1
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Lecocq de Pletincx N, Cerdà X, Kiran K, Karaman C, Taheri A, Aron S. Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants. iScience 2024; 27:109852. [PMID: 38779477 PMCID: PMC11109030 DOI: 10.1016/j.isci.2024.109852] [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: 11/30/2023] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Biological diversity often arises as organisms adapt to new ecological conditions (i.e., ecological opportunities) or colonize suitable areas (i.e., spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ∼18 million years ago and became a taxon of diverse species specializing in prey of different masses. The genus then colonized the Mediterranean Basin around 9 million years ago. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification preceded geographical expansion, resulting in a clade composed of ecologically homogeneous subclades.
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Affiliation(s)
- Nathan Lecocq de Pletincx
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
| | - Xim Cerdà
- Department of Ethology and Biodiversity Conservation, Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - Kadri Kiran
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Celal Karaman
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Ahmed Taheri
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences of El Jadida, University Chouaïb Doukkali, El Jadida, Morocco
| | - Serge Aron
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
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2
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Sternes PC, Schmitz L, Higham TE. The rise of pelagic sharks and adaptive evolution of pectoral fin morphology during the Cretaceous. Curr Biol 2024; 34:2764-2772.e3. [PMID: 38834065 DOI: 10.1016/j.cub.2024.05.016] [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: 02/29/2024] [Revised: 04/05/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024]
Abstract
The emergence and subsequent evolution of pectoral fins is a key point in vertebrate evolution, as pectoral fins are dominant control surfaces for locomotion in extant fishes.1,2,3 However, major gaps remain in our understanding of the diversity and evolution of pectoral fins among cartilaginous fishes (Chondrichthyes), a group with an evolutionary history spanning over 400 million years with current selachians (modern sharks) appearing about 200 million years ago.4,5,6 Modern sharks are a charismatic group of vertebrates often thought to be predators roaming the open ocean and coastal areas, but most extant species occupy the seafloor.4 Here we use an integrative approach to understand what facilitated the expansion to the pelagic realm and what morphological changes accompanied this shift. On the basis of comparative analyses in the framework of a time-calibrated molecular phylogeny,7 we show that modern sharks expanded to the pelagic realm no later than the Early Cretaceous (Barremian). The pattern of pectoral fin aspect ratios across selachians is congruent with adaptive evolution, and we identify an increase of the subclade disparity of aspect ratio at a time when sea surface temperatures were at their highest.8 The expansion to open ocean habitats likely involved extended bouts of sustained fast swimming, which led to the selection for efficient movement via higher aspect ratio pectoral fins. Swimming performance was likely enhanced in pelagic sharks during this time due to the elevated temperatures in the sea, highlighting that shark evolution has been greatly impacted by climate change.
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Affiliation(s)
- Phillip C Sternes
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
| | - Lars Schmitz
- Kravis Department of Integrated Sciences, Claremont McKenna College, Claremont, CA 91711, USA
| | - Timothy E Higham
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
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3
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Bastide P, Rocu P, Wirtz J, Hassler GW, Chevenet F, Fargette D, Suchard MA, Dellicour S, Lemey P, Guindon S. Modeling the velocity of evolving lineages and predicting dispersal patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597755. [PMID: 38895258 PMCID: PMC11185746 DOI: 10.1101/2024.06.06.597755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, the very concept of instan-taneous speed simply does not exist under one of the most popular approaches that models the evolution of spatial coordinates as Brownian trajectories running along a phylogeny [30]. Here, we introduce a new family of models - the so-called "Phylogenetic Integrated Velocity" (PIV) models - that use Gaussian processes to explicitly model the velocity of evolving lineages instead of focusing on the fluctuation of spatial coordinates over time. We describe the properties of these models and show an increased accuracy of velocity estimates compared to previous approaches. Analyses of West Nile virus data in the U.S.A. indicate that PIV models provide sensible predictions of the dispersal of evolving pathogens at a one-year time horizon. These results demonstrate the feasibility and relevance of predictive phylogeography in monitoring epidemics in time and space.
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4
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Zhang R, Drummond AJ, Mendes FK. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 2024; 73:102-124. [PMID: 38085256 PMCID: PMC11129596 DOI: 10.1093/sysbio/syad067] [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: 11/06/2023] [Revised: 03/23/2023] [Accepted: 11/07/2023] [Indexed: 05/28/2024] Open
Abstract
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.
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Affiliation(s)
- Rong Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School 169857, Singapore
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Fábio K Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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5
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Adams R, Cain Z, Assis R, DeGiorgio M. Robust Phylogenetic Regression. Syst Biol 2024; 73:140-157. [PMID: 38035624 PMCID: PMC11129599 DOI: 10.1093/sysbio/syad070] [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: 08/25/2022] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023] Open
Abstract
Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships. Over the past few decades, the phylogenetic regression framework has become a paradigm of modern comparative biology that has been widely embraced as a remedy for shared ancestry. However, recent evidence has shown doubt over the efficacy of phylogenetic regression, and PCMs more generally, with the suggestion that many of these methods fail to provide an adequate defense against unreplicated evolution-the primary justification for using them in the first place. Importantly, some of the most compelling examples of biological innovation in nature result from abrupt lineage-specific evolutionary shifts, which current regression models are largely ill equipped to deal with. Here we explore a solution to this problem by applying robust linear regression to comparative trait data. We formally introduce robust phylogenetic regression to the PCM toolkit with linear estimators that are less sensitive to model violations than the standard least-squares estimator, while still retaining high power to detect true trait associations. Our analyses also highlight an ingenuity of the original algorithm for phylogenetic regression based on independent contrasts, whereby robust estimators are particularly effective. Collectively, we find that robust estimators hold promise for improving tests of trait associations and offer a path forward in scenarios where classical approaches may fail. Our study joins recent arguments for increased vigilance against unreplicated evolution and a better understanding of evolutionary model performance in challenging-yet biologically important-settings.
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Affiliation(s)
- Richard Adams
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, USA
- Agricultural Statistics Laboratory, University of Arkansas, Fayetteville, AR, USA
| | - Zoe Cain
- Department of Biological and Environmental Sciences, Georgia College, Milledgeville, GA, USA
| | - Raquel Assis
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
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6
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Gayford JH, Brazeau MD, Naylor GJP. Evolutionary trends in the elasmobranch neurocranium. Sci Rep 2024; 14:11471. [PMID: 38769415 PMCID: PMC11106257 DOI: 10.1038/s41598-024-62004-3] [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: 02/23/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
The neurocranium (braincase) is one of the defining vertebrate characters. Housing the brain and other key sensory organs, articulating with the jaws and contributing to the shape of the anteriormost portion of the body, the braincase is undoubtedly of great functional importance. Through studying relationships between braincase shape and ecology we can gain an improved understanding of form-function relationships in extant and fossil taxa. Elasmobranchii (sharks and rays) represent an important case study of vertebrate braincase diversity as their neurocranium is simplified and somewhat decoupled from other components of the cranium relative to other vertebrates. Little is known about the associations between ecology and braincase shape in this clade. In this study we report patterns of mosaic cranial evolution in Elasmobranchii that differ significantly from those present in other clades. The degree of evolutionary modularity also differs between Selachii and Batoidea. In both cases innovation in the jaw suspension appears to have driven shifts in patterns of integration and modularity, subsequently facilitating ecological diversification. Our results confirm the importance of water depth and biogeography as drivers of elasmobranch cranial diversity and indicate that skeletal articulation between the neurocranium and jaws represents a major constraint upon the evolution of braincase shape in vertebrates.
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Affiliation(s)
- Joel H Gayford
- Department of Life Sciences, Silwood Park Campus, Imperial College London, London, UK.
- Shark Measurements, London, UK.
| | - Martin D Brazeau
- Department of Life Sciences, Silwood Park Campus, Imperial College London, London, UK
- The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Gavin J P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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7
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Hay EM, McGee MD, White CR, Chown SL. Body size shapes song in honeyeaters. Proc Biol Sci 2024; 291:20240339. [PMID: 38654649 PMCID: PMC11040244 DOI: 10.1098/rspb.2024.0339] [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: 02/08/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Birdsongs are among the most distinctive animal signals. Their evolution is thought to be shaped simultaneously by habitat structure and by the constraints of morphology. Habitat structure affects song transmission and detectability, thus influencing song (the acoustic adaptation hypothesis), while body size and beak size and shape necessarily constrain song characteristics (the morphological constraint hypothesis). Yet, support for the acoustic adaptation and morphological constraint hypotheses remains equivocal, and their simultaneous examination is infrequent. Using a phenotypically diverse Australasian bird clade, the honeyeaters (Aves: Meliphagidae), we compile a dataset consisting of song, environmental, and morphological variables for 163 species and jointly examine predictions of these two hypotheses. Overall, we find that body size constrains song frequency and pace in honeyeaters. Although habitat type and environmental temperature influence aspects of song, that influence is indirect, likely via effects of environmental variation on body size, with some evidence that elevation constrains the evolution of song peak frequency. Our results demonstrate that morphology has an overwhelming influence on birdsong, in support of the morphological constraint hypothesis, with the environment playing a secondary role generally via body size rather than habitat structure. These results suggest that changing body size (a consequence of both global effects such as climate change and local effects such as habitat transformation) will substantially influence the nature of birdsong.
