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Lin Q, Goldberg EE, Leitner T, Molina-París C, King AA, Romero-Severson EO. The number and pattern of viral genomic reassortments are not necessarily identifiable from segment trees. Mol Biol Evol 2024:msae078. [PMID: 38648521 DOI: 10.1093/molbev/msae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Because large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the `first-infection tree', a typically but not always counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our perception of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment but also the four additional situations that can complicate the inference of reassortment.
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Affiliation(s)
- Qianying Lin
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
| | - Emma E Goldberg
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
| | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
| | - Carmen Molina-París
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
| | - Aaron A King
- Center for the Study of Complex Systems and Departments of Ecology & Evolutionary Biology and Mathematics, University of Michigan, Ann Arbor MI, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM, USA
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2
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Goldberg EE, Lundgren EJ, Romero-Severson EO, Leitner T. Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs. Mol Biol Evol 2024; 41:msad282. [PMID: 38149995 PMCID: PMC10776241 DOI: 10.1093/molbev/msad282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023] Open
Abstract
When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source's infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model-which make use of different information within a tree-suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.
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Affiliation(s)
- Emma E Goldberg
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Erik J Lundgren
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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3
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Goldberg EE, Lundgren EJ, Romero-Severson EO, Leitner T. Inferring viral transmission time from phylogenies for known transmission pairs. bioRxiv 2023:2023.09.12.557404. [PMID: 37745490 PMCID: PMC10515827 DOI: 10.1101/2023.09.12.557404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously-described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source's infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time-calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model-which make use of different information within a tree-suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.
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Affiliation(s)
- Emma E. Goldberg
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
| | - Erik J. Lundgren
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
| | | | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
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4
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Lin Q, Goldberg EE, Leitner T, Molina-París C, King AA, Romero-Severson EO. Modeling the evolution of segment trees reveals deficiencies in current inferential methods for genomic reassortment. bioRxiv 2023:2023.09.20.558687. [PMID: 37790507 PMCID: PMC10542121 DOI: 10.1101/2023.09.20.558687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to new viral variants. Large-scale genome rearrangements, such as reassortment, have the potential to quickly generate new phenotypes, making the understanding of viral reassortment important to both evolutionary biology and public health research. In this paper, we argue that reassortment cannot be reliably inferred from incongruities between segment phylogenies using the established remove-and-rejoin or coalescent approaches. We instead show that reassortment must be considered in the context of a broader population process that includes the dynamics of the infected hosts. Using illustrative examples and simulation we identify four types of evolutionary events that are difficult or impossible to reconstruct with incongruence-based methods. Further, we show that these specific situations are very common and will likely occur even in small samples. Finally, we argue that existing methods can be augmented or modified to account for all the problematic situations that we identify in this paper. Robust assessment of the role of reassortment in viral evolution is difficult, and we hope to provide conceptual clarity on some important methodological issues that can arise in the development of the next generation of tools for studying reassortment.
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Goldberg EE, Lin Q, Romero-Severson EO, Ke R. Swift and extensive Omicron outbreak in China after sudden exit from 'zero-COVID' policy. Nat Commun 2023; 14:3888. [PMID: 37393346 PMCID: PMC10314942 DOI: 10.1038/s41467-023-39638-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023] Open
Abstract
In late 2022, China transitioned from a strict 'zero-COVID' policy to rapidly abandoning nearly all interventions and data reporting. This raised great concern about the presumably-rapid but unreported spread of the SARS-CoV-2 Omicron variant in a very large population of very low pre-existing immunity. By modeling a combination of case count and survey data, we show that Omicron spread extremely rapidly, at a rate of 0.42/day (95% credibility interval: [0.35, 0.51]/day), translating to an epidemic doubling time of 1.6 days ([1.6, 2.0] days) after the full exit from zero-COVID on Dec. 7, 2022. Consequently, we estimate that the vast majority of the population (97% [95%, 99%], sensitivity analysis lower limit of 90%) was infected during December, with the nation-wide epidemic peaking on Dec. 23. Overall, our results highlight the extremely high transmissibility of the variant and the importance of proper design of intervention exit strategies to avoid large infection waves.
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Affiliation(s)
- Emma E Goldberg
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Qianying Lin
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Ethan O Romero-Severson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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6
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Goldberg EE, Price T. Effects of plasticity on elevational range size and species richness. Am Nat 2022; 200:316-329. [DOI: 10.1086/720412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Dorp CHV, Goldberg EE, Hengartner N, Ke R, Romero-Severson EO. Estimating the strength of selection for new SARS-CoV-2 variants. Nat Commun 2021; 12:7239. [PMID: 34907182 PMCID: PMC8671537 DOI: 10.1038/s41467-021-27369-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/10/2021] [Indexed: 01/15/2023] Open
Abstract
Controlling the SARS-CoV-2 pandemic becomes increasingly challenging as the virus adapts to human hosts through the continual emergence of more transmissible variants. Simply observing that a variant is increasing in frequency is relatively straightforward, but more sophisticated methodology is needed to determine whether a new variant is a global threat and the magnitude of its selective advantage. We present two models for quantifying the strength of selection for new and emerging variants of SARS-CoV-2 relative to the background of contemporaneous variants. These methods range from a detailed model of dynamics within one country to a broad analysis across all countries, and they include alternative explanations such as migration and drift. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. Cutting back data to earlier time horizons reveals that uncertainty is large very soon after emergence, but that estimates of selection stabilize after several weeks. Our results also show substantial heterogeneity among countries, demonstrating the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.
