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Stephen Robertson - One of the best experts on this subject based on the ideXlab platform.
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Challenges posed by web-based retrieval of scientific papers: Okapi participation in TIPS
Journal of Information Science, 2002Co-Authors: Murat Karamuftuoglu, Stephen Robertson, Susan Jones, Fabio Venuti, Xinkun WangAbstract:This paper reviews some of the past Okapi research and discusses the role of Okapi in the current TIPS project. The main purpose is to report new challenges faced by probabilistic text retrieval in the web environment and to indicate some of the solutions that are currently under investigation. In this context, extraction of indexing units from formatted document sources, user interface design, implementation of field searching and query expansion within the framework of probabilistic searching are discussed. The problem of maintaining session continuity in the web environment and a possible solution to this problem are outlined. Other challenges posed by the open nature of the web environment are also indicated. These include the difficulty of delimiting the boundaries of a search session and the potential of the web for collaborative information retrieval. A system for collaboratively filtering documents based on their contents is described in this connection. Issues surrounding the integration of Okapi with other pieces of software being developed for the TIPS project are also briefly discussed.
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Overview of the Okapi projects
Journal of Documentation, 1997Co-Authors: Stephen RobertsonAbstract:This paper gives a brief description of the Okapi projects and the work of the Centre for Interactive Systems research, as an introduction to this special issue of the Journal of Documentation. Okapi is the name given to an experimental text retrieval system (or rather, family of systems, as will be discussed below), based at City University, London. The current systems and their predecessors have been used as the basis for a series of projects, generally addressing aspects of user information‐seeking behaviour and user‐system interaction, as well as system design. The projects have been supported extensively by the British Library, and to some degree by a number of other funders. They have been at City since 1989; for the previous seven years they were based at the Polytechnic of Central London (now the University of Westminster). In order to give a picture of the system(s) that now constitute Okapi, it is appropriate to describe one version containing some of the features that have become central to the Okapi projects, and then to indicate the variety of systems now implemented or implementable within the present setup, as well as the directions it may go in the future. In what follows, papers in this issue are referred to by brief titles.
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Laboratory experiments with Okapi : Participation in the TREC programme
Journal of Documentation, 1997Co-Authors: Stephen Robertson, Steve Walker, Micheline BeaulieuAbstract:A brief review of the history of laboratory testing of information retrieval systems focuses on the idea of a general‐purpose test collection of documents, queries and relevance judgements. The TREC programme is introduced in this context, and an overview is given of the methods used in TREC. The Okapi team’s participation in TREC is then discussed. The team has made use of TREC to improve some of the automatic techniques used in Okapi, specifically the term weighting function and the algorithms for term selection for query expansion. The consequence of this process has been a very good showing for Okapi in terms of the TREC evaluation results. Some of the issues around the much more difficult problem of interactive evaluation in TREC are then discussed. Although some interesting interactive experiments have been performed at TREC, the problems of reconciling the requirements of the laboratory context with the concerns of interactive retrieval are still largely unresolved.
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TREC - Okapi at TREC-6 automatic ad hoc, VLC, routing, filtering and QSDR
1997Co-Authors: Steve Walker, Stephen Robertson, Mohand Boughanem, Gareth J. F. Jones, Karen Sparck JonesAbstract:Recherche d'information sur le catalogue en ligne Okapi. VLC= Very Large Collection SDR= Spoken Document Retrieval
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Okapi at trec 6 automatic ad hoc vlc routing filtering and qsdr
Text REtrieval Conference, 1997Co-Authors: Steve Walker, Stephen Robertson, Mohand Boughanem, Gareth J. F. Jones, Karen Sparck JonesAbstract:Recherche d'information sur le catalogue en ligne Okapi. VLC= Very Large Collection SDR= Spoken Document Retrieval
Steve Walker - One of the best experts on this subject based on the ideXlab platform.
