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tina so the structure is effectively upside down in contrast the cephalopod eye has the retina then a layer of nerve fibres then the wall of the eye the right way around 44 the evidence of pax 6 however was that the same genes controlled the development of the eyes of all these animals suggesting that they all evolved from a common ancestor 9 ancient genes had been conserved through millions of years of evolution to create dissimilar structures for similar functions demonstrating deep homology between structures once thought to be purely analogous 45 46 this notion was later extended to the evolution of embryogenesis 47 and has caused a radical revision of the meaning of homology in evolutionary biology 45 46 1 gene toolkit edit main article evo devo gene toolkit further information plant evolutionary developmental biology expression of homeobox hox genes in the fruit fly a small fraction of the genes in an organism s genome control the organism s development these genes are called the developmental genetic toolkit they are highly conserved among phyla meaning that they are ancient and very similar in widely separated groups of animals differences in deployment of toolkit genes affect the body plan and the number identity and pattern of body parts most toolkit genes are parts of signalling pathways they encode transcription factors cell adhesion proteins cell surface receptor proteins and signalling ligands that bind to them and secreted morphogens that diffuse through the embryo all of these help to define the fate of undifferentiated cells in the embryo together they generate the patterns in time and space which shape the embryo and ultimately form the body plan of the organism among the most important toolkit genes are the hox genes these transcription factors contain the homeobox protein binding dna motif also found in other toolkit genes and create the basic pattern of the body along its front to back axis 1 hox genes determine where repeating parts such as the many vertebrae of snakes will grow in a developing embryo or larva 9 pax 6 already mentioned is a classic toolkit gene 48 although other toolkit genes are involved in establishing the plant bodyplan 49 homeobox genes are also found in plants implying they are common to all eukaryotes 50 51 52 the embryo s regulatory networks edit further information regulation of gene expression and transcriptional regulation a gene regulatory network the protein products of the regulatory toolkit are reused not by duplication and modification but by a complex mosaic of pleiotropy i e being applied unchanged in many independent developmental processes giving pattern to many dissimilar body structures 1 the loci of these pleiotropic toolkit genes have large complicated and modular cis regulatory elements for example while a non pleiotropic rhodopsin gene in the fruit fly has a cis regulatory element just a few hundred base pairs long the pleiotropic eyeless cis regulatory region contains 6 cis regulatory elements in over 7000 base pairs 1 the regulatory networks involved are often very large each regulatory protein controls scores to hundreds of cis regulatory elements for instance 67 fruit fly transcription factors controlled on average 124 target genes each 1 all this complexity enables genes involved in the development of the embryo to be switched on and off at exactly the right times and in exactly the right places some of these genes are structural directly forming enzymes tissues and organs of the embryo but many others are themselves regulatory genes so what is switched on is often a precisely timed cascade of switching involving turning on one developmental process after another in the developing embryo 1 gene product distributions along the long axis of the early embryo of a fruit fly such a cascading regulatory network has been studied in detail in the development of the fruit fly embryo the young embryo is oval in shape like a rugby ball a small number of genes produce messenger rnas that set up concentration gradients along the long axis of the embryo in the early embryo the bicoid and hunchback genes are at high concentration near the anterior end and give pattern to the future head and thorax the caudal and nanos genes are at high concentration near the posterior end and give pattern to the hindmost abdominal segments the effects of these genes interact for instance the bicoid protein blocks the translation of caudal s messenger rna so the caudal protein concentration becomes low at the anterior end caudal later switches on genes which create the fly s hindmost segments but only at the posterior end where it is most concentrated 53 54 gap genes in the fruit fly are switched on by genes such as bicoid setting up stripes across the embryo which start to pattern the body s segments the bicoid hunchback and caudal proteins in turn regulate the transcription of gap genes such as giant knirps krüppel and tailless in a