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April 9, 2013

Department of Life Sciences Seminar


A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini) and its implication for biogeography and Indo-Pacific Rattini systematics


Pierre-Henri Fabre

Synthesys visitor, University of Montpellier


Friday 12th April 11:00
Sir Neil Chalmers seminar room, Darwin Centre LG16 (below Attenborough studio)

We describe Halmaheramys bokimekot Fabre et al. a new genus and new species of murine rodent from the North Moluccas and study its phylogenetic placement using both molecular and morphological data. We generated a taxonomically densely sampled mitochondrial and nuclear DNA data set that included almost all genera of Indo-Pacific Murinae. We then used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a LAGRANGE analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo-Pacific archipelagos. We provide a new comprehensive molecular phylogenetic reconstruction for the Indo-Pacific Murinae with a focus on the Rattus division. Based on previous results and those presented in this study, we define a new Indo-Pacific group within the Rattus division: comprised of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstruction reveals a relatively recent diversification from the Middle-Miocene to Plio-Pleistocene associated with several major dispersal events. We identified two independent Indo-Pacific origins from both Western and Eastern Indo-Pacific archipelagoes to the isolated Halmahera island that led to the speciations of Halmaheramys bokimekot and Rattus morotaiensis. We propose that Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival from the Eastern Wallacea of the Halmaheramys ancestors. Halmaheramys bokimekot Fabre et al. sp. nov., is described in detail and its systematics and biogeography documented and illustrated.




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Protists, other small organisms, and Next Generation Sequencing: A forum for ideas, news, information, and exchange


10-12 April 2013, Flett Theatre, Natural History Museum


Joint meeting between the British Society for Protist Biology and the Linnean Society


This meeting will be an exciting forum for exchange of knowledge, experiences, and learning about new experimental and analytical methods associated with NGS, from data generation to analysis.




Weds 10 April


1500                         Registration & poster hanging


1700                        Keynote Lecture: Chris Quince

                        The challenges and opportunities of microbial metagenomics



Thurs 11 April


0900                        Sequencing – a field guide

                        Konrad Paskiewicz & Karen Moore


1100                        Coffee


1130                        Macroecological patterns and processes in the benthic marine microbial biosphere

                        Si Creer


1215                        Placing short environmental next generation sequencing amplicons from microbial eukaryotes into a phylogenetic context

                        Micah Dunthorn


1300                        Lunch & poster session


1410                        Can amoebae ‘see’ red?

                        Jackie Parry


1435                        The curiosity of histidine phosphatases in trypanosomatid parasites

                        Amber Lynch


1500                        Desmodesmus: a model organism for investigating the origin of multicellularity

                        Elliot Shubert


1525                        Genotypic diversity of endosymbiotic algae originating from Paramecium bursaria and Euplotes daidaleos

                        Undine Achilles-Day


1550                        Tea


1620                        Revealing hidden plankton diversity in the Orkney Islands, UK; 18S rRNA gene amplicon sequencing using an Ion torrent PGM

                        Joe Taylor


1645                        Isolating genomic DNA from Lagenophrys tattersalli (Ciliophora: Peritrichia) and new insights into lagenophryid biology

                        Robert Mansergh


1710                        AGM - all welcome




Fri 12 April


0900                        The use of QIIME (Quantitative Insights Into Microbial Ecology) in  microbial community ecology – a case study

                         Serena Thomson


0945                        High performance computing infrastructure developed for phylogenomic analyses           

                        Kamran Shalchian-Tabrizi           


1030                        Transparent clustering method for cryptic molecular species of protists

                        Frédéric Mahé


1100                       Coffee


1130                        Ocean Sampling Day (OSD)

                        Dawn Field


1215                        Comparative and functional genomics in Entamoeba parasites

                        Neil Hall


1300                        Lunch & poster session


1410                        Flow cytometric identification of Mamiellales clade II in the Southern Atlantic Ocean

                        Mike Zubkov


1435                        Targeting essential amino acid biosynthesis pathways within Acanthamoeba spp.

                        Chris Rice


1500                        Eukaryotic fauna on the sand filters of water treatment plants: Artificial lake bottoms dominated by protozoa

                        Christoffer Bugge Harder


1525                        A six-gene phylogeny provides new insights into choanoflagellate evolution

                        Martin Carr


1550                        Tea & end of meeting



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Thursday 11th April




4.00 pm

One way of forest plants to make their living in deep shade: eating mycorrhizal fungi.

Mark Andre Selosse, Muséum national d’Histoire Naturelle,Paris, & Centre d'Ecologie Fonctionnelle et Evolutive Montpellier  


The evolution of land plants provided repeated emergences of mycoheterotrophy, where achlorophyllous plants exploit carbon from their mycorrhizal fungi. I will briefly review the current knowledge on mycoheterotrophs, mainly orchids and Montropoideae (Ericaceae), and their specific basidiomycetous fungal partners, that also form ectomycorrhizae with surrounding trees. By contrast, subtropical and tropical species often connect to arbuscular-mycorrhizal fungi, or even to saprotrophic basidiomycetes. I will then focus on the evolution from the ‘usual’ mycorrhizal functioning (where autotrophic plants furnish carbon to fungi) to mycoheterotrophy. Intermediate evolutionarily steps were discovered, i.e. green, photosynthetic plants that partly use carbon from their mycorrhizal fungi. This mixotrophic nutrition pre-disposed to evolution of mycoheterotrophy. In some mixotrophic, green orchids, the rare survival of achlorophyllous plants (albinos) further supports the use of fungal carbon. Our investigations of albinos‘ nutrition and fitness nevertheless clarify why emergence of mycoheterotrophy is rare in evolution of mixotrophs, and thus why mixotrophy can be evolutionarily metastable.




