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ogy programming linguistics phylogeny systematics 01 july 2014 the evolution of cranial capacity in humans and stem humans hey i m actually writing on the blog s title subject today here s a chart i ve been working on for a while this shows all known human and stem human individuals plotted according to stratigraphy and cranial capacity endocranial volume the fossil individuals with known cranial capacity are highlighted as white circles other fossil individuals probable capacity is inferred from these the chimpanzee range shows the span between a normal female bonobo chimpanzee pan paniscus and a normal male common chimpanzee pan troglodytes begun kordos 2004 the full range for chimpanzees pan is slightly larger but not much the human range shows where about 90 of living humans fall burenhult 1993 update my mistake it s the range of 90 of living humans combined with the range of upper pleistocene humans which is actually higher on average some notes read more posted by mike keesey at 1 19 pm 6 comments labels anthropology charts evolution paleontology primatology stratigraphy 04 march 2014 deeper dive on the phylopic t shirt just to review phylopic is a website featuring freely reusable silhouettes of organisms anybody may submit images under a creative commons license i am attempting to raise funds to host phylopic for the next two years by selling a phylopic t shirt depicting the past half billion years of our evolutionary lineage with free silhouettes we ve come a long way in this post i ll go into more detail about what exactly is on the shirt starting with the final silhouette and going back in time in each entry the taxonomic name links to a page for the image with artist and license information some terminology first concestor means most recent shared ancestor and stem x means not x but more closely related to x than to anything else alive the final silhouette is a modern human homo sapiens sapiens specifically a melanesian woman melanesians and other oceanians represent one of the furthest migrations of humanity from our original geographical range immediately behind her is another homo sapiens sapiens this one a subsaharan african man subsaharan africa is the wellspring of modern humanity this isn t meant to imply an ancestor descendant relationship between the two figures they re just coexisting members of the same subspecies read more posted by mike keesey at 8 00 am no comments labels anthropology evolution funding illustration mammalia paleontology phylogeny phylopic primatology synapsida vertebrata zoology 24 february 2014 half a billion years in the making the phylopic t shirt yes now you can wear phylopic the phylopic t shirt phylopic s silhouettes are free but hosting the site costs money with this shirt i m trying to raise enough to cover basic expenses if 100 of you buy a shirt you will cover phylopic s hosting for the next two years the design uses phylopic silhouettes to depict the evolutionary lineage of humanity starting with the earliest bilaterian animals all of the silhouettes are public domain or available under a creative commons attribution or attibution sharealike license which means the design itself is under a creative commons attibution sharealike license the works of ten artists are featured dmitry bogdanov steven coombs ghedoghedo t michael keesey myself gareth monger william g scott rna enzyme on the back smokeybjb brian swartz nobu tamura mateus zica the shirt is only available through march 15 as of this morning 25 shirts have been purchased meaning that we are exactly one quarter of the way to the goal so help phylopic out and get a great t shirt or if you can t at least help spread the word do you have phylopic s back apologies but shipping is only available in the u s canada and army or fleet post offices but if this campaign does well i ll certainly look into a more global option for future shirts yes plural why should homo sapiens get all the fun phylopic has good coverage of many other lineages posted by mike keesey at 7 05 am 2 comments labels anthropology evolution funding illustration mammalia phylopic primatology synapsida vertebrata zoology 18 october 2013 the phylocode has a deadline as most of you probably know the phylocode more verbosely the international code of phylogenetic nomenclature is a proposed nomenclatural code intended as an alternative to the rank based codes it was first draft ed in april 2000 and at that time the starting date was given as 1 january 200n on this date the code would be enacted and published along with a companion volume which would provide the first definitions under the code establishing best practices and defining the most commonly used clade names across all fields of biology well the 00s the zeroes the aughts came and went without the code being enacted the hold up was not the code itself which has been at least close to its final form since 2007 the last revision in january 2010 was