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Bromham L. Combining Molecular, Macroevolutionary, and Macroecological Perspectives on the Generation of Diversity. Cold Spring Harb Perspect Biol 2024; 16:a041453. [PMID: 38503506 PMCID: PMC11368193 DOI: 10.1101/cshperspect.a041453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Charles Darwin presented a unified process of diversification driven by the gradual accumulation of heritable variation. The growth in DNA databases and the increase in genomic sequencing, combined with advances in molecular phylogenetic analyses, gives us an opportunity to realize Darwin's vision, connecting the generation of variation to the diversification of lineages. The rate of molecular evolution is correlated with the rate of diversification across animals and plants, but the relationship between genome change and speciation is complex: Mutation rates evolve in response to life history and niche; substitution rates are influenced by mutation, selection, and population size; rates of acquisition of reproductive isolation vary between populations; and traits, niches, and distribution can influence diversification rates. The connection between mutation rate and diversification rate is one part of the complex and varied story of speciation, which has theoretical importance for understanding the generation of biodiversity and also practical impacts on the use of DNA to understand the dynamics of speciation over macroevolutionary timescales.
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Affiliation(s)
- Lindell Bromham
- Macroevolution and Macroecology, Research School of Biology, Australian National University, ACT 0200, Australia
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Feng K, Walker JF, Marx HE, Yang Y, Brockington SF, Moore MJ, Rabeler RK, Smith SA. The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae. AMERICAN JOURNAL OF BOTANY 2024; 111:e16350. [PMID: 38825760 DOI: 10.1002/ajb2.16350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024]
Abstract
PREMISE The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae. METHODS We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift. RESULTS The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations. CONCLUSIONS Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.
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Affiliation(s)
- Keyi Feng
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Joseph F Walker
- Department of Biological Sciences, University of Illinois Chicago, Chicago, 60607, IL, USA
| | - Hannah E Marx
- Department of Biology, University of New Mexico, Albuquerque, 87131, NM, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, 55108, MN, USA
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, 44074, OH, USA
| | - Richard K Rabeler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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Duran-Nebreda S, Bentley RA, Vidiella B, Spiridonov A, Eldredge N, O'Brien MJ, Valverde S. On the multiscale dynamics of punctuated evolution. Trends Ecol Evol 2024; 39:734-744. [PMID: 38821781 DOI: 10.1016/j.tree.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
For five decades, paleontologists, paleobiologists, and ecologists have investigated patterns of punctuated equilibria in biology. Here, we step outside those fields and summarize recent advances in the theory of and evidence for punctuated equilibria, gathered from contemporary observations in geology, molecular biology, genetics, anthropology, and sociotechnology. Taken in the aggregate, these observations lead to a more general theory that we refer to as punctuated evolution. The quality of recent datasets is beginning to illustrate the mechanics of punctuated evolution in a way that can be modeled across a vast range of phenomena, from mass extinctions hundreds of millions of years ago to the possible future ahead in the Anthropocene. We expect the study of punctuated evolution to be applicable beyond biological scenarios.
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Affiliation(s)
- Salva Duran-Nebreda
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain
| | - R Alexander Bentley
- Department of Anthropology, University of Tennessee, Knoxville, TN 37996, USA
| | - Blai Vidiella
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain
| | - Andrej Spiridonov
- Department of Geology and Mineralogy, Vilnius University, Vilnius, Lithuania
| | - Niles Eldredge
- The American Museum of Natural History, New York, NY 10024, USA
| | - Michael J O'Brien
- Department of History, Philosophy, and Geography and Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX 78224, USA; Department of Anthropology, University of Missouri, Columbia, MO 65205, USA.
| | - Sergi Valverde
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain; European Centre for Living Technology, Ca' Bottacin, Dorsoduro 3911, 30123 Venice, Italy.
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Jung H, Strait D, Rolian C, Baab KL. Evaluating modularity in the hominine skull related to feeding biomechanics. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:39-59. [PMID: 37982349 DOI: 10.1002/ajpa.24875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
OBJECTIVES Modular architecture of traits in complex organisms can be important for morphological evolution at micro- and sometimes macroevolutionary scales as it may influence the tempo and direction of changes to groups of traits that are essential for particular functions, including food acquisition and processing. We tested several distinct hypotheses about craniofacial modularity in the hominine skull in relation to feeding biomechanics. MATERIALS AND METHODS First, we formulated hypothesized functional modules for craniofacial traits reflecting specific demands of feeding biomechanics (e.g., masseter leverage/gape or tooth crown mechanics) in Homo sapiens, Pan troglodytes, and Gorilla gorilla. Then, the pattern and strength of modular signal was quantified by the covariance ratio coefficient and compared across groups using covariance ratio effect size. Hierarchical clustering analysis was then conducted to examine whether a priori-defined functional modules correspond to empirically recovered clusters. RESULTS There was statistical support for most a priori-defined functional modules in the cranium and half of the functional modules in the mandible. Modularity signal was similar in the cranium and mandible, and across the three taxa. Despite a similar strength of modularity, the empirically recovered clusters do not map perfectly onto our priori functional modules, indicating that further work is needed to refine our hypothesized functional modules. CONCLUSION The results suggest that modular structure of traits in association with feeding biomechanics were mostly shared with humans and the two African apes. Thus, conserved patterns of functional modularity may have facilitated evolutionary changes to the skull during human evolution.
