Species as a Heuristic: Reconciling Theory and Practice.

Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the "species problem" stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and comparable unit of biology. Here, we suggest that treating species as a heuristic can be consistent with a theoretical definition of what species are and with the practical means by which they are identified and delimited. Specifically, we suggest that theoretically species are heuristic since they comprise clusters of closely related individuals responding in a similar manner to comparable sets of evolutionary and ecological forces, whilst they are practically heuristic because they are identifiable by the congruence of contingent properties indicative of those forces. This reconciliation of the theoretical basis of species with their practical applications in biological research allows for a loose but relatively consistent definition of species based on the strategic analysis and integration of genotypic, phenotypic, and ecotypic data. [Cohesion; heuristic; homeostasis; lineage; species problem.].

Discovery and characterization of sweetpotato's closest tetraploid relative.

The origin of sweetpotato, a hexaploid species, is poorly understood, partly because the identity of its tetraploid progenitor remains unknown. In this study, we identify, describe and characterize a new species of Ipomoea that is sweetpotato's closest tetraploid relative known to date and probably a direct descendant of its tetraploid progenitor. We integrate morphological, phylogenetic, and genomic analyses of herbarium and germplasm accessions of the hexaploid sweetpotato, its closest known diploid relative Ipomoea trifida, and various tetraploid plants closely related to them from across the American continent. We identify wild autotetraploid plants from Ecuador that are morphologically distinct from Ipomoea batatas and I. trifida, but monophyletic and sister to I. batatas in phylogenetic analysis of nuclear data. We describe this new species as Ipomoea aequatoriensis T. Wells & P. Muñoz sp. nov., distinguish it from hybrid tetraploid material collected in Mexico; and show that it likely played a direct role in the origin of sweetpotato's hexaploid genome. This discovery transforms our understanding of sweetpotato's origin.

The temporal dynamics of evolutionary diversification in Ipomoea.

Molecular phylogenies are used as a basis for making inferences about macroevolutionary history. However, a robust phylogeny does not contain the information that is necessary to make many of these inferences. Complex methodologies that incorporate important assumptions about the nature of evolutionary history are therefore required. Here, we explore the implications of these assumptions for making inferences about the macroevolutionary history of Ipomoea - a large pantropical genus of flowering plants that contains the sweet potato (Ipomoea batatas), a crop of global economic importance. We focus on assumptions that underlie inferences of divergence times, and diversification parameters (speciation rates, extinction rates, and net diversification rates). These are among the most fundamental variables in macroevolutionary research. We use a series of novel approaches to explore the implications of these assumptions for inferring the age of Ipomoea, the ages of major clades within Ipomoea, whether there are significant differences in diversification parameters among clades within Ipomoea, and whether the storage root of I. batatas evolved in pre-human times. We show that inferring an age estimate for Ipomoea and major clades within Ipomoea is highly problematic. Inferred divergence times are sensitive to uncertain fossil calibrations and differing assumptions about among-branch-substitution-rate-variation. Despite this uncertainty, we are able to make robust inferences about patterns of variation in diversification parameters within Ipomoea, and that the storage root of I. batatas evolved in pre-human times. Taken together, this study presents novel and generalizable insights into the implications of methodological assumptions for making inferences about macroevolutionary history. Further, by presenting novel findings relating to the temporal dynamics of evolution in Ipomoea, as well as more specifically to I. batatas, this study makes a valuable contribution to our understanding of tropical plant evolution, and the evolutionary context in which economically important crops evolve.

Additional notes on Ipomoea (Convolvulaceae) in Bolivia.

109 species of Ipomoea L. are recorded from Bolivia. This total includes six new country records and two species, I. prolifera J. R. I. Wood & Scotland and I. inaccessa J. R. I. Wood & Scotland, which are described as new, while I. jujuyensis O'Donell is excluded having been included previously in error. The little-known I. subalata Hassl. is described in full and compared with I. chondrosepala Hallier f. and other species with which it has been confused. The paper is illustrated with line drawings, photographs and distribution maps of the main species discussed.

Evolutionary Biology: A New Phylogenetic Framework for an Iconic Plant Radiation.

Studies in island systems underpin much of our knowledge of macroevolution. A new study of the Galápagos giant daisies adds to this tradition. A time-calibrated phylogeny is presented that offers insights into the factors associated with diversification, providing a framework for further studies to investigate processes underlying these findings.