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Affiliation(s)
- Christiaan H van Dorp
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Emma E Goldberg
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Ethan O Romero-Severson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA.
- New Mexico Consortium, Los Alamos, NM, USA.
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8
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Abstract
Controlling the SARS-CoV-2 pandemic becomes increasingly challenging as the virus adapts to human hosts through the continual emergence of more transmissible variants. Simply observing that a variant is increasing in frequency is relatively straightforward, but more sophisticated methodology is needed to determine whether a new variant is a global threat and the magnitude of its selective advantage. We present three methods for quantifying the strength of selection for new and emerging variants of SARS-CoV-2 relative to the background of contemporaneous variants. These methods range from a detailed model of dynamics within one country to a broad analysis across all countries, and they include alternative explanations such as migration and drift. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. Cutting back data to earlier time horizons reveals large uncertainty very soon after emergence, but that estimates of selection stabilize after several weeks. Our results also show substantial heterogeneity among countries, demonstrating the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.
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Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
| | - Emma E. Goldberg
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
| | - Ethan O. Romero-Severson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM, USA
- New Mexico Consortium, Los Alamos NM, USA
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9
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Harkness A, Goldberg EE, Brandvain Y. Diversification or Collapse of Self-Incompatibility Haplotypes as a Rescue Process. Am Nat 2021; 197:E89-E109. [DOI: 10.1086/712424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Shafir A, Azouri D, Goldberg EE, Mayrose I. Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates. Evolution 2020; 74:1620-1639. [PMID: 32510165 DOI: 10.1111/evo.14036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/17/2020] [Indexed: 12/01/2022]
Abstract
As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel.,School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | | | - Itay Mayrose
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
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12
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Zenil-Ferguson R, Burleigh JG, Freyman WA, Igić B, Mayrose I, Goldberg EE. Interaction among ploidy, breeding system and lineage diversification. New Phytol 2019; 224:1252-1265. [PMID: 31617595 DOI: 10.1111/nph.16184] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/14/2019] [Indexed: 05/28/2023]
Abstract
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs polyploid states) and breeding system (self-incompatible vs self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit 29 diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.
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Affiliation(s)
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - William A Freyman
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Boris Igić
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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13
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Ballen CJ, Aguillon SM, Awwad A, Bjune AE, Challou D, Drake AG, Driessen M, Ellozy A, Ferry VE, Goldberg EE, Harcombe W, Jensen S, Jørgensen C, Koth Z, McGaugh S, Mitry C, Mosher B, Mostafa H, Petipas RH, Soneral PAG, Watters S, Wassenberg D, Weiss SL, Yonas A, Zamudio KR, Cotner S. Smaller Classes Promote Equitable Student Participation in STEM. Bioscience 2019. [DOI: 10.1093/biosci/biz069] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
As science, technology, engineering, and mathematics (STEM) classrooms in higher education transition from lecturing to active learning, the frequency of student interactions in class increases. Previous research documents a gender bias in participation, with women participating less than would be expected on the basis of their numeric proportions. In the present study, we asked which attributes of the learning environment contribute to decreased female participation: the abundance of in-class interactions, the diversity of interactions, the proportion of women in class, the instructor's gender, the class size, and whether the course targeted lower division (first and second year) or upper division (third or fourth year) students. We calculated likelihood ratios of female participation from over 5300 student–instructor interactions observed across multiple institutions. We falsified several alternative hypotheses and demonstrate that increasing class size has the largest negative effect. We also found that when the instructors used a diverse range of teaching strategies, the women were more likely to participate after small-group discussions.