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Laboratory experiments with Okapi : Participation in the TREC programme
Journal of Documentation, 1997Co-Authors: Stephen Robertson, Steve Walker, Micheline BeaulieuAbstract:A brief review of the history of laboratory testing of information retrieval systems focuses on the idea of a general‐purpose test collection of documents, queries and relevance judgements. The TREC programme is introduced in this context, and an overview is given of the methods used in TREC. The Okapi team’s participation in TREC is then discussed. The team has made use of TREC to improve some of the automatic techniques used in Okapi, specifically the term weighting function and the algorithms for term selection for query expansion. The consequence of this process has been a very good showing for Okapi in terms of the TREC evaluation results. Some of the issues around the much more difficult problem of interactive evaluation in TREC are then discussed. Although some interesting interactive experiments have been performed at TREC, the problems of reconciling the requirements of the laboratory context with the concerns of interactive retrieval are still largely unresolved.
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Peeling the Onion: Okapi System Architecture and Software Design Issues
Journal of Documentation, 1997Co-Authors: Susan Jones, Steve Walker, Mike GatfordAbstract:At the heart of the Okapi system is a formula referring to some half a dozen variables, which estimate the probability that a given document is relevant to a given query. User interface design for Okapi aims to present its search capabilities as clearly and simply as possible. But between the basic formula and the simple interface lie several layers of complex software, which must support both probabilistic and non‐probabilistic retrieval functions, and combine them in a logical and consistent way. We describe the evolution, and some of the functions, of these software layers.
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TREC - Okapi at TREC-6 automatic ad hoc, VLC, routing, filtering and QSDR
1997Co-Authors: Steve Walker, Stephen Robertson, Mohand Boughanem, Gareth J. F. Jones, Karen Sparck JonesAbstract:Recherche d'information sur le catalogue en ligne Okapi. VLC= Very Large Collection SDR= Spoken Document Retrieval
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Okapi at trec 6 automatic ad hoc vlc routing filtering and qsdr
Text REtrieval Conference, 1997Co-Authors: Steve Walker, Stephen Robertson, Mohand Boughanem, Gareth J. F. Jones, Karen Sparck JonesAbstract:Recherche d'information sur le catalogue en ligne Okapi. VLC= Very Large Collection SDR= Spoken Document Retrieval
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Okapi at trec
Text REtrieval Conference, 1994Co-Authors: Stephen Robertson, Steve Walker, Susan Jones, Micheline Hancockbeaulieu, Mike GatfordAbstract:City submitted two runs each for the automatic ad hoc, very large collection track, automatic routing and Chinese track; and took part in the interactive and filtering tracks. The method used was : expansion using terms from the top documents retrieved by a pilot search on topic terms. Additional runs seem to show that we would have done better without expansion. Twor runs using the method of city96al were also submitted for the Very Large Collection track. The training database and its relevant documents were partitioned into three parts. Working on a pool of terms extracted from the relevant documents for one partition, an iterative procedure added or removed terms and/or varied their weights. After each change in query content or term weights a score was calculated by using the current query to search a second protion of the training database and evaluating the results against the corresponding set of relevant documents. Methods were compared by evaluating queries predictively against the third training partition. Queries from different methods were then merged and the results evaluated in the same way. Two runs were submitted, one based on character searching and the other on words or phrases. Much of the work involved investigating plausible methods of applying Okapi-style weighting to phrases
Mike Gatford - One of the best experts on this subject based on the ideXlab platform.
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Peeling the Onion: Okapi System Architecture and Software Design Issues
Journal of Documentation, 1997Co-Authors: Susan Jones, Steve Walker, Mike GatfordAbstract:At the heart of the Okapi system is a formula referring to some half a dozen variables, which estimate the probability that a given document is relevant to a given query. User interface design for Okapi aims to present its search capabilities as clearly and simply as possible. But between the basic formula and the simple interface lie several layers of complex software, which must support both probabilistic and non‐probabilistic retrieval functions, and combine them in a logical and consistent way. We describe the evolution, and some of the functions, of these software layers.
