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Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity
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- Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.
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- Aki Mimoto
- IRMACS, Simon Fraser University, Burnaby, Canada.
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- Arne Ø Mooers
- IRMACS, Simon Fraser University, Burnaby, Canada.
Description
<jats:p> If predictions for species extinctions hold, then the ‘tree of life’ today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to contribute to future biodiversity, as measured by its expected contribution to phylogenetic diversity. Our approach considers all possible scenarios for the set of species that will be extant at some future time, and weights them according to their likelihood under an independent (but not identical) distribution on species extinctions. Although the number of extinction scenarios can typically be very large, we show that there is a simple algorithm that will quickly compute this index. The method is implemented and applied to the prosimian primates as a test case, and the associated species ranking is compared to a related measure (the ‘Shapley index’). We describe indices for rooted and unrooted trees, and a modification that also includes the focal taxon's probability of extinction and which links two complementary approaches to conserving phylogenetic diversity. </jats:p>
Journal
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- Evolutionary Bioinformatics
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Evolutionary Bioinformatics 3 47-, 2007-01
SAGE Publications
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Keywords
- gametic phase estimation
- function prediction
- proteome evolution
- neutral model
- ALFRED
- neighbor-nets
- polymorphism
- dating speciation events
- ancestral sequence reconstruction
- biodiversity
- ribosomal DNA
- Sciences bio-médicales et agricoles
- Serial Samples
- tree search heuristics
- Trophic interaction
- phylogenetics
- feedforward neural network
- phylogenetic diversity
- PD
- feature diversity
- allele frequency
- mixed models
- 570
- Bacterial genomes
- Bioinformatics
- Virulence Factors
- Sequence Simulation
- Evolution
- taxon sampling
- selection
- Exotoxins
- NP-hard
- 333
- RAxML
- diversity
- Evolutionary history
- Domain architecture
- Functional divergence
- QH359-425
- FOS: Mathematics
- protein interaction
- Bacteriophage
- EM algorithm
- protein evolution
- Quantitative Biology - Populations and Evolution
- paralogy
- Bipartition networks
- motif
- molecular evolution
- phylogenetic analysis
- Fields of Research::230000 Mathematical Sciences::239900 Other Mathematical Sciences::239901 Biological Mathematics
- Spatial expansion
- DNA
- tree search strategies
- Indels
- speciation
- lattice models
- FOS: Biological sciences
- HIV-1
- Biochemistry and Cell Biology
- Gene expression
- phylogenetic
- orthology
- evolutionary history
- Population genetics
- gene order
- 511
- Genome context
- perception
- phylogeny
- individual haplotyping
- genome doubling
- edge lengths
- Markov Chain Monte Carlo
- network analysis
- Migration
- database
- dynamic programming
- cereals
- Measurably Evolving Populations
- lateral transfer
- synteny
- conservation
- genetic diversity
- structural search and retrieval
- minimum conflict individual haplotyping
- matrix representation with flipping
- species problem
- systematic nomenclature
- Coalescent
- Combinatorics (math.CO)
- genetic data analysis
- Functional convergence
- Mathematics - Probability
- Sciences exactes et naturelles
- Genetic data analysis
- AMOVA
- spatial expansion
- Environmental Science and Management
- gene content
- likelihood
- protein domains
- ITS sequence motifs
- large-scale maximum likelihood analyses
- Sciences de l'ingénieur
- Taxonomic distribution
- algorithms
- Supertree
- FDR
- matrix representation with parsimony
- protein thermodynamics
- Mathematics - Combinatorics
- DNA barcoding
- population sample
- Gametic phase estimation
- rational vaccine design
- Computer package
- continuous traits
- genome rearrangement
- model
- Non-stationarity
- Structural pattern matching
- Probability (math.PR)
- Populations and Evolution (q-bio.PE)
- population genetics
- Computation Theory and Mathematics
- invertebrates
- phylogenetic trees
- tetraploid
- center of tree
- Phage
- Bayesian Inference
- Brownian motion
- Protein family classification
- Maximum likelihood
- reconstruction rate
Details 詳細情報について
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- CRID
- 1360011143585513088
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- DOI
- 10.1177/117693430700300024
