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Dimayacyac JR, Wu S, Jiang D, Pennell M. Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution. Genome Biol Evol 2023; 15:evad211. [PMID: 38000902 PMCID: PMC10709115 DOI: 10.1093/gbe/evad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Phylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown whether the distributional assumptions of phylogenetic models designed for quantitative phenotypic traits are realistic for expression data and importantly, the reliability of conclusions of phylogenetic comparative studies of gene expression may depend on whether the data is well described by the chosen model. To evaluate this, we first fit several phylogenetic models of trait evolution to 8 previously published comparative expression datasets, comprising a total of 54,774 genes with 145,927 unique gene-tissue combinations. Using a previously developed approach, we then assessed how well the best model of the set described the data in an absolute (not just relative) sense. First, we find that Ornstein-Uhlenbeck models, in which expression values are constrained around an optimum, were the preferred models for 66% of gene-tissue combinations. Second, we find that for 61% of gene-tissue combinations, the best-fit model of the set was found to perform well; the rest were found to be performing poorly by at least one of the test statistics we examined. Third, we find that when simple models do not perform well, this appears to be typically a consequence of failing to fully account for heterogeneity in the rate of the evolution. We advocate that assessment of model performance should become a routine component of phylogenetic comparative expression studies; doing so can improve the reliability of inferences and inspire the development of novel models.
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Affiliation(s)
- Jose Rafael Dimayacyac
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Shanyun Wu
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daohan Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Matt Pennell
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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Dimayacyac JR, Wu S, Jiang D, Pennell M. Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527893. [PMID: 37645857 PMCID: PMC10461906 DOI: 10.1101/2023.02.09.527893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Phylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown whether the distributional assumptions of phylogenetic models designed for quantitative phenotypic traits are realistic for expression data and importantly, the reliability of conclusions of phylogenetic comparative studies of gene expression may depend on whether the data is well-described by the chosen model. To evaluate this, we first fit several phylogenetic models of trait evolution to 8 previously published comparative expression datasets, comprising a total of 54,774 genes with 145,927 unique gene-tissue combinations. Using a previously developed approach, we then assessed how well the best model of the set described the data in an absolute (not just relative) sense. First, we find that Ornstein-Uhlenbeck models, in which expression values are constrained around an optimum, were the preferred model for 66% of gene-tissue combinations. Second, we find that for 61% of gene-tissue combinations, the best fit model of the set was found to perform well; the rest were found to be performing poorly by at least one of the test statistics we examined. Third, we find that when simple models do not perform well, this appears to be typically a consequence of failing to fully account for heterogeneity in the rate of the evolution. We advocate that assessment of model performance should become a routine component of phylogenetic comparative expression studies; doing so can improve the reliability of inferences and inspire the development of novel models.
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Affiliation(s)
- Jose Rafael Dimayacyac
- Department of Zoology, University of British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Canada
| | - Shanyun Wu
- Department of Zoology, University of British Columbia, Canada
- Department of Genetics, Washington University School of Medicine, USA
| | - Daohan Jiang
- Department of Quantitative and Computational Biology, University of Southern California, USA
| | - Matt Pennell
- Department of Zoology, University of British Columbia, Canada
- Department of Quantitative and Computational Biology, University of Southern California, USA
- Department of Biological Sciences, University of Southern California, USA
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Jiang D, Cope AL, Zhang J, Pennell M. On the Decoupling of Evolutionary Changes in mRNA and Protein Levels. Mol Biol Evol 2023; 40:msad169. [PMID: 37498582 PMCID: PMC10411491 DOI: 10.1093/molbev/msad169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/19/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is closer to the target of natural selection but gene expression is typically measured as the amount of mRNA. The broad assumption that mRNA levels are good proxies for protein levels has been undermined by a number of studies reporting moderate or weak correlations between the two measures across species. One biological explanation for this discrepancy is that there has been compensatory evolution between the mRNA level and regulation of translation. However, we do not understand the evolutionary conditions necessary for this to occur nor the expected strength of the correlation between mRNA and protein levels. Here, we develop a theoretical model for the coevolution of mRNA and protein levels and investigate the dynamics of the model over time. We find that compensatory evolution is widespread when there is stabilizing selection on the protein level; this observation held true across a variety of regulatory pathways. When the protein level is under directional selection, the mRNA level of a gene and the translation rate of the same gene were negatively correlated across lineages but positively correlated across genes. These findings help explain results from comparative studies of gene expression and potentially enable researchers to disentangle biological and statistical hypotheses for the mismatch between transcriptomic and proteomic data.
