The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Arcady Mushegian - One of the best experts on this subject based on the ideXlab platform.
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reconstructing gene content in the Last Common Ancestor of cellular life is it possible should it be done and are we making any progress
bioRxiv, 2014Co-Authors: Arcady MushegianAbstract:I review recent literature on the reconstruction of gene repertoire of the Last Universal Common Ancestor of cellular life (LUCA). The form of the phylogenetic record of cellular life on Earth is important to know in order to reconstruct any ancestral state; therefore I also discuss the emerging understanding that this record does not take the form of a tree. I argue that despite this, “tree-thinking” remains an essential component in evolutionary thinking and that “pattern pluralism” in evolutionary biology can be only epistemological, but not ontological.
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models of gene gain and gene loss for probabilistic reconstruction of gene content in the Last universal Common Ancestor of life
Biology Direct, 2013Co-Authors: Lavanya Kannan, Boris Rubinstein, Arcady MushegianAbstract:Background The problem of probabilistic inference of gene content in the Last Common Ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their Last Common Ancestor.
David J Green - One of the best experts on this subject based on the ideXlab platform.
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scapular shape of extant hominoids and the african ape modern human Last Common Ancestor
Journal of Human Evolution, 2016Co-Authors: David J Green, Ted A Spiewak, Brielle C Seitelman, Philipp GunzAbstract:Newly discovered early hominin fossil scapulae have bolstered investigations of scapular shape, which have long been used to interpret behavioral variation among primates. However, unexpected similarities between Pongo and Homo - particularly in scapular spine orientation - have raised questions about the functional utility of scapular morphology and its phylogenetic context in the hominin lineage. Not surprisingly, significant disagreement surrounds disparate morphological reconstructions of the modern human/African ape Last Common Ancestor (LCA). Our study utilizes geometric morphometric (GM) approaches - two employing homologous, anatomical landmarks and a "spine-free" alternative using 98 sliding semilandmarks along the boundary of the subscapular fossa. The landmark-based "wireframe" GM analysis principally sorted groups by spine orientation: Homo and Pongo were similar to one another with more transversely-oriented spines as compared to Hylobates and the African apes. In contrast, Homo and Gorilla clustered together in our semilandmark analysis with superoinferiorly broad blades. Pan scapulae were similar, but had more mediolaterally compressed blades and laterally-positioned superior angles. Hylobates was superoinferiorly narrow, yet obliquely expanded relative to the vertebral border. Pongo scapulae were unique among hominoids in being nearly as broad as they were long. Previously documented 'convergence' of Homo and Pongo scapulae appears to be principally driven by similarities in spine orientation, rather than overall blade shape. Therefore, we contend that it is more parsimonious to reconstruct the African ape/Homo LCA scapula as being Gorilla-like, especially in light of similar characterizations of certain fossil hominin scapulae. Accordingly, the evolution of Pan (highly oblique spine and laterally-situated superior angle) and Homo (transversely-oriented spine) scapular morphology would have involved relatively minor shifts from this ancestral condition. These results support the prevailing molecular phylogeny and provide further insight into the behavioral implications of scapular shape in the LCA and fossil hominins.
P W H Holland - One of the best experts on this subject based on the ideXlab platform.
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Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs
Heredity, 2016Co-Authors: N J Kenny, W Nong, H S Kwan, K.w. Chan, Z Qu, Ignacio Maeso, T F Chan, P W H HollandAbstract:Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the Last Common Ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs— Carcinoscorpius rotundicauda , Limulus polyphemus and Tachypleus tridentatus . Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the Last Common Ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
Zeresenay Alemseged - One of the best experts on this subject based on the ideXlab platform.
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reply to almecija a new direction for reconstructing our Last Common Ancestor with chimpanzees
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Nathan M Young, Neil T Roach, Terence D Capellini, Zeresenay AlemsegedAbstract:We welcome Almecija’s critique (1), but his claims of “bias” in our conclusions are unfounded. All available evidence continues to support an African ape-like shoulder and pattern of forelimb use in our Last Common Ancestor (LCA) with chimpanzees and bonobos ( Pan ). First, controlling for within-group size variation is uncontroversial (2), and neither biases our results nor obscures their biological meaning. Gorilla and Pan shape differences may still be size-related. Specifically, Gorilla ’s expansive supraspinous fossa is plausibly associated with increased body mass and functional demands to stabilize the joint during knuckle-walking (3). Second, although we note that a “ Pan -like” LCA may be … [↵][1]1To whom correspondence should be addressed. Email: nathan.m.young{at}gmail.com. [1]: #xref-corresp-1-1
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fossil hominin shoulders support an african ape like Last Common Ancestor of humans and chimpanzees
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Nathan M Young, Neil T Roach, Terence D Capellini, Zeresenay AlemsegedAbstract:Reconstructing the behavioral shifts that drove hominin evolution requires knowledge of the timing, magnitude, and direction of anatomical changes over the past ∼6–7 million years. These reconstructions depend on assumptions regarding the morphotype of the Homo–Pan Last Common Ancestor (LCA). However, there is little consensus for the LCA, with proposed models ranging from African ape to orangutan or generalized Miocene ape-like. The ancestral state of the shoulder is of particular interest because it is functionally associated with important behavioral shifts in hominins, such as reduced arboreality, high-speed throwing, and tool use. However, previous morphometric analyses of both living and fossil taxa have yielded contradictory results. Here, we generated a 3D morphospace of ape and human scapular shape to plot evolutionary trajectories, predict ancestral morphologies, and directly test alternative evolutionary hypotheses using the hominin fossil evidence. We show that the most parsimonious model for the evolution of hominin shoulder shape starts with an African ape-like ancestral state. We propose that the shoulder evolved gradually along a single morphocline, achieving modern human-like configuration and function within the genus Homo. These data are consistent with a slow, progressive loss of arboreality and increased tool use throughout human evolution.
Lavanya Kannan - One of the best experts on this subject based on the ideXlab platform.
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models of gene gain and gene loss for probabilistic reconstruction of gene content in the Last universal Common Ancestor of life
Biology Direct, 2013Co-Authors: Lavanya Kannan, Boris Rubinstein, Arcady MushegianAbstract:Background The problem of probabilistic inference of gene content in the Last Common Ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their Last Common Ancestor.