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Affiliation(s)
- Hyunwoo Jung
- Department of Anatomy, College of Graduate Studies, Midwestern University, Glendale, Arizona, USA
| | - David Strait
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- DFG Center for Advanced Studies "Words, Bones, Genes, Tools", University of Tübingen, Tübingen, Germany
| | - Campbell Rolian
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Karen L Baab
- Department of Anatomy, College of Graduate Studies, Midwestern University, Glendale, Arizona, USA
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Guillerme T, Bright JA, Cooney CR, Hughes EC, Varley ZK, Cooper N, Beckerman AP, Thomas GH. Innovation and elaboration on the avian tree of life. SCIENCE ADVANCES 2023; 9:eadg1641. [PMID: 37878701 PMCID: PMC10599619 DOI: 10.1126/sciadv.adg1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/22/2023] [Indexed: 10/27/2023]
Abstract
Widely documented, megaevolutionary jumps in phenotypic diversity continue to perplex researchers because it remains unclear whether these marked changes can emerge from microevolutionary processes. Here, we tackle this question using new approaches for modeling multivariate traits to evaluate the magnitude and distribution of elaboration and innovation in the evolution of bird beaks. We find that elaboration, evolution along the major axis of phenotypic change, is common at both macro- and megaevolutionary scales, whereas innovation, evolution away from the major axis of phenotypic change, is more prominent at megaevolutionary scales. The major axis of phenotypic change among species beak shapes at megaevolutionary scales is an emergent property of innovation across clades. Our analyses suggest that the reorientation of phenotypes via innovation is a ubiquitous route for divergence that can arise through gradual change alone, opening up further avenues for evolution to explore.
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Affiliation(s)
- Thomas Guillerme
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jen A. Bright
- School of Natural Science, University of Hull, Hull HU6 7RX, UK
| | | | - Emma C. Hughes
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Zoë K. Varley
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Bird Group, Department of Life Sciences, the Natural History Museum at Tring, Tring, UK
| | - Natalie Cooper
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | - Gavin H. Thomas
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Bird Group, Department of Life Sciences, the Natural History Museum at Tring, Tring, UK
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Horowitz J, Quattrini AM, Brugler MR, Miller DJ, Pahang K, Bridge TCL, Cowman PF. Bathymetric evolution of black corals through deep time. Proc Biol Sci 2023; 290:20231107. [PMID: 37788705 PMCID: PMC10547549 DOI: 10.1098/rspb.2023.1107] [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: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 10/05/2023] Open
Abstract
Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250-3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of 'source' slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.
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Affiliation(s)
- Jeremy Horowitz
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th street and Constitution avenue North West, Washington, DC 20560, USA
| | - Andrea M. Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th street and Constitution avenue North West, Washington, DC 20560, USA
| | - Mercer R. Brugler
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th street and Constitution avenue North West, Washington, DC 20560, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary Street, Beaufort, SC 29902, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - David J. Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Molecular and Cell Biology, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
| | - Kristina Pahang
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
| | - Tom C. L. Bridge
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
- College of Science and Engineering, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
| | - Peter F. Cowman
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, 70-102 Flinders street, Townsville, Queensland 4810, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Molecular and Cell Biology, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
- College of Science and Engineering, James Cook University, 101 Angus Smith Drive, Townsville, Queensland 4811, Australia
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Alfieri F, Botton-Divet L, Wölfer J, Nyakatura JA, Amson E. A macroevolutionary common-garden experiment reveals differentially evolvable bone organization levels in slow arboreal mammals. Commun Biol 2023; 6:995. [PMID: 37770611 PMCID: PMC10539518 DOI: 10.1038/s42003-023-05371-3] [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: 02/20/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023] Open
Abstract
Eco-morphological convergence, i.e., similar phenotypes evolved in ecologically convergent taxa, naturally reproduces a common-garden experiment since it allows researchers to keep ecological factors constant, studying intrinsic evolutionary drivers. The latter may result in differential evolvability that, among individual anatomical parts, causes mosaic evolution. Reconstructing the evolutionary morphology of the humerus and femur of slow arboreal mammals, we addressed mosaicism at different bone anatomical spatial scales. We compared convergence strength, using it as indicator of evolvability, between bone external shape and inner structure, with the former expected to be less evolvable and less involved in convergent evolution, due to anatomical constraints. We identify several convergent inner structural traits, while external shape only loosely follows this trend, and we find confirmation for our assumption in measures of convergence magnitude. We suggest that future macroevolutionary reconstructions based on bone morphology should include structural traits to better detect ecological effects on vertebrate diversification.