- 10.1177/117693430500100001
- 10.1177/117693430700300027
- 10.1177/117693430700300007
- 10.1177/117693430600200033
- 10.1177/117693430700300006
- 10.1177/117693430700300011
- 10.1177/117693430600200024
- 10.1177/117693430700300016
- 10.1177/117693430700300014
- 10.1177/117693430600200007
- 10.1177/117693430700300008
- 10.1177/117693430500100006
- 10.1177/117693430500100003
- 10.1177/117693430700300028
- 10.1177/117693430800400001
- 10.1177/117693430600200006
- 10.1177/117693430700300013
- 10.1177/117693430600200030
- 10.1177/117693430600200018
- 10.1177/117693430600200021
- 10.1177/117693430700300001
- 10.1177/117693430600200019
- 10.1177/117693430500100009
- 10.1177/117693430600200004
- 10.1177/117693430700300002
- 10.1177/117693430500100002
- 10.1177/117693430700300029
- 10.1177/117693430500100007
- 10.1177/117693430600200027
- 10.1177/117693430600200005
- 10.1177/117693430600200013
- 10.1177/117693430600200012
- 10.1177/117693430600200032
- 10.1177/117693430600200010
- 10.1177/117693430500100004
- 10.1177/117693430600200031
- 10.1177/117693430800400004
- 10.1177/117693430600200029
- 10.1177/117693430600200020
- 10.1177/117693430700300015
- 10.1177/117693430600200023
- 10.1177/117693430700300019
- 10.1177/117693430600200008
- 10.1177/117693430700300026
- 10.1177/117693430700300005
- 10.1177/117693430700300004
- 10.1177/117693430700300022
- 10.1177/117693430700300018
- 10.1177/117693430600200015
- 10.1177/117693430500100008
- 10.1177/117693430600200028
- 10.1177/117693430600200014
- 10.1177/117693430600200011
- 10.1177/117693430700300025
- 10.1177/117693430600200034
- 10.1177/117693430600200003
- 10.1177/117693430600200001
- 10.1177/117693430600200026
- 10.1177/117693430600200022
- 10.1177/117693430700300010
- 10.5282/ubm/epub.14646
- 10.48550/arxiv.math/0610840
- 10.17615/rj6k-8x92
- 10.48550/arxiv.0704.2649
- 10.4137/ebo.s0
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- ISSN
- 11769343
- http://id.crossref.org/issn/11769343
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- PubMed
- 19455209
- 19325852
- 19455222
- 19461973
- 19461977
- 19455200
- 19204806
- 19468312
- 19204809
- 19455216
- 19468310
- 19455205
- 19461979
- 19461975
- 19455211
- 19455215
- 19461982
- 19461976
- 19325855
- 19455206
- 19430600
- 19455203
- 19468311
- 21760704
- 19455202
- 19455197
- 19455213
- 19461983
- 19430606
- 19455199
- 19455229
- 19455221
- 19455217
- 19325857
- 19461971
- 19455226
- 19325851
- 19455212
- 19461986
- 19325850
- 19461985
- 19325856
- 19468313
- 19455201
- 19461974
- 19455207
- 19455219
- 19455204
- 19455208
- 19455218
- 19455198
- 19461980
- 19455228
- 19455223
- 19325853
- 19468314
- 19430604
- 19455225
- 19325849
- 19461984
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- Web Site
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300024
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300024
- https://journals.sagepub.com/doi/pdf/10.1177/117693430500100001
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430500100001
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300027
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300027
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300007
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300007
- https://journals.sagepub.com/doi/pdf/10.1177/117693430600200033
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430600200033
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300006
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300006
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300011
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300011
- https://journals.sagepub.com/doi/pdf/10.1177/117693430600200024
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430600200024
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300016
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300016
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300014
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300014
- https://journals.sagepub.com/doi/pdf/10.1177/117693430600200007
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430600200007
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300008
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300008
- https://journals.sagepub.com/doi/pdf/10.1177/117693430500100006
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430500100006
- https://journals.sagepub.com/doi/pdf/10.1177/117693430500100003
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430500100003
- https://journals.sagepub.com/doi/pdf/10.1177/117693430700300028
- https://journals.sagepub.com/doi/full-xml/10.1177/117693430700300028
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- Data Source
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- Crossref
- OpenAIRE