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Affiliation(s)
- Eleanor M. Hay
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Craig R. White
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Steven L. Chown
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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8
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Sansalone G, Wroe S, Coates G, Attard MRG, Fruciano C. Unexpectedly uneven distribution of functional trade-offs explains cranial morphological diversity in carnivores. Nat Commun 2024; 15:3275. [PMID: 38627430 PMCID: PMC11021405 DOI: 10.1038/s41467-024-47620-x] [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: 06/28/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Functional trade-offs can affect patterns of morphological and ecological evolution as well as the magnitude of morphological changes through evolutionary time. Using morpho-functional landscape modelling on the cranium of 132 carnivore species, we focused on the macroevolutionary effects of the trade-off between bite force and bite velocity. Here, we show that rates of evolution in form (morphology) are decoupled from rates of evolution in function. Further, we found theoretical morphologies optimising for velocity to be more diverse, while a much smaller phenotypic space was occupied by shapes optimising force. This pattern of differential representation of different functions in theoretical morphological space was highly correlated with patterns of actual morphological disparity. We hypothesise that many-to-one mapping of cranium shape on function may prevent the detection of direct relationships between form and function. As comparatively only few morphologies optimise bite force, species optimising this function may be less abundant because they are less likely to evolve. This, in turn, may explain why certain clades are less variable than others. Given the ubiquity of functional trade-offs in biological systems, these patterns may be general and may help to explain the unevenness of morphological and functional diversity across the tree of life.
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Affiliation(s)
- Gabriele Sansalone
- Institute for Marine Biological Resources and Biotechnology (CNR-IRBIM), National Research Council, Via S. Raineri 4, 98122, Messina, Italy.
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia.
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 213D, 41125, Modena, Italy.
| | - Stephen Wroe
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Geoffrey Coates
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Marie R G Attard
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
- British Antarctic Survey, High Cross, Madingley Road, CB3 0ET, Cambridge, UK
| | - Carmelo Fruciano
- Institute for Marine Biological Resources and Biotechnology (CNR-IRBIM), National Research Council, Via S. Raineri 4, 98122, Messina, Italy.
- National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy.
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124, Catania, Italy.
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9
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Grossnickle DM, Sadier A, Patterson E, Cortés-Viruet NN, Jiménez-Rivera SM, Sears KE, Santana SE. The hierarchical radiation of phyllostomid bats as revealed by adaptive molar morphology. Curr Biol 2024; 34:1284-1294.e3. [PMID: 38447572 DOI: 10.1016/j.cub.2024.02.027] [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: 09/04/2023] [Revised: 12/11/2023] [Accepted: 02/13/2024] [Indexed: 03/08/2024]
Abstract
Adaptive radiations are bursts in biodiversity that generate new evolutionary lineages and phenotypes. However, because they typically occur over millions of years, it is unclear how their macroevolutionary dynamics vary through time and among groups of organisms. Phyllostomid bats radiated extensively for diverse diets-from insects to vertebrates, fruit, nectar, and blood-and we use their molars as a model system to examine the dynamics of adaptive radiations. Three-dimensional shape analyses of lower molars of Noctilionoidea (Phyllostomidae and close relatives) indicate that different diet groups exhibit distinct morphotypes. Comparative analyses further reveal that phyllostomids are a striking example of a hierarchical radiation; phyllostomids' initial, higher-level diversification involved an "early burst" in molar morphological disparity as lineages invaded new diet-affiliated adaptive zones, followed by subsequent lower-level diversifications within adaptive zones involving less dramatic morphological changes. We posit that strong selective pressures related to initial shifts to derived diets may have freed molars from morpho-functional constraints associated with the ancestral molar morphotype. Then, lineages with derived diets (frugivores and nectarivores) diversified within broad adaptive zones, likely reflecting finer-scale niche partitioning. Importantly, the observed early burst pattern is only evident when examining molar traits that are strongly linked to diet, highlighting the value of ecomorphological traits in comparative studies. Our results support the hypothesis that adaptive radiations are commonly hierarchical and involve different tempos and modes at different phylogenetic levels, with early bursts being more common at higher levels.
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Affiliation(s)
- David M Grossnickle
- Natural Sciences Department, Oregon Institute of Technology, Campus Drive, Klamath Falls, OR 97601, USA.
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Charles E. Young Drive East, Los Angeles, CA 90095, USA; Institut des Sciences de l'Evolution de Montpellier, Universite de Montpellier, Place Eugene Bataillon, Montpellier 34095, France
| | - Edward Patterson
- Department of Biology, University of Washington, Stevens Way NE, Seattle, WA 98195, USA
| | - Nashaly N Cortés-Viruet
- Department of Animal Science, University of Puerto Rico at Mayagüez, Calle Post, Mayagüez, PR 00681, USA
| | - Stephanie M Jiménez-Rivera
- Caribbean Manatee Conservation Center, Inter American University of Puerto Rico, 500 Dr. John Will Harris Street, Bayamón, PR 00957, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Charles E. Young Drive East, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Sharlene E Santana
- Department of Biology, University of Washington, Stevens Way NE, Seattle, WA 98195, USA; Burke Museum of Natural History and Culture, University of Washington, Memorial Way NE, Seattle, WA 98195, USA.
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10
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Astudillo-Clavijo V, Mankis T, López-Fernández H. Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data. Am Nat 2024; 203:305-322. [PMID: 38358812 DOI: 10.1086/728422] [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] [Indexed: 02/17/2024]
Abstract
AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.
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11
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Gayford JH, Sternes PC. The origins and drivers of sexual size dimorphism in sharks. Ecol Evol 2024; 14:e11163. [PMID: 38500855 PMCID: PMC10944705 DOI: 10.1002/ece3.11163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
While sexual size dimorphism (SSD) is abundant in nature, there is huge variation in both the intensity and direction of SSD. SSD results from a combination of sexual selection for large male size, fecundity selection for large female size and ecological selection for either. In most vertebrates, it is variation in the intensity of male-male competition that primarily underlies variation in SSD. In this study, we test four hypotheses regarding the adaptive value of SSD in sharks-considering the potential for each of fecundity, sexual, ecological selection and reproductive mode as the primary driver of variation in SSD between species. We also estimate past macroevolutionary shifts in SSD direction/intensity through shark phylogeny. We were unable to find evidence of significant SSD in early sharks and hypothesise that SSD is a derived state in this clade, that has evolved independently of SSD observed in other vertebrates. Moreover, there is no significant relationship between SSD and fecundity, testes mass or oceanic depth in sharks. However, there is evidence to support previous speculation that reproductive mode is an important determinant of interspecific variation in SSD in sharks. This is significant as in most vertebrates sexual selection is thought to be the primary driver of SSD trends, with evidence for the role of fecundity selection in other clades being inconsistent at best. While the phylogenetic distribution of SSD among sharks is superficially similar to that observed in other vertebrate clades, the relative importance of selective pressures underlying its evolution appears to differ.
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Affiliation(s)
- Joel H. Gayford
- Department of Life SciencesSilwood Park Campus, Imperial College LondonLondonUK
- Shark MeasurementsLondonUK
| | - Phillip C. Sternes
- Shark MeasurementsLondonUK
- Department of Evolution, Ecology and Organismal BiologyUniversity of CaliforniaRiversideCaliforniaUSA
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12
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Bartoszek K, Fuentes-González J, Mitov V, Pienaar J, Piwczyński M, Puchałka R, Spalik K, Voje KL. Analytical advances alleviate model misspecification in non-Brownian multivariate comparative methods. Evolution 2024; 78:389-400. [PMID: 37897801 DOI: 10.1093/evolut/qpad185] [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: 09/30/2023] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023]
Abstract
Adams and Collyer argue that contemporary multivariate (Gaussian) phylogenetic comparative methods are prone to favouring more complex models of evolution and sometimes rotation invariance can be an issue. Here we dissect the concept of rotation invariance and point out that, depending on the understanding, this can be an issue with any method that relies on numerical instead of analytical estimation approaches. We relate this to the ongoing discussion concerning phylogenetic principal component analysis. Contrary to what Adams and Collyer found, we do not observe a bias against the simpler Brownian motion process in simulations when we use the new, improved, likelihood evaluation algorithm employed by mvSLOUCH, which allows for studying much larger phylogenies and more complex model setups.