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Affiliation(s)
- Cissy J Ballen
- Department of Biological Sciences at Auburn University, Auburn, Alabama
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, Minnesota
| | - Stepfanie M Aguillon
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
- Fuller Evolutionary Biology Program, at the Cornell Lab of Ornithology, Ithaca, New York
| | - Azza Awwad
- Center for Learning and Teaching at The American University in Cairo, Cairo, Egypt
| | - Anne E Bjune
- Department of Biological Sciences at the University of Bergen, Bergen, Norway
| | - Daniel Challou
- Department of Computer Science and Engineering at the University of Minnesota, Minneapolis, Minnesota
| | - Abby Grace Drake
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Michelle Driessen
- Department of Chemistry at the University of Minnesota, Minneapolis, Minnesota
| | - Aziza Ellozy
- Center for Learning and Teaching at The American University in Cairo, Cairo, Egypt
| | - Vivian E Ferry
- Department of Chemical Engineering and Materials Science at the University of Minnesota, Minneapolis, Minnesota
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior at the University of Minnesota, Minneapolis, Minnesota
| | - William Harcombe
- Department of Ecology, Evolution, and Behavior at the University of Minnesota, Minneapolis, Minnesota
| | - Steve Jensen
- Department of Computer Science and Engineering at the University of Minnesota, Minneapolis, Minnesota
| | - Christian Jørgensen
- Department of Biological Sciences at the University of Bergen, Bergen, Norway
| | - Zoe Koth
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, Minnesota
| | - Suzanne McGaugh
- Department of Ecology, Evolution, and Behavior at the University of Minnesota, Minneapolis, Minnesota
| | - Caroline Mitry
- Center for Learning and Teaching at The American University in Cairo, Cairo, Egypt
| | - Bryan Mosher
- School of Mathematics at the University of Minnesota, Minneapolis, Minnesota
| | - Hoda Mostafa
- Center for Learning and Teaching at The American University in Cairo, Cairo, Egypt
| | - Renee H Petipas
- Department of Plant Pathology at Washington State University, Pullman, Washington
| | - Paula A G Soneral
- Department of Biological Sciences at Bethel University, Saint Paul, Minnesota
| | - Shana Watters
- Department of Computer Science and Engineering at the University of Minnesota, Minneapolis, Minnesota
| | - Deena Wassenberg
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, Minnesota
| | - Stacey L Weiss
- Department of Biology at the University of Puget Sound, Tacoma, Washington
| | - Azariah Yonas
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, Minnesota
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Sehoya Cotner
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, Minnesota
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14
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Harmon LJ, Andreazzi CS, Débarre F, Drury J, Goldberg EE, Martins AB, Melián CJ, Narwani A, Nuismer SL, Pennell MW, Rudman SM, Seehausen O, Silvestro D, Weber M, Matthews B. Detecting the macroevolutionary signal of species interactions. J Evol Biol 2019; 32:769-782. [DOI: 10.1111/jeb.13477] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Luke J. Harmon
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Department of Biological Sciences University of Idaho Moscow Idaho
| | | | - Florence Débarre
- Sorbonne Université, UPMC Univ Paris 06, CNRS, IRD, INRA, Université Paris Diderot, Institute of Ecology and Environmental Sciences (UMR7618) Paris France
| | | | - Emma E. Goldberg
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul Minnesota
| | - Ayana B. Martins
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Instituto de Física ‘Gleb Wataghin’ Universidade Estadual de Campinas Campinas Brazil
| | - Carlos J. Melián
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
| | - Anita Narwani
- Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology Eawag Dübendorf Switzerland
| | - Scott L. Nuismer
- Department of Biological Sciences University of Idaho Moscow Idaho
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre University of British Columbia Vancouver British Columbia
| | - Seth M. Rudman
- Department of Biology University of Pennsylvania Philadelphia Pennsylvania
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences Global Gothenburg Biodiversity Centre University of Gothenburg Gothenburg Sweden
| | - Marjorie Weber
- Department of Plant Biology & Program in Ecology, Evolution, and Behavior Michigan State University East Lansing Michigan
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry Eawag Kastanienbaum Switzerland
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution University of Bern Bern Switzerland
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15
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Harkness A, Brandvain Y, Goldberg EE. The evolutionary response of mating system to heterosis. J Evol Biol 2019; 32:476-490. [DOI: 10.1111/jeb.13430] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Harkness
- Department of Ecology, Evolution, and BehaviorUniversity of Minnesota St. Paul Minnesota
| | - Yaniv Brandvain
- Department of Plant and Microbial BiologyUniversity of Minnesota St. Paul Minnesota
| | - Emma E. Goldberg
- Department of Ecology, Evolution, and BehaviorUniversity of Minnesota St. Paul Minnesota
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16
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Blackmon H, Justison J, Mayrose I, Goldberg EE. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 2019; 73:511-523. [PMID: 30690715 PMCID: PMC6590138 DOI: 10.1111/evo.13682] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all bibrachial or all monobrachial chromosomes than in species with a mix of both types of morphologies. We suggest that species with homogeneous karyotypes may represent cases where meiotic drive acts to stabilize the karyotype, favoring the chromosome morphologies already present in the genome. In contrast, rapid bouts of chromosome number evolution in taxa with mixed karyotypes may indicate that a switch in the polarity of female meiotic drive favors changes in chromosome number. We do not find any evidence that karyotype morphology affects rates of speciation or extinction. Furthermore, we document that switches in meiotic drive polarity are likely common and have occurred in most major clades of mammals, and that rapid remodeling of karyotypes may be more common than once thought.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Joshua Justison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
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17
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Huang D, Goldberg EE, Chou LM, Roy K. The origin and evolution of coral species richness in a marine biodiversity hotspot. Evolution 2017; 72:288-302. [PMID: 29178128 DOI: 10.1111/evo.13402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 10/30/2017] [Accepted: 11/12/2017] [Indexed: 12/25/2022]
Abstract
The Coral Triangle (CT) region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here, we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the CT are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the CT is low, and the CT endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the CT is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the CT requires protecting not just reefs within the hotspot, but also those in the surrounding areas.
