1
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Brennan IG, Chapple DG, Keogh JS, Donnellan S. Evolutionary bursts drive morphological novelty in the world's largest skinks. Curr Biol 2024:S0960-9822(24)00943-6. [PMID: 39137786 DOI: 10.1016/j.cub.2024.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 06/26/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024]
Abstract
Animal phenotypes evolve and diverge as a result of differing selective pressures and drift. These processes leave unique signatures in patterns of trait evolution, impacting the tempo and mode of morphological macroevolution. While there is a broad understanding of the history of some organismal traits (e.g., body size), there is little consensus about the evolutionary mode of most others. This includes the relative contribution of prolonged (Darwinian gradualist) and episodic (Simpsonian jump) changes toward the evolution of novel morphologies. Here, we use new exon-capture and linear morphological datasets to investigate the tempo and mode of morphological evolution in Australo-Melanesian Tiliquini skinks. We generate a well-supported time-calibrated phylogenomic tree from ∼400 nuclear markers for more than 100 specimens, including undescribed diversity, and provide unprecedented resolution of the rapid Miocene diversification of these lizards. By collecting a morphological dataset that encompasses the lizard body plan (19 traits across the head, body, limb, and tail), we are able to identify that most traits evolve conservatively, but infrequent evolutionary bursts result in morphological novelty. These phenotypic discontinuities occur via rapid rate increases along individual branches, inconsistent with both gradualistic and punctuated equilibrial evolutionary modes. Instead, this "punctuated gradualism" has resulted in the rapid evolution of blue-tongued giants and armored dwarves in the ∼20 million years since colonizing Australia. These results outline the evolutionary pathway toward new morphologies and highlight the heterogeneity of evolutionary tempo and mode, even within individual traits.
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Affiliation(s)
- Ian G Brennan
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Australian National University, Division of Ecology & Evolution, Linnaeus Way, Canberra, ACT 2600, Australia.
| | - David G Chapple
- Monash University, School of Biological Sciences, Wellington Road, Melbourne, VIC 3800, Australia
| | - J Scott Keogh
- Australian National University, Division of Ecology & Evolution, Linnaeus Way, Canberra, ACT 2600, Australia
| | - Stephen Donnellan
- The University of Adelaide, School of Biological Sciences, North Terrace, Adelaide, SA 5005, Australia; South Australian Museum, North Terrace, Adelaide, SA 5000, Australia; Australian Museum, Australian Museum Research Institute, William Street, Sydney, NSW 2010, Australia
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2
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Venditti C, Baker J, Barton RA. Co-evolutionary dynamics of mammalian brain and body size. Nat Ecol Evol 2024; 8:1534-1542. [PMID: 38977833 PMCID: PMC11310075 DOI: 10.1038/s41559-024-02451-3] [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: 01/15/2024] [Accepted: 05/29/2024] [Indexed: 07/10/2024]
Abstract
Despite decades of comparative studies, puzzling aspects of the relationship between mammalian brain and body mass continue to defy satisfactory explanation. Here we show that several such aspects arise from routinely fitting log-linear models to the data: the correlated evolution of brain and body mass is in fact log-curvilinear. This simultaneously accounts for several phenomena for which diverse biological explanations have been proposed, notably variability in scaling coefficients across clades, low encephalization in larger species and the so-called taxon-level problem. Our model implies a need to revisit previous findings about relative brain mass. Accounting for the true scaling relationship, we document dramatically varying rates of relative brain mass evolution across the mammalian phylogeny, and we resolve the question of whether there is an overall trend for brain mass to increase through time. We find a trend in only three mammalian orders, which is by far the strongest in primates, setting the stage for the uniquely rapid directional increase ultimately producing the computational powers of the human brain.