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Affiliation(s)
- Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Jesualdo Fuentes-González
- Department of Biological Sciences and the Institutes of Environment, Florida International University, Miami, FL, United States
| | | | - Jason Pienaar
- Department of Biological Sciences and the Institutes of Environment, Florida International University, Miami, FL, United States
| | - Marcin Piwczyński
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Radosław Puchałka
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Krzysztof Spalik
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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13
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Singh SA, Elsler A, Stubbs TL, Rayfield EJ, Benton MJ. Predatory synapsid ecomorphology signals growing dynamism of late Palaeozoic terrestrial ecosystems. Commun Biol 2024; 7:201. [PMID: 38368492 PMCID: PMC10874460 DOI: 10.1038/s42003-024-05879-2] [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: 12/16/2022] [Accepted: 02/01/2024] [Indexed: 02/19/2024] Open
Abstract
Terrestrial ecosystems evolved substantially through the Palaeozoic, especially the Permian, gaining much new complexity, especially among predators. Key among these predators were non-mammalian synapsids. Predator ecomorphology reflect interactions with prey and competitors, which are key controls on carnivore diversity and ecology. Therefore, carnivorous synapsids may offer insight on wider ecological evolution as the first complex, tetrapod-dominated, terrestrial ecosystems formed through the late Palaeozoic. Using morphometric and phylogenetic comparative methods, we chart carnivorous synapsid trophic morphology from the latest Carboniferous to the earliest Triassic (307-251.2 Ma). We find a major morphofunctional shift in synapsid carnivory between the early and middle Permian, via the addition of new feeding modes increasingly specialised for greater biting power or speed that captures the growing antagonism and dynamism of terrestrial tetrapod predator-prey interactions. The further evolution of new hypo- and hypercarnivorous synapsids highlight the nascent intrinsic pressures and complexification of terrestrial ecosystems across the mid-late Permian.
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Affiliation(s)
- Suresh A Singh
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Armin Elsler
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Thomas L Stubbs
- School of Life, Health and Chemical Sciences, Open University, Milton Keynes, MK7 6AE, UK
| | - Emily J Rayfield
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Michael J Benton
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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14
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Popescu SM, Tigae C, Dobrițescu A, Ștefănescu DM. Exploring the Climatic Niche Evolution of the Genus Falco (Aves: Falconidae) in Europe. BIOLOGY 2024; 13:113. [PMID: 38392331 PMCID: PMC10886973 DOI: 10.3390/biology13020113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
By integrating species distribution modeling techniques, phylogenetic comparative methods, and climatic data, we analyzed how European falcon climatic niches have changed over evolutionary time in order to understand their tempo and mode of evolution and gain phylogenetic insights related to the ecological context of falcon evolution. For this purpose, we tested the relative contributions of niche conservatism, convergent evolution, and divergent evolution in the evolutionary history of this group of species in Europe. The occupation of climatic niche spaces by falcon species in Europe was not similar, considering that their climatic niche evolution was characterized by heterotachy, especially after ca. 4 Mya. Our results indicate that convergent evolution and niche divergence played an important role in the evolutionary history of these species, with no significant evidence of closely related species retaining their fundamental niche over time (phylogenetic niche conservatism). In most analyses, less closely related falcon species occupied similar climatic environments. We found that speciation in the European genus Falco was influenced by climatic niche differentiation, more prevalent in the last 4 million years, with the main climatic niche shifts occurring between closely related falcon species.
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Affiliation(s)
- Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A.I. Cuza, 13, 200585 Craiova, Romania
| | - Cristian Tigae
- Faculty of Science, University of Craiova, A.I. Cuza, 13, 200585 Craiova, Romania
| | - Aurelian Dobrițescu
- Faculty of Science, University of Craiova, A.I. Cuza, 13, 200585 Craiova, Romania
| | - Dragoș Mihail Ștefănescu
- Department of Biology and Environmental Engineering, University of Craiova, A.I. Cuza, 13, 200585 Craiova, Romania
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15
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Drury JP, Clavel J, Tobias JA, Rolland J, Sheard C, Morlon H. Limited ecological opportunity influences the tempo of morphological evolution in birds. Curr Biol 2024; 34:661-669.e4. [PMID: 38218182 DOI: 10.1016/j.cub.2023.12.055] [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: 08/24/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 01/15/2024]
Abstract
According to classic models of lineage diversification and adaptive radiation, phenotypic evolution should accelerate in the context of ecological opportunity and slow down when niches become saturated.1,2 However, only weak support for these ideas has been found in nature, perhaps because most analyses make the biologically unrealistic assumption that clade members contribute equally to reducing ecological opportunity, even when they occur in different continents or specialize on different habitats and diets. To view this problem through a different lens, we adapted a new phylogenetic modeling approach that accounts for the fact that competition for ecological opportunity only occurs between species that coexist and share similar habitats and diets. Applying this method to trait data for nearly all extant species of landbirds,3 we find a widespread signature of decelerating trait evolution in lineages adapted to similar habitats or diets. The strength of this pattern was consistent across latitudes when comparing tropical and temperate assemblages. Our results provide little support for the idea that increased diversity and tighter packing of niches accentuates evolutionary slowdowns in the tropics and instead suggest that limited ecological opportunity can be an important factor determining the rate of morphological diversification at a global scale.
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Affiliation(s)
- Jonathan P Drury
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK.
| | - Julien Clavel
- Université Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, F-69622 Villeurbanne, France
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, UK
| | - Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, 31062 Toulouse, France
| | - Catherine Sheard
- School of Earth Sciences, University of Bristol, Bristol BS8 1RL, UK; School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Hélène Morlon
- Institut de Biologie - École Normale Supérieure, Université PSL, CNRS, INSERM, 75005 Paris, France
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16
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Coombs EJ, Knapp A, Park T, Bennion RF, McCurry MR, Lanzetti A, Boessenecker RW, McGowen MR. Drivers of morphological evolution in the toothed whale jaw. Curr Biol 2024; 34:273-285.e3. [PMID: 38118449 DOI: 10.1016/j.cub.2023.11.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/22/2023]
Abstract
Toothed whales (odontocetes) emit high-frequency underwater sounds (echolocate)-an extreme and unique innovation allowing them to sense their prey and environment. Their highly specialized mandible (lower jaw) allows high-frequency sounds to be transmitted back to the inner ear. Echolocation is evident in the earliest toothed whales, but little research has focused on the evolution of mandibular form regarding this unique adaptation. Here, we use a high-density, three-dimensional geometric morphometric analysis of 100 living and extinct cetacean species spanning their ∼50-million-year evolutionary history. Our analyses demonstrate that most shape variation is found in the relative length of the jaw and the mandibular symphysis. The greatest morphological diversity was obtained during two periods of rapid evolution: the initial evolution of archaeocetes (stem whales) in the early to mid-Eocene as they adapted to an aquatic lifestyle, representing one of the most extreme adaptive transitions known, and later on in the mid-Oligocene odontocetes as they became increasingly specialized for a range of diets facilitated by increasingly refined echolocation. Low disparity in the posterior mandible suggests the shape of the acoustic window, which receives sound, has remained conservative since the advent of directional hearing in the aquatic archaeocetes, even as the earliest odontocetes began to receive sounds from echolocation. Diet, echolocation, feeding method, and dentition type strongly influence mandible shape. Unlike in the toothed whale cranium, we found no significant asymmetry in the mandible. We suggest that a combination of refined echolocation and associated dietary specializations have driven morphology and disparity in the toothed whale mandible.
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Affiliation(s)
- Ellen J Coombs
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St & Constitution Ave NW, Washington, DC 20560, USA; Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Andrew Knapp
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK; University College London, Gower Street, London WC1E 6BT, UK
| | - Travis Park
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK; School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Rebecca F Bennion
- Evolution & Diversity Dynamics Lab, Department of Geology, University of Liege, 4000 Liege, Belgium; O.D. Earth and History of Life, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Matthew R McCurry
- Australian Museum Research Institute, 1 William Street, Sydney, NSW 2010, Australia; Earth & Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences (BEES), University of New South Wales, Kensington, NSW 2052, Australia; Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Agnese Lanzetti
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK; School of Geography, Earth, and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert W Boessenecker
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael R McGowen
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St & Constitution Ave NW, Washington, DC 20560, USA
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17
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Campelo dos Santos AL, DeGiorgio M, Assis R. Predicting evolutionary targets and parameters of gene deletion from expression data. BIOINFORMATICS ADVANCES 2024; 4:vbae002. [PMID: 38282974 PMCID: PMC10812876 DOI: 10.1093/bioadv/vbae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/08/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024]
Abstract
Motivation Gene deletion is traditionally thought of as a nonadaptive process that removes functional redundancy from genomes, such that it generally receives less attention than duplication in evolutionary turnover studies. Yet, mounting evidence suggests that deletion may promote adaptation via the "less-is-more" evolutionary hypothesis, as it often targets genes harboring unique sequences, expression profiles, and molecular functions. Hence, predicting the relative prevalence of redundant and unique functions among genes targeted by deletion, as well as the parameters underlying their evolution, can shed light on the role of gene deletion in adaptation. Results Here, we present CLOUDe, a suite of machine learning methods for predicting evolutionary targets of gene deletion events from expression data. Specifically, CLOUDe models expression evolution as an Ornstein-Uhlenbeck process, and uses multi-layer neural network, extreme gradient boosting, random forest, and support vector machine architectures to predict whether deleted genes are "redundant" or "unique", as well as several parameters underlying their evolution. We show that CLOUDe boasts high power and accuracy in differentiating between classes, and high accuracy and precision in estimating evolutionary parameters, with optimal performance achieved by its neural network architecture. Application of CLOUDe to empirical data from Drosophila suggests that deletion primarily targets genes with unique functions, with further analysis showing these functions to be enriched for protein deubiquitination. Thus, CLOUDe represents a key advance in learning about the role of gene deletion in functional evolution and adaptation. Availability and implementation CLOUDe is freely available on GitHub (https://github.com/anddssan/CLOUDe).
