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All posts; Tags Include "Phylogenetics"

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  • April 28, 2016
  • 10:45 AM
  • 673 views

Phylo.io a new interactive way of visualising and comparing trees

by Christophe Dessimoz in Open Reading Frame

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 »

  • March 24, 2016
  • 04:16 AM
  • 704 views

What are homoeologs? (story behind the paper)

by Christophe Dessimoz in Open Reading Frame

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 »

  • March 15, 2016
  • 06:42 PM
  • 829 views

New paper “Clustering Genes of Common Evolutionary History”

by Christophe Dessimoz in Open Reading Frame

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 »

Gori K, Suchan T, Alvarez N, Goldman N, & Dessimoz C. (2016) Clustering genes of common evolutionary history. Molecular biology and evolution. PMID: 26893301  

  • February 13, 2015
  • 10:47 AM
  • 1,077 views

The Tree of Earthworms

by Marc in Teaching Biology

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  

  • September 19, 2012
  • 04:00 AM
  • 2,277 views

Extinct Carolina parakeet provides glimpse into evolution of American parrots | @GrrlScientist

by GrrlScientist in GrrlScientist

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

  • July 31, 2012
  • 08:48 AM
  • 1,202 views

Morphology of immature stages of the butterfly genus Junea and its implications

by Carlos Pena in NSG's databases blog

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  

  • May 15, 2012
  • 03:29 PM
  • 816 views

Testing for common ancestry

by Leonardo Martins in bioMCMC

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

  • January 4, 2012
  • 02:39 AM
  • 1,033 views

The Good, the Bad, and the Zombees

by Morgan Jackson in Biodiversity in Focus

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 »

  • August 6, 2011
  • 04:46 PM
  • 738 views

How to summarise a collection of trees that came from a Bayesian analysis

by Leonardo Martins in bioMCMC

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 »

Huggins, P., Li, W., Haws, D., Friedrich, T., Liu, J., & Yoshida, R. (2011) Bayes Estimators for Phylogenetic Reconstruction. Systematic Biology, 60(4), 528-540. DOI: 10.1093/sysbio/syr021  

  • April 11, 2011
  • 01:13 AM
  • 1,948 views

The Fly Tree of Life – Big Science, Big Results?

by Morgan Jackson in Biodiversity in Focus

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 »

Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim JW, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM.... (2011) Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences of the United States of America, 108(14), 5690-5. PMID: 21402926  

  • January 27, 2011
  • 11:58 AM
  • 1,517 views

Africa’s new, old gray wolf

by DeLene Beeland in Wild Muse

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

  • October 28, 2010
  • 10:25 AM
  • 3,577 views

Who's Your Momma? The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares

by GrrlScientist in GrrlScientist

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 »

  • July 12, 2010
  • 06:09 PM
  • 1,700 views

Distribution of recombination distances between trees – poster at SMBE2010

by Leonardo Martins in bioMCMC

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 »

  • June 23, 2010
  • 02:13 AM
  • 1,228 views

Sequence space and the ongoing expansion of the protein universe

by Victor Hanson-Smith in Evolution, Development, and Genomics

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 »

  • May 16, 2010
  • 10:17 PM
  • 1,190 views

fault-tolerant conversion between sequence alignments

by Leonardo Martins in bioMCMC

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  

  • April 27, 2010
  • 07:04 PM
  • 1,285 views

The specialization of novel genes

by Leonardo Martins in bioMCMC

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  

  • March 20, 2010
  • 11:10 PM
  • 2,776 views

Using System-on-a-Chip hardware to speed up alignments

by Leonardo Martins in bioMCMC

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 »

  • October 5, 2009
  • 05:20 AM
  • 3,828 views

Sunday Protist - Euglyphids

by Psi Wavefunction in Skeptic Wonder

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 »

Javaux EJ. (2007) The early eukaryotic fossil record. Advances in experimental medicine and biology, 1-19. PMID: 17977455  

KEELING, P., & ARCHIBALD, J. (2008) Organelle Evolution: What's in a Name?. Current Biology, 18(8). DOI: 10.1016/j.cub.2008.02.065  

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  

  • May 8, 2009
  • 12:00 PM
  • 1,331 views

Stickleblog: The stickleback family tree, part 2

by Sticklematt in Wainwright Lab

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 »

  • March 27, 2009
  • 12:00 PM
  • 1,515 views

Stickleblog: The stickleback family tree

by Sticklematt in Wainwright Lab

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 »

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