scispace - formally typeset
Search or ask a question
Author

Sophie von der Heyden

Other affiliations: University of Oxford
Bio: Sophie von der Heyden is an academic researcher from Stellenbosch University. The author has contributed to research in topics: Population & Biodiversity. The author has an hindex of 25, co-authored 67 publications receiving 2138 citations. Previous affiliations of Sophie von der Heyden include University of Oxford.


Papers
More filters
Journal ArticleDOI
TL;DR: This review describes the state of marine phylogeography in southern Africa, that is, the study of evolutionary relationships at the species level, or amongst closely related species, in relation to the region’s marine environment, and focuses particularly on coastal phylegeography.
Abstract: The southern African marine realm is located at the transition zone between the Atlantic and Indo-Pacific biomes. Its biodiversity is particularly rich and comprises faunal and floral elements from the two major oceanic regions, as well as a large number of endemics. Within this realm, strikingly different biota occur in close geographic proximity to each other, and many of the species with distributions spanning two or more of the region’s marine biogeographic provinces are divided into evolutionary units that can often only be distinguished on the basis of genetic data. In this review, we describe the state of marine phylogeography in southern Africa, that is, the study of evolutionary relationships at the species level, or amongst closely related species, in relation to the region’s marine environment. We focus particularly on coastal phylogeography, where much progress has recently been made in identifying phylogeographic breaks and explaining how they originated and are maintained. We also highlight numerous shortcomings that should be addressed in the near future. These include: the limited data available for commercially important organisms, particularly offshore species; the paucity of oceanographic data for nearshore areas; a dearth of studies based on multilocus data; and the fact that studying the role of diversifying selection in speciation has been limited to physiological approaches to the exclusion of genetics. It is becoming apparent that the southern African marine realm is one of the world’s most interesting environments in which to study the evolutionary processes that shape not only regional, but also global patterns of marine biodiversity.

186 citations

Journal ArticleDOI
TL;DR: The results suggest that combined SSU+LSU rDNA phylogenies can help to resolve several ambiguous regions of the eukaryotic tree and identify key taxa for subsequent multi-gene analyses.

160 citations

Journal ArticleDOI
TL;DR: Euglenozoa is a major phylum of excavate protozoa with highly unusual nuclear, mitochondrial, and chloroplast genomes with three phagotrophic euglenoid orders: Petalomonadida (holophyletic), Ploeotiida (probably holophyletsic), Peranemida (paraphyletic).
Abstract: Euglenozoa is a major phylum of excavate protozoa (comprising euglenoids, kinetoplastids, and diplonemids) with highly unusual nuclear, mitochondrial, and chloroplast genomes. To improve understanding of euglenozoan evolution, we sequenced nuclear small-subunit rRNA genes from 34 bodonids (Bodo, Neobodo, Parabodo, Dimastigella-like, Rhynchobodo, Rhynchomonas, and unidentified strains), nine diplonemids (Diplonema, Rhynchopus), and a euglenoid (Entosiphon). Phylogenetic analysis reveals that diplonemids and bodonids are more diverse than previously recognised, but does not clearly establish the branching order of kinetoplastids, euglenoids, and diplonemids. Rhynchopus is holophyletic; parasitic species arose from within free-living species. Kinetoplastea (bodonids and trypanosomatids) are robustly holophyletic and comprise a major clade including all trypanosomatids and most bodonids ('core bodonids') and a very divergent minor one including Ichthyobodo. The root of the major kinetoplastid clade is probably between trypanosomatids and core bodonids. Core bodonids have three distinct subclades. Clade 1 has two distinct Rhynchobodo-like lineages; a lineage comprising Dimastigella and Rhynchomonas; and another including Cruzella and Neobodo. Clade 2 comprises Cryptobia/ Trypanoplasma, Procryptobia, and Parabodo. Clade 3 is an extensive Bodo saltans species complex. Neobodo designis is a vast genetically divergent species complex with mutually exclusive marine and freshwater subclades. Our analysis supports three phagotrophic euglenoid orders: Petalomonadida (holophyletic), Ploeotiida (probably holophyletic), Peranemida (paraphyletic).