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Raquel Assis
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, United States
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL 33431, United States
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18
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Revell LJ. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 2024; 12:e16505. [PMID: 38192598 PMCID: PMC10773453 DOI: 10.7717/peerj.16505] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/31/2023] [Indexed: 01/10/2024] Open
Abstract
Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.
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Affiliation(s)
- Liam J. Revell
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
- Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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19
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Law CJ, Hlusko LJ, Tseng ZJ. Uncovering the mosaic evolution of the carnivoran skeletal system. Biol Lett 2024; 20:20230526. [PMID: 38263882 PMCID: PMC10806395 DOI: 10.1098/rsbl.2023.0526] [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: 11/09/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
The diversity of vertebrate skeletons is often attributed to adaptations to distinct ecological factors such as diet, locomotion, and sensory environment. Although the adaptive evolution of skull, appendicular skeleton, and vertebral column is well studied in vertebrates, comprehensive investigations of all skeletal components simultaneously are rarely performed. Consequently, we know little of how modes of evolution differ among skeletal components. Here, we tested if ecological and phylogenetic effects led to distinct modes of evolution among the cranial, appendicular and vertebral regions in extant carnivoran skeletons. Using multivariate evolutionary models, we found mosaic evolution in which only the mandible, hindlimb and posterior (i.e. last thoracic and lumbar) vertebrae showed evidence of adaptation towards ecological regimes whereas the remaining skeletal components reflect clade-specific evolutionary shifts. We hypothesize that the decoupled evolution of individual skeletal components may have led to the origination of distinct adaptive zones and morphologies among extant carnivoran families that reflect phylogenetic hierarchies. Overall, our work highlights the importance of examining multiple skeletal components simultaneously in ecomorphological analyses. Ongoing work integrating the fossil and palaeoenvironmental record will further clarify deep-time drivers that govern the carnivoran diversity we see today and reveal the complexity of evolutionary processes in multicomponent systems.
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Affiliation(s)
- Chris J. Law
- Department of Integrative Biology, University of Texas, Austin, TX, USA
- Burke Museum and Department of Biology, University of Washington, Seattle, WA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Leslea J. Hlusko
- National Research Center on Human Evolution (CENIEH), Burgos, Spain
| | - Z. Jack Tseng
- Department of Integrative Biology, University of California, Berkeley, CA, USA
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20
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Bastide P, Didier G. The Cauchy Process on Phylogenies: A Tractable Model for Pulsed Evolution. Syst Biol 2023; 72:1296-1315. [PMID: 37603537 DOI: 10.1093/sysbio/syad053] [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: 04/06/2023] [Revised: 08/05/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
Phylogenetic comparative methods use random processes, such as the Brownian Motion, to model the evolution of continuous traits on phylogenetic trees. Growing evidence for non-gradual evolution motivated the development of complex models, often based on Lévy processes. However, their statistical inference is computationally intensive and currently relies on approximations, high-dimensional sampling, or numerical integration. We consider here the Cauchy Process (CP), a particular pure-jump Lévy process in which the trait increment along each branch follows a centered Cauchy distribution with a dispersion proportional to its length. In this work, we derive an exact algorithm to compute both the joint probability density of the tip trait values of a phylogeny under a CP and the ancestral trait values and branch increments posterior densities in quadratic time. A simulation study shows that the CP generates patterns in comparative data that are distinct from any Gaussian process, and that restricted maximum likelihood parameter estimates and root trait reconstruction are unbiased and accurate for trees with 200 tips or less. The CP has only two parameters but is rich enough to capture complex-pulsed evolution. It can reconstruct posterior ancestral trait distributions that are multimodal, reflecting the uncertainty associated with the inference of the evolutionary history of a trait from extant taxa only. Applied on empirical datasets taken from the Evolutionary Ecology and Virology literature, the CP suggests nuanced scenarios for the body size evolution of Greater Antilles Lizards and for the geographical spread of the West Nile Virus epidemics in North America, both consistent with previous studies using more complex models. The method is efficiently implemented in C with an R interface in package cauphy, which is open source and freely available online.
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Affiliation(s)
- Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Gilles Didier
- IMAG, Université de Montpellier, CNRS, Montpellier, France
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21
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Mendes FK, Landis MJ. PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571907. [PMID: 38168278 PMCID: PMC10760140 DOI: 10.1101/2023.12.15.571907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction - which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models - and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.
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Affiliation(s)
- Fábio K. Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO
| | - Michael J. Landis
- Department of Biology, Washington University in St. Louis, St. Louis, MO
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22
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Liao W, Jiang Y, Jin L, Lüpold S. How hibernation in frogs drives brain and reproductive evolution in opposite directions. eLife 2023; 12:RP88236. [PMID: 38085091 PMCID: PMC10715729 DOI: 10.7554/elife.88236] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Environmental seasonality can promote the evolution of larger brains through cognitive and behavioral flexibility but can also hamper it when temporary food shortage is buffered by stored energy. Multiple hypotheses linking brain evolution with resource acquisition and allocation have been proposed for warm-blooded organisms, but it remains unclear how these extend to cold-blooded taxa whose metabolism is tightly linked to ambient temperature. Here, we integrated these hypotheses across frogs and toads in the context of varying brumation (hibernation) durations and their environmental correlates. We showed that protracted brumation covaried negatively with brain size but positively with reproductive investment, likely in response to brumation-dependent changes in the socio-ecological context and associated selection on different tissues. Our results provide novel insights into resource allocation strategies and possible constraints in trait diversification, which may have important implications for the adaptability of species under sustained environmental change.
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Affiliation(s)
- Wenbo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal UniversitySichuanChina
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal UniversityNanchongChina
- Institute of Eco-Adaptation in Amphibians and Reptiles, China West Normal UniversityNanchongChina
| | - Ying Jiang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal UniversitySichuanChina
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal UniversityNanchongChina
- Institute of Eco-Adaptation in Amphibians and Reptiles, China West Normal UniversityNanchongChina
| | - Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal UniversitySichuanChina
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal UniversityNanchongChina
- Institute of Eco-Adaptation in Amphibians and Reptiles, China West Normal UniversityNanchongChina
| | - Stefan Lüpold
- Department of Evolutionary Biology and Environmental Studies, University of ZurichZurichSwitzerland
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23
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Overcast I, Noguerales V, Meramveliotakis E, Andújar C, Arribas P, Creedy TJ, Emerson BC, Vogler AP, Papadopoulou A, Morlon H. Inferring the ecological and evolutionary determinants of community genetic diversity. Mol Ecol 2023; 32:6093-6109. [PMID: 37221561 DOI: 10.1111/mec.16958] [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: 04/21/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.
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Affiliation(s)
- Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Víctor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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24
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Anthwal N, Hall RP, de la Rosa Hernandez FA, Koger M, Yohe LR, Hedrick BP, Davies KTJ, Mutumi GL, Roseman CC, Dumont ER, Dávalos LM, Rossiter SJ, Sadier A, Sears KE. Cochlea development shapes bat sensory system evolution. Anat Rec (Hoboken) 2023. [PMID: 37994725 DOI: 10.1002/ar.25353] [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: 08/05/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023]
Abstract
Sensory organs must develop alongside the skull within which they are largely encased, and this relationship can manifest as the skull constraining the organs, organs constraining the skull, or organs constraining one another in relative size. How this interplay between sensory organs and the developing skull plays out during the evolution of sensory diversity; however, remains unknown. Here, we examine the developmental sequence of the cochlea, the organ responsible for hearing and echolocation, in species with distinct diet and echolocation types within the ecologically diverse bat super-family Noctilionoidea. We found the size and shape of the cochlea largely correlates with skull size, with exceptions of Pteronotus parnellii, whose high duty cycle echolocation (nearly constant emission of sound pulses during their echolocation process allowing for detailed information gathering, also called constant frequency echolocation) corresponds to a larger cochlear and basal turn, and Monophyllus redmani, a small-bodied nectarivorous bat, for which interactions with other sensory organs restrict cochlea size. Our findings support the existence of developmental constraints, suggesting that both developmental and anatomical factors may act synergistically during the development of sensory systems in noctilionoid bats.