4.30 pm

Evolutionary history of mycorrhizas

Christine Strullu-Derrien, Dept. of Earth Sciences, NHM


Nowadays fungi form widespread mutualistic associations with over 90% of plant species. Of the two predominant types, the most common and widespread are the arbuscular mycorrhizas (AM), which are endomycorrhizas in which hyphae form distinctive branched structures (arbuscules) in cells. In contrast, in ectomycorrhizas  (ECM) the fungus ensheaths the outer surface of roots and forms a net-like reticulum between the cells of the root epidermis and the cells of the cortex. The link between plants and their fungal associates is known to go back to the dawn of life on land, and endomycorrhizas are among the first documented in the Early Devonian. The earliest well-documented fossils with diagnostic evidence for ECM symbioses are reported from the Eocene. I will present an overview of the current knowledge on fossil mycorrhizas including our recent findings from the investigation of the NHM slide collections.




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The roles of paleoclimates, mineralogy and geochemistry in forming anomalies on interfaces in areas of basin cover: implications for exploration



Ravi Anand

CSIRO Earth Science and Resource Engineering, Western Australia


Wednesday 10th April - 12.00

Mineralogy Seminar Room 



Transported cover provides significant challenges to geochemical exploration as dispersion of indicator elements to the surface is restricted. Conventional approaches (e.g. soil and lag sampling) may not be viable in many areas of transported cover and various selective extraction methods have had only limited success in deeply weathered and arid terrains than in terrains with recent glacial or volcanic cover. An alternative approach to the direct detection of element dispersion from mineralisation through transported regolith is the identification of the more general effects of oxidising sulphide mineralisation on regolith mineralogy and pH. Approaches to detect these features have been developed, but their application has met with limited success.

In Australia, exploration is progressively moving to areas of deep transported cover (>30 m). Given the cost of deep drilling, high density sampling of weathered basement beneath the unconformity is no longer cost effective and so new exploration approaches are needed. A variety of transported cover sediments, ranging from Quaternary to Permian, are common in Australian landscapes. These have been subjected to weathering under a variety of climates. The Quaternary climate differed from Tertiary and Cretaceous climates, resulting in distinct styles of weathering and mineralogical features. This presentation provides a  synthesis on the  importance of an integrated approach combining different metal migration mechanisms with the nature of transported regolith, landscape history and climate settings to obtain the best prediction of anomaly formation and guide exploration strategies. 

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Department of Life Sciences Seminar



What a difference a decade makes – Recapping the last 10 years of bryozoan phylogenetics and future prospects


Andrea Waeschenbach

Parasites and Vectors, Dept.of Life Sciences, NHM


Wednesday 10 of April 11:00
Sir Neil Chalmers seminar room, Darwin Centre LG16 (below Attenborough studio)

Since the first bryozoan molecular phylogenetic study just over decade ago, the field has come a long way, battling the enemies of sequence contamination, long-branch attraction, and misidentification. In this talk I will recount how some of these obstacles have been overcome, recap key results that were gathered along the way, and outline some future research lines of molecular bryozoology in the era of next-generation sequencing (NGS). Bryozoan colonies provide microhabitats for many other organisms including bacteria, fungi, diatoms, ciliates, nematodes, copepods, ostracods, sponges, molluscs, entoprocts and turbellarian flatworms, providing ample opportunities for co-extraction and co-amplification during PCR, resulting in frequently contaminated datasets. This has been having important implications for bryozoan interrelationships and metazoan-wide phylogenetic inferences, which will be discussed. The comparatively fast rate of molecular evolution of bryozoans often results in them forming clades with other long-branching taxa, such as chaetognaths and platyhelminths. By using a model of sequence evolution that accounts for heterogeneity in amino acid composition across sites and across lineages, our results provide an alternative hypothesis, placing phoronids as the sister group to bryozoans, contradicting recent hypotheses of Bryozoa sensu lato, i.e. (Ectoprocta, Entoprocta), and Polyzoa (Ectoprocta (Cycliophora, Entoprocta)). Phylogenetic reconstructions have revealed numerous examples of morphological convergence and plasticity, as well as cryptic species, in all three bryozoans classes, highlighting the importance of using molecular data in assessing species interrelationships and species boundaries, and thus in providing a true estimate of diversity at multiple taxonomic hierarchies. Future work is planned to utilize these instances of convergence to study their effect on species diversification rates, by interpreting a densely sampled phylogenetic framework, constructed using NGS technology, in light of the well-preserved fossil record of bryozoans. Furthermore, using RNA-seq, future work is projected to provide insights into the underlying gene-expression processes involved in the generation of different zooid types produced by a single colony genotype, thus taking the first step in developing bryozoans as a model to study the underlying molecular processes of morphological and functional disparity.





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