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7 Posts tagged with the phylogenetics tag
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Large centipedes and larger datasets

 

Dr Greg Edgecombe, Department of Earth Sciences, NHM

 

27th January - 4.00 pm

 

Earth Sciences Seminar Room (Basement, WEB 05, formerly Mineralogy Seminar Room)

                                         

Scolopendromorpha includes the largest and most fiercely predatory centipedes, totalling more than 700 species.  Subjected to phylogenetic analysis since the late 1990s, early studies drew on small sets of external morphological characters, mostly those used in classical taxonomic works.

 

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Scolopendra gigantea

 

In order to bolster the character sample, new anatomical data were worked up by systematically sampling the group’s diversity in order to formulate new characters from understudied structures/organ systems. Simultaneously, targeted sequencing of a few markers for a small (but growing) number of species provided the first molecular estimates of phylogeny.  These have resulted in stable higher-level relationships that predict a single origin of blindness in three lineages that share this trait, and are now backed up by transcriptomic datasets with high gene occupancy. Explicit matrices of morphological characters and fossils coded as terminal taxa remain vital to “total evidence” dating/tip dating of the tree.

 

More information on attending seminars at http://www.nhm.ac.uk/research-curation/news-events/seminars/

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Robert W. Scotland, Department of Plant Sciences, University of Oxford

 

Wednesday 9 July 11:00

 

Sir Neil Chalmers seminar room, Darwin Centre LG16 (below Attenborough studio)

 

 

The collective efforts of taxonomists over time has played a pivotal role in identifying many natural groups of monophyletic taxa.  How this task has been achieved is by no means clear given that for much of the history of taxonomy there has been no universally agreed method for discovering taxa. Nevertheless, many monophyletic taxa were discovered through the identification of shared characters (novelties, special similarities, synapomorphies, taxic homologues, good characters, conserved characters).  It seems the history of taxonomy is the history of ‘character weighting’ in favour of some characters being useful and others not. In more recent times all characters have been considered phylogenetically useful but only at the appropriate hierarchical level. Thus phylogenetic analysis of morphological data has become akin to the study of character evolution. 

 

In this talk I will show that morphological traits are poorly correlated with phylogeny and that measures ofphylogenetic diversity in conservation may not maximize feature diversity. Furthermore, because the probability of two random binary characters being compatible with each other converges to zero exponentially quickly as the number of taxa grows, then compatibility is best able to accurately discover and distinguish evolutionary novelty.

 

More information on attending seminars at http://www.nhm.ac.uk/research-curation/news-events/seminars/

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Monotropa.jpg

 

Phylogenetics and evolution of some early and oddball plants

 

Sean Graham

University of British Columbia

 

Friday 8 November 11:00
Sir Neil Chalmers seminar room, Darwin Centre LG16 (below Attenborough studio)


My research group works on multiple problematic nodes in the plant Tree of Life. Here I focus on two major subjects from phylogenetic and evolutionary perspectives: (1) The 'early' aquatic flowering-plant family Hydatellaceae; (2) the mycoheterotophic plants, which are diverse lineages of non-photosynthetic plants that rely on fungi for their carbon budget.

 

 

For additional details on attending this or other seminars see http://www.nhm.ac.uk/research-curation/seminars-events/index.html

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Thomas Simonsen has published an invited peer-reviewed paper in Arthropod Structure and Development in collaboration with co-workers from the Finnish Museum of Natural History and Naturalis (Dutch Museum of Natural History) on the continuing importance of morphology in Lepidoptera systematics.

 

Taxonomy and systematics are areas of science that are focused on description, naming, classification and evolutionary relationships of living things.  Such science is the fundamental reason for the existence of large natural history collections, and traditionally the focus has been on morphology - the use of combinations of physical characters such as number of legs, wing patterns or body form.  The differences in these characters between species can be compared and allow identification - so a fly will have one pair of wings but a bee will have two pairs, for example. Over time, different species and groups have diverged as a result of evolution and in general become progressively more different in form.

