Author
Joeri S. Strijk
Other affiliations: Paul Sabatier University, Centre national de la recherche scientifique, Ghent University ...read more
Bio: Joeri S. Strijk is an academic researcher from Guangxi University. The author has contributed to research in topics: Genome & Biodiversity. The author has an hindex of 11, co-authored 41 publications receiving 436 citations. Previous affiliations of Joeri S. Strijk include Paul Sabatier University & Centre national de la recherche scientifique.
Topics: Genome, Biodiversity, Biological dispersal, Monophyly, Biogeography
Papers
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TL;DR: The biogeography of the tropical plant family Monimiaceae has long been thought to reflect the break‐up of West and East Gondwana, followed by limited transoceanic dispersal.
Abstract: Aim The biogeography of the tropical plant family Monimiaceae has long been thought to reflect the break-up of West and East Gondwana, followed by limited transoceanic dispersal.
Location Southern Hemisphere, with fossils in East and West Gondwana.
Methods We use phylogenetic analysis of DNA sequences from 67 of the c. 200 species, representing 26 of the 28 genera of Monimiaceae, and a Bayesian relaxed clock model with fossil prior constraints to estimate species relationships and divergence times. Likelihood optimization is used to infer switches between biogeographical regions on the highest likelihood tree.
Results Peumus from Chile, Monimia from the Mascarenes and Palmeria from eastern Australia/New Guinea form a clade that is sister to all other Monimiaceae. The next-deepest split is between the Sri Lankan Hortonia and the remaining genera. The African Monimiaceae, Xymalos monospora, then forms the sister clade to a polytomy of five clades: (I) Mollinedia and allies from South America; (II) Tambourissa and allies from Madagascar and the Mascarenes; (III) Hedycarya, Kibariopsis and Leviera from New Zealand, New Caledonia and Australia; (IV) Wilkiea, Kibara, Kairoa; and (V) Steganthera and allies, all from tropical Australasia.
Main conclusions Tree topology, fossils, inferred divergence times and ances-tral area reconstruction fit with the break-up of East Gondwana having left a still discernible signature consisting of sister clades in Chile and Australia. There is no support for previous hypotheses that the break-up of West Gondwana (Africa/South America) explains disjunctions in the Monimiaceae. The South American Mollinedia clade is only 28–16 Myr old, and appears to have arrived via trans-Pacific dispersal from Australasia. The clade apparently spread in southern South America prior to the Andean orogeny, fitting with its first-diverging lineage (Hennecartia) having a southern-temperate range. The crown ages of the other major clades (II–V) range from 20 to 29 Ma, implying over-water dispersal between Australia, New Caledonia, New Zealand, and across the Indian Ocean to Madagascar and the Mascarenes. The endemic genus Monimia on the Mascarenes provides an interesting example of an island lineage being much older than the islands on which it presently occurs.
101 citations
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TL;DR: It is discussed how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales and factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification.
Abstract: Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.
53 citations
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TL;DR: In this paper, the relative contributions of the great Asiatic floristic interchanges with India and Sahul, respectively, to the flora of Malesia comes from contemporary lineage distributions, the fossil record, time-calibrated phylogenies, functional traits, and the spatial structure of genetic diversity.
Abstract: Unraveling the origins of Malesia's once vast, hyperdiverse rainforests is a perennial challenge. Major contributions to rainforest assembly came from floristic elements carried on the Indian Plate and montane elementsfrom the Australian Plate (Sahul). The Sahul component is now understood to include substantial two-way exchanges with Sunda inclusive of lowland taxa. Evidence for the relative contributions of the great Asiatic floristic interchanges (GAFIs) with India and Sahul, respectively, to the flora of Malesia comes from contemporary lineage distributions, the fossil record, time-calibrated phylogenies, functional traits, and the spatial structure of genetic diversity. Functional-trait and biome conservatism are noted features of montane austral lineages from Sahul (e.g., diverse Podocarpaceae), whereas the abundance and diversity of lowland lineages, including Syzygium (Myrtaceae) and the Asian dipterocarps (Dipterocarpoideae), reflect a less well understood combination of dispersal, ecology, and adaptive radiations. Thus, Malesian rainforest assembly has been shaped by sharply contrasting evolutionary origins and biogeographic histories.
48 citations
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TL;DR: The two genera Macaranga and Mallotus show congruence in dispersal patterns, which corroborate divergence time estimates, although the overall mode and tempo of dispersal and diversification differ significantly as shown by distribution patterns of extant species.
