A foundation monograph of Ipomoea (Convolvulaceae) in the New World

DNA sequencing
Perhaps the most significant element in our methodology has been the integration of morphological and molecular data. During the course of the five years that we have been studying Ipomoea we have been able to sequence 1,560 specimens and approximately 450 species of Ipomoea from all over the world for ITS and two chloroplast markers (matK and trnH-psbA), 3,035 DNA barcode sequences in total (Muñoz-Rodríguez et al. 2019, supplementary data 3–8). A smaller number of 211 selected species were sequenced for 605 nuclear genes and the whole chloroplast genome (Muñoz-Rodríguez et al. 2019, supplementary data 3–8). Figure 1 summarises the results showing the main clades into which Ipomoea divides. We are particularly grateful to Kew and the Natural History Museum in London for allowing us to sequence large numbers of specimens in their collections and it is from these herbarium collections that the main bulk of our sequence data has been taken. We have had permission to sequence selected examples of species from other herbaria including E, L, MA and P and in the Americas from A, ARIZ, F, GH, HUEFS, IEB, LPB, MEXU, MO, NY, US. Obviously, field collections have provided additional samples for sequencing and we are grateful to several botanists for sending us samples including George Staples, Deng Yunfei (SCIB), Moises Mendoza (UB) and Barbara Kennedy (BISH).
Species concept
Nowhere in biology is the disparity between theory and practice more evident than at the level of species. In an influential and widely cited contribution Kevin de Queiroz (2005, 2007) proposed the ‘unified species concept’ to treat existence of species as ‘separately evolving metapopulation lineages’ as the only necessary property of species and that the plethora of species concepts in existence merely represent different lines of evidence relevant to assessing lineage separation. In this way Queiroz (2005, 2007) separated the theoretical idea of what species are from the operational criteria of how to discover them. An important issue for the recognition of species is that as lineages diverge they can become distinguishable as separate species with diagnostic characters of fixed traits. Species can evolve distinctive ecologies and they can pass through polyphyletic, paraphyletic, and monophyletic stages in terms of their component genes. The problem is that these changes do not all necessarily occur, or if they do occur, do not do so at the same time and they do not even necessarily occur in a regular order (Queiroz et al. 1998). What this dynamic system of divergence means is that there is a certain pragmatic and heuristic nature to species delimitation whereby, although the expectation is that many species are clearly monophyletic, there will be other situations where the estimate of the degree of separation comes down to taxonomic judgement. Therefore, in this monograph we consider species to be separately evolving metapopulation lineages and in the discussion that follows we describe the operational criteria we used to infer, delimit and make taxonomic judgements about species boundaries. From experience gained studying Ipomoea we consider that species delimitation is usually relatively straightforward, given a representative sample of specimens and an understanding of the important diagnostic characters in the genus. Thus, a first task is to gain access to a wide range of specimens for comparison purposes, followed by a study of publications by reliable taxonomists who have worked on the genus. At the same time as specimens are studied morphologically, representative leaf samples from each putative species are sequenced for a few DNA barcode markers to provide an independent data source to corroborate or refute a species hypothesis based on morphological analysis or literature sources. Species delimitation is facilitated if DNA sequencing and specimen examination take place nearly simultaneously but this is only possible when DNA samples can be extracted from the available material. Conceptually as discussed above, we follow Queiroz (2005, 2007), whose framework includes the idea that disagreements about the limits of species are especially prevalent in those species at the active interface of speciation. This explains why many species have universally agreed boundaries whereas others are more difficult to interpret. We take the view that, in the context of taxonomy, for those instances where species delimitation is particularly problematic, it is best to flag up the variation, make a pragmatic, discursive and explicit taxonomic decision and move onto those other species delimitation problems that taxonomy can readily solve. This is especially true in large tropical groups such as Ipomoea in which many of the taxonomic problems can be readily solved by having a good sample of specimens combined with good knowledge of the group’s literature and nomenclature. Our view is that species and species delimitation can be viewed as a heuristic allowing an approach to problem solving or discovery that employs a practical method not guaranteed to be optimal or perfect, but sufficient for the immediate goals. To a greater extent than in Convolvulus (Wood et al. 2015), Evolvulus L. or even Jacquemontia, most species of Ipomoea are, as a generalization, well-defined. Hybridization is rarely reported, and that principally in the Batatas Clade. Claims by Austin that I. leucantha and I. grandifolia are of hybrid origin require corroboration. There are, of course, species complexes where delimitation is difficult, as intermediates occur between recognized species and these may be hybrids but a lot of the difficulty faced by the taxonomist arises from the lack of available material for study. Almost 20 species in the following account are only known from the type collection, another 50 or so are only known from less than five collections, and not all of these have been available for study. In about 20 cases, we have not seen authentic material and have relied on images and original descriptions to describe and delimit species. Inevitably, we are tentative in our decisions on the validity of some individual species. Examples include I. leucantha mentioned above as well as several species in Clade A1 (Figure 1; Muñoz-Rodríguez et al. 2019), such as I. vivianae or I. pseudomalvaeoides. A particular case is the pantropical I. indica. Molecular studies show that this is polyphyletic (Muñoz-Rodríguez et al. 2019, supplementary data 3), but it is clear that a more exhaustive study with extensive sampling is necessary before the components of this entity can be unravelled.
We have tried to make use of so-called conservative characters in accepting species and the value of these is discussed in the notes that follow. Pollination syndromes as reflected in corolla shape and to some extent in colouring and the structure of the androecium are seen as important for species delimitation (Rosas-Guerrero et al. 2011). Ideally each species will be delimited by a combination of distinctive characters. Species defined by a single character, unless it is exceptionally strong, are regarded with suspicion. We do take into account ecological and geographical factors. We would expect different species to have different ecological requirements or occupy a different geographical area from obviously related species. Where morphology, ecology and geography intergrade we have indicated by notes and in some cases by the recognition of subspecies. We have used insights from molecular sequence data, keeping separate apparently similar species like I. marginisepala and I. cardiophylla or I. asarifolia and I. paludicola where uniting them would render them non-monophyletic. We have been reassured in our species level decisions by molecular data in the recognition of numerous species, for example, I. huayllae, I. graniticola, I. chiquitensis and I. juliagutierreziae from Bolivia and I. kraholandica and I. chapadensis from Brazil. Molecular data has been less helpful for species delimitation within some of the relatively large clades such as Clades A, 1–2 (Figure 1) where multiple accessions of several species are not resolved partly due to the limited variation provided by regions used.