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Affiliation(s)
- Danwei Huang
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Loke Ming Chou
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, California 92093
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18
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Grossenbacher DL, Brandvain Y, Auld JR, Burd M, Cheptou PO, Conner JK, Grant AG, Hovick SM, Pannell JR, Pauw A, Petanidou T, Randle AM, Rubio de Casas R, Vamosi J, Winn A, Igic B, Busch JW, Kalisz S, Goldberg EE. Self-compatibility is over-represented on islands. New Phytol 2017; 215:469-478. [PMID: 28382619 DOI: 10.1111/nph.14534] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/20/2017] [Indexed: 06/07/2023]
Abstract
Because establishing a new population often depends critically on finding mates, individuals capable of uniparental reproduction may have a colonization advantage. Accordingly, there should be an over-representation of colonizing species in which individuals can reproduce without a mate, particularly in isolated locales such as oceanic islands. Despite the intuitive appeal of this colonization filter hypothesis (known as Baker's law), more than six decades of analyses have yielded mixed findings. We assembled a dataset of island and mainland plant breeding systems, focusing on the presence or absence of self-incompatibility. Because this trait enforces outcrossing and is unlikely to re-evolve on short timescales if it is lost, breeding system is especially likely to reflect the colonization filter. We found significantly more self-compatible species on islands than mainlands across a sample of > 1500 species from three widely distributed flowering plant families (Asteraceae, Brassicaceae and Solanaceae). Overall, 66% of island species were self-compatible, compared with 41% of mainland species. Our results demonstrate that the presence or absence of self-incompatibility has strong explanatory power for plant geographical patterns. Island floras around the world thus reflect the role of a key reproductive trait in filtering potential colonizing species in these three plant families.
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Affiliation(s)
- Dena L Grossenbacher
- Department of Biology, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Josh R Auld
- Department of Biology, West Chester University, West Chester, PA, 19383, USA
| | - Martin Burd
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Pierre-Olivier Cheptou
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valery Montpellier, EPHE, CEFE, 34293, Montpellier Cedex 05, France
| | - Jeffrey K Conner
- Kellogg Biological Station and Department of Plant Biology, Michigan State University, Hickory Corners, MI, 49060, USA
| | - Alannie G Grant
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Stephen M Hovick
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Anton Pauw
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Theodora Petanidou
- Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, 81100, Mytilene, Lesvos, Greece
| | - April M Randle
- Department of Environmental Science, University of San Francisco, San Francisco, CA, 94117, USA
| | - Rafael Rubio de Casas
- Departmento Ecología, Facultad de Ciencias, Universidad de Granada, Granada, UGR, 18071, Granada, Spain
| | - Jana Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada, T2N 1N4
| | - Alice Winn
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Boris Igic
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Susan Kalisz
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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Rabosky DL, Goldberg EE. FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates. Evolution 2017; 71:1432-1442. [DOI: 10.1111/evo.13227] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/06/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan 48103
| | - Emma E. Goldberg
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul Minnesota 55108
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20
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Goldberg EE, Otto SP, Vamosi JC, Mayrose I, Sabath N, Ming R, Ashman TL. Macroevolutionary synthesis of flowering plant sexual systems. Evolution 2017; 71:898-912. [PMID: 28085192 DOI: 10.1111/evo.13181] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 01/22/2023]
Abstract
Sexual system is a key determinant of genetic variation and reproductive success, affecting evolution within populations and within clades. Much research in plants has focused on evolutionary transitions away from the most common state of hermaphroditism and toward the rare state of dioecy (separate sexes). Rather than transitions predominantly toward greater sexual differentiation, however, evolution may proceed in the direction of lesser sexual differentiation. We analyzed the macroevolutionary dynamics of sexual system in angiosperm genera that contain both dioecious and nondioecious species. Our phylogenetic analyses encompass a total of 2145 species from 40 genera. Overall, we found little evidence that rates of sexual system transitions are greater in any direction. Counting the number of inferred state changes revealed a mild prevalence of transitions away from hermaphroditism and away from dioecy, toward states of intermediate sexual differentiation. We identify genera in which future studies of sexual system evolution might be especially productive, and we discuss how integrating genetic or population-level studies of sexual system could improve the power of phylogenetic comparative analyses. Our work adds to the evidence that different selective pressures and constraints act in different groups, helping maintain the variety of sexual systems observed among plants.
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Affiliation(s)
- Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, 55108
| | - Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, BC, V6J 3S7, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Niv Sabath
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.,Department of Plant Biology, University of Illinois, Urbana, Illinois, 61801
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260
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21
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Zhan SH, Drori M, Goldberg EE, Otto SP, Mayrose I. Phylogenetic evidence for cladogenetic polyploidization in land plants. Am J Bot 2016; 103:1252-1258. [PMID: 27466054 DOI: 10.3732/ajb.1600108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation". Whether polyploidization is associated with the formation of new species (cladogenesis) or simply occurs over time within a lineage (anagenesis), however, has never been assessed systematically. METHODS We tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. KEY RESULTS Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. CONCLUSIONS Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera.