striped pattern creating the first level of structures that will become segments 37 the proteins from these in turn control the pair rule genes which in the next stage set up 7 bands across the embryo s long axis finally the segment polarity genes such as engrailed split each of the 7 bands into two creating 14 future segments 53 54 this process explains the accurate conservation of toolkit gene sequences which has resulted in deep homology and functional equivalence of toolkit proteins in dissimilar animals seen for example when a mouse protein controls fruit fly development the interactions of transcription factors and cis regulatory elements or of signalling proteins and receptors become locked in through multiple usages making almost any mutation deleterious and hence eliminated by natural selection 1 the mechanism that sets up every animal s front back axis is the same implying a common ancestor there is a similar mechanism for the back belly axis for bilaterian animals but it is reversed between arthropods and vertebrates 55 another process gastrulation of the embryo is driven by myosin ii molecular motors which are not conserved across species the process may have been started by movements of sea water in the environment later replaced by the evolution of tissue movements in the embryo 56 57 58 the origins of novelty edit further information history of evolutionary thought 21st century among the more surprising and perhaps counterintuitive from a neo darwinian viewpoint results of recent research in evolutionary developmental biology is that the diversity of body plans and morphology in organisms across many phyla are not necessarily reflected in diversity at the level of the sequences of genes including those of the developmental genetic toolkit and other genes involved in development indeed as john gerhart and marc kirschner have noted there is an apparent paradox where we most expect to find variation we find conservation a lack of change 59 so if the observed morphological novelty between different clades does not come from changes in gene sequences such as by mutation where does it come from novelty may arise by mutation driven changes in gene regulation 1 60 61 62 variations in the toolkit edit heliconius erato heliconius melpomene different species of heliconius butterfly have independently evolved similar patterns apparently both facilitated and constrained by the available developmental genetic toolkit genes controlling wing pattern formation variations in the toolkit may have produced a large part of the morphological evolution of animals the toolkit can drive evolution in two ways a toolkit gene can be expressed in a different pattern as when the beak of darwin s large ground finch was enlarged by the bmp gene 63 or when snakes lost their legs as distal less became under expressed or not expressed at all in the places where other reptiles continued to form their limbs 64 or a toolkit gene can acquire a new function as seen in the many functions of that same gene distal less which controls such diverse structures as the mandible in vertebrates 65 66 legs and antennae in the fruit fly 67 and eyespot pattern in butterfly wings 68 given that small changes in toolbox genes can cause significant changes in body structures they have often enabled the same function convergently or in parallel distal less generates wing patterns in the butterflies heliconius erato and heliconius melpomene which are müllerian mimics in so called facilitated variation 69 their wing patterns arose in different evolutionary events but are controlled by the same genes 70 developmental changes can contribute directly to speciation 71 consolidation of epigenetic changes edit main articles genetic assimilation and transgenerational epigenetic inheritance further information extended evolutionary synthesis evolutionary innovation may sometimes begin in lamarckian style with epigenetic alterations of gene regulation or phenotype generation subsequently consolidated by changes at the gene level epigenetic changes include modification of dna by reversible methylation 72 as well as nonprogrammed remoulding of the organism by physical and other environmental effects due to the inherent plasticity of developmental mechanisms 73 the biologists stuart a newman and gerd b müller have suggested that organisms early in the history of multicellular life were more susceptible to this second category of epigenetic determination than are modern organisms providing a basis for early macroevolutionary changes 74 developmental bias edit main article developmental bias among the centipedes all members of the geophilomorpha are constrained by a developmental bias to have an odd number of segments whether as few as 27 or as many as 191 development in specific lineages can be biased either positively towards a given trajectory or phenotype b or negatively away from producing certain types of change either may be absolute the change is always or never produced or