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Affiliation(s)
- Neal Anthwal
- King's College London, Centre for Craniofacial and Regenerative Biology, London, UK
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Ronald P Hall
- Department of Life and Environment Sciences, University of California Merced, Merced, California, USA
| | | | - Michael Koger
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, North Carolina, USA
| | - Brandon P Hedrick
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Kalina T J Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Gregory L Mutumi
- Department of Life and Environment Sciences, University of California Merced, Merced, California, USA
| | - Charles C Roseman
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA
| | - Elizabeth R Dumont
- Department of Life and Environment Sciences, University of California Merced, Merced, California, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, USA
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
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25
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Burress ED, Muñoz MM. Phenotypic rate and state are decoupled in response to river-to-lake transitions in cichlid fishes. Evolution 2023; 77:2365-2377. [PMID: 37624672 DOI: 10.1093/evolut/qpad143] [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: 01/21/2023] [Revised: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Geographic access to isolated ecosystems is an important catalyst of adaptive radiation. Cichlid fishes repeatedly colonized rift, crater, and volcanic lakes from surrounding rivers. We test the "lake effect" on the phenotypic rate and state across 253 cichlid species. The rate of evolution was consistently higher (~10-fold) in lakes, and consistent across different dimensions of the phenotype. Rate shifts tended to occur coincident with or immediately following river-to-lake transitions, generally resulting in 2- to 5-fold faster rates than in the founding riverine lineage. By contrast, river- and lake-dwelling cichlids exhibit considerable overlap in phenotypes, generally with less disparity in lakes, but often different evolutionary optima. Taken together, these results suggest that lake radiations rapidly expand into niches largely already represented by ancestral riverine lineages, albeit in different frequencies. Lakes may provide ecological opportunity via ecological release (e.g., from predators/competitors) but need not be coupled with access to novel ecological niches.
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Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolution, Yale University, New Haven, CT, United States
| | - Martha M Muñoz
- Department of Ecology and Evolution, Yale University, New Haven, CT, United States
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26
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Hellert SM, Grossnickle DM, Lloyd GT, Kammerer CF, Angielczyk KD. Derived faunivores are the forerunners of major synapsid radiations. Nat Ecol Evol 2023; 7:1903-1913. [PMID: 37798433 DOI: 10.1038/s41559-023-02200-y] [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: 04/22/2022] [Accepted: 08/06/2023] [Indexed: 10/07/2023]
Abstract
Evolutionary radiations generate most of Earth's biodiversity, but are there common ecomorphological traits among the progenitors of radiations? In Synapsida (the mammalian total group), 'small-bodied faunivore' has been hypothesized as the ancestral state of most major radiating clades, but this has not been quantitatively assessed across multiple radiations. To examine macroevolutionary patterns in a phylogenetic context, we generated a time-calibrated metaphylogeny ('metatree') comprising 1,888 synapsid species from the Carboniferous through the Eocene (305-34 Ma) based on 269 published character matrices. We used comparative methods to investigate body size and dietary evolution during successive synapsid radiations. Faunivory is the ancestral dietary regime of each major synapsid radiation, but relatively small body size is only established as the common ancestral state of radiations near the origin of Mammaliaformes in the Late Triassic. The faunivorous ancestors of synapsid radiations typically have numerous novel characters compared with their contemporaries, and these derived traits may have helped them to survive faunal turnover events and subsequently radiate.
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Affiliation(s)
- Spencer M Hellert
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA.
- Department of Science and Mathematics, Columbia College Chicago, Chicago, IL, USA.
| | - David M Grossnickle
- Department of Biology, University of Washington, Seattle, WA, USA
- Natural Sciences Department, Oregon Institute of Technology, Klamath Falls, OR, USA
| | | | | | - Kenneth D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
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Voje KL. Fitting and evaluating univariate and multivariate models of within-lineage evolution. PALEOBIOLOGY 2023; 49:747-764. [PMID: 37859727 PMCID: PMC7615219 DOI: 10.1017/pab.2023.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The nature of phenotypic evolution within lineages is central to many unresolved questions in paleontology and evolutionary biology. Analyses of evolutionary time-series of ancestor-descendant populations in the fossil record are likely to make important contributions to many of these debates. However, the limited number of models that have been applied to these types of data may restrict our ability to interpret phenotypic evolution in the fossil record. Using uni- and multivariate models of trait evolution that make different assumptions regarding the dynamics of the adaptive landscape, I evaluate contrasting hypotheses to explain evolution of size in the radiolarian Eucyrtidium calvertense and armor in the stickleback Gaserosteus doryssus. Body size evolution in E. calvertense is best explained by a model where the lineage evolves as a consequence of a shift in the adaptive landscape that coincides with the initiation of neosympatry with its sister lineage. Multivariate evolution of armor traits in a stickleback lineage (Gasterosteus doryssus) show evidence of adaptation towards independent optima on the adaptive landscape at the same time as traits change in a correlated fashion. The fitted models are available in a the R package evoTS, which builds on the commonly used paleoTS framework.
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Kiel CA, Manzitto-Tripp E, Fisher AE, Porter JM, McDade LA. Remarkable variation in androecial morphology is closely associated with corolla traits in Western Hemisphere Justiciinae (Acanthaceae: Justicieae). ANNALS OF BOTANY 2023; 132:43-60. [PMID: 37279362 PMCID: PMC10550274 DOI: 10.1093/aob/mcad068] [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: 12/11/2022] [Accepted: 05/30/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Few studies of angiosperms have focused on androecial evolution in conjunction with evolutionary shifts in corolla morphology and pollinator relationships. The Western Hemisphere clade of Justiciinae (Acanthaceae) presents the rare opportunity to examine remarkable diversity in staminal morphology. We took a phylogenetically informed approach to examine staminal diversity in this hypervariable group and asked whether differences in anther thecae separation is associated with phylogenetically informed patterns of variation in corolla morphology. We further discuss evidence for associations between anther diversity and pollinators in this lineage. METHODS For the Dianthera/Sarotheca/Plagiacanthus (DSP) clade of Western Hemisphere Justiciinae, we characterized floral diversity based on a series of corolla measurements and using a model-based clustering approach. We then tested for correlations between anther thecae separation and corolla traits, and for shifts in trait evolution, including evidence for convergence. KEY RESULTS There is evolutionary vagility in corolla and anther traits across the DSP clade with little signal of phylogenetic constraint. Floral morphology clusters into four distinct groups that are, in turn, strongly associated with anther thecae separation, a novel result in Acanthaceae and, to our knowledge, across flowering plants. These cluster groups are marked by floral traits that strongly point to associations with pollinating animals. Specifically, species that are known or likely to be hummingbird pollinated have stamens with parallel thecae, whereas those that are likely bee or fly pollinated have stamens with offset, divergent thecae. CONCLUSIONS Our results suggest that anther thecae separation is likely under selection in concert with other corolla characters. Significant morphological shifts detected by our analyses corresponded to putative shifts from insect to hummingbird pollination. Results from this study support the hypothesis that floral structures function in an integrated manner and are likely subject to selection as a suite. Further, these changes can be hypothesized to represent adaptive evolution.
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Affiliation(s)
- Carrie A Kiel
- California Botanic Garden, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Erin Manzitto-Tripp
- University of Colorado, Museum of Natural History and Department of Ecology and Evolutionary Biology, Boulder, CO 80309, USA
| | - Amanda E Fisher
- California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90807, USA
| | - J Mark Porter
- California Botanic Garden, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Lucinda A McDade
- California Botanic Garden, 1500 North College Avenue, Claremont, CA 91711, USA
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29
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Heuer K, Traut N, de Sousa AA, Valk SL, Clavel J, Toro R. Diversity and evolution of cerebellar folding in mammals. eLife 2023; 12:e85907. [PMID: 37737580 PMCID: PMC10617990 DOI: 10.7554/elife.85907] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023] Open
Abstract
The process of brain folding is thought to play an important role in the development and organisation of the cerebrum and the cerebellum. The study of cerebellar folding is challenging due to the small size and abundance of its folia. In consequence, little is known about its anatomical diversity and evolution. We constituted an open collection of histological data from 56 mammalian species and manually segmented the cerebrum and the cerebellum. We developed methods to measure the geometry of cerebellar folia and to estimate the thickness of the molecular layer. We used phylogenetic comparative methods to study the diversity and evolution of cerebellar folding and its relationship with the anatomy of the cerebrum. Our results show that the evolution of cerebellar and cerebral anatomy follows a stabilising selection process. We observed two groups of phenotypes changing concertedly through evolution: a group of 'diverse' phenotypes - varying over several orders of magnitude together with body size, and a group of 'stable' phenotypes varying over less than 1 order of magnitude across species. Our analyses confirmed the strong correlation between cerebral and cerebellar volumes across species, and showed in addition that large cerebella are disproportionately more folded than smaller ones. Compared with the extreme variations in cerebellar surface area, folial anatomy and molecular layer thickness varied only slightly, showing a much smaller increase in the larger cerebella. We discuss how these findings could provide new insights into the diversity and evolution of cerebellar folding, the mechanisms of cerebellar and cerebral folding, and their potential influence on the organisation of the brain across species.