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Affiliation(s)
- Shing H Zhan
- Department of Zoology, 4200-6270 University Boulevard, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - Michal Drori
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, P. O. Box 39040, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, & Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, Minnesota 55108 USA
| | - Sarah P Otto
- Department of Zoology, 4200-6270 University Boulevard, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, P. O. Box 39040, Tel Aviv 69978, Israel
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22
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Sabath N, Goldberg EE, Glick L, Einhorn M, Ashman TL, Ming R, Otto SP, Vamosi JC, Mayrose I. Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms. New Phytol 2016; 209:1290-1300. [PMID: 26467174 DOI: 10.1111/nph.13696] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver.
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Affiliation(s)
- Niv Sabath
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution & Behavior, University of Minnesota, St Paul, MN, 55108-6097, USA
| | - Lior Glick
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Einhorn
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute for Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6J 3S7, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
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23
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Grossenbacher D, Briscoe Runquist RD, Goldberg EE, Brandvain Y. No association between plant mating system and geographic range overlap. Am J Bot 2016; 103:110-117. [PMID: 26643886 DOI: 10.3732/ajb.1500078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 06/15/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Automatic self-fertilization may influence the geography of speciation, promote reproductive isolation between incipient species, and lead to ecological differentiation. As such, selfing taxa are predicted to co-occur more often with their closest relatives than are outcrossing taxa. Despite suggestions that this pattern may be general, the extent to which mating system influences range overlap in close relatives has not been tested formally across a diverse group of plant species pairs. METHODS We tested for a difference in range overlap between species pairs for which zero, one, or both species are selfers, using data from 98 sister species pairs in 20 genera across 15 flowering plant families. We also used divergence time estimates from time-calibrated phylogenies to ask how range overlap changes with divergence time and whether this effect depends on mating system. KEY RESULTS We found no evidence that automatic self-fertilization influenced range overlap of closely related plant species. Sister pairs with more recent divergence times had modestly greater range overlap, but this effect did not depend on mating system. CONCLUSIONS The absence of a strong influence of mating system on range overlap suggests that mating system plays a minor or inconsistent role compared with many other mechanisms potentially influencing the co-occurrence of close relatives.
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Affiliation(s)
- Dena Grossenbacher
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 USA
| | | | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 USA
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24
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Pannell JR, Auld JR, Brandvain Y, Burd M, Busch JW, Cheptou PO, Conner JK, Goldberg EE, Grant AG, Grossenbacher DL, Hovick SM, Igic B, Kalisz S, Petanidou T, Randle AM, de Casas RR, Pauw A, Vamosi JC, Winn AA. The scope of Baker's law. New Phytol 2015; 208:656-67. [PMID: 26192018 DOI: 10.1111/nph.13539] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/27/2015] [Indexed: 05/13/2023]
Abstract
Baker's law refers to the tendency for species that establish on islands by long-distance dispersal to show an increased capacity for self-fertilization because of the advantage of self-compatibility when colonizing new habitat. Despite its intuitive appeal and broad empirical support, it has received substantial criticism over the years since it was proclaimed in the 1950s, not least because it seemed to be contradicted by the high frequency of dioecy on islands. Recent theoretical work has again questioned the generality and scope of Baker's law. Here, we attempt to discern where the idea is useful to apply and where it is not. We conclude that several of the perceived problems with Baker's law fall away when a narrower perspective is adopted on how it should be circumscribed. We emphasize that Baker's law should be read in terms of an enrichment of a capacity for uniparental reproduction in colonizing situations, rather than of high selfing rates. We suggest that Baker's law might be tested in four different contexts, which set the breadth of its scope: the colonization of oceanic islands, metapopulation dynamics with recurrent colonization, range expansions with recurrent colonization, and colonization through species invasions.
