Pub Date : 2022-01-24DOI: 10.1007/s11692-021-09557-7
Matthew O. Moreira, Carlos Fonseca, Danny Rojas
Identifying the role of quantitative variables on speciation rates is among the main purposes of trait-dependent diversification methods. ES-sim, a recent simulation-based approach that relies on Pearson’s correlations, allows testing trait-dependent diversification for single regression models. Here, we modified this approach to include generalized linear models and two independent variables. To examine the effects of multiple traits on speciation we modified ES-sim and integrated generalized linear models instead of Pearson’s correlations. We named the new approach as ES-sim-GLM. We further evaluated how this modified method performs in both single and multiple regression modelling. For this, we analyzed the relationship of speciation rates with geographic range size and snout-to-vent length in 216 species from the family Liolaemidae, a South American radiation of Andean lizards. Based on simulations, ES-sim-GLM for single regression models shows high power, low false discovery rates and is robust to incomplete taxon sampling. ES-sim-GLM for multiple regression models shows lower power but also low false-discovery rates. Both remained computationally efficient. Using Liolaemidae data, we found that larger species but with smaller species geographic range sizes were associated with higher speciation rates. To the best of our knowledge, no study as addressed these relationships in this clade. Our results provide new insights on macroevolutionary methods that should be relevant to all organisms and facilitate future studies that aim to understand diversification patterns across the Tree of Life.
{"title":"ES-sim-GLM, a Multiple Regression Trait-Dependent Diversification Approach","authors":"Matthew O. Moreira, Carlos Fonseca, Danny Rojas","doi":"10.1007/s11692-021-09557-7","DOIUrl":"https://doi.org/10.1007/s11692-021-09557-7","url":null,"abstract":"<p>Identifying the role of quantitative variables on speciation rates is among the main purposes of trait-dependent diversification methods. <i>ES-sim</i>, a recent simulation-based approach that relies on Pearson’s correlations, allows testing trait-dependent diversification for single regression models. Here, we modified this approach to include generalized linear models and two independent variables. To examine the effects of multiple traits on speciation we modified <i>ES-sim</i> and integrated generalized linear models instead of Pearson’s correlations. We named the new approach as <i>ES-sim</i>-GLM. We further evaluated how this modified method performs in both single and multiple regression modelling. For this, we analyzed the relationship of speciation rates with geographic range size and snout-to-vent length in 216 species from the family Liolaemidae, a South American radiation of Andean lizards. Based on simulations, <i>ES-sim</i>-GLM for single regression models shows high power, low false discovery rates and is robust to incomplete taxon sampling. <i>ES-sim</i>-GLM for multiple regression models shows lower power but also low false-discovery rates. Both remained computationally efficient. Using Liolaemidae data, we found that larger species but with smaller species geographic range sizes were associated with higher speciation rates. To the best of our knowledge, no study as addressed these relationships in this clade. Our results provide new insights on macroevolutionary methods that should be relevant to all organisms and facilitate future studies that aim to understand diversification patterns across the Tree of Life.</p>","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138532947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-12DOI: 10.1093/obo/9780199941728-0139
Cancer develops through the evolution of somatic cells in multicellular bodies. The familiar dynamics of organismal evolution, including mutations, natural selection, genetic drift, and migration, also occur among the cells of multicellular organisms. In some cases, but not all, these evolutionary processes lead to cancer. This has profound implications for both our understanding of cancer and our treatment of the disease, as well as its prevention. All of our medical interventions impose selective pressures on the heterogeneous populations of billions of cells in tumors, and tend to select for mutant cells that are resistant to the intervention, regardless of whether the intervention is a drug, radiation, the immune system, or anything else that has been tried. We will likely need evolutionary and ecological approaches to cancer to manage its evolution in response to our interventions. The field of the evolutionary biology and ecology of cancer is still young and relatively small. We are in the early stages of translating ideas and tools from evolutionary biology and ecology to study and manage cancers. There is a desperate need for more researchers with expertise in evolutionary biology and ecology to apply their skills and ideas to cancer. Currently, there are far more important questions that need to be addressed than there are people to address them.
