Phylogenetic Character Reconstruction

Author(s):  
J.S. Albert
Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 769-777
Author(s):  
Michael A Cantrell ◽  
Brian J Filanoski ◽  
Angela R Ingermann ◽  
Katherine Olsson ◽  
Nicole DiLuglio ◽  
...  

Abstract Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. Mys elements are a type of LTR-containing retrotransposon present in Sigmodontine rodents. In this study we have shown that one particular insert, mys-9, is an extremely old insert present in multiple species of the genus Peromyscus. We have found that different copies of this insert show a surprising range of sizes, due primarily to a continuing series of SINE (short interspersed element) insertions into this locus. We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers.


PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6703 ◽  
Author(s):  
Jonathan A. Coddington ◽  
Ingi Agnarsson ◽  
Chris A. Hamilton ◽  
Jason E. Bond

Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolvedde novo10–14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding theabsenceof webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. “Absence” of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as “?” because these codes—or their equivalent—are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5–7 times, not gained 10–14 times. The orb web, specifically, may be homologous (originated only once) although lost 2–6 times.


2020 ◽  
Vol 190 (1) ◽  
pp. 114-139
Author(s):  
Philippe J R Kok ◽  
Milan A J van der Velden ◽  
D Bruce Means ◽  
Sebastian Ratz ◽  
Iván Josipovic ◽  
...  

Abstract The only study of the osteology of the toad genus Oreophrynella dates back to 1971 and was based on a single species. Here, we use high-resolution X-ray microcomputed tomography to analyse the osteology of all nine described Oreophrynella species, which are compared with representatives of other bufonid lineages. Oreophrynella is unique among bufonids in having opposable digits. Osteological synapomorphies confirmed for the genus are as follows: presence of parietal fontanelles and exposed frontoparietal fontanelle, absence of quadratojugal, five presacral vertebrae, distally enlarged terminal phalanges and urostyle greatly expanded into flanges. Ancestral character reconstruction indicates that arboreal habits in some Oreophrynella species are likely to have evolved after the evolution of opposable digits. Opposable digits, in combination with an extension of the interdigital integument and the relative length/orientation of the digits, are likely to be adaptations to facilitate life on rocky tepui summits and an exaptation to arboreality. Cranial simplification in Oreophrynella, in the form of cranial fontanelles and absence of the quadratojugal, is possibly driven by a reduction of developmental costs, increase in flexibility and reduction of body weight. Cranial simplification combined with the shortening of the vertebral column and the shift towards a partly firmisternal girdle might be adaptations to the peculiar tumbling behaviour displayed by Oreophrynella.


It is now firmly established that the coordination of chromatic response in Amphibia is predominantly, if not exclusively, due to the liberation of hormones by reflexes involving visual and skin receptors, and in Reptiles to direct innervation of the pigmentary effector organs (Hogben and Mirvish, 1928; Zoond and Eyre,1934). Among aquatic vertebrates examples of both types of coordination occur. The bulk of available evidence points to the conclusion that the chromatophores of Teleostean fishes are directly innervated and that the comparatively rapid responses which are exhibited by several species are brought about by simple reflex action. That this is not true of cyclostomes has recently been shown by J. Z. Young (1935) whose experiments demonstrate the archaic phylogenetic character of the control exercised by the Amphibian pituitary gland. From an evolutionary standpoint it would not be surprising to find among physiological mechanisms in Teleostean fishes examples of specialization comparable to the strikingly aberrant features which their anatomical organization displays. On the other hand it would be remarkable if the cartilaginous fishes proved an exception to a rule which applies both to Cyclostomes and to Amphibia. Recent work on the colour changes of Elasmobranchs supports the conclusion that the coordination of colour change in Teleostean fishes is highly specialized. Lundstrom and Bard (1932) have shown that total removal of the pituitary gland in Mustelis canis results in a state of pallor which ensues within a few hours after operation, reaching its limit about the twelfth post-operative hour. In their experiments the animals usually succumbed after three or four days with loss of righting reactions. Only a few survived as long as a week. The effect was not produced by removal of the anterior lobe alone, nor by severe traumatization of the hypothalamus. Complete darkening of the pale operated animals followed injections or extracts of ox pituitary and of the pituitary of the fish itself, the quantity present in the fish gland being greatly in excess of the amount requisite to induce full expansion of the dermal melanophores. The present investigation, undertaken to throw further light on the evolution of the chromatic function in Vertebrates, is based on several species of Elasmobranch fishes, namely the skates, Raia Brachiura, R. clavata, R. maculata, R. microcelatus , the speckled dogfish Scyllium canicula , the banded dogfish or nursehound S. catulus (Scylliorhinusstellaris) , and the monkfish Rhina squatina . The writer is indebted to Mr. G. A. Steven for invaluable assistance in identifying the various species used. In all these species the pigmentary effector system of the integument, like that of the American dogfish Mustelis canis , closely resembles that of Amphibia, and consists of three types of chromatophores which are more or less evenly distributed. These are the epidermal melanophores, larger more richly branched dermal melanophores, and xanthophores containing an orange yellow pigment. The same agencies, in the fishes to be described, evoked or maintained pigment diffusion (“expansion”) of all three types, and the concentration of pigment in the centre of the cell (“contraction”) in all three types. That is to say, the xanthophores of a skate or dogfish which was maximally pale were always fully contracted like the melanophores of both kinds, and the xanthophores of a dark animal were fully expanded. This is true of some—but not all—Amphibia. In general appearance the chromatophores of the species studied are more like those of a Urodele than those of a Teleost.


2015 ◽  
Vol 7 (3) ◽  
pp. 352-357 ◽  
Author(s):  
Carl Boettiger ◽  
Scott Chamberlain ◽  
Rutger Vos ◽  
Hilmar Lapp

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