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Affiliation(s)
- John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Josh R Auld
- Department of Biology, West Chester University, West Chester, PA, 19383, USA
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Martin Burd
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Pierre-Olivier Cheptou
- CEFE UMR 5175, CNRS, Universite de Montpellier, Université Paul-Valery Montpellier, EPHE, CEFE 34293, Montpellier Cedex 05, France
| | - Jeffrey K Conner
- Kellogg Biological Station and Department of Plant Biology, Michigan State University, Hickory Corners, MI, 49060, USA
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | | | | | - Stephen M Hovick
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Boris Igic
- Department of Biological Sciences, University of Illinois at Chicago, 840 W Taylor St, M/C 067, Chicago, IL, 60607, USA
| | - Susan Kalisz
- Department of Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Theodora Petanidou
- Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, 81100 Mytilene, Lesvos, Greece
| | - April M Randle
- Department of Environmental Science, University of San Francisco, San Francisco, CA, 94117-1049, USA
| | - Rafael Rubio de Casas
- CEFE UMR 5175, CNRS, Universite de Montpellier, Université Paul-Valery Montpellier, EPHE, CEFE 34293, Montpellier Cedex 05, France
- Departmento Ecología, Facultad de Ciencias, Universidad de Granada, UGR, 18071, Granada, Spain
- Estación Experimental de Zonas Áridas, EEZA-CSIC, Carretera de Sacramento s/n, La Cañada de San Urbano, EEZA 04120, Almeria, Spain
| | - Anton Pauw
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N1N4, Canada
| | - Alice A Winn
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
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25
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Grossenbacher D, Briscoe Runquist R, Goldberg EE, Brandvain Y. Geographic range size is predicted by plant mating system. Ecol Lett 2015; 18:706-13. [PMID: 25980327 DOI: 10.1111/ele.12449] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/13/2015] [Accepted: 04/09/2015] [Indexed: 11/30/2022]
Abstract
Species' geographic ranges vary enormously, and even closest relatives may differ in range size by several orders of magnitude. With data from hundreds of species spanning 20 genera in 15 families, we show that plant species that autonomously reproduce via self-pollination consistently have larger geographic ranges than their close relatives that generally require two parents for reproduction. Further analyses strongly implicate autonomous self-fertilisation in causing this relationship, as it is not driven by traits such as polyploidy or annual life history whose evolution is sometimes correlated with selfing. Furthermore, we find that selfers occur at higher maximum latitudes and that disparity in range size between selfers and outcrossers increases with time since their evolutionary divergence. Together, these results show that autonomous reproduction--a critical biological trait that eliminates mate limitation and thus potentially increases the probability of establishment--increases range size.
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Affiliation(s)
- Dena Grossenbacher
- Department of Plant Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, St. Paul, MN, 55108, USA
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26
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Affiliation(s)
- Daniel L. Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109; and 2Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Emma E. Goldberg
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109; and 2Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
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27
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Servedio MR, Brandvain Y, Dhole S, Fitzpatrick CL, Goldberg EE, Stern CA, Van Cleve J, Yeh DJ. Not just a theory--the utility of mathematical models in evolutionary biology. PLoS Biol 2014; 12:e1002017. [PMID: 25489940 PMCID: PMC4260780 DOI: 10.1371/journal.pbio.1002017] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Models have made numerous contributions to evolutionary biology, but misunderstandings persist regarding their purpose. By formally testing the logic of verbal hypotheses, proof-of-concept models clarify thinking, uncover hidden assumptions, and spur new directions of study. thumbnail image credit: modified from the Biodiversity Heritage Library
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Affiliation(s)
- Maria R. Servedio
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Sumit Dhole
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Courtney L. Fitzpatrick
- National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States of America
| | - Emma E. Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Caitlin A. Stern
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Jeremy Van Cleve
- National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States of America
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - D. Justin Yeh
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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28
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Fagan WF, Pearson YE, Larsen EA, Lynch HJ, Turner JB, Staver H, Noble AE, Bewick S, Goldberg EE. Phylogenetic prediction of the maximum per capita rate of population growth. Proc Biol Sci 2013; 280:20130523. [PMID: 23720545 DOI: 10.1098/rspb.2013.0523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The maximum per capita rate of population growth, r, is a central measure of population biology. However, researchers can only directly calculate r when adequate time series, life tables and similar datasets are available. We instead view r as an evolvable, synthetic life-history trait and use comparative phylogenetic approaches to predict r for poorly known species. Combining molecular phylogenies, life-history trait data and stochastic macroevolutionary models, we predicted r for mammals of the Caniformia and Cervidae. Cross-validation analyses demonstrated that, even with sparse life-history data, comparative methods estimated r well and outperformed models based on body mass. Values of r predicted via comparative methods were in strong rank agreement with observed values and reduced mean prediction errors by approximately 68 per cent compared with two null models. We demonstrate the utility of our method by estimating r for 102 extant species in these mammal groups with unknown life-history traits.
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Affiliation(s)
- William F Fagan
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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Abstract
Classic questions about trait evolution-including the directionality of character change and its interactions with lineage diversification-intersect in the study of plant breeding systems. Transitions from self-incompatibility to self-compatibility are frequent, and they may proceed within a species ("anagenetic" mode of breeding system change) or in conjunction with speciation events ("cladogenetic" mode of change). We apply a recently developed phylogenetic model to the nightshade family Solanaceae, quantifying the relative contributions of these two modes of evolution along with the tempo of breeding system change, speciation, and extinction. We find that self-incompatibility, a genetic mechanism that prevents self-fertilization, is lost largely by the cladogenetic mode. Self-compatible species are thus more likely to arise from the isolation of a newly self-compatible population than from species-wide fixation of self-compatible mutants. Shared polymorphism at the locus that governs self-incompatibility shows it to be ancestral and not regained within this family. We demonstrate that failing to account for cladogenetic character change misleads phylogenetic tests of evolutionary irreversibility, both for breeding system in Solanaceae and on simulated trees.
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Affiliation(s)
- Emma E Goldberg
- Department of Biological Sciences, University of Illinois at Chicago, 840 West Taylor Street MC067, Chicago, Illinois 60607, USA.