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Affiliation(s)
- Fabio Alfieri
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany.
- Museum Für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany.
| | - Léo Botton-Divet
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Jan Wölfer
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - John A Nyakatura
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Eli Amson
- Paleontology Department, Staatliches Museum für Naturkunde, Rosenstein 1-3, 70191, Stuttgart, Germany
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Watanabe J. Exact expressions and numerical evaluation of average evolvability measures for characterizing and comparing [Formula: see text] matrices. J Math Biol 2023; 86:95. [PMID: 37217733 DOI: 10.1007/s00285-023-01930-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/28/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Theory predicts that the additive genetic covariance ([Formula: see text]) matrix determines a population's short-term (in)ability to respond to directional selection-evolvability in the Hansen-Houle sense-which is typically quantified and compared via certain scalar indices called evolvability measures. Often, interest is in obtaining the averages of these measures across all possible selection gradients, but explicit formulae for most of these average measures have not been known. Previous authors relied either on approximations by the delta method, whose accuracy is generally unknown, or Monte Carlo evaluations (including the random skewers analysis), which necessarily involve random fluctuations. This study presents new, exact expressions for the average conditional evolvability, average autonomy, average respondability, average flexibility, average response difference, and average response correlation, utilizing their mathematical structures as ratios of quadratic forms. The new expressions are infinite series involving top-order zonal and invariant polynomials of matrix arguments, and can be numerically evaluated as their partial sums with, for some measures, known error bounds. Whenever these partial sums numerically converge within reasonable computational time and memory, they will replace the previous approximate methods. In addition, new expressions are derived for the average measures under a general normal distribution for the selection gradient, extending the applicability of these measures into a substantially broader class of selection regimes.
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Affiliation(s)
- Junya Watanabe
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, UK.
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Zhou S, Edie SM, Collins KS, Crouch NMA, Jablonski D. Cambrian origin but no early burst in functional disparity for Class Bivalvia. Biol Lett 2023; 19:20230157. [PMID: 37254520 PMCID: PMC10230185 DOI: 10.1098/rsbl.2023.0157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Both the Cambrian explosion, more than half a billion years ago, and its Ordovician aftermath some 35 Myr later, are often framed as episodes of widespread ecological opportunity, but not all clades originating during this interval showed prolific rises in morphological or functional disparity. In a direct analysis of functional disparity, instead of the more commonly used proxy of morphological disparity, we find that ecological functions of Class Bivalvia arose concordantly with and even lagged behind taxonomic diversification, rather than the early-burst pattern expected for clades originating in supposedly open ecological landscapes. Unlike several other clades originating in the Cambrian explosion, the bivalves' belated acquisition of key anatomical novelties imposed a macroevolutionary lag, and even when those novelties evolved in the Early Ordovician, functional disparity never surpassed taxonomic diversity. Beyond this early period of animal evolution, the founding and subsequent diversification of new major clades and their functions might be expected to follow the pattern of the early bivalves-one where interactions between highly dynamic environmental and biotic landscapes and evolutionary contingencies need not promote prolific functional innovation.
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Affiliation(s)
- Sharon Zhou
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Stewart M. Edie
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | | | - Nicholas M. A. Crouch
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
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Leventhal S, Jamison-Todd S, Simpson C. Aggregate Trait Evolvability and Macroevolution in Two Sister Species of the Bryozoan Stylopoma. Evol Biol 2022. [DOI: 10.1007/s11692-022-09588-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractThe study of trait evolution in modular animals is more complicated than that in solitary animals, because a single genotype of a modular colony can express an enormous range of phenotypic variation. Furthermore, traits can occur either at the module level or at the colony level. However, it is unclear how the traits at the colony level evolve. We test whether colony-level aggregate traits, defined as the summary statistics of a phenotypic distribution, can evolve. To quantify this evolutionary potential, we use parent-offspring pairs in two sister species of the bryozoan Stylopoma, grown and bred in a common garden breeding experiment. We find that the medians of phenotypic distributions are evolvable between generations of colonies. We also find that the structure of this evolutionary potential differs between these two species. Ancestral species align more closely with the direction of species divergence than the descendent species. This result indicates that aggregate trait evolvability can itself evolve.
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