The paper introducing our new tree visualisation tool Phylo.io was just published in MBE.
Yet another tool to display trees, you might say, and indeed, so it is. But for all the tools that have been developed over the years, there are very few that scale to large trees, make it easy to compare trees side-by-side, and simply run in a browser on any computer or mobile device.
To fill this gap, we created Phylo.io.
Story behind the paper
The project started as a student summer internshi........ Read more »
Robinson, O., Dylus, D., & Dessimoz, C. (2016) Phyla.io: interactive viewing and comparison of large phylogenetic trees on the web . Molecular Biology and Evolution. DOI: 10.1093/molbev/msw080
We know homologs are genes related by common ancestry. But throw complex evolutionary events into the mix and things can get little dicey. Under the umbrella of homologs exist many different categories: orthologs, paralogs, ohnologs, xenologs, co-ortholog, in-paralogs, out-paralogs, paleologs, among others. All of these —log terms have a specific meaning (see my previous blog post on orthology and paralogy), but now we will focus on one in particular: homoeologs.
But before we get into ........ Read more »
Glover, N., Redestig, H., & Dessimoz, C. (2016) Homoeologs: What Are They and How Do We Infer Them?. Trends in Plant Science. DOI: 10.1016/j.tplants.2016.02.005
This is how molecular systematics has worked since the sixties: you take some identifiable feature (e.g. a gene or a protein) common to a group of species and take some measurements of it (e.g. sequencing the DNA). By comparing the results of these measurements you can estimate the evolutionary tree that links the species. Shortly after people started doing this they realised there was a problem: when analyses are based different genes they often estimate different —incongruent — evo........ Read more »
Earthworm taxonomists describing what they do to a layperson is hilarious to watch. Laypeople often have a difficult time understanding the concept of a species – you will regularly hear statements that there are only 50 insect species, for example. Insect species often differ in colour and patterning, so it’s easy to then correct a layman’s misconceptions about […]
The post The Tree of Earthworms appeared first on Teaching Biology.
... Read more »
Domínguez, J., Aira, M., Breinholt, J., Stojanovic, M., James, S., & Pérez-Losada, M. (2015) Underground evolution: New roots for the old tree of lumbricid earthworms. Molecular Phylogenetics and Evolution, 7-19. DOI: 10.1016/j.ympev.2014.10.024
DNA obtained for the first time from extinct Carolina parakeets reveals their closest relatives and provides insight into the evolution of New World parrots... Read more »
Jeremy J. Kirchman, Erin E. Schirtzinger, & Timothy F. Wright. (2012) Phylogenetic relationships of the extinct Carolina Parakeet (Conuropsis carolinensis) inferred from DNA sequence Data. The Auk, 129(2), 197-204. info:/10.1525/auk.2012.11259
Manuel Schweizer, Ole Seehausen, & Stefan T. Hertwig. (2011) Macroevolutionary patterns in the diversification of parrots: Effects of climate change, geological events and key innovations. Journal of Biogeography, 38(11), 2176-2194. info:/10.1111/j.1365-2699.2011.02555.x
Fredy Montero was very kind to send me his recent publication (with Maira Ortiz) describing morphological characters of eggs, larvae and pupae of the satyrine butterfly genus Junea.
They raised the specimens on the hostplant Chusquea in Colombia. What I found most interesting is the morphology of the last instars of the larva. They have very long "horns" and long bifid "tails".... Read more »
Carlos Peña, Niklas Wahlberg, Elisabet Weingartner, Ullasa Kodandaramaiah, Sören Nylin, André V.L. Freitas, Andrew V.Z. Brower. (2006) Higher level phylogeny of Satyrinae butterflies (Lepidoptera: Nymphalidae) based on DNA sequence data. Molecular Phylogenetics and Evolution, 40(1), 29-49. DOI: 10.1016/j.ympev.2006.02.007
Our commentary on Douglas Theobald's test from Universal Common Ancestry (UCA) just went online. The original idea was to make a user-friendly review of his analysis described in "A formal test of the theory of universal common ancestry", but after a long e-mail exchange between Douglas and us -- actually between him and David, I didn't say much -- we decided to expand the article to include some remaining points of skepticism and spell out the basic problem with his approach.His work His test f........ Read more »
Leonardo de Oliveira Martins, David Posada. (2012) Proving universal common ancestry with similar sequences. Trends in Evolutionary Biology, 14(1). info:/10.4081/eb.2012.e5
Theobald, D. (2010) A formal test of the theory of universal common ancestry. Nature, 465(7295), 219-222. DOI: 10.1038/nature09014
It’s not often that flies make headlines, and when they do it’s usually in a negative connotation (malaria, mosquitoes, black flies, etc). A new paper published Tuesday in PLoS ONE (Core et al, 2011) is certainly not helping this Detrimental Diptera Dillema (DDD), announcing that a species of scuttle fly (Phoridae) has been discovered parasitizing [...]