 

However, while morphology is a key tool in understanding diversity, evolutionary difference can be seen also in molecules, particularly DNA.  DNA of different species can be compared and the degree of difference used to assess patterns of evolution and relationships.  The use of DNA in taxonomy and systematics is of increasing importance and museum collections are of great value in this new science - a purpose never suspected by those who started to assemble them in the 18th and 19th Centuries.

 

Wallace birdwing NaturalHistoryMuseum_PictureLibrary_056153_IA.jpgOrnithoptera croesus, Wallace's golden birdwing butterfly - a member of the Paplionidae family

 

Some scientists have argued that DNA alone will be used in future to assess diversity and to identify species: it is after all DNA differences that are the root cause of morphological difference - so why use both?  There are in fact a number of reasons why morphological techniques will be of continuing importance - Thomas and colleagues explore the relative value of morphology and molecular information for large groups of butterflies in this paper.

 

They reviewed the morphological characters that are important for understanding butterfly phylogeny and evolution in the context of large-scale molecular phylogenies (evolutionary classifications) of the group. In particular, they were interested in what the molecular evidence was able to tell them about the evolution of morphological features - so for example, were characters that are used to separate distantly related groups actually caused by large genetic differences?

 

They looked in particular at the families Papilionidae, Nymphalidae and Hesperiidae which have all been studied with a combination of morphological and molecular data in recent years. What they found was that a  scientifically more valuable classification emerged not from using either molecular or morphological techniques, but from using both in combination. They argue that morphology still has an immensely important role to play in butterfly (and insect) phylogenetics - including its value in understanding how the whole organism is important in evolutionary changes, natural selection and diversity.  

 

Simonsen, T. J., de Jong, R., Heikkilä, M. & Kaila, L. (2012). Butterfly morphology in a molecular age – does it still matter in butterfly systematics? Arthropod Structure and Development. 41: pp. 307-322.

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Different ideas of the relationship between the crustacea (crabs, barnacles, copepods and others) and insects have been discussed at length over the past century. The emergence of more and better DNA information is allowing the evolutionary relationships to be explored and clarified.


Ronald Jenner (Zoology) co-authored a first phylogenomic test of the recent hypothesis of a sister group relationship between hexapods (insects) and remipede crustaceans. Numerous data and testing of different interpretations led the authors to robustly find hexapods and remipedes as sister groups.


Remipede crustaceans were first described as Carboniferous fossils in the 1950s (around 310 million years old).  However, living species have been discovered since 1979, living only in underground aquifers connected to the sea. They are slow-moving with relatively basic segmented body plans, but can have specialised characteristics such as poison fangs and advanced sense of scent, important for securing prey in their unusual habitat.

 

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A Remipede from Mexico

 

The paper looks at the idea of the Pancrustacea - a large group containing both crustaceans and insects.  The data support the idea that the Pancrustacea can be divided into two major groups.  In the first are the marine decapods (crabs, prawns and lobsters), barnacles and copepods.  In the second group are found the freshwater Branchiopoda (such as the familar waterflea Daphnia), the Remipedes and the insects.  This supports the insects as a part of the Pancrustacea, possibly as part of a subgroup that moved from shallow marine environments to specialist freshwater, groundwater and terrestrial habitats.

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von Reumont, B. M., Jenner, R. A., Wills, M. A., Dell’Ampio, E., Pass, G., Ebersberger, I., Meyer, B., Koenemann, S., Iliffe, T. M., Stamatakis, A., Niehuis, O., Meusemann, K. and Misof, B. Early online. Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the sister group of Hexapoda. Molecular Biology and Evolution (doi:10.1093/molbev/msr270)  Abstract

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Bryozoans are widespread aquatic colonial animals living both in the sea (sea mats) and fresh waters, with an extensive marine fossil record over almost 500 million years. Collaborating research groups in the NHM Departments of Zoology and Palaeontology represent arguably the strongest concentration of bryozoan research expertise anywhere in the world.

 

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Wilbertopora woodwardi (Brydone) from the Upper Cretaceous Chalk, Hampshire

 

Andrea Waeschenbach (NERC Postdoctoral Fellow, Zoology), Paul Taylor (Palaeontology) and Tim Littlewood (Zoology) have had accepted for publication the most comprehensive molecular phylogeny of bryozoans to date, using mitochondrial and ribosomal genes.