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Affiliation(s)
- Daohan Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Alexander L Cope
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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Jiang D, Cope AL, Zhang J, Pennell M. Decoupling of evolutionary changes in mRNA and protein levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536110. [PMID: 37066157 PMCID: PMC10104238 DOI: 10.1101/2023.04.08.536110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is closer to the target of natural selection but gene expression is typically measured as the amount of mRNA. The broad assumption that mRNA levels are good proxies for protein levels has been undermined by a number of studies reporting moderate or weak correlations between the two measures across species. One biological explanation for this discrepancy is that there has been compensatory evolution between the mRNA level and regulation of translation. However, we do not understand the evolutionary conditions necessary for this to occur nor the expected strength of the correlation between mRNA and protein levels. Here we develop a theoretical model for the coevolution of mRNA and protein levels and investigate the dynamics of the model over time. We find that compensatory evolution is widespread when there is stabilizing selection on the protein level, which is true across a variety of regulatory pathways. When the protein level is under directional selection, the mRNA level of a gene and its translation rate of the same gene were negatively correlated across lineages but positively correlated across genes. These findings help explain results from comparative studies of gene expression and potentially enable researchers to disentangle biological and statistical hypotheses for the mismatch between transcriptomic and proteomic studies.
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Affiliation(s)
- Daohan Jiang
- Department of Quantitative and Computational Biology, University of Southern California, USA
| | | | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, USA
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, USA
- Department of Biological Sciences, University of Southern California, USA
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Evolvability and trait function predict phenotypic divergence of plant populations. Proc Natl Acad Sci U S A 2023; 120:e2203228120. [PMID: 36580593 PMCID: PMC9910613 DOI: 10.1073/pnas.2203228120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Understanding the causes and limits of population divergence in phenotypic traits is a fundamental aim of evolutionary biology, with the potential to yield predictions of adaptation to environmental change. Reciprocal transplant experiments and the evaluation of optimality models suggest that local adaptation is common but not universal, and some studies suggest that trait divergence is highly constrained by genetic variances and covariances of complex phenotypes. We analyze a large database of population divergence in plants and evaluate whether evolutionary divergence scales positively with standing genetic variation within populations (evolvability), as expected if genetic constraints are evolutionarily important. We further evaluate differences in divergence and evolvability-divergence relationships between reproductive and vegetative traits and between selfing, mixed-mating, and outcrossing species, as these factors are expected to influence both patterns of selection and evolutionary potentials. Evolutionary divergence scaled positively with evolvability. Furthermore, trait divergence was greater for vegetative traits than for floral (reproductive) traits, but largely independent of the mating system. Jointly, these factors explained ~40% of the variance in evolutionary divergence. The consistency of the evolvability-divergence relationships across diverse species suggests substantial predictability of trait divergence. The results are also consistent with genetic constraints playing a role in evolutionary divergence.
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Opedal ØH, Hildesheim LS, Armbruster WS. Evolvability and constraint in the evolution of three-dimensional flower morphology. AMERICAN JOURNAL OF BOTANY 2022; 109:1906-1917. [PMID: 36371715 PMCID: PMC9827957 DOI: 10.1002/ajb2.16092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 05/31/2023]
Abstract
PREMISE Flower phenotypes evolve to attract pollinators and to ensure efficient pollen transfer to and from the bodies of pollinators or, in self-compatible bisexual flowers, between anthers and stigmas. If functionally interacting traits are genetically correlated, response to selection may be subject to genetic constraints. Genetic constraints can be assessed by quantifying standing genetic variation in (multivariate) phenotypic traits and by asking how much the available variation is reduced under specific assumptions about phenotypic selection on functionally interacting and genetically correlated traits. METHODS We evaluated multivariate evolvability and potential genetic constraints underlying the evolution of the three-dimensional structure of Dalechampia blossoms. First, we used data from a greenhouse crossing design to estimate the G matrix for traits representing the relative positions of male and female sexual organs (anthers and stigmas) and used the G matrix to ask how genetic variation is distributed in multivariate space. To assess the evolutionary importance of genetic constraints, we related standing genetic variation across phenotypic space to evolutionary divergence of population and species in the same phenotypic directions. RESULTS Evolvabilities varied substantially across phenotype space, suggesting that certain traits or trait combinations may be subject to strong genetic constraint. Traits involved functionally in flower-pollinator fit and autonomous selfing exhibited considerable independent evolutionary potential, but population and species divergence tended to occur in phenotypic directions associated with greater-than-average evolvability. CONCLUSIONS These results are consistent with the hypothesis that genetic constraints can hamper joint trait evolution towards optimum flower-pollinator fit and optimum self-pollination rates.