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

A monograph of the 425 New World species of Ipomoea is presented. All 425 species are described and information is provided on their ecology and distribution, with citations from all countries from which they are reported. Notes are provided on salient characteristics and taxonomic issues related to individual species. A full synonymy is provided and 272 names are lectotypified. An extensive introduction discusses the delimitation and history of Ipomoea arguing that a broad generic concept is the only rational solution in the light of recent phylogenetic advances. Although no formal infrageneric classification is proposed, attention is drawn to the major clades of the genus and several morphologically well-defined clades are discussed including those traditionally treated under the names Arborescens, Batatas, Pharbitis, Calonyction and Quamoclit, sometimes as distinct genera, subgenera, sections or series. Identification keys are provided on a regional basis including multi-entry keys for the main continental blocks. Six species are described as new, Ipomoea nivea J.R.I. Wood & Scotland from Peru, I. apodiensis J.R.I. Wood & Scotland from Brazil, I. calcicola J.R.I. Wood & Scotland, I. pochutlensis J.R.I. Wood & Scotland, I. zacatecana J.R.I. Wood & Scotland and I. ramulosa J.R.I. Wood & Scotland from Mexico, while var. australis of I. cordatotriloba is raised to specific status as I. australis (O'Donell) J.R.I. Wood & P. Muñoz. New subspecies for I. nitida (subsp. krapovickasii J.R.I. Wood & Scotland) and for I. chenopodiifolia (subsp. bellator J.R.I. Wood & Scotland) are described. The status of previously recognized species and varieties is changed so the following new subspecies are recognized: I. amnicola subsp. chiliantha (Hallier f.) J.R.I. Wood & Scotland, I. chenopodiifolia subsp. signata (House) J.R.I. Wood & Scotland, I. orizabensis subsp. collina (House) J.R.I. Wood & Scotland, I. orizabensis subsp. austromexicana (J.A. McDonald) J.R.I. Wood & Scotland, I. orizabensis subsp. novogaliciana (J.A. McDonald) J.R.I. Wood & Scotland, I. setosa subsp. pavonii (Hallier f.) J.R.I. Wood & Scotland, I. setosa subsp. melanotricha (Brandegee) J.R.I. Wood & Scotland, I. setosa subsp. sepacuitensis (Donn. Sm.) J.R.I. Wood & Scotland, I. ternifolia subsp. leptotoma (Torr.) J.R.I. Wood & Scotland. Ipomoea angustata and I. subincana are treated as var. angustata (Brandegee) J.R.I. Wood & Scotland and var. subincana (Choisy) J.R.I. Wood & Scotland of I. barbatisepala and I. brasiliana respectively. Attention is drawn to a number of hitherto poorly recognized phenomena in the genus including a very large radiation centred on the Parana region of South America and another on the Caribbean Islands, a strong trend towards an amphitropical distribution in the New World, the existence of a relatively large number of species with a pantropical distribution and of many species in different clades with storage roots, most of which have never been evaluated for economic purposes. The treatment is illustrated with over 200 figures composed of line drawings and photographs.

A taxonomic monograph of Ipomoea integrated across phylogenetic scales.

Taxonomic monographs have the potential to make a unique contribution to the understanding of global biodiversity. However, such studies, now rare, are often considered too daunting to undertake within a realistic time frame, especially as the world's collections have doubled in size in recent times. Here, we report a global-scale monographic study of morning glories (Ipomoea) that integrated DNA barcodes and high-throughput sequencing with the morphological study of herbarium specimens. Our approach overhauled the taxonomy of this megadiverse group, described 63 new species and uncovered significant increases in net diversification rates comparable to the most iconic evolutionary radiations in the plant kingdom. Finally, we show that more than 60 species of Ipomoea, including sweet potato, independently evolved storage roots in pre-human times, indicating that the storage root is not solely a product of human domestication but a trait that predisposed the species for cultivation. This study demonstrates how the world's natural history collections can contribute to global challenges in the Anthropocene.

Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia.

The sweet potato is one of the world's most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our research combined genome skimming and target DNA capture to sequence whole chloroplasts and 605 single-copy nuclear regions from 199 specimens representing the sweet potato and all of its crop wild relatives (CWRs). We present strongly supported nuclear and chloroplast phylogenies demonstrating that the sweet potato had an autopolyploid origin and that Ipomoea trifida is its closest relative, confirming that no other extant species were involved in its origin. Phylogenetic analysis of nuclear and chloroplast genomes shows conflicting topologies regarding the monophyly of the sweet potato. The process of chloroplast capture explains these conflicting patterns, showing that I. trifida had a dual role in the origin of the sweet potato, first as its progenitor and second as the species with which the sweet potato introgressed so one of its lineages could capture an I. trifida chloroplast. In addition, we provide evidence that the sweet potato was present in Polynesia in pre-human times. This, together with several other examples of long-distance dispersal in Ipomoea, negates the need to invoke ancient human-mediated transport as an explanation for its presence in Polynesia. These results have important implications for understanding the origin and evolution of a major global food crop and question the existence of pre-Columbian contacts between Polynesia and the American continent.

New species of Ipomoea (Convolvulaceae) from South America.

The importance of discovering, describing and cataloguing poorly known species in herbarium collections is discussed. It is a spur to efforts at rediscovery and consequent conservation efforts. The problems faced in describing species from limited material are discussed and our methods and criteria in making a decision are described. Prospects for future novelties are briefly assessed. Fifteen new species are described and illustrated with line drawings and distribution maps: Ipomoea attenuata J.R.I. Wood & Scotland, I. cuscoensis J.R.I. Wood & P. Muñoz, I. dasycarpa J.R.I. Wood & Scotland, I. dolichopoda J.R.I. Wood & R. Degen, I. ensiformis J.R.I.Wood & Scotland, I. fasciculata J.R.I. Wood & Scotland, I. graminifolia J.R.I. Wood & Scotland, I. kraholandica J.R.I. Wood & Scotland, I. longirostra J.R.I. Wood & Scotland, I. revoluta J.R.I. Wood & Scotland, I. scopulina J.R.I. Wood &. Scotland, I. uninervis J.R.I. Wood & Scotland, I. veadeirosii J.R.I. Wood & Scotland, I. velutinifolia J.R.I. Wood & Scotland, I. walteri J.R.I. Wood & Scotland. All species are narrow endemics except I. velutinifolia which is found in Brazil and Peru; of the others, 12 are found in Brazil and one each in Paraguay and Peru.