Alex Sumadijaya

Bio: Alex Sumadijaya is an academic researcher from University of Oxford. The author has contributed to research in topics: Bothriochloa & Reinwardtia. The author has an hindex of 3, co-authored 10 publications receiving 36 citations. Previous affiliations of Alex Sumadijaya include Indonesian Institute of Sciences.

A taxonomic monograph of Ipomoea integrated across phylogenetic scales

Abstract: 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.

Structure and composition of subalpine summit habitats on Mt. Gede-Pangrango complex, Cibodas Biosphere Reserve, West Java, Indonesia

Abstract: SADILI, A., KARTAWINATA, K., KARTONEGORO, A., SOEDJITO, H. & SUMADIJAYA, A. 2009. Structure and composition of subalpine summit habitats on Mt. Gede-Pangrango complex, Cibodas Biosphere Reserve, West Java, Indonesia. Reinwardtia 12 (5): 391–404. We undertook a phytosociological analysis of the subalpine herbaceous and shrubby vegetation at the Mandalawangi and Suryakencana meadows and the scrub at the Crater Side at the tops of Mt. Gede and Mt. Pangrango in the Cibodas Biosphere Reserve. We recorded 30 species of 18 families of saplings, shrubs, seedlings and herbs in 78 quadrats with a total area of 7,800 m2. Anaphalis javanica, a woody tall herb and long-lived pioneer was the dominant species in the sapling and shrub stratum, while Isachne pangerangensis, Tripogon exiguus and Carex verticillata were prevalent in the seedling and herb stratum at Mandalawangi and Suryakencana. Stunted shrub is Vaccinium varingaeifolium, dominant in the Crater Side scrub. Based on the importance values, the Mandalawangi meadow may be designated as the Anaphalis javanica-Isachne pangerangensis community type, the Suryakencana meadow as Anaphalis javanica-Tripogon exiguus community type and the Crater Side scrub as Vaccinium varingiaefolium-Seliguea feei community type. The similarity indices between Mandalawangi and Suryakencana community types were very high (>75 %) while those between the Crater Side and Mandalawangi and the Crater Side and Suryakencana were very low (<10 %). Poor soil conditions and fire seem responsible for the perpetual existence of A. javanica.

Morphology, Molecular Phylogeny and Genome content of Bothriochloa focusing on Australian taxa

Abstract: The study focuses on the genus Bothriochloa (Andropogoneae, Poaceae) in Australia. Despite morphological features separating this genus from the closely related two genera Capillipedium and Dichanthium, (the three hereafter will be called BCD), De Wet and Harlan introduced the compilospecies complex to show the interbreeding phenomena that occurred among species of these genera. This study was carried out to assess species/genus relatedness of the BCD complex using different evidences from morphology, molecular information and genomic content. Nineteen morphological characters were observed, three regions (trnT-F, rps16 intron and 3’trnK) of chloroplast genome phylogenetic were used in phylogenetic reconstruction, and chromosome counting as well as flow cytometry for chromosome number and genome size were conducted during the study. Phylogenetic trees were constructed using MP with NJ for morphological data, and MP, RAxML, and BI for molecular data. Based on morphology, all three genera were separated as monophyletic units. Bothriochloa consisted of two clades. However, phylogenetic analyses based on chloroplast genomic regions reveal that Bothriochloa and Dichanthium are paraphyletic clades and only Capillipedium is resolved as a monophyletic clade. The concatenated data set has performed better than individual data sets in terms of resolution and support for clades. Flow-cytometry and chromosome counting only found diploid and tetraploid but not hexaplod species. TCS network reveals that tetraploidization followed different pathways from the ancestral diploid species. This study provided new insight onto the evolution of the chloroplast genome in the compilospecies and empirical evidence of species grouping of the compilospecies based on morphology.

Notes on bothriochloa kuntze (gramineae: andropogoneae) in malesia

Abstract: SUMADIJAYA, A. & VELDKAMP, J.F. 2009. Notes on Bothriochloa Kuntze (Gramineae: Andropogoneae) in Malesia. Reinwardtia 12(5): 415 – 417. — The note is preliminary part for studies of Bothriochloa Kuntze in Malesia. Special caution should be given to Bothriochloa intermedia (R. Br.) A. Camus, now B. bladhii (Retz.) S.T. Blake, because of the variation, synonyms, and natural hybridization to generic level.

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

Abstract: 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. Munoz. 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.

Germplasm Acquisition and Distribution by CGIAR Genebanks.

Abstract: The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization’s global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks’ trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers’ acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers’ distributions of PGRFA included the extent of accession-level information, users’ capacity to identify the materials they want, and policies. The genebanks’ rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA.

Richness and Distribution of Salvia Subg. Calosphace (Lamiaceae)

Abstract: Premise of research. Salvia is one of the most species-rich genera in the world. Its outstanding diversity and subcosmopolitan distribution have prevented the preparation of a modern comprehensive ...

The Central Role of Taxonomy in the Study of Neotropical Biodiversity

Abstract: The Neotropics are the most species-rich area of the planet. Understanding the origin and maintenance of this diversity is an important goal of ecology and evolutionary biology. Success in this endeavor relies heavily on the past work of taxonomists who have collected specimens and produced the floras and monographs that constitute the foundation for the study of plant diversity. To illustrate this, we visualize collecting efforts through time and identify the importance of past taxonomic and collection efforts in generating the bulk of specimen data that broad-scale analyses rely on today. To demonstrate the importance of taxonomy for the study of Neotropical biodiversity, we showcase selected plant groups in which in-depth taxonomic understanding has facilitated exciting evolutionary and ecological research and highlight the teams of scientists who have built on the legacy of Alwyn Gentry, one of the most prolific taxonomists of the late 20th century. We also discuss challenges faced by taxonomists, including perceived subjectivity, difficulty in measuring impact, and the need to become more interdisciplinary. We end with potential solutions going forward, including integration of taxonomists in interdisciplinary research, advocacy for continued collection efforts, increased funding for alpha taxonomic research that is performed with increasingly replicable methodology, and explicit decolonization efforts to increase inclusivity and equity in the field of taxonomy. Acknowledging the central role of taxonomy and taxonomists is essential to accurately and completely describe Neotropical biodiversity patterns in an age of unprecedented extinction risk and conservation need.

Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

Abstract: Abstract Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.