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Affiliation(s)
- Chris Venditti
- School of Biological Sciences, University of Reading, Reading, UK.
| | - Joanna Baker
- School of Biological Sciences, University of Reading, Reading, UK
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3
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Li Y, Moritz C, Brennan IG, Zwick A, Nicholls J, Grealy A, Slipinski A. Evolution across the adaptive landscape in a hyperdiverse beetle radiation. Curr Biol 2024:S0960-9822(24)00898-4. [PMID: 39067451 DOI: 10.1016/j.cub.2024.06.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
The extraordinary diversification of beetles on Earth is a textbook example of adaptive evolution. Yet, the tempo and drivers of this super-radiation remain largely unclear. Here, we address this problem by investigating macroevolutionary dynamics in darkling beetles (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse beetle families (with over 30,000 species). Using multiple genomic datasets and analytical approaches, we resolve the long-standing inconsistency over deep relationships in the family. In conjunction with a landmark-based dataset of body shape morphology, we show that the evolutionary history of darkling beetles is marked by ancient rapid radiations, frequent ecological transitions, and rapid bursts of morphological diversification. On a global scale, our analyses uncovered a significant pulse of phenotypic diversification proximal to the Cretaceous-Palaeogene (K/Pg) mass extinction and convergence of body shape associated with recurrent ecological specializations. On a regional scale, two major Australasian radiations, the Adeliini and the Heleine clade, exhibited contrasting patterns of ecomorphological diversification, representing phylogenetic niche conservatism versus adaptive radiation. Our findings align with the Simpsonian model of adaptive evolution across the macroevolutionary landscape and highlight a significant role of ecological opportunity in driving the immense ecomorphological diversity in a hyperdiverse beetle group.
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Affiliation(s)
- Yun Li
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia.
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - James Nicholls
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - Alicia Grealy
- Australian National Herbarium, CSIRO, Canberra, ACT 2601, Australia
| | - Adam Slipinski
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
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4
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Fromm B, Sorger T. Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy. iScience 2024; 27:108740. [PMID: 38327773 PMCID: PMC10847693 DOI: 10.1016/j.isci.2023.108740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 09/13/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024] Open
Abstract
The metabolic efficiency of mammalian cells depends on the attenuation of intrinsic translation noise by microRNAs. We devised a metric of cellular metabolic rate (cMR), rMR/Mexp optimally fit to the number of microRNA families (mirFam), that is robust to variation in mass and sensitive to body temperature (Tb), consistent with the heat dissipation limit theory of Speakman and Król (2010). Using mirFam as predictor, an Ornstein-Uhlenbeck process of stabilizing selection, with an adaptive shift at the divergence of Boreoeutheria, accounted for 95% of the variation in cMR across mammals. Branchwise rates of evolution of cMR, mirFam and Tb concurrently increased 6- to 7-fold at the divergence of Boreoeutheria, independent of mass. Cellular MR variation across placental mammals was also predicted by the sum of model conserved microRNA-target interactions, revealing an unexpected degree of integration of the microRNA-target apparatus into the energy economy of the mammalian cell.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Thomas Sorger
- Department of Biology, Roger Williams University, Bristol, RI 02809, USA
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5
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Olivier CA, Martin JS, Pilisi C, Agnani P, Kauffmann C, Hayes L, Jaeggi AV, Schradin C. Primate social organization evolved from a flexible pair-living ancestor. Proc Natl Acad Sci U S A 2024; 121:e2215401120. [PMID: 38154063 PMCID: PMC10769843 DOI: 10.1073/pnas.2215401120] [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: 09/09/2022] [Accepted: 10/26/2023] [Indexed: 12/30/2023] Open
Abstract
Explaining the evolution of primate social organization has been fundamental to understand human sociality and social evolution more broadly. It has often been suggested that the ancestor of all primates was solitary and that other forms of social organization evolved later, with transitions being driven by various life history traits and ecological factors. However, recent research showed that many understudied primate species previously assumed to be solitary actually live in pairs, and intraspecific variation in social organization is common. We built a detailed database from primary field studies quantifying the number of social units expressing different social organizations in each population. We used Bayesian phylogenetic models to infer the probability of each social organization, conditional on several socioecological and life history predictors. Here, we show that when intraspecific variation is accounted for, the ancestral social organization of primates was inferred to be variable, with the most common social organization being pair-living but with approximately 10 to 20% of social units of the ancestral population deviating from this pattern by being solitary living. Body size and activity patterns had large effects on transitions between types of social organizations. As in other mammalian clades, pair-living is closely linked to small body size and likely more common in ancestral species. Our results challenge the assumption that ancestral primates were solitary and that pair-living evolved afterward emphasizing the importance of focusing on field data and accounting for intraspecific variation, providing a flexible statistical framework for doing so.