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Abstract
Geographic characters--traits describing the spatial distribution of a species-may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of ranges and the growth of phylogenetic trees. Here, we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model in which these processes are interdependent. We demonstrate the method with simulation tests that accurately recover parameters relating to the mode of speciation and source-sink dynamics. We then apply it to the evolution of habitat occupancy in Californian plant communities, where we find higher rates of speciation in chaparral than in forests and evidence for expanding habitat tolerances.
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Affiliation(s)
- Emma E Goldberg
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Abstract
Identifying traits that affect rates of speciation and extinction and, hence, explain differences in species diversity among clades is a major goal of evolutionary biology. Detecting such traits is especially difficult when they undergo frequent transitions between states. Self-incompatibility, the ability of hermaphrodites to enforce outcrossing, is frequently lost in flowering plants, enabling self-fertilization. We show, however, that in the nightshade plant family (Solanaceae), species with functional self-incompatibility diversify at a significantly higher rate than those without it. The apparent short-term advantages of potentially self-fertilizing individuals are therefore offset by strong species selection, which favors obligate outcrossing.
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Affiliation(s)
- Emma E Goldberg
- Department of Biological Sciences, University of Illinois at Chicago, 840 West Taylor Street, M/C 067, Chicago, IL 60607, USA
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Abstract
Habitat specialization plays an important role in the creation and loss of biodiversity over ecological and evolutionary time scales. In California, serpentine soils have a distinctive flora, with 246 serpentine habitat specialists (i.e., endemics). Using molecular phylogenies for 23 genera containing 784 taxa and 51 endemics, we infer few transitions out of the endemic state, which is shown by an analysis of transition rates to simply reflect the low frequency of endemics (i.e., reversal rates were high). The finding of high reversal rates, but a low number of reversals, is consistent with the widely hypothesized trade-off between serpentine tolerance and competitive ability, under which serpentine endemics are physiologically capable of growing in less-stressful habitats but competitors lead to their extirpation. Endemism is also characterized by a decrease in speciation and extinction rates and a decrease in the overall diversification rate. We also find that tolerators (species with nonserpentine and serpentine populations) undergo speciation in serpentine habitats to give rise to new serpentine endemics but are several times more likely to lose serpentine populations to produce serpentine-intolerant taxa. Finally, endemics were younger on average than nonendemics, but this alone does not explain their low diversification.
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Affiliation(s)
- Brian L Anacker
- Department of Environmental Science and Policy, One Shields Avenue, University of California, Davis, California 95616, USA.
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Abstract
Breakdown of self-incompatibility occurs repeatedly in flowering plants with important evolutionary consequences. In plant families in which self-incompatibility is mediated by S-RNases, previous evidence suggests that polyploidy may often directly cause self-compatibility through the formation of diploid pollen grains. We use three approaches to examine relationships between self-incompatibility and ploidy. First, we test whether evolution of self-compatibility and polyploidy is correlated in the nightshade family (Solanaceae), and find the expected close association between polyploidy and self-compatibility. Second, we compare the rate of breakdown of self-incompatibility in the absence of polyploidy against the rate of breakdown that arises as a byproduct of polyploidization, and we find the former to be greater. Third, we apply a novel extension to these methods to show that the relative magnitudes of the macroevolutionary pathways leading to self-compatible polyploids are time dependent. Over small time intervals, the direct pathway from self-incompatible diploids is dominant, whereas the pathway through self-compatible diploids prevails over longer time scales. This pathway analysis is broadly applicable to models of character evolution in which sequential combinations of rates are compared. Finally, given the strong evidence for both irreversibility of the loss of self-incompatibility in the family and the significant association between self-compatibility and polyploidy, we argue that ancient polyploidy is highly unlikely to have occurred within the Solanaceae, contrary to previous claims based on genomic analyses.
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Affiliation(s)
- Kelly Robertson
- Department of Biological Sciences, 840 West Taylor St., M/C 067, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
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Goldberg EE, Lynch HJ, Neubert MG, Fagan WF. Effects of branching spatial structure and life history on the asymptotic growth rate of a population. THEOR ECOL-NETH 2009. [DOI: 10.1007/s12080-009-0058-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Species diversity gradients seen today are, to a large degree, a product of history. Spatially nonrandom originations, extinctions, and changes in geographic distributions can create gradients in species and higher-taxon richness, but the relative roles of each of these processes remain poorly documented. Existing explanations of diversity gradients have tended to focus on either macroevolutionary or biogeographic processes; integrative models that include both are largely lacking. We used simple models that incorporate origination and extinction rates along with dispersal of taxa between regions to show that dispersal not only affects regional richness patterns but also has a strong influence on the average age of taxa present in a region. Failure to take into account the effects of dispersal can, in principle, lead to biased estimates of diversification rates and potentially wrong conclusions regarding processes driving latitudinal and other gradients in diversity. Thus, it is critical to include the effects of dispersal when formulating and testing hypotheses about the causes of large-scale gradients in diversity. Finally, the model results, in conjunction with the results of existing empirical studies, suggest that the nature of macroevolutionary and biogeographic processes may differ between terrestrial and marine diversity gradients.