133 citations

Journal ArticleDOI
TL;DR: This work compiled population genetic studies of deep‐sea fauna and estimated dispersal distances for 51 studies using a method based on isolation‐by‐distance slopes to provide the first rough estimate of the range of disperseal distances in the deep sea.
Abstract: With anthropogenic impacts rapidly advancing into deeper waters, there is growing interest in establishing deep-sea marine protected areas (MPAs) or reserves. Reserve design depends on estimates of connectivity and scales of dispersal for the taxa of interest. Deep-sea taxa are hypothesized to disperse greater distances than shallow-water taxa, which implies that reserves would need to be larger in size and networks could be more widely spaced; however, this paradigm has not been tested. We compiled population genetic studies of deep-sea fauna and estimated dispersal distances for 51 studies using a method based on isolation-by-distance slopes. Estimates of dispersal distance ranged from 0.24 km to 2028 km with a geometric mean of 33.2 km and differed in relation to taxonomic and life-history factors as well as several study parameters. Dispersal distances were generally greater for fishes than invertebrates with the Mollusca being the least dispersive sampled phylum. Species that are pelagic as adults were more dispersive than those with sessile or sedentary lifestyles. Benthic species from soft-substrate habitats were generally less dispersive than species from hard substrate, demersal or pelagic habitats. As expected, species with pelagic and/or feeding (planktotrophic) larvae were more dispersive than other larval types. Many of these comparisons were confounded by taxonomic or other life-history differences (e.g. fishes being more dispersive than invertebrates) making any simple interpretation difficult. Our results provide the first rough estimate of the range of dispersal distances in the deep sea and allow comparisons to shallow-water assemblages. Overall, dispersal distances were greater for deeper taxa, although the differences were not large (0.3-0.6 orders of magnitude between means), and imbalanced sampling of shallow and deep taxa complicates any simple interpretation. Our analyses suggest the scales of dispersal and connectivity for reserve design in the deep sea might be comparable to or slightly larger than those in shallow water. Deep-sea reserve design will need to consider the enormous variety of taxa, life histories, hydrodynamics, spatial configuration of habitats and patterns of species distributions. The many caveats of our analyses provide a strong impetus for substantial future efforts to assess connectivity of deep-sea species from a variety of habitats, taxonomic groups and depth zones.

100 citations

Journal ArticleDOI
18 Aug 2005-Protist
TL;DR: A single or double amino acid insertion at the monomer-monomer junction of the universal eukaryotic protein polyubiquitin is unique to Cercozoa and Foraminifera, closely related 'core' phyla in the protozoan infrakingdom Rhizaria.

98 citations


Cited by
More filters
Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations

01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Book ChapterDOI
15 Mar 2012

1,516 citations

Journal ArticleDOI
Colomban de Vargas1, Colomban de Vargas2, Stéphane Audic1, Stéphane Audic2, Nicolas Henry1, Nicolas Henry2, Johan Decelle1, Johan Decelle2, Frédéric Mahé1, Frédéric Mahé3, Frédéric Mahé2, Ramiro Logares4, Enrique Lara, Cédric Berney2, Cédric Berney1, Noan Le Bescot2, Noan Le Bescot1, Ian Probert1, Ian Probert2, Margaux Carmichael5, Margaux Carmichael2, Margaux Carmichael1, Julie Poulain6, Sarah Romac2, Sarah Romac1, Sébastien Colin2, Sébastien Colin5, Sébastien Colin1, Jean-Marc Aury6, Lucie Bittner, Samuel Chaffron7, Samuel Chaffron8, Micah Dunthorn3, Stefan Engelen6, Olga Flegontova9, Olga Flegontova10, Lionel Guidi2, Lionel Guidi1, Aleš Horák9, Aleš Horák10, Olivier Jaillon6, Olivier Jaillon2, Olivier Jaillon11, Gipsi Lima-Mendez7, Gipsi Lima-Mendez8, Julius Lukeš12, Julius Lukeš9, Julius Lukeš10, Shruti Malviya5, Raphael Morard13, Raphael Morard1, Raphael Morard2, Matthieu Mulot, Eleonora Scalco14, Raffaele Siano15, Flora Vincent5, Flora Vincent7, Adriana Zingone14, Céline Dimier2, Céline Dimier5, Céline Dimier1, Marc Picheral2, Marc Picheral1, Sarah Searson2, Sarah Searson1, Stefanie Kandels-Lewis16, Tara Oceans Coordinators17, Silvia G. Acinas4, Peer Bork18, Peer Bork16, Chris Bowler5, Gabriel Gorsky1, Gabriel Gorsky2, Nigel Grimsley19, Nigel Grimsley2, Pascal Hingamp20, Daniele Iudicone14, Fabrice Not1, Fabrice Not2, Hiroyuki Ogata17, Stephane Pesant13, Jeroen Raes7, Jeroen Raes8, Michael E. Sieracki21, Michael E. Sieracki22, Sabrina Speich23, Sabrina Speich5, Lars Stemmann1, Lars Stemmann2, Shinichi Sunagawa16, Jean Weissenbach11, Jean Weissenbach6, Jean Weissenbach2, Patrick Wincker11, Patrick Wincker6, Patrick Wincker2, Eric Karsenti16, Eric Karsenti5 
22 May 2015-Science
TL;DR: Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies.
Abstract: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

1,378 citations