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Affiliation(s)
- Katja Heuer
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et ThéoriqueParisFrance
| | - Nicolas Traut
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et ThéoriqueParisFrance
| | | | - Sofie Louise Valk
- Otto Hahn Group Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, FZ JülichJülichGermany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Julien Clavel
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNAVilleurbanneFrance
| | - Roberto Toro
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et ThéoriqueParisFrance
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30
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Grabowski M, Pienaar J, Voje KL, Andersson S, Fuentes-González J, Kopperud BT, Moen DS, Tsuboi M, Uyeda J, Hansen TF. A Cautionary Note on "A Cautionary Note on the Use of Ornstein Uhlenbeck Models in Macroevolutionary Studies". Syst Biol 2023; 72:955-963. [PMID: 37229537 PMCID: PMC10405355 DOI: 10.1093/sysbio/syad012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 01/08/2023] [Accepted: 03/16/2023] [Indexed: 05/27/2023] Open
Abstract
Models based on the Ornstein-Uhlenbeck process have become standard for the comparative study of adaptation. Cooper et al. (2016) have cast doubt on this practice by claiming statistical problems with fitting Ornstein-Uhlenbeck models to comparative data. Specifically, they claim that statistical tests of Brownian motion may have too high Type I error rates and that such error rates are exacerbated by measurement error. In this note, we argue that these results have little relevance to the estimation of adaptation with Ornstein-Uhlenbeck models for three reasons. First, we point out that Cooper et al. (2016) did not consider the detection of distinct optima (e.g. for different environments), and therefore did not evaluate the standard test for adaptation. Second, we show that consideration of parameter estimates, and not just statistical significance, will usually lead to correct inferences about evolutionary dynamics. Third, we show that bias due to measurement error can be corrected for by standard methods. We conclude that Cooper et al. (2016) have not identified any statistical problems specific to Ornstein-Uhlenbeck models, and that their cautions against their use in comparative analyses are unfounded and misleading. [adaptation, Ornstein-Uhlenbeck model, phylogenetic comparative method.].
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Affiliation(s)
- Mark Grabowski
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Jason Pienaar
- Department of Biological Sciences and the Institutes of Environment, Florida International University Miami, Miami, FL, USA
| | - Kjetil L Voje
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Jesualdo Fuentes-González
- Department of Biological Sciences and the Institutes of Environment, Florida International University Miami, Miami, FL, USA
| | - Bjørn T Kopperud
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Thomas F Hansen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
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31
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Goswami A, Noirault E, Coombs EJ, Clavel J, Fabre AC, Halliday TJD, Churchill M, Curtis A, Watanabe A, Simmons NB, Beatty BL, Geisler JH, Fox DL, Felice RN. Developmental origin underlies evolutionary rate variation across the placental skull. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220083. [PMID: 37183904 PMCID: PMC10184245 DOI: 10.1098/rstb.2022.0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The placental skull has evolved into myriad forms, from longirostrine whales to globular primates, and with a diverse array of appendages from antlers to tusks. This disparity has recently been studied from the perspective of the whole skull, but the skull is composed of numerous elements that have distinct developmental origins and varied functions. Here, we assess the evolution of the skull's major skeletal elements, decomposed into 17 individual regions. Using a high-dimensional morphometric approach for a dataset of 322 living and extinct eutherians (placental mammals and their stem relatives), we quantify patterns of variation and estimate phylogenetic, allometric and ecological signal across the skull. We further compare rates of evolution across ecological categories and ordinal-level clades and reconstruct rates of evolution along lineages and through time to assess whether developmental origin or function discriminate the evolutionary trajectories of individual cranial elements. Our results demonstrate distinct macroevolutionary patterns across cranial elements that reflect the ecological adaptations of major clades. Elements derived from neural crest show the fastest rates of evolution, but ecological signal is equally pronounced in bones derived from neural crest and paraxial mesoderm, suggesting that developmental origin may influence evolutionary tempo, but not capacity for specialisation. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Anjali Goswami
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Eve Noirault
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Ellen J Coombs
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Julien Clavel
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622 Villeurbanne, France
| | - Anne-Claire Fabre
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Naturhistorisches Museum Bern, 3005 Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Thomas J D Halliday
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Morgan Churchill
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
| | - Abigail Curtis
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Akinobu Watanabe
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
- Division of Paleontology, American Museum of Natural History, New York, NY 10024, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Brian L Beatty
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Jonathan H Geisler
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - David L Fox
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryan N Felice
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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32
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Weisbecker V, Beck RMD, Guillerme T, Harrington AR, Lange-Hodgson L, Lee MSY, Mardon K, Phillips MJ. Multiple modes of inference reveal less phylogenetic signal in marsupial basicranial shape compared with the rest of the cranium. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220085. [PMID: 37183893 PMCID: PMC10184248 DOI: 10.1098/rstb.2022.0085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Incorporating morphological data into modern phylogenies allows integration of fossil evidence, facilitating divergence dating and macroevolutionary inferences. Improvements in the phylogenetic utility of morphological data have been sought via Procrustes-based geometric morphometrics (GMM), but with mixed success and little clarity over what anatomical areas are most suitable. Here, we assess GMM-based phylogenetic reconstructions in a heavily sampled source of discrete characters for mammalian phylogenetics-the basicranium-in 57 species of marsupial mammals, compared with the remainder of the cranium. We show less phylogenetic signal in the basicranium compared with a 'Rest of Cranium' partition, using diverse metrics of phylogenetic signal (Kmult, phylogenetically aligned principal components analysis, comparisons of UPGMA/neighbour-joining/parsimony trees and cophenetic distances to a reference phylogeny) for scaled, Procrustes-aligned landmarks and allometry-corrected residuals. Surprisingly, a similar pattern emerged from parsimony-based analyses of discrete cranial characters. The consistent results across methods suggest that easily computed metrics such as Kmult can provide good guidance on phylogenetic information in a landmarking configuration. In addition, GMM data may be less informative for intricate but conservative anatomical regions such as the basicranium, while better-but not necessarily novel-phylogenetic information can be expected for broadly characterized shapes such as entire bones. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Vera Weisbecker
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT, UK
| | - Thomas Guillerme
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | | - Leonie Lange-Hodgson
- School of Biological Sciences, University of Queensland, Saint Lucia, Queensland, 4072, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
- Earth Sciences Section, South Australian Museum, Adelaide, South Australia, 5000 Australia
| | - Karine Mardon
- Centre of Advanced Imaging, University of Queensland, Saint Lucia, Queensland, 4072, Australia
| | - Matthew J Phillips
- School of Biology & Environmental Science, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
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Simon MN, Moen DS. Bridging Performance and Adaptive Landscapes to Understand Long-Term Functional Evolution. Physiol Biochem Zool 2023; 96:304-320. [PMID: 37418608 DOI: 10.1086/725416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
AbstractUnderstanding functional adaptation demands an integrative framework that captures the complex interactions between form, function, ecology, and evolutionary processes. In this review, we discuss how to integrate the following two distinct approaches to better understand functional evolution: (1) the adaptive landscape approach (ALA), aimed at finding adaptive peaks for different ecologies, and (2) the performance landscape approach (PLA), aimed at finding performance peaks for different ecologies. We focus on the Ornstein-Uhlenbeck process as the evolutionary model for the ALA and on biomechanical modeling to estimate performance for the PLA. Whereas both the ALA and the PLA have each given insight into functional adaptation, separately they cannot address how much performance contributes to fitness or whether evolutionary constraints have played a role in form-function evolution. We show that merging these approaches leads to a deeper understanding of these issues. By comparing the locations of performance and adaptive peaks, we can infer how much performance contributes to fitness in species' current environments. By testing for the relevance of history on phenotypic variation, we can infer the influence of past selection and constraints on functional adaptation. We apply this merged framework in a case study of turtle shell evolution and explain how to interpret different possible outcomes. Even though such outcomes can be quite complex, they represent the multifaceted relations among function, fitness, and constraints.
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Hunt ESE, Felice RN, Tobias JA, Goswami A. Ecological and life-history drivers of avian skull evolution. Evolution 2023; 77:1720-1729. [PMID: 37105944 DOI: 10.1093/evolut/qpad079] [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: 02/03/2023] [Revised: 04/04/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023]
Abstract
One of the most famous examples of adaptive radiation is that of the Galápagos finches, where skull morphology, particularly the beak, varies with feeding ecology. Yet increasingly studies are questioning the strength of this correlation between feeding ecology and morphology in relation to the entire neornithine radiation, suggesting that other factors also significantly affect skull evolution. Here, we broaden this debate to assess the influence of a range of ecological and life-history factors, specifically habitat density, migration, and developmental mode, in shaping avian skull evolution. Using 3D geometric morphometric data to robustly quantify skull shape for 354 extant species spanning avian diversity, we fitted flexible phylogenetic regressions and estimated evolutionary rates for each of these factors across the full data set. The results support a highly significant relationship between skull shape and both habitat density and migration, but not developmental mode. We further found heterogenous rates of evolution between different character states within habitat density, migration, and developmental mode, with rapid skull evolution in species that occupy dense habitats, are migratory, or are precocial. These patterns demonstrate that diverse factors affect the tempo and mode of avian phenotypic evolution and that skull evolution in birds is not simply a reflection of feeding ecology.