... Read more »
Core, A., Runckel, C., Ivers, J., Quock, C., Siapno, T., DeNault, S., Brown, B., DeRisi, J., Smith, C., & Hafernik, J. (2012) A New Threat to Honey Bees, the Parasitic Phorid Fly Apocephalus borealis. PLoS ONE, 7(1). DOI: 10.1371/journal.pone.0029639
BROWN, B. (1993) Taxonomy and preliminary phylogeny of the parasitic genus Apocephalus, subgenus Mesophora (Diptera: Phoridae). Systematic Entomology, 18(3), 191-230. DOI: 10.1111/j.1365-3113.1993.tb00662.x
After running a Bayesian phylogenetic analysis we are usually left with a large collection of trees, that came from the posterior distribution of the model given our data. Then if we want to work with a single tree - that is, to have a point estimate of this posterior distribution of trees - the most usual ways are to calculate the consensus tree or to select the most frequent tree. There are other ways, but let's fix on those by now.We might not be aware of it, but when we choose for one or ano........ Read more »
This post is going to be longer and a little more technical than normal; feel free to jump in and out, or just check out some of the photos on your way to the conclusions. Although I may come across as critical and occasionally cynical at times, I’m not picking on anyone just to be [...]... Read more »
Africa has a new, old wolf. An animal that was previously called a subspecies of the golden jackal in Egypt has now been found to be a very rare relict species hiding in plain sight — an ancient gray wolf line still living today. Previously, it was thought that the Ethiopian wolf (Canis simensis) was [...]... Read more »
Eli Knispel Rueness, Maria Gulbrandsen Asmyhr, Claudio Sillero-Zubiri, David W. Macdonald, Afework Bekele, Anagaw Atickem, Nils Chr. Stenseth. (2011) The Cryptic African Wolf: Canis aureus lupaster Is Not a Golden Jackal and Is Not Endemic to Egypt . PLoS ONE, 6(1). info:/10.1371/journal.pone.0016385
This newly published study finds that thoroughbred racehorses, which originated in Europe, descended from a number of British and Irish native breed foundation mares... Read more »
Bower, M., Campana, M., Whitten, M., Edwards, C., Jones, H., Barrett, E., Cassidy, R., Nisbet, R., Hill, E., Howe, C.... (2010) The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares. Biology Letters. DOI: 10.1098/rsbl.2010.0800
I just came back from SMBE2010, where I presented a poster about our recombination detection software and had the chance to see awesome research other people are doing. The poster can be downloaded here (1.MB in pdf format) and I’m distributing it under the Creative Commons License. Given the great feedback I got from other [...]... Read more »
de Oliveira Martins, L., Leal, É., & Kishino, H. (2008) Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees. PLoS ONE, 3(7). DOI: 10.1371/journal.pone.0002651
Oliveira Martins, L., & Kishino, H. (2009) Distribution of distances between topologies and its effect on detection of phylogenetic recombination. Annals of the Institute of Statistical Mathematics, 62(1), 145-159. DOI: 10.1007/s10463-009-0259-8
Posted by Victor Hanson-Smith Check-out this paper by Inna S. Povolotskaya and Fyodor A. Kondrashov. (It’s a closed-access Nature article; I’m sorry if you do not have a subscription!) The premise of this paper begins with two claims. First, protein-sequence space is finite. Second, proteins have been evolving away from one other (“expanding in sequence [...]... Read more »
Povolotskaya, I., & Kondrashov, F. (2010) Sequence space and the ongoing expansion of the protein universe. Nature, 465(7300), 922-926. DOI: 10.1038/nature09105
Despite I’m very charitable when testing my own programs, I’m not so nice when asked to scrutinize other people’s work. That’s why I was happy to see the announcement about the ALTER web server being published at Nucleic Acids Research (open access!). I am not involved in the project, but I was in the very [...]... Read more »
Glez-Pena, D., Gomez-Blanco, D., Reboiro-Jato, M., Fdez-Riverola, F., & Posada, D. (2010) ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Research. DOI: 10.1093/nar/gkq321
Recently a paper about the software MANTiS called my attention, and I’ve been trying to write about it for a while. This announcement at the EvolDir list seemed like the perfect opportunity. I must warn you though that I’ve never used the software and I don’t have any intimacy with the underlying databases, but the [...]... Read more »