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Affiliation(s)
- Charlotte-Anaïs Olivier
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg2050, South Africa
| | - Jordan S. Martin
- Human Ecology Group, Institute of Evolutionary Medicine, University of Zurich, ZurichCH-8057, Switzerland
| | - Camille Pilisi
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
| | - Paul Agnani
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
| | - Cécile Kauffmann
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
| | - Loren Hayes
- Department of Biology, Geology, and Environmental Science, University of Tennessee, Chattanooga37403, TN
| | - Adrian V. Jaeggi
- Human Ecology Group, Institute of Evolutionary Medicine, University of Zurich, ZurichCH-8057, Switzerland
| | - C. Schradin
- Institut Pluridisciplinaire Hubert Curien, CNRS, Department of Ethology and Evolutionary Physiology, University of Strasbourg, Strasbourg67200, France
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg2050, South Africa
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6
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Asar Y, Sauquet H, Ho SYW. Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution. Syst Biol 2023; 72:1337-1356. [PMID: 37695237 PMCID: PMC10924723 DOI: 10.1093/sysbio/syad055] [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: 08/02/2022] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023] Open
Abstract
Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of 5 statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all 5 methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.
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Affiliation(s)
- Yasmin Asar
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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7
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Caetano DS, Quental TB. How Important Is Budding Speciation for Comparative Studies? Syst Biol 2023; 72:1443-1453. [PMID: 37586404 DOI: 10.1093/sysbio/syad050] [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: 05/30/2022] [Revised: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with 3 or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here, we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here, we show that many PCMs assume that divergence happens as a symmetric split, even if these methods do not explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.
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Affiliation(s)
- Daniel S Caetano
- Department of Biological Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
- Department of Ecology, University of São Paulo, Rua do Matão, 321 - Trav. 14, São Paulo, SP, 05508-090, Brazil
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, Rua do Matão, 321 - Trav. 14, São Paulo, SP, 05508-090, Brazil
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8
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Jones ME, Sheard C. The macroevolutionary dynamics of mammalian sexual size dimorphism. Proc Biol Sci 2023; 290:20231211. [PMID: 37964522 PMCID: PMC10646455 DOI: 10.1098/rspb.2023.1211] [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: 05/31/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Sexual size dimorphism (SSD) is a common phenomenon across the animal kingdom. Mammals are unusual in primarily displaying male-biased SSD, where males of a species are typically larger than females. The driving factors behind the evolution of this SSD have been much debated, with popular hypotheses invoking the influence of mating system and social organization via sexual selection, dietary niche divergence and broad-scale correlations with body size (Rensch's rule). Here, we investigate the macroevolutionary origins and maintenance of SSD among mammals, using phylogenetic general mixed linear models and a comprehensive global dataset to evaluate correlations of diet, body mass, seasonality, social organization and mating system with SSD type. We find that SSD as a whole is lost at a greater rate than it is gained, with female-biased SSD being particularly unstable. Non-monogamous mating systems, vertebrate prey consumption and temperature seasonality correlate with male-biased SSD, while polyandry correlates with female-biased SSD, and both types of SSD are positively correlated with body mass. This is in partial contrast to the predictions of Rensch's rule, which predicts that female-biased SSD would correlate negatively with body size. Taken together, our results highlight the importance of considering multiple ecological and social drivers when evaluating the macroevolutionary trajectory of sex differences in body size.
