Towards integrative taxonomy in Neotropical botany: disentangling the Pagamea guianensis species complex (Rubiaceae)

Abstract

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 variation. Here we present the most comprehensive population and molecular sampling across the geographical distribution of the P. guianensis complex to date in order to test the monophyly of this group and to clarify species limits. Using a high-throughput DNA sequencing approach, we sequenced 431 loci (>34 M bases) for 179 individuals. We applied phylogenetic and species tree analyses to resolve phylogenetic relationships among the sampled individuals. Species delimitation was inferred based on genomic data, and we tested whether hypothesized species could be differentiated using morphological, ecological and near-infrared spectroscopy data. We confirm the monophyly of the P. guianensis complex and accept 15 distinct and well-supported lineages, here proposed as 14 species and one subspecies. Our findings highlight the importance of multiple lines of evidence from independent datasets in the process of species delimitation and species discovery in species complexes in the Neotropics.

Reestablishment of Protium cordatum (Burseraceae) based on integrative taxonomy

“…Recent studies of two diverse Amazonian genera, Eschweilera (Durgante & al., ) and Protium (Lang & al., ), showed that NIR spectra could accurately discriminate distinct species with over 96% success. Regarding closely related plant groups, this technology has been effective to discriminate cryptic species within Pagamea (Rubiaceae) (Prata & al., ). In addition to the morphological and phylogenetic results, the NIR data indicate that P. cordatum and P. heptaphyllum have distinct spectral signatures.…”

“…The spectrometer generates an absorbance response that is a function of the chemical composition and internal anatomy of leaves, which has been shown to be conserved within populations of the same species in a large study with more than 1000 tropical tree species (Asner & al., ). Analyzing the spectral signatures of near‐infrared reflectance of herbarium specimens can allow the discrimination of morphotypes even when there is a high phenotypic overlap among samples, and informative vegetative and reproductive traits are unknown (Durgante & al., ; Prata & al., ).…”

Using near-infrared spectroscopy to discriminate closely related species: A case study of neotropical ferns

“…Our best results show that the best models and validations can, on average, correctly predict the identification of species 96.7 % of the time when using all wavelengths to construct the models, which is comparable to previously published taxonomic works. Prata et al (2018) demonstrated for the first time that near-infrared spectroscopy on leaves of subspecies of the Pagamea guianensis complex can discriminate taxa with high precision. Fan et al (2010) tested and proved the reliability of the technique at discriminating Ephedra plants from different habitats and collection seasons, while Lang et al (2017) showed the effectiveness of the technique at discriminating species, genera, and families of tree species from eighteen different angiosperm families.…”

“…Research using near-infrared spectroscopy to discriminate plant species is gaining more and more attention in plant taxonomy, especially for angiosperms (Durgante et al 2013; Kim et al 2004; Krajšek et al 2008; Lang et al 2017). The tool has been shown to be more practical and accurate than genetic or morphological methods (Castillo et al 2008), is capable of consistently discriminating phylogenetic relationships of flowering plant species (Kim et al 2004), and has been used in different works to aid in species circumscription and identification of several plant groups (Damasco et al 2019; Durgante et al 2013; Lang et al 2017; Prata et al 2018; Shen et al 2020). However, the technique has not been tested to identify other groups of embryophytes, such as ferns and lycophytes, or bryophytes.…”

The Central Role of Taxonomy in the Study of Neotropical Biodiversity

“…Species delimitation methods are also catching up to the statistical rigor of phylogenetics, with model-based methods (e.g., Zapata & Jiménez, 2012; Yang, 2015) Lagomarsino & Frost Taxonomy in the Study of Neotropical Biodiversity frequently applied instead of, or in addition to, a taxonomic expert's gestalt. This has resulted in a blooming subfield known as "integrative taxonomy" (Schlick-Steiner et al, 2010;Fujita et al, 2012;Prata et al, 2018), which reduces subjectivity and facilitates stability in classification schemes. As a result, descriptive taxonomy is becoming a more rigorous discipline (Sangster & Luksenberg, 2015).…”