Milinkovitch, M., Helaers, R., & Tzika, A. (2009) Historical Constraints on Vertebrate Genome Evolution. Genome Biology and Evolution, 13-18. DOI: 10.1093/gbe/evp052
Tzika, A., Helaers, R., Van de Peer, Y., & Milinkovitch, M. (2007) MANTIS: a phylogenetic framework for multi-species genome comparisons. Bioinformatics, 24(2), 151-157. DOI: 10.1093/bioinformatics/btm567
In recent years there has been an explosion of parallel algorithms for solving bioinformatics problems, namely phylogenetic reconstruction and sequence alignment. These algorithms follow the growth of new hardware solutions like Field-Programmable Gate Arrays (integrated circuits capable of performing simple instructions in parallel), Cell microprocessors (like the one inside Playstation 3), Graphics Processing Units (nvidia [...]... Read more »
Galvez, S., Diaz, D., Hernandez, P., Esteban, F., Caballero, J., & Dorado, G. (2010) Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment. Bioinformatics, 26(5), 683-686. DOI: 10.1093/bioinformatics/btq017
Manavski, S., & Valle, G. (2008) CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics, 9(Suppl 2). DOI: 10.1186/1471-2105-9-S2-S10
I'm going to be lazy and leech off the Mystery Micrograph again. None of you saner people (non-protistgeeks) seem to have taken advantage of the massive handicap, and subsequent hint. Seriously, type in "testate amoebae" in Google image search, and it's on the first page! Perhaps I should do a tutorial on some methods of attacking those mystery images...Quite shockingly(not!), Opisthokont got the last one. I agree with his statement that that was like shooting fish in a barrel, but easier since ........ Read more »
BODYL, A., MACKIEWICZ, P., & STILLER, J. (2007) The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles?. Trends in Microbiology, 15(7), 295-296. DOI: 10.1016/j.tim.2007.05.002
Keeling, P. (2004) Diversity and evolutionary history of plastids and their hosts. American Journal of Botany, 91(10), 1481-1493. DOI: 10.3732/ajb.91.10.1481
LARA, E., HEGER, T., MITCHELL, E., MEISTERFELD, R., & EKELUND, F. (2007) SSU rRNA Reveals a Sequential Increase in Shell Complexity Among the Euglyphid Testate Amoebae (Rhizaria: Euglyphida). Protist, 158(2), 229-237. DOI: 10.1016/j.protis.2006.11.006
NOWACK, E., MELKONIAN, M., & GLOCKNER, G. (2008) Chromatophore Genome Sequence of Paulinella Sheds Light on Acquisition of Photosynthesis by Eukaryotes. Current Biology, 18(6), 410-418. DOI: 10.1016/j.cub.2008.02.051
THEISSEN, U., & MARTIN, W. (2006) The difference between organelles and endosymbionts. Current Biology, 16(24). DOI: 10.1016/j.cub.2006.11.020
Yoon, H., Reyes-Prieto, A., Melkonian, M., & Bhattacharya, D. (2006) Minimal plastid genome evolution in the Paulinella endosymbiont. Current Biology, 16(17). DOI: 10.1016/j.cub.2006.08.018
Some weeks ago, I discussed a large phylogenetic study that separated sticklebacks from the seahorses and pipefishes - today we're going to discuss a phylogenetics paper that zooms in on the relationships between different sticklebacks(and their very closest relatives).Many of the same scientists from the earlier stickleback phylogeny were involved in this paper, though there is one new face, Yale's Tom Near, a longtime Wainwright Lab collaborator and former CPB Postdoc.The group sequenced the m........ Read more »
KAWAHARA, R., MIYA, M., MABUCHI, K., NEAR, T., & NISHIDA, M. (2009) Stickleback phylogenies resolved: Evidence from mitochondrial genomes and 11 nuclear genes. Molecular Phylogenetics and Evolution, 50(2), 401-404. DOI: 10.1016/j.ympev.2008.10.014
Until recently, sticklebacks were thought to be pretty closely related to seahorses and pipefish. At first glance, it seems reasonable: both groups of fish have bony armor plates, male parental care, and species with elongated bodies and snouts. Many of the species also share a mode of swimming called "labriform" that I'll be talking about more in a later entry.So, the pipefishes and sticklebacks share parental care, bony armor, elongation, swimming mode - seems like a slam dunk, right? Wrong.T........ Read more »
KAWAHARA, R., MIYA, M., MABUCHI, K., LAVOUE, S., INOUE, J., SATOH, T., KAWAGUCHI, A., & NISHIDA, M. (2008) Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts. Molecular Phylogenetics and Evolution, 46(1), 224-236. DOI: 10.1016/j.ympev.2007.07.009
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
Research Blogging is powered by SMG Technology.
To learn more, visit seedmediagroup.com.