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TREC - Interactive Okapi at TREC-6
1997Co-Authors: Micheline Hancock-beaulieu, Mike GatfordAbstract:Evaluation comparative des catalogues en ligne Okapi et ZPrise, effectuee sur un ensemble de 58 requetes menees par 8 personnes
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interactive Okapi at trec 6
Text REtrieval Conference, 1997Co-Authors: Micheline Hancockbeaulieu, Mike GatfordAbstract:Evaluation comparative des catalogues en ligne Okapi et ZPrise, effectuee sur un ensemble de 58 requetes menees par 8 personnes
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Okapi at trec
Text REtrieval Conference, 1994Co-Authors: Stephen Robertson, Steve Walker, Susan Jones, Micheline Hancockbeaulieu, Mike GatfordAbstract:City submitted two runs each for the automatic ad hoc, very large collection track, automatic routing and Chinese track; and took part in the interactive and filtering tracks. The method used was : expansion using terms from the top documents retrieved by a pilot search on topic terms. Additional runs seem to show that we would have done better without expansion. Twor runs using the method of city96al were also submitted for the Very Large Collection track. The training database and its relevant documents were partitioned into three parts. Working on a pool of terms extracted from the relevant documents for one partition, an iterative procedure added or removed terms and/or varied their weights. After each change in query content or term weights a score was calculated by using the current query to search a second protion of the training database and evaluating the results against the corresponding set of relevant documents. Methods were compared by evaluating queries predictively against the third training partition. Queries from different methods were then merged and the results evaluated in the same way. Two runs were submitted, one based on character searching and the other on words or phrases. Much of the work involved investigating plausible methods of applying Okapi-style weighting to phrases
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TREC - Okapi at TREC
1993Co-Authors: Stephen Robertson, Micheline Hancock-beaulieu, Steve Walker, Susan Jones, Mike GatfordAbstract:City submitted two runs each for the automatic ad hoc, very large collection track, automatic routing and Chinese track; and took part in the interactive and filtering tracks. The method used was : expansion using terms from the top documents retrieved by a pilot search on topic terms. Additional runs seem to show that we would have done better without expansion. Twor runs using the method of city96al were also submitted for the Very Large Collection track. The training database and its relevant documents were partitioned into three parts. Working on a pool of terms extracted from the relevant documents for one partition, an iterative procedure added or removed terms and/or varied their weights. After each change in query content or term weights a score was calculated by using the current query to search a second protion of the training database and evaluating the results against the corresponding set of relevant documents. Methods were compared by evaluating queries predictively against the third training partition. Queries from different methods were then merged and the results evaluated in the same way. Two runs were submitted, one based on character searching and the other on words or phrases. Much of the work involved investigating plausible methods of applying Okapi-style weighting to phrases
Edson Ishengoma - One of the best experts on this subject based on the ideXlab platform.
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evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and Okapi
PeerJ, 2017Co-Authors: Edson Ishengoma, Morris Agaba, Douglas R CavenerAbstract:Background The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to Okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe's visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe's unique visual capacity and its difference with Okapi is reflected by changes in their vision genes is not understood. Methods The recent availability of giraffe and Okapi genomes provided opportunity to identify giraffe and Okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and Okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and Okapi vision genes and orthologous sequences from other mammals. Results Signatures of selection were identified in key genes that could potentially underlie giraffe and Okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW. Significant selection divergence was identified in SAG while positive selection was detected in LUM when Okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. Discussion By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and Okapi vision adaptations. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and Okapi habitat. We hypothesize that requirement for long distance vision associated with predation and communication with conspecifics likely played an important role in the adaptive pressure on giraffe vision genes.
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Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification
BMC Evolutionary Biology, 2017Co-Authors: Edson Ishengoma, Morris AgabaAbstract:Background Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and Okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Results Sequence analysis shows that giraffe has 94–99% nucleotide identity with Okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, Okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, Okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. Conclusion There is overall structural conservation in TLRs among giraffe, Okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans.
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Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and Okapi
2016Co-Authors: Edson Ishengoma, Morris Agaba, Douglas R CavenerAbstract:Background. The capacity of species to respond and perceive visual signal is integral to their evolutionary success. Giraffe is closely related to Okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with most of them. To what extent giraffe unique visual capacity and its difference with Okapi is reflected by changes in their vision genes is not understood. Methods. The recent availability of giraffe and Okapi genome provided opportunity to identify giraffe and Okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and Okapi genomes. Quantification of selection pressure was performed by a combination of branch-site test of positive selection and clade models of selection divergence through comparing giraffe and Okapi vision genes and their corresponding orthologous sequences from other mammals obtained from public gene banks. Results. Signatures of selection was identified in key genes that could potentially underlie giraffe and Okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW in giraffe. Significant selection divergence was identified in SAG while positive selection was detected in LUM when Okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. Discussion. By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and Okapi vision adaptation. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and Okapi habitat. Moreover, requirement for long distance vision associated with predation likely played an important role in the adaptive pressure on giraffe vision genes.