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Affiliation(s)
- Megan E. Jones
- Department of Earth and Environmental Sciences, University of Manchester, 176 Oxford Road, Manchester M13 9QQ, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Catherine Sheard
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biological Sciences, University of Aberdeen, Tillydrone Ave, Aberdeen, AB24 2TZ, UK
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9
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Mao J, Cao Y, Zhang Y, Huang B, Zhao Y. A novel method for identifying key genes in macroevolution based on deep learning with attention mechanism. Sci Rep 2023; 13:19727. [PMID: 37957311 PMCID: PMC10643560 DOI: 10.1038/s41598-023-47113-9] [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: 06/27/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023] Open
Abstract
Macroevolution can be regarded as the result of evolutionary changes of synergistically acting genes. Unfortunately, the importance of these genes in macroevolution is difficult to assess and hence the identification of macroevolutionary key genes is a major challenge in evolutionary biology. In this study, we designed various word embedding libraries of natural language processing (NLP) considering the multiple mechanisms of evolutionary genomics. A novel method (IKGM) based on three types of attention mechanisms (domain attention, kmer attention and fused attention) were proposed to calculate the weights of different genes in macroevolution. Taking 34 species of diurnal butterflies and nocturnal moths in Lepidoptera as an example, we identified a few of key genes with high weights, which annotated to the functions of circadian rhythms, sensory organs, as well as behavioral habits etc. This study not only provides a novel method to identify the key genes of macroevolution at the genomic level, but also helps us to understand the microevolution mechanisms of diurnal butterflies and nocturnal moths in Lepidoptera.
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Affiliation(s)
- Jiawei Mao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China
| | - Yong Cao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China
| | - Yan Zhang
- College of Mathematics and Physics, Southwest Forestry University, Kunming, 650224, China
| | - Biaosheng Huang
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China
| | - Youjie Zhao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, China.
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10
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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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11
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Danis T, Rokas A. The evolution of gestation length in eutherian mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563491. [PMID: 37961105 PMCID: PMC10634735 DOI: 10.1101/2023.10.22.563491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Gestation length, or the duration of pregnancy, is a critical component of mammalian reproductive biology1. Eutherian mammals exhibit striking variation in their gestation lengths2-5, which has traditionally been linked to and allometrically scales with variation in other life history traits, including body mass and lifespan5-8. How the phenotypic landscape of gestation length variation, including its associations with body mass and lifespan variation, changed over mammalian evolution remains unknown. Phylogeny-informed analyses of 845 representative extant eutherian mammals showed that gestation length variation substantially differed in both whether and how strongly it was associated with body mass and lifespan across mammalian clades. For example, gestation length variation in Chiroptera and Cetacea was not associated with lifespan or body mass but was strongly associated only with body mass in Carnivora. We also identified 52 adaptive shifts in gestation length variation across the mammal phylogeny and 14 adaptive shifts when considering all three life history traits; the placements of six adaptive shifts are common in the two analyses. Notably, two of these shifts occurred at the roots of Cetacea and Pinnipedia, respectively, coinciding with the transition of these clades to the marine environment. The varying dynamics of the phenotypic landscape of gestation length, coupled with the varying patterns of associations between gestation length and two other major life history traits, raise the hypothesis that evolutionary constraints on gestation length have varied substantially across mammalian phylogeny. This variation in constraints implies that the genetic architecture of gestation length differs between mammal clades.
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Affiliation(s)
- Thodoris Danis
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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12
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Rolland J, Henao-Diaz LF, Doebeli M, Germain R, Harmon LJ, Knowles LL, Liow LH, Mank JE, Machac A, Otto SP, Pennell M, Salamin N, Silvestro D, Sugawara M, Uyeda J, Wagner CE, Schluter D. Conceptual and empirical bridges between micro- and macroevolution. Nat Ecol Evol 2023; 7:1181-1193. [PMID: 37429904 DOI: 10.1038/s41559-023-02116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/13/2023] [Indexed: 07/12/2023]
Abstract
Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
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Affiliation(s)
- Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Toulouse, France.