minor and it hasn t been the software for the registration database which has been completed the hold up was the companion volume which turned out to be a much more daunting project than expected and considering that the zoological code took 66 years to go from being proposed to being published perhaps the initial estimate should have been hedged anyway at the 2008 meeting of the international society for phylogenetic nomenclature ispn this problem was discussed it was decided that the companion volume should be narrowed in scope instead of waiting to get definitions for commonly used clade names across all fields of biology many of which did not even have willing authors entries would be limited to those already in progress later on a revision was also made to the editorial process to help speed things up now for some news at the website for the ispn recently revamped by yrs trly there is a new progress report for phylonyms the companion volume to the phylocode there will be at most 268 entries currently 186 of those over two thirds have already been accepted the rest are at various stages of review but perhaps most excitingly there is a deadline the contract with university of california press calls for the manuscript to be submitted by september 1 2014 yes folks we will see the phylocode enacted in our lifetime pending nuclear holocaust or alien invasion posted by mike keesey at 9 58 am 3 comments labels clade nomenclature phylocode phylogeny phyloreferencing publication systematics 06 september 2013 solution to rampant monotypy subgenera genus names are stupid they have two jobs and they do them both poorly refer to a taxon form the first part of the names of all species within that taxon they do 1 poorly because they re defined typologically the definition for a genus is just some taxon that includes the type species but they could do this task well if they were given phylogenetic definitions instead but that doesn t work either because it conflicts with 2 taxa defined by phylogenetic definitions may overlap or be empty for 2 to work every single species has to be part of one genus and only one genus phylogenetically defined taxa don t really work that way so genus names are stupid but we have to use them because there s no other system for naming species because they refer to taxa poorly different disciplines often have wildly different ways of using genus names in entomology a genus may have hundreds of species but increasingly in dinosaur paleontology each genus gets one species nearly every single mesozoic dinosaur genus is monotypic this is a pattern we see over and over in recent years a new dinosaur species is discovered researchers do a cladistic analysis and determine that it is the sister group to another species already named originalgenus oldschoolensis at this point most researchers in other fields would name the new species something like originalgenus noobius but no even though it s barely different from o oldschoolensis it gets a new genus so it s newguy noobius today s researchers do have an excuse prepared for 3 it goes like this sure this analysis shows it as the sister group of originalgenus oldschoolensis but what if a future analysis shifts it a bit so that they no longer form a clade cladistic taxonomies may require it to be placed it in a new genus we sure as hell aren t going to let anyone else name that genus not after all the work we did describing it ignoring the mild egomania in 2 this sounds reasonable enough but this way of thinking has given us a huge number of completely redundant names as well as pushing dinosaur paleontology into an extreme corner of the splitter vs lumper debate isn t there a better way there is a better way just give your species a new subgenus taxonomy genus originalgenus original author 1900 subgenus newguy subgen nov species originalgenus noobius sp nov now as long as o noobius continues to be regarded as the sister group or otherwise close enough to o oldschoolensis you just keep the status quo but if things get shaken up and o noobius requires a different genus name by the rules of the iczn it has to be newguy and you still get the credit i know it s stupid but it works posted by mike keesey at 4 46 pm 9 comments labels dinosauria nomenclature paleontology 20 may 2013 phylopic submissions come in fits and bursts api example the recent surge of activity as phylopic neared its 1000th image got me to wondering about the pattern of image submissions over time fortunately it s very easy to collect this data using the phylopic api step 1 determine the number of submissions this is a very simple api call http phylopic org api a image count which yields result 1024 success true step 2 pull down the submission time data for all images now that we have the total number we can grab data for all of the images at once like so http phylopic org api a image list 0 1024 but this just yields a list of 1024 image entries that each look like this uid 1353c901 f652 4563 941d 7b12bc7a86df