstrand et al., 2019;Borges et al., 2021;Razafimandimbison et al., 2021;Amenu et al., 2022), as well for the entire family (Bremer and Eriksson, 2009), these have mostly relied on a few loci. Only a handful of studies have used genomic-scale phylogenetic data to resolve relationships within Rubiaceae, with most of these using the Angiosperms353 data (Antonelli et al., 2021;Canales et al., 2022;Thureborn et al., 2022) and another using microarray technology (Prata et al., 2018). ...
Premise
Rubiaceae is among the most species‐rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large‐scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single‐copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae‐specific probe set that allows for comparable phylogenetic inference across clades is lacking.
Methods
Here, we use publicly accessible genomic resources to identify putatively single‐copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent‐aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.
Results
We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.
Discussion
Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.
... Several tools have been used to study species complexes, such as near-infrared spectroscopy (NIR) (Durgante et al. 2013;Lang et al. 2017;Prata et al. 2018;Paiva et al. 2021), cytogenetics (Assis et al. 2013;Medeiros-Neto et al. 2017;Querino et al. 2020;Pessoa et al. 2021;Camelo-Júnior et al. 2022), population genetics Esteves & Vicentini 2013;Rodrigues et al. 2014), and geometric morphometrics (GM) (Pinheiro & Barros 2007;Nery & Fiaschi 2019;Aristizábal et al. 2020;Pessoa et al. 2021;Camelo-Júnior et al. 2022). This latter phenetic approach allows, through statistical analysis of shape variation among individuals and populations, to test taxon delimitation using highly variable structures. ...
Scaphyglottis Poepp. & Endl. (Orchidaceae) is a neotropical genus with 78 species, 14 of which are found in Brazil. Some of these taxa have an intricate taxonomy, especially due to the morphological similarity among species and the existence of species complexes. Our study aims to test if the labellum shape, the main source of species diagnostic characters, can confirm the proposed circumscription of Brazilian species of Scaphyglottis. We analyzed 136 flowers from 12 species, to which we applied 12 landmarks, using a geometric morphometrics approach. Our results show that most species can be distinguished. Most of the variation is observed in the claw and apices of labellum lobes, confirming that the labellum is important tool in taxon distinction. Species with distinctly 3-lobed labellum showed some overlap but, for these taxa, we have found distinction specially in the lateral lobes. Our study showed new morphologically variable features in Scaphyglottis that can be used in future taxonomic studies. For widely distributed species we suggest a population-level approach, as local environmental factors can impact morphology, causing expected intraspecific variation.
... These factors together may result in a serious underestimation of biodiversity. The study of morphological variation in time and space, based on detailed sampling of fresh material at the population level of sympatric morphotypes, may therefore reveal characters and patterns not observed on dried herbarium specimens (Ikabanga et al., 2017;Prata et al., 2018;Lissambou et al., 2019). Using multivariate analyses of morphological data may facilitate the identification and selection of diagnostic morphological characters (Henderson, 2006;Marhold, 2011). ...
... Using multivariate analyses of morphological data may facilitate the identification and selection of diagnostic morphological characters (Henderson, 2006;Marhold, 2011). The further inclusion of molecular techniques can be used to assess whether morphological variants are genetically distinct, thereby contributing to quantification of reproductive isolation (Østbye et al., 2005;Lowry et al., 2008;Xu & Schlüter, 2015;Prata et al., 2018). Genetic data can provide additional insight into the evolutionary history and phylogenetic relationships (e.g. ...
Species-level taxonomy is traditionally based on herbarium collections that typically include few, or even single, representatives per site. This can lead to underestimation of diversity when there are sympatric populations of superficially similar plants belonging to different lineages. Satyrium longicauda (Orchidaceae) represents a taxonomic challenge for the delimitation of species boundaries due to the high degree of morphological variation detected within and among populations. Currently, just two varieties are accepted based mainly on length differences of the lateral sepal and nectar spur. However, there is extensive morphological variation within South African populations and evidence for several pollination ecotypes, indicating that this taxon represents an actively diverging species complex. Here, we evaluate intraspecific morphological variation through uni- and multivariate morphometrics and analyse internal transcribed spacer sequences for individuals sampled from 36 sites, including 14 sites where divergent morphotypes occur sympatrically. Morphometric analyses of 1802 individuals revealed the presence of eight morphotypes based on vegetative and floral characters. Up to six morphologically and genetically distinct morphotypes can coexist in sympatry. Morphological and genetic distances among populations were significantly correlated. Phylogenetic analyses of 120 accessions indicated that neither of the two varieties nor S. longicauda as a species is monophyletic, and provided evidence for the monophyly of some of the morphotypes including the newly described S. cernuiflorum. The presence of distinct morphological and genetic sympatric variants, which in several cases scale up to distinct evolutionary lineages, is consistent with the existence of different taxa according to morphological and biological species concepts. Our results therefore confirm that taxonomy based mainly on herbarium collections can grossly under-estimate actual diversity of disparate lineages, although further work is required to finalize taxonomic decisions. These findings have implications for efforts to estimate species diversity in groups that are in the process of diversifying and for conservation practice.
... Its subsequent uses include phenotyping in breeding programs (Cabrera-Bosquet et al., 2012) and vegetation analyses focusing on diversity (Hill et al., 1988) and vegetation health (Pontius et al., 2005). A number of taxonomic studies have used IRS to differentiate species (Lu et al., 2008a;Lang et al., 2015;Prata et al., 2018), hybrids (Stasinski et al., 2021), or even intraspecific units (Gao et al., 2012), sometimes demonstrating superior results to DNA barcoding (Durgante et al., 2013). Meireles et al. (2020) even studied spectra across seed plants and found a phylogenetic signal. ...
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.
... (Damasco & al., 2021) and Pagamea guianensis Aubl. (Prata & al., 2018). However, these are very few studies considering the 227 hyperdominant tree species found in Amazonia (Ter Steege & al., 2013). ...
Hyperdominant trees in Amazonia account for half of the individual trees (>10 cm dbh) in the forest, and thus play a crucial role in ecosystem dynamics. However, several of these widespread hyperdominant species may be complexes hiding cryptic diversity that can affect species richness estimates and conservation priorities. Here, we study the intraspecific variation of Astrocaryum murumuru
(Arecaceae), a keystone and hyperdominant species in Amazonia, also known as Astrocaryum sect. Huicungo, a complex of 15 understory to subcanopy palm species. Using chloroplast DNA from genome skimming (>66 kbp alignment) in a Bayesian framework, we present evidence that A. sect. Huicungo represents three separately evolving lineages, suggesting that the section is not a
single hyperdominant species, and that the 15 morphology-based species may be an over-representation. Genome skimming chloroplast data did not fully resolve the species-level phylogenetic relationships in A. sect. Huicungo mostly because of gene discordance and the paraphyly of most species. Contrary to a previous nuclear-based phylogenetic analysis, the chloroplast genomic data did not
recover A. sect. Huicungo monophyletic, but yielded monophyly in an increased number of species (six) in the complex. Interspecific phylogenetic relationships showed a geographic pattern, and the traditional morphology-based classification was not supported. Our phylogenomic results are discussed in light of earlier phylogeographical studies using Sanger sequencing. Our findings show
the utility of genome skimming data in species delimitation analyses to uncover intraspecific variation of hyperdominant species in Amazonia, the largest evergreen tropical forest.