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Affiliation(s)
| | | | - W. Scott Armbruster
- School of Biological SciencesUniversity of PortsmouthPortsmouthPO1 2DYUK
- Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAK99775USA
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Brand JN, Harmon LJ, Schärer L. Frequent origins of traumatic insemination involve convergent shifts in sperm and genital morphology. Evol Lett 2022; 6:63-82. [PMID: 35127138 PMCID: PMC8802240 DOI: 10.1002/evl3.268] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Traumatic insemination is a mating behavior during which the (sperm) donor uses a traumatic intromittent organ to inject an ejaculate through the epidermis of the (sperm) recipient, thereby frequently circumventing the female genitalia. Traumatic insemination occurs widely across animals, but the frequency of its evolution, the intermediate stages via which it originates, and the morphological changes that such shifts involve remain poorly understood. Based on observations in 145 species of the free-living flatworm genus Macrostomum, we identify at least nine independent evolutionary origins of traumatic insemination from reciprocal copulation, but no clear indication of reversals. These origins involve convergent shifts in multivariate morphospace of male and female reproductive traits, suggesting that traumatic insemination has a canalizing effect on morphology. We also observed sperm in both the sperm receiving organ and within the body tissue of two species. These species had intermediate trait values indicating that traumatic insemination evolves through initial internal wounding during copulation. Finally, signatures of male-female coevolution of genitalia across the genus indicate that sexual selection and sexual conflict drive the evolution of traumatic insemination, because it allows donors to bypass postcopulatory control mechanisms of recipients.
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Affiliation(s)
- Jeremias N. Brand
- Department of Environmental Sciences, Zoological InstituteUniversity of BaselBaselCH‐4051Switzerland
- Department of Tissue Dynamics and RegenerationMax Planck Institute for Biophysical ChemistryGöttingenDE‐37077Germany
| | - Luke J. Harmon
- Department of Biological SciencesUniversity of IdahoMoscowIdaho83843
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological InstituteUniversity of BaselBaselCH‐4051Switzerland
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Johansson F, Watts PC, Sniegula S, Berger D. Natural selection mediated by seasonal time constraints increases the alignment between evolvability and developmental plasticity. Evolution 2021; 75:464-475. [PMID: 33368212 PMCID: PMC7986058 DOI: 10.1111/evo.14147] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 12/26/2022]
Abstract
Phenotypic plasticity can either hinder or promote adaptation to novel environments. Recent studies that have quantified alignments between plasticity, genetic variation, and divergence propose that such alignments may reflect constraints that bias future evolutionary trajectories. Here, we emphasize that such alignments may themselves be a result of natural selection and do not necessarily indicate constraints on adaptation. We estimated developmental plasticity and broad sense genetic covariance matrices (G) among damselfly populations situated along a latitudinal gradient in Europe. Damselflies were reared at photoperiod treatments that simulated the seasonal time constraints experienced at northern (strong constraints) and southern (relaxed constraints) latitudes. This allowed us to partition the effects of (1) latitude, (2) photoperiod, and (3) environmental novelty on G and its putative alignment with adaptive plasticity and divergence. Environmental novelty and latitude did not affect G, but photoperiod did. Photoperiod increased evolvability in the direction of observed adaptive divergence and developmental plasticity when G was assessed under strong seasonal time constraints at northern (relative to southern) photoperiod. Because selection and adaptation under time constraints is well understood in Lestes damselflies, our results suggest that natural selection can shape the alignment between divergence, plasticity, and evolvability.
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Affiliation(s)
- Frank Johansson
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, 752 36, Sweden
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Szymon Sniegula
- Department of Ecosystem Conservation, Institute of Nature Conservation, Polish Academy of Sciences, Krakow, 31-120, Poland
| | - David Berger
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, 752 36, Sweden
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