relative evidence for any such direction in evolution is however hard to acquire and can also result from developmental constraints that limit diversification 47 for example in the gastropods the snail type shell is always built as a tube that grows both in length and in diameter selection has created a wide variety of shell shapes such as flat spirals cowries and tall turret spirals within these constraints among the centipedes the lithobiomorpha always have 15 trunk segments as adults probably the result of a developmental bias towards an odd number of trunk segments another centipede order the geophilomorpha the number of segments varies in different species between 27 and 191 but the number is always odd making this an absolute constraint almost all the odd numbers in that range are occupied by one or another species 75 76 77 ecological evolutionary developmental biology edit ecological evolutionary developmental biology informally known as eco evo devo integrates research from developmental biology and ecology to examine their relationship with evolutionary theory 78 researchers study concepts and mechanisms such as developmental plasticity epigenetic inheritance genetic assimilation niche construction and symbiosis 79 80 see also edit arthropod head problem cell signaling evolution development journal human evolutionary developmental biology just so stories as seen by evolutionary developmental biologists plant evolutionary developmental biology recapitulation theory notes edit though c h waddington had called for embryology to be added to the synthesis in his 1953 paper epigenetics and evolution 26 positive bias is sometimes called developmental drive 75 references edit citations edit 1 2 3 4 5 6 7 8 9 10 carroll sean b 2008 evo devo and an expanding evolutionary synthesis a genetic theory of morphological evolution cell 134 1 25 36 doi 10 1016 j cell 2008 06 030 pmid 18614008 s2cid 2513041 leroi armand marie 2014 the lagoon how aristotle invented science bloomsbury pp 181 182 isbn 978 1 4088 3622 4 richardson keuck 2002 p 516 o connell lindsey 10 july 2013 the meckel serres conception of recapitulation the embryo project encyclopedia retrieved 10 october 2016 desmond adrian j 1989 the politics of evolution morphology medicine and reform in radical london chicago university of chicago press pp 53 53 86 88 337 340 490 491 isbn 978 0 226 14374 3 secord 2003 pp 252 253 bowler peter j 2003 evolution the history of an idea berkeley university of california press pp 120 128 190 191 208 isbn 978 0 520 23693 6 secord 2003 pp 424 512 1 2 3 4 5 6 carroll sean b the origins of form natural history retrieved 9 october 2016 biologists could say with confidence that forms change and that natural selection is an important force for change yet they could say nothing about how that change is accomplished how bodies or body parts change or how new structures arise remained complete mysteries 1 2 3 4 5 6 gilbert scott f 2003 the morphogenesis of evolutionary developmental biology pdf international journal of developmental biology 47 7 8 467 477 pmid 14756322 darwin charles 1859 on the origin of species london john murray pp 439 440 isbn 978 0 8014 1319 3 cirripedes afford a good instance of this even the illustrious cuvier did not perceive that a barnacle was as it certainly is a crustacean but a glance at the larva shows this to be the case in an unmistakeable manner cite book isbn date incompatibility help richmond marsha january 2007 darwin s study of the cirripedia darwin online retrieved 9 october 2016 1 2 hall b k 2003 evo devo evolutionary developmental mechanisms international journal of developmental biology 47 7 8 491 495 pmid 14756324 ridley mark 2003 evolution wiley blackwell isbn 978 1 4051 0345 9 gould 1977 pp 221 222 1 2 turing alan m 14 august 1952 the chemical basis of morphogenesis philosophical transactions of the royal society of london b 237 641 37 72 bibcode 1952rsptb 237 37t doi 10 1098 rstb 1952 0012 s2cid 120437796 ball philip 7 february 2013 in retrospect on growth and form nature 494 32 33 32 33 bibcode 2013natur 494 32b doi 10 1038 494032a s2cid 205076253 shalizi cosma review the self made tapestry by philip ball university of michigan retrieved 14 october 2016 gribbin john 2004 deep simplicity random house p 126 bock walter j july 1981 reviewed work the evolutionary synthesis perspectives on the unification of biology the auk 98 3 644 646 jstor 4086148 held lewis i 2014 how the snake lost its legs curious tales from the frontier of evo devo cambridge university press p 67 isbn 978 1 107 62139 8 gould 1977 pp 221 222 brigandt ingo 2006 homology and heterochrony the evolutionary embryologist gavin rylands de beer 1899 1972 pdf journal of experimental zoology 306b 4 317 328 bibcode 2006jezb 306 317b doi 10 1002 jez b 21100 pmid 16506229 gilbert s f opitz j m raff r a 1996 resynthesizing evolutionary and developmental biology developmental biology 173 2 357 372 doi 10 1006 dbio 1996 0032 pmid 8605997 adams m 1991...