{"title":"Evolutionary Processes in Cancer","authors":"","doi":"10.1093/obo/9780199941728-0139","DOIUrl":"https://doi.org/10.1093/obo/9780199941728-0139","url":null,"abstract":"Cancer develops through the evolution of somatic cells in multicellular bodies. The familiar dynamics of organismal evolution, including mutations, natural selection, genetic drift, and migration, also occur among the cells of multicellular organisms. In some cases, but not all, these evolutionary processes lead to cancer. This has profound implications for both our understanding of cancer and our treatment of the disease, as well as its prevention. All of our medical interventions impose selective pressures on the heterogeneous populations of billions of cells in tumors, and tend to select for mutant cells that are resistant to the intervention, regardless of whether the intervention is a drug, radiation, the immune system, or anything else that has been tried. We will likely need evolutionary and ecological approaches to cancer to manage its evolution in response to our interventions. The field of the evolutionary biology and ecology of cancer is still young and relatively small. We are in the early stages of translating ideas and tools from evolutionary biology and ecology to study and manage cancers. There is a desperate need for more researchers with expertise in evolutionary biology and ecology to apply their skills and ideas to cancer. Currently, there are far more important questions that need to be addressed than there are people to address them.","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44643363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-11-10DOI: 10.1007/s11692-021-09555-9
B. Esteve-Altava
{"title":"Cranial Anatomical Integration and Disparity Among Bones Discriminate Between Primates and Non-primate Mammals","authors":"B. Esteve-Altava","doi":"10.1007/s11692-021-09555-9","DOIUrl":"https://doi.org/10.1007/s11692-021-09555-9","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2021-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43769664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-11-08DOI: 10.1007/s11692-021-09554-w
M. R. Ruiz-Monachesi, C. Abdala, James A. Schulte, Felix Benjamin Cruz
{"title":"Predictive Factors of Chemical and Visual Sensory Organ Size: The Roles of Sex, Environment, and Evolution","authors":"M. R. Ruiz-Monachesi, C. Abdala, James A. Schulte, Felix Benjamin Cruz","doi":"10.1007/s11692-021-09554-w","DOIUrl":"https://doi.org/10.1007/s11692-021-09554-w","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2021-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48131957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-10-21DOI: 10.1007/s11692-021-09553-x
M. Gilg, Emily V. Kerns, Natalia E Gutierrez-Bayona, Catherine Kooyomjian, N. A. Hinojosa
{"title":"Dynamic Cohort Analysis Reveals Fluctuating Patterns of Selection Within a Hybrid Zone Between the Killifish Fundulus heteroclitus and F. grandis","authors":"M. Gilg, Emily V. Kerns, Natalia E Gutierrez-Bayona, Catherine Kooyomjian, N. A. Hinojosa","doi":"10.1007/s11692-021-09553-x","DOIUrl":"https://doi.org/10.1007/s11692-021-09553-x","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2021-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46593766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-23DOI: 10.1007/s11692-021-09551-z
Michael Andrade, Daubian Santos, Gabriel M. Bueno, C. M. D. Santos
{"title":"What if… Sponges Originated 890 Million Years Ago? On the Emergence of Some Precursors of Animal Sentience","authors":"Michael Andrade, Daubian Santos, Gabriel M. Bueno, C. M. D. Santos","doi":"10.1007/s11692-021-09551-z","DOIUrl":"https://doi.org/10.1007/s11692-021-09551-z","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2021-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47166290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-01DOI: 10.1007/s11692-021-09550-0
J. Thioulouse, S. Renaud, A. Dufour, S. Dray
{"title":"Overcoming the Spurious Groups Problem in Between-Group PCA","authors":"J. Thioulouse, S. Renaud, A. Dufour, S. Dray","doi":"10.1007/s11692-021-09550-0","DOIUrl":"https://doi.org/10.1007/s11692-021-09550-0","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48954923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-28DOI: 10.1007/s11692-021-09548-8
F. Bookstein
{"title":"A New Method for Landmark-Based Studies of the Dynamic Stability of Growth, with Implications for Evolutionary Analyses","authors":"F. Bookstein","doi":"10.1007/s11692-021-09548-8","DOIUrl":"https://doi.org/10.1007/s11692-021-09548-8","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2021-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11692-021-09548-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41367910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-18DOI: 10.1007/s11692-021-09549-7
B. Rothschild
{"title":"Consistent Prevalence of Spondyloarthropathy Over 2300 Years: Ancient Egyptians and the Synchronic Baboon Catacomb","authors":"B. Rothschild","doi":"10.1007/s11692-021-09549-7","DOIUrl":"https://doi.org/10.1007/s11692-021-09549-7","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2021-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11692-021-09549-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44284021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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