| | - L Francisco Henao-Diaz
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Michael Doebeli
- Department of Zoology, and Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel Germain
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke J Harmon
- Dept. of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | | | - Judith E Mank
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonin Machac
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Sarah P Otto
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Pennell
- Departments of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mauro Sugawara
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Mário Schenberg Institute, São Paulo, Brazil
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Catherine E Wagner
- Department of Botany, and Program in Ecology and Evolution, University of Wyoming, Laramie, WY, USA
| | - Dolph Schluter
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Jiang B, He Y, Elsler A, Wang S, Keating JN, Song J, Kearns SL, Benton MJ. Extended embryo retention and viviparity in the first amniotes. Nat Ecol Evol 2023; 7:1131-1140. [PMID: 37308704 PMCID: PMC10333127 DOI: 10.1038/s41559-023-02074-0] [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: 11/04/2022] [Accepted: 04/17/2023] [Indexed: 06/14/2023]
Abstract
The amniotic egg with its complex fetal membranes was a key innovation in vertebrate evolution that enabled the great diversification of reptiles, birds and mammals. It is debated whether these fetal membranes evolved in eggs on land as an adaptation to the terrestrial environment or to control antagonistic fetal-maternal interaction in association with extended embryo retention (EER). Here we report an oviparous choristodere from the Lower Cretaceous period of northeast China. The ossification sequence of the embryo confirms that choristoderes are basal archosauromorphs. The discovery of oviparity in this assumed viviparous extinct clade, together with existing evidence, suggests that EER was the primitive reproductive mode in basal archosauromorphs. Phylogenetic comparative analyses on extant and extinct amniotes suggest that the first amniote displayed EER (including viviparity).
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Affiliation(s)
- Baoyu Jiang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China.
| | - Yiming He
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Armin Elsler
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
| | - Shengyu Wang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Joseph N Keating
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Junyi Song
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Stuart L Kearns
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
| | - Michael J Benton
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
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14
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Burin G, Park T, James TD, Slater GJ, Cooper N. The dynamic adaptive landscape of cetacean body size. Curr Biol 2023; 33:1787-1794.e3. [PMID: 36990088 DOI: 10.1016/j.cub.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/28/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023]
Abstract
Adaptive landscapes are central to evolutionary theory, forming a conceptual bridge between micro- and macroevolution.1,2,3,4 Evolution by natural selection across an adaptive landscape should drive lineages toward fitness peaks, shaping the distribution of phenotypic variation within and among clades over evolutionary timescales.5 The location and breadth of these peaks in phenotypic space can also evolve,4 but whether phylogenetic comparative methods can detect such patterns has largely remained unexplored.6 Here, we characterize the global and local adaptive landscape for total body length in cetaceans (whales, dolphins, and relatives), a trait that spans 5 orders of magnitude, across their ∼53 million year evolutionary history. Using phylogenetic comparative methods, we analyze shifts in long-term mean body length7 and directional changes in average trait values8 for 345 living and fossil cetacean taxa. Remarkably, we find that the global macroevolutionary adaptive landscape of cetacean body length is relatively flat, with very few peak shifts occurring after cetaceans entered the oceans. Local peaks are more numerous and manifest as trends along branches linked to specific adaptations. These results contrast with previous studies using only extant taxa,9 highlighting the vital role of fossil data for understanding macroevolution.10,11,12 Our results indicate that adaptive peaks are dynamic and are associated with subzones of local adaptations, creating moving targets for species adaptation. In addition, we identify limits in our ability to detect some evolutionary patterns and processes and suggest that multiple approaches are required to characterize complex hierarchical patterns of adaptation in deep time.