not very useful to get any actual data fields from the phylopic api you have to be more specific http phylopic org api a image list 0 1024 options submitted now each entry is a lot more useful uid 1353c901 f652 4563 941d 7b12bc7a86df submitted 2013 05 19 16 05 12 step 3 process the data once you have this it s a pretty simple matter for a javascript programmer to strip out the month and tally the images i did this and generated a bar chart using google s code playground here it is i left out may since it s not over yet apologies for the gaps phylopic was officially launched on 21 february 2011 most of the submissions for that month are ones that i presubmitted during development a lot are from scott hartman s skeletal drawings including the very first submission submissions were strong going into march but then completely slacked off i m sure a lot of this was due to technical problems the site became incredibly slow after a while there were major architecture flaws i mostly fixed these and relaunched in january 2012 interest was strong and in february phylopic had its best month ever but then submissions slacked off again a year later in march 2013 i was getting ready to do another major upgrade i added dozens of images in anticipation then i relaunched at the very end of the month sure enough april was one of the best months ever second only to february 2012 may 2013 is currently going strong but looking at this trend i start to wonder how long will it last and although i recently swore off doing massive updates are they actually better for driving up submissions posted by mike keesey at 11 48 am no comments labels phylopic 11 may 2013 phylopic passes a thousand images just a little while ago phylopic reached its first 1000 silhouettes here s the thousandth the eusauropod dinosaur cetiosaurus oxoniensis by michael p taylor public domain several contributors seem to have all been vying for the spot around the same time we got some other lovely contributions gareth monger contributed this upside down butterfly aglais urticae creative commons attribution sharealike 3 0 unported he missed the 1000th spot and got 1002nd matt martyniuk missed it on the opposite side with this lambeosaurus hadrosaurid dinosaur at 993rd creative commons attribution noncommercial sharealike 3 0 unported emily willoughby got quite close too and intended this rather recognizable angiosperm leaf cannabis sativa for the 1000th spot alas it s 1007th creative commons attribution sharealike 3 0 unported as she noted 420 would have been a good number as well thanks to everyone who contributed to the first thousand silhouettes it took two years to get here may the next thousand be even faster posted by mike keesey at 4 24 pm 4 comments labels illustration phylopic web applications older posts home subscribe to posts atom philosophy is the art of understanding the universe using a three pound monkey brain what is this blog about for that you d better see the first post the author mike keesey view my complete profile search this blog my other stuff résumé phylopic dragabok flickr names on nodes parry carney friends for life reference material actionscript language reference typescript archives of the dinosaur mailing list the phylocode the tree of life web project blog archive 2014 3 july 1 the evolution of cranial capacity in humans and st march 1 february 1 2013 15 october 1 september 1 may 2 april 1 march 3 february 4 january 3 2012 17 december 3 october 1 august 4 may 1 april 1 february 4 january 3 2011 13 december 1 november 2 october 1 september 1 august 2 may 1 march 2 february 2 january 1 2010 34 december 3 october 1 august 3 july 4 june 1 may 7 april 5 march 3 february 5 january 2 2009 26 december 2 november 2 september 1 august 1 july 2 june 2 may 4 march 3 february 7 january 2 2008 48 december 2 november 3 october 4 september 3 august 2 june 7 may 6 april 3 march 2 february 6 january 10 2007 17 december 4 november 13 popular posts brand new forum for discussion of phylogenetic nomenclature the title says it all as some of you may know the ispn s online forum has been down for a while daniel madzia of wild prehistory human clades a look at a complex phylogeny most methods of phylogenetic analysis deal with simple trees in these phylogenies every taxonomic unit has a single direct ancestor or using typescript to define json data json has gradually been wearing away at xml s position as the primary format for data communication on the web in some ways that the dinosauricon is dead long live the dinosauricon as some of you may know i used to run a website devoted to dinosaur information and illustration called the di the evolution of cranial capacity in humans and stem humans hey i m actually writing on the blog s title subject today here s a chart i ve been working on for a while t guest post similarities between macaque and human brains despite the title of this blog i ve rarely if ever actually discussed simian brains the title refers to my ow...