Abstract: Molecular phylogenies and estimates of divergence times within the sister genera Macaranga and Mallotus were estimated using Bayesian relaxed clock analyses of two generic data sets, one per genus. Both data sets were based on different molecular markers and largely different samples. Per genus three calibration points were utilised. The basal calibration point (crown node of all taxa used) was taken from literature and used for both taxa. The other three calibrations were based on fossils of which two were used per genus. We compared patterns of dispersal and diversification in Macaranga and Mallotus using ancestral area reconstruction in RASP (S-DIVA option) and contrasted our results with biogeographical and geological records to assess accuracy of inferred age estimates. A check of the fossil calibration point showed that the Japanese fossil, used for dating the divergence of Mallotus, probably had to be attached to a lower node, the stem node of all pioneer species, but even then the divergence time was still younger than the estimated age of the fossil. The African (only used in the Macaranga data set) and New Zealand fossils (used for both genera) seemed reliably placed. Our results are in line with existing geological data and the presence of stepping stones that provided dispersal pathways from Borneo to New Guinea-Australia, from Borneo to mainland Asia and additionally at least once to Africa and Madagascar via land and back to India via Indian Ocean island chains. The two genera show congruence in dispersal patterns, which corroborate divergence time estimates, although the overall mode and tempo of dispersal and diversification differ significantly as shown by distribution patterns of extant species.
33 citations
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05 Apr 2016
TL;DR: The Syzygium Working Group (SYZWG) presents a meta-modelling framework for estimating the phytochemical properties of the SyzyGium and its applications in agriculture, ecology, and the environment.
Abstract: 1 Recommended citation: SYZWG (2016) Syzygium Working Group 2 Faculty of Science & Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia. 3 The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security; R. E. Vaughan Building, Reduit, Mauritius. 4 Plant Gateway, 5 Talbot Street, Hertford, Hertfordshire, SG13 7BX, UK. 5 School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK. 6 School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia. 7 Ecology & Ecosystem Research, Georg-August-University Gottingen, Untere Karspule 2, 37073 Gottingen, Germany. 8 Naturalis Biodiversity Center, Botany, P.O. Box 9517, 2300 RA, Leiden, The Netherlands. 9 Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK. 10 Department of Biosciences, University of Mauritius, Reduit, Mauritius. 11 Centre for Ecological Sciences, Indian Institute of Sciences, Bengaluru, 560012, India. 12 Ashoka Trust for Research in Ecology and the Environment (ATREE), Bengaluru, India 13 Department of Biology, Pittsburg State University, Pittsburg, Kansas, U.S.A. 14 College of Forestry, Guangxi University, Nanning, Guangxi 530005, PR China. 15 Royal Botanic Gardens, Mrs Macquaries Road, Sydney, NSW 2000, Australia
32 citations
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TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201
14,171 citations
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TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.
2,436 citations
10 Dec 2007
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
1,528 citations
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TL;DR: In this article, the authors re-evaluated the biogeographical history and relationships of Macaronesia in the light of geological evidence, which suggests that large and high islands may have been continuously available in the region for very much longer than is indicated by the maximum surface area of the oldest current island (27 Ma) -possibly for as long as 60 million years.
Abstract: Macaronesia is a biogeographical region comprising five Atlantic Oceanic archipelagos: the Azores, Madeira, Selvagen (Savage Islands), Canaries and Cape Verde. It has strong affinities with the Atlantic coast of the Iberian Peninsula and the north-western fringes of Africa. This paper re-evaluates the biogeographical history and relationships of Macaronesia in the light of geological evidence, which suggests that large and high islands may have been continuously available in the region for very much longer than is indicated by the maximum surface area of the oldest current island (27 Ma) – possibly for as long as 60 million years. We review this literature, attempting a sequential reconstruction of Palaeo-Macaronesia from 60 Ma to the present. We consider the implications of these geological dynamics for our understanding of the history of colonization of the present islands of Macaronesia. We also evaluate the role of these archipelagos as stepping stones and as both repositories of palaeo-endemic forms and crucibles of neoendemic radiations of plant and animal groups. Our principal focus is on the laurel forest communities, long considered impoverished relicts of the Palaeotropical Tethyan flora. This account is therefore contextualized by reference to the long-term climatic and biogeographical history of Southern Europe and North Africa and by consideration of the implications of changes in land–sea configuration, climate and ocean circulation for Macaronesian biogeography. We go on to provide a synthesis of the more recent history of Macaronesian forests, which has involved a process of impoverishment of the native elements of the biota that has accelerated since human conquest of the islands. We comment briefly on these processes and on the contemporary status and varied conservation opportunities and threats facing these forests across the Macaronesian biogeographical region.
311 citations