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Affiliation(s)
- Eloise S E Hunt
- Department of Life Sciences and Grantham Institute, Imperial College London, London, United Kingdom
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Ryan N Felice
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Anjali Goswami
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
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35
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Monclús-Gonzalo O, Alba DM, Duhamel A, Fabre AC, Marigó J. Early euprimates already had a diverse locomotor repertoire: Evidence from ankle bone morphology. J Hum Evol 2023; 181:103395. [PMID: 37320961 DOI: 10.1016/j.jhevol.2023.103395] [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: 08/09/2022] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023]
Abstract
The morphological adaptations of euprimates have been linked to their origin and early evolution in an arboreal environment. However, the ancestral and early locomotor repertoire of this group remains contentious. Although some tarsal bones like the astragalus and the calcaneus have been thoroughly studied, the navicular remains poorly studied despite its potential implications for foot mobility. Here, we evaluate early euprimate locomotion by assessing the shape of the navicular-an important component of the midtarsal region of the foot-using three-dimensional geometric morphometrics in relation to quantified locomotor repertoire in a wide data set of extant primates. We also reconstruct the locomotor repertoire of representatives of the major early primate lineages with a novel phylogenetically informed discriminant analysis and characterize the changes that occurred in the navicular during the archaic primate-euprimate transition. To do so, we included in our study an extensive sample of naviculars (36 specimens) belonging to different species of adapiforms, omomyiforms, and plesiadapiforms. Our results indicate that navicular shape embeds a strong functional signal, allowing us to infer the type of locomotion of extinct primates. We demonstrate that early euprimates displayed a diverse locomotor behavior, although they did not reach the level of specialization of some living forms. Finally, we show that the navicular bone experienced substantial reorganization throughout the archaic primate-euprimate transition, supporting the major functional role of the tarsus during early primate evolution. This study demonstrates that navicular shape can be used as a reliable proxy for primate locomotor behavior. In addition, it sheds light on the diverse locomotor behavior of early primates as well as on the archaic primate-euprimate transition, which involved profound morphological changes within the tarsus, including the navicular bone.
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Affiliation(s)
- Oriol Monclús-Gonzalo
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - David M Alba
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Anaïs Duhamel
- University of Lyon, ENSL, CNRS, LGL-TPE, Villeurbanne 69622, France
| | - Anne-Claire Fabre
- Naturhistorisches Museum Bern, 3005 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; Life Sciences Department, Vertebrates Division, Natural History Museum, London SW7 5BD, UK.
| | - Judit Marigó
- Universitat Autònoma de Barcelona, Departament de Geologia, 08193 Cerdanyola del Vallès, Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain.
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36
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Nevers Y, Glover NM, Dessimoz C, Lecompte O. Protein length distribution is remarkably uniform across the tree of life. Genome Biol 2023; 24:135. [PMID: 37291671 PMCID: PMC10251718 DOI: 10.1186/s13059-023-02973-2] [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: 02/03/2022] [Accepted: 05/16/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND In every living species, the function of a protein depends on its organization of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different evolutionary pressures, the protein length distribution, much like other genomic features, is expected to vary across species but has so far been scarcely studied. RESULTS Here we evaluate this diversity by comparing protein length distribution across 2326 species (1688 bacteria, 153 archaea, and 485 eukaryotes). We find that proteins tend to be on average slightly longer in eukaryotes than in bacteria or archaea, but that the variation of length distribution across species is low, especially compared to the variation of other genomic features (genome size, number of proteins, gene length, GC content, isoelectric points of proteins). Moreover, most cases of atypical protein length distribution appear to be due to artifactual gene annotation, suggesting the actual variation of protein length distribution across species is even smaller. CONCLUSIONS These results open the way for developing a genome annotation quality metric based on protein length distribution to complement conventional quality measures. Overall, our findings show that protein length distribution between living species is more uniform than previously thought. Furthermore, we also provide evidence for a universal selection on protein length, yet its mechanism and fitness effect remain intriguing open questions.
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Affiliation(s)
- Yannis Nevers
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland.
| | - Natasha M Glover
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland
- Department of Computer Science, University College London, London, UK
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Odile Lecompte
- Department of Computer Science, Centre de Recherche en Biomédecine de Strasbourg, ICube, UMR 7357, University of Strasbourg, CNRS, Strasbourg, France
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Jantzen JR, Laliberté E, Carteron A, Beauchamp-Rioux R, Blanchard F, Crofts AL, Girard A, Hacker PW, Pardo J, Schweiger AK, Demers-Thibeault S, Coops NC, Kalacska M, Vellend M, Bruneau A. Evolutionary history explains foliar spectral differences between arbuscular and ectomycorrhizal plant species. THE NEW PHYTOLOGIST 2023; 238:2651-2667. [PMID: 36960543 DOI: 10.1111/nph.18902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Leaf spectra are integrated foliar phenotypes that capture a range of traits and can provide insight into ecological processes. Leaf traits, and therefore leaf spectra, may reflect belowground processes such as mycorrhizal associations. However, evidence for the relationship between leaf traits and mycorrhizal association is mixed, and few studies account for shared evolutionary history. We conduct partial least squares discriminant analysis to assess the ability of spectra to predict mycorrhizal type. We model the evolution of leaf spectra for 92 vascular plant species and use phylogenetic comparative methods to assess differences in spectral properties between arbuscular mycorrhizal and ectomycorrhizal plant species. Partial least squares discriminant analysis classified spectra by mycorrhizal type with 90% (arbuscular) and 85% (ectomycorrhizal) accuracy. Univariate models of principal components identified multiple spectral optima corresponding with mycorrhizal type due to the close relationship between mycorrhizal type and phylogeny. Importantly, we found that spectra of arbuscular mycorrhizal and ectomycorrhizal species do not statistically differ from each other after accounting for phylogeny. While mycorrhizal type can be predicted from spectra, enabling the use of spectra to identify belowground traits using remote sensing, this is due to evolutionary history and not because of fundamental differences in leaf spectra due to mycorrhizal type.
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Affiliation(s)
- Johanna R Jantzen
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Etienne Laliberté
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Alexis Carteron
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Rosalie Beauchamp-Rioux
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Florence Blanchard
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Anna L Crofts
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2X9, Canada
| | - Alizée Girard
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Paul W Hacker
- Department of Forest Resources Management, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Juliana Pardo
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Anna K Schweiger
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
- Department of Geography, Remote Sensing Laboratories, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Sabrina Demers-Thibeault
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Nicholas C Coops
- Department of Forest Resources Management, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Margaret Kalacska
- Department of Geography, McGill University, Montréal, QC, H3A 0B9, Canada
| | - Mark Vellend
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2X9, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
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Siqueira AC, Yan HF, Morais RA, Bellwood DR. The evolution of fast-growing coral reef fishes. Nature 2023:10.1038/s41586-023-06070-z. [PMID: 37198484 DOI: 10.1038/s41586-023-06070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/11/2023] [Indexed: 05/19/2023]
Abstract
Individual growth is a fundamental life history trait1-4, yet its macroevolutionary trajectories have rarely been investigated for entire animal assemblages. Here we analyse the evolution of growth in a highly diverse vertebrate assemblage-coral reef fishes. We combine state-of-the-art extreme gradient boosted regression trees with phylogenetic comparative methods to detect the timing, number, location and magnitude of shifts in the adaptive regime of somatic growth. We also explored the evolution of the allometric relationship between body size and growth. Our results show that the evolution of fast growth trajectories in reef fishes has been considerably more common than the evolution of slow growth trajectories. Many reef fish lineages shifted towards faster growth and smaller body size evolutionary optima in the Eocene (56-33.9 million years ago), pointing to a major expansion of life history strategies in this Epoch. Of all lineages examined, the small-bodied, high-turnover cryptobenthic fishes shifted most towards extremely high growth optima, even after accounting for body size allometry. These results suggest that the high global temperatures of the Eocene5 and subsequent habitat reconfigurations6 might have been critical for the rise and retention of the highly productive, high-turnover fish faunas that characterize modern coral reef ecosystems.