 

This has resulted in a well supported topology (the shape of the phylogenetic tree), providing unambiguous evidence for the interrelationship of the taxonomic classes.  It also provides strong evidence that several presently recognized taxonomic units at various hierarchical levels are each in fact of more than one origin in evolutionary terms - they are non-monophyletic (a monophyletic group has a single ancestor)

 

Using this topology, the work tried to establish the likely larval form and strategy of the ancestral bryozoans, but this gave ambiguous results.  It seems most likely that multiple shifts have occurred between different types of larval nutrition – dependency on yolk provided to the egg (lecithotrophy) and feeding by the bryozoan larva on phytoplankton (planktotrophy).

 

This result, combined with their long fossil record, promises bryozoans to be a suitable phylum to studying links between reproductive strategy and large scale evolutionary patterns, such as speciation rates. This paper is a significant contribution for assessing the interrelationships in a relatively neglected group that offers much promise as an evolutionary model. This work was funded by NERC (NE/E015298/1).

 

Waeschenbach, A., Taylor, P.D., Littlewood, D.T.J. (2011) A molecular phylogeny of bryozoans, Molecular Phylogenetics and Evolution. http://dx.doi.org/10.1016/j.ympev.2011.11.011

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Myxozoans are a diverse group of microscopic endoparasites - tiny worm-like parasites that live within other organisms, depending on their hosts for nutrition, oxygen and other needs.  Examples of myxozoans featured as NHM species of the day in 2010 were  Buddenbrockia plumatellae  and Tetracapsuloides bryosalmonae.

Scientific study of evolution and evolutionary relationships has in the past often depended on study of the physical forms of organisms (morphology) and comparing particular characteristics, such as body plan, organs, limbs or other features. Similarities and differences in these characters are used to classify the organisms.  However, with some organisms, particularly parasites, evolution can result in the loss of features with an apparently more simple body form.  This makes clarification of relationships difficult.  However, the use of DNA sequences can provide additional information that leads to understanding of evolutionary relationships and a clear evolutionary classification (phylogeny).

Myxozoans have been the focus of much controversy regarding their phylogenetic position. Two dramatically different hypotheses have been put forward for the position of the Myxozoa within Metazoa (all multicelled animals).

The first hypothesis, supported by rDNA sequence data (a specific kind of DNA from the ribosomes of the cell), suggests that Myxozoa is a sister group to Bilateria (all organisms with a single line of symmetry to their body plan, ranging from simple worms to humans, and representing most groups of animals). However, the alternative hypothesis, supported by phylogenomic data (a broader range of DNA) and morphology, suggests that Myxozoan are cnidarian. Cnidarians are an animal group containing sea anemones, coral and jellyfish that have radial symmetry and a very different body plan from the Bilateria.  These different ideas represent evolutionary events that would have occurred hundreds of millions of years ago.

Professor Beth Okamura (NHM department of Zoology) and colleagues, funded by the US National Science Foundation, investigated these conflicting hypotheses with Buddenbrockia and explored the effects of missing data, different statistical methods, and different models on evolutionary classification.  In addition, they identified subsets of the data that most influence the placement of Myxozoa and explored their effects by removing them from the datasets.

The results confirm the existence of two relatively stable placements for myxozoans and demonstrate that conflicting signal exists not only between the two types of data but also within the phylogenomic dataset. These analyses underscore the importance of careful model selection, taxon and data sampling, and in-depth data exploration, when investigating the phylogenetic placement of highly divergent taxa.

In other words, the  available information does not yet allow Myxozoans to be placed  definitely within one or other fundamental group - further development of data, and new scientific techniques will be needed to answer this question, but the work in the paper is important in defining the current limits and uncertainties of this area of science, and suggests ways forward for the future.

Evans, N.M., Holder, M.T., Barbeitos, M.S., Okamura, B. & Cartwright, P. 2010. The phylogenetic position of Myxozoa: Exploring conflicting signals in phylogenomic and ribosomal datasets. Molecular Biology and Evolution 27: 2733-2746. doi:10.1093/molbev/msq159