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Giraffe genome sequence reveals clues to its unique morphology and physiology
Nature Communications, 2016Co-Authors: Morris Agaba, Edson Ishengoma, Webb C. Miller, Barbara C. Mcgrath, Chelsea N. Hudson, Oscar C. Bedoya Reina, Aakrosh Ratan, Rico Burhans, Rayan Chikhi, Paul MedvedevAbstract:The origins of giraffe’s imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe’s closest relative and provides a useful comparison, to identify genetic variation underlying giraffe’s long neck and cardiovascular system. The genomes of giraffe and Okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe’s unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe’s stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and Okapi in double-strand break repair and centrosome functions. Giraffe’s unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novo genome assemblies of giraffe and its closest relative Okapi and provide comparative analyses to infer insights into evolution and adaptation.
Morris Agaba - One of the best experts on this subject based on the ideXlab platform.
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evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and Okapi
PeerJ, 2017Co-Authors: Edson Ishengoma, Morris Agaba, Douglas R CavenerAbstract:Background The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to Okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe's visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe's unique visual capacity and its difference with Okapi is reflected by changes in their vision genes is not understood. Methods The recent availability of giraffe and Okapi genomes provided opportunity to identify giraffe and Okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and Okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and Okapi vision genes and orthologous sequences from other mammals. Results Signatures of selection were identified in key genes that could potentially underlie giraffe and Okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW. Significant selection divergence was identified in SAG while positive selection was detected in LUM when Okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. Discussion By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and Okapi vision adaptations. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and Okapi habitat. We hypothesize that requirement for long distance vision associated with predation and communication with conspecifics likely played an important role in the adaptive pressure on giraffe vision genes.
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Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification
BMC Evolutionary Biology, 2017Co-Authors: Edson Ishengoma, Morris AgabaAbstract:Background Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and Okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Results Sequence analysis shows that giraffe has 94–99% nucleotide identity with Okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, Okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, Okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. Conclusion There is overall structural conservation in TLRs among giraffe, Okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans.
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Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and Okapi
2016Co-Authors: Edson Ishengoma, Morris Agaba, Douglas R CavenerAbstract:Background. The capacity of species to respond and perceive visual signal is integral to their evolutionary success. Giraffe is closely related to Okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with most of them. To what extent giraffe unique visual capacity and its difference with Okapi is reflected by changes in their vision genes is not understood. Methods. The recent availability of giraffe and Okapi genome provided opportunity to identify giraffe and Okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and Okapi genomes. Quantification of selection pressure was performed by a combination of branch-site test of positive selection and clade models of selection divergence through comparing giraffe and Okapi vision genes and their corresponding orthologous sequences from other mammals obtained from public gene banks. Results. Signatures of selection was identified in key genes that could potentially underlie giraffe and Okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW in giraffe. Significant selection divergence was identified in SAG while positive selection was detected in LUM when Okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. Discussion. By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and Okapi vision adaptation. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and Okapi habitat. Moreover, requirement for long distance vision associated with predation likely played an important role in the adaptive pressure on giraffe vision genes.
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Giraffe genome sequence reveals clues to its unique morphology and physiology
Nature Communications, 2016Co-Authors: Morris Agaba, Edson Ishengoma, Webb C. Miller, Barbara C. Mcgrath, Chelsea N. Hudson, Oscar C. Bedoya Reina, Aakrosh Ratan, Rico Burhans, Rayan Chikhi, Paul MedvedevAbstract:The origins of giraffe’s imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe’s closest relative and provides a useful comparison, to identify genetic variation underlying giraffe’s long neck and cardiovascular system. The genomes of giraffe and Okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe’s unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe’s stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and Okapi in double-strand break repair and centrosome functions. Giraffe’s unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novo genome assemblies of giraffe and its closest relative Okapi and provide comparative analyses to infer insights into evolution and adaptation.