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15
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Way to big cats: Directional selection in body size evolution in living felids. J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09639-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Martin BS, Bradburd GS, Harmon LJ, Weber MG. Modeling the Evolution of Rates of Continuous Trait Evolution. Syst Biol 2022:6830631. [PMID: 36380474 DOI: 10.1093/sysbio/syac068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/17/2022] Open
Abstract
Rates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called "living fossils". Such rate variation has important consequences for large-scale evolutionary dynamics, generating vast disparities in phenotypic diversity across space, time, and taxa. Despite this, most methods for estimating trait evolution rates assume rates vary deterministically with respect to some variable of interest or change infrequently during a clade's history. These assumptions may cause underfitting of trait evolution models and mislead hypothesis testing. Here, we develop a new trait evolution model that allows rates to vary gradually and stochastically across a clade. Further, we extend this model to accommodate generally decreasing or increasing rates over time, allowing for flexible modeling of "early/late bursts" of trait evolution. We implement a Bayesian method, termed "evolving rates" (evorates for short), to efficiently fit this model to comparative data. Through simulation, we demonstrate that evorates can reliably infer both how and in which lineages trait evolution rates varied during a clade's history. We apply this method to body size evolution in cetaceans, recovering substantial support for an overall slowdown in body size evolution over time with recent bursts among some oceanic dolphins and relative stasis among beaked whales of the genus Mesoplodon. These results unify and expand on previous research, demonstrating the empirical utility of evorates.
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Affiliation(s)
- B S Martin
- Department of Plant Biology, Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - G S Bradburd
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - L J Harmon
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83843, USA
| | - M G Weber
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Newman SA. Inherency and agency in the origin and evolution of biological functions. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Although discussed by 20th century philosophers in terms drawn from the sciences of non-living systems, in recent decades biological function has been considered in relationship to organismal capability and purpose. Bringing two phenomena generally neglected in evolutionary theory (i.e. inherency and agency) to bear on questions of function leads to a rejection of the adaptationist ‘selected effects’ notion of biological function. I review work showing that organisms such as the placozoans can thrive with almost no functional embellishments beyond those of their constituent cells and physical properties of their simple tissues. I also discuss work showing that individual tissue cells and their artificial aggregates exhibit agential behaviours that are unprecedented in the histories of their respective lineages. I review findings on the unique metazoan mechanism of developmental gene expression that has recruited, during evolution, inherent ancestral cellular functionalities into specialized cell types and organs of the different animal groups. I conclude that most essential functions in animal species are inherent to the cells from which they evolved, not selected effects, and that many of the others are optional ‘add-ons’, a status inimical to fitness-based models of evolution positing that traits emerge from stringent cycles of selection to meet external challenges.
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Affiliation(s)
- Stuart A Newman
- Department of Cell Biology & Anatomy, New York Medical College , Valhalla, NY 10595 , USA
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18
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Slater GJ. Topographically distinct adaptive landscapes for teeth, skeletons, and size explain the adaptive radiation of Carnivora (Mammalia). Evolution 2022; 76:2049-2066. [PMID: 35880607 PMCID: PMC9546082 DOI: 10.1111/evo.14577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/08/2022] [Indexed: 01/22/2023]
Abstract
Models of adaptive radiation were originally developed to explain the early, rapid appearance of distinct modes of life within diversifying clades. Phylogenetic tests of this hypothesis have yielded limited support for temporally declining rates of phenotypic evolution across diverse clades, but the concept of an adaptive landscape that links form to fitness, while also crucial to these models, has received more limited attention. Using methods that assess the temporal accumulation of morphological variation and estimate the topography of the underlying adaptive landscape, I found evidence of an early partitioning of mandibulo-dental morphological variation in Carnivora (Mammalia) that occurs on an adaptive landscape with multiple peaks, consistent with classic ideas about adaptive radiation. Although strong support for this mode of adaptive radiation is present in traits related to diet, its signal is not present in body mass data or for traits related to locomotor behavior and substrate use. These findings suggest that adaptive radiations may occur along some axes of ecomorphological variation without leaving a signal in others and that their dynamics are more complex than simple univariate tests might suggest.
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Affiliation(s)
- Graham J. Slater
- Department of the Geophysical SciencesUniversity of ChicagoChicagoIllinois60637
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