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Affiliation(s)
- Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California 92093, USA.
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Abstract
Range limits of species are determined by combined effects of physical, historical, ecological, and evolutionary forces. We consider a subset of these factors by using spatial models of competition, hybridization, and local adaptation to examine the effects of partial dispersal barriers on the locations of borders between similar species. Prompted by results from population genetic models and biogeographic observations, we investigate the conditions under which species' borders are attracted to regions of reduced dispersal. For borders maintained by competition or hybridization, we find that dispersal barriers can attract borders whose positions would otherwise be either neutrally stable or moving across space. Borders affected strongly by local adaptation and gene flow, however, are repelled from dispersal barriers. These models illustrate how particular biotic and abiotic factors may combine to limit species' ranges, and they help to elucidate mechanisms by which range limits of many species may coincide.
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Affiliation(s)
- Emma E Goldberg
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92903, USA.
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Goldberg EE, Lande R. Ecological and reproductive character displacement on an environmental gradient. Evolution 2006; 60:1344-57. [PMID: 16929652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Character displacement, in which coevolution of similar species alters their phenotypes, can be difficult to identify on the basis of observational data alone. In two-species systems, the most commonly identified (i.e., classic) resulting pattern is greater phenotypic difference between species in sympatry than allopatry. We show that restricting studies to this pattern may exclude many instances of character displacement, particularly in the presence of spatial environmental gradients. We present four spatial models of character displacement in quantitative traits affecting competition and hybridization between the species. Our models highlight the connections between range limits and character displacement in continuous space. We conclude that the classic pattern is less likely to occur for a trait affecting resource acquisition than for a trait affecting mate choice. We also show that interspecific hybridization (when hybrids are inviable), even in very small amounts, has marked effects on the shape and stability of borders between species and the nature of character displacement. A survey of the empirical literature shows that character displacement studies often lack analysis of spatial phenotype and abundance data. We recommend more careful spatial sampling in character displacement studies, and we illustrate how comparison of clines in mean phenotype in sympatry and allopatry can be used to suggest the action of character displacement.
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Affiliation(s)
- Emma E Goldberg
- Division of Biological Sciences, University of California-San Diego, La Jolla, California 92093-0116, USA.
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Goldberg EE, Lande R. ECOLOGICAL AND REPRODUCTIVE CHARACTER DISPLACEMENT ON AN ENVIRONMENTAL GRADIENT. Evolution 2006. [DOI: 10.1554/05-696.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Goldberg EE, Roy K, Lande R, Jablonski D. Diversity, Endemism, and Age Distributions in Macroevolutionary Sources and Sinks. Am Nat 2005; 165:623-33. [PMID: 15937743 DOI: 10.1086/430012] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Accepted: 02/08/2005] [Indexed: 11/03/2022]
Abstract
Quantitative tests of historical hypotheses are necessary to advance our understanding of biogeographic patterns of species distributions, but direct tests are often hampered by incomplete fossil or historical records. Here we present an alternative approach in which we develop a dynamic model that allows us to test hypotheses about regional rates of taxon origination, extinction, and dispersal using information on ages and current distributions of taxa. With this model, we test two assumptions traditionally made in the context of identifying regions as "centers of origin"--that regions with high origination rates will have high diversity and high endemism. We find that these assumptions are not necessarily valid. We also develop expressions for the regional age distributions of extant taxa and show that these may yield better insight into regional evolutionary rates. We then apply our model to data on the biogeography and ages of extant genera of marine bivalves and conclude that diversity in polar regions predominantly reflects dispersal of taxa that evolved elsewhere rather than in situ origination-extinction dynamics.
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Affiliation(s)
- Emma E Goldberg
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA.
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Ponomareva TI, Grodnitskaya NA, Goldberg EE, Chaplygina NM, Naroditsky BS, Tikchonenko TI. Biological activity of the intact and cleaved DNA of the simian adenovirus 7. Nucleic Acids Res 1979; 6:3119-31. [PMID: 114980 PMCID: PMC327920 DOI: 10.1093/nar/6.9.3119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Only the deproteinized DNA preparations of the simian adenovirus of the type 7 (SA 7) exhibited transforming and tumorigenic activity. The complex of the SA7 DNA with terminal protein (TP) did not exhibit either transforming or tumorigenic activity in cell cultures. In contrast to the transforming potential the infectious titers of the DNA - TP complex for the monkey kidney cells were 30-50 times higher than those of pure DNA. Cleavage of the SA7 DNA by specific endonucleases enhanced the tumorigenic potential of pure DNA, suppressed its infectivity and did not affect the lack of transformation capacity of the DNA - TP complex. The onc-gene was localized in the left terminal fragment with the minimal size 4,3x10(6)D in the case of R.Sal I. The tumorigenic activity was found to decrease with an increase in the size of the DNA fragment containing the onc-gene.
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Young LW, Goldberg EE, Morrison J. Radiological case of the month. Dyschondrosteosis. Am J Dis Child 1978; 132:1037-8. [PMID: 717295 DOI: 10.1001/archpedi.1978.02120350105021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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