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Affiliation(s)
- Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.
| | - Helen F Yan
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Renato A Morais
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Paris Sciences et Lettres Université, École Pratique des Hautes Études, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Perpignan, France
| | - David R Bellwood
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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39
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Piya AA, DeGiorgio M, Assis R. Predicting gene expression divergence between single-copy orthologs in two species. Genome Biol Evol 2023; 15:evad078. [PMID: 37170892 PMCID: PMC10220509 DOI: 10.1093/gbe/evad078] [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: 08/12/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Predicting gene expression divergence is integral to understanding the emergence of new biological functions and associated traits. Whereas several sophisticated methods have been developed for this task, their applications are either limited to duplicate genes or require expression data from more than two species. Thus, here we present PiXi, the first machine learning framework for predicting gene expression divergence between single-copy orthologs in two species. PiXi models gene expression evolution as an Ornstein-Uhlenbeck process, and overlays this model with multi-layer neural network, random forest, and support vector machine architectures for making predictions. It outputs the predicted class "conserved" or "diverged" for each pair of orthologs, as well as their predicted expression optima in the two species. We show that PiXi has high power and accuracy in predicting gene expression divergence between single-copy orthologs, as well as high accuracy and precision in estimating their expression optima in the two species, across a wide range of evolutionary scenarios, with the globally best performance achieved by a multi-layer neural network. Moreover, application of our best performing PiXi predictor to empirical gene expression data from single-copy orthologs residing at different loci in two species of Drosophila reveals that approximately 23% underwent expression divergence after positional relocation. Further analysis shows that several of these "diverged" genes are involved in the electron transport chain of the mitochondrial membrane, suggesting that new chromatin environments may impact energy production in Drosophila. Thus, by providing a toolkit for predicting gene expression divergence between single-copy orthologs in two species, PiXi can shed light on the origins of novel phenotypes across diverse biological processes and study systems.
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Affiliation(s)
- Antara Anika Piya
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FloridaUSA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FloridaUSA
| | - Raquel Assis
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FloridaUSA
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FloridaUSA
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40
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Rickman J, Burtner AE, Linden TJ, Santana SE, Law CJ. Size And Locomotor Ecology Have Differing Effects on the External and Internal Morphologies of Squirrel (Rodentia: Sciuridae) Limb Bones. Integr Org Biol 2023; 5:obad017. [PMID: 37361915 PMCID: PMC10286724 DOI: 10.1093/iob/obad017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/19/2023] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
Mammals exhibit a diverse range of limb morphologies that are associated with different locomotor ecologies and structural mechanics. Much remains to be investigated, however, about the combined effects of locomotor modes and scaling on the external shape and structural properties of limb bones. Here, we used squirrels (Sciuridae) as a model clade to examine the effects of locomotor mode and scaling on the external shape and structure of the two major limb bones, the humerus and femur. We quantified humeral and femoral morphologies using 3D geometric morphometrics and bone structure analyses on a sample of 76 squirrel species across their four major ecotypes. We then used phylogenetic generalized linear models to test how locomotor ecology, size, and their interaction influenced morphological traits. We found that size and locomotor mode exhibit different relationships with the external shape and structure of the limb bones, and that these relationships differ between the humerus and femur. External shapes of the humerus and, to a lesser extent, the femur are best explained by locomotor ecology rather than by size, whereas structures of both bones are best explained by interactions between locomotor ecology and scaling. Interestingly, the statistical relationships between limb morphologies and ecotype were lost when accounting for phylogenetic relationships among species under Brownian motion. That assuming Brownian motion confounded these relationships is not surprising considering squirrel ecotypes are phylogenetically clustered; our results suggest that humeral and femoral variation partitioned early between clades and their ecomorphologies were maintained to the present. Overall, our results show how mechanical constraints, locomotor ecology, and evolutionary history may enact different pressures on the shape and structure of limb bones in mammals.
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Affiliation(s)
| | | | - T J Linden
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
| | - S E Santana
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
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41
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Wilson LAB, López-Aguirre C, Archer M, Hand SJ, Flores D, Abdala F, Giannini NP. Patterns of ontogenetic evolution across extant marsupials reflect different allometric pathways to ecomorphological diversity. Nat Commun 2023; 14:2689. [PMID: 37164950 PMCID: PMC10172307 DOI: 10.1038/s41467-023-38365-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
The relatively high level of morphological diversity in Australasian marsupials compared to that observed among American marsupials remains poorly understood. We undertake a comprehensive macroevolutionary analysis of ontogenetic allometry of American and Australasian marsupials to examine whether the contrasting levels of morphological diversity in these groups are reflected in their patterns of allometric evolution. We collate ontogenetic series for 62 species and 18 families of marsupials (n = 2091 specimens), spanning across extant marsupial diversity. Our results demonstrate significant lability of ontogenetic allometric trajectories among American and Australasian marsupials, yet a phylogenetically structured pattern of allometric evolution is preserved. Here we show that species diverging more than 65 million years ago converge in their patterns of ontogenetic allometry under animalivorous and herbivorous diets, and that Australasian marsupials do not show significantly greater variation in patterns of ontogenetic allometry than their American counterparts, despite displaying greater magnitudes of extant ecomorphological diversity.
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Affiliation(s)
- Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 2600, Australia.
- Earth & Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Camilo López-Aguirre
- Department of Anthropology, University of Toronto Scarborough, Toronto, ON, Canada
| | - Michael Archer
- Earth & Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Suzanne J Hand
- Earth & Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - David Flores
- Unidad Ejecutora Lillo (Consejo Nacional de Investigaciones Científicas y Técnicas-Fundación Miguel Lillo). Instituto de Vertebrados, Fundación Miguel Lillo. Miguel Lillo 251, CP 4000, Tucumán, Argentina
| | - Fernando Abdala
- Unidad Ejecutora Lillo (Consejo Nacional de Investigaciones Científicas y Técnicas-Fundación Miguel Lillo), Miguel Lillo 251, CP4000, Tucumán, Argentina
| | - Norberto P Giannini
- Unidad Ejecutora Lillo (Consejo Nacional de Investigaciones Científicas y Técnicas-Fundación Miguel Lillo), Miguel Lillo 251, CP4000, Tucumán, Argentina
- Cátedra de Biogeografía, Universidad Nacional de Tucumán, Tucumán, Argentina
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42
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López-Romero FA, Stumpf S, Kamminga P, Böhmer C, Pradel A, Brazeau MD, Kriwet J. Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification. Commun Biol 2023; 6:496. [PMID: 37156994 PMCID: PMC10167336 DOI: 10.1038/s42003-023-04882-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.
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Affiliation(s)
- Faviel A López-Romero
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria.
- University of Vienna, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, 1030, Vienna, Austria.
| | - Sebastian Stumpf
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria
| | - Pepijn Kamminga
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Christine Böhmer
- MECADEV UMR 7179 CNRS/MNHN, Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, CP 55, 57 rue Cuvier, 75231, Paris, France
- Department für Geo- und Umweltwissenschaften und GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333, München, Germany
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Alan Pradel
- CR2P, Centre de Recherche en Paléontologie - Paris, Muséum National d'Histoire Naturelle-Sorbonne Université-CNRS, CP 38, 57 rue Cuvier, F75231, Paris, Cedex 05, France
| | - Martin D Brazeau
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, London, UK
- The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jürgen Kriwet
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria
- University of Vienna, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, 1030, Vienna, Austria
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43
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Schwartz E, Nenning KH, Heuer K, Jeffery N, Bertrand OC, Toro R, Kasprian G, Prayer D, Langs G. Evolution of cortical geometry and its link to function, behaviour and ecology. Nat Commun 2023; 14:2252. [PMID: 37080952 PMCID: PMC10119184 DOI: 10.1038/s41467-023-37574-x] [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: 03/14/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Studies in comparative neuroanatomy and of the fossil record demonstrate the influence of socio-ecological niches on the morphology of the cerebral cortex, but have led to oftentimes conflicting theories about its evolution. Here, we study the relationship between the shape of the cerebral cortex and the topography of its function. We establish a joint geometric representation of the cerebral cortices of ninety species of extant Euarchontoglires, including commonly used experimental model organisms. We show that variability in surface geometry relates to species' ecology and behaviour, independent of overall brain size. Notably, ancestral shape reconstruction of the cortical surface and its change during evolution enables us to trace the evolutionary history of localised cortical expansions, modal segregation of brain function, and their association to behaviour and cognition. We find that individual cortical regions follow different sequences of area increase during evolutionary adaptations to dynamic socio-ecological niches. Anatomical correlates of this sequence of events are still observable in extant species, and relate to their current behaviour and ecology. We decompose the deep evolutionary history of the shape of the human cortical surface into spatially and temporally conscribed components with highly interpretable functional associations, highlighting the importance of considering the evolutionary history of cortical regions when studying their anatomy and function.
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Affiliation(s)
- Ernst Schwartz
- Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab, Medical University of Vienna, Vienna, Austria
| | - Karl-Heinz Nenning
- Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab, Medical University of Vienna, Vienna, Austria
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute, Orangeburg, NY, USA
| | - Katja Heuer
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015, Paris, France
| | - Nathan Jeffery
- Institute of Life Course & Medical Sciences, University of Liverpool, Liverpool, England
| | - Ornella C Bertrand
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona Edifici ICTA-ICP, c/ Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès., Barcelona, Spain
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, Scotland, EH9 3FE, United Kingdom
| | - Roberto Toro
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015, Paris, France
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab, Medical University of Vienna, Vienna, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab, Medical University of Vienna, Vienna, Austria
| | - Georg Langs
- Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab, Medical University of Vienna, Vienna, Austria.
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Zelditch ML, Swiderski DL. Effects of Procrustes Superimposition and Semilandmark Sliding on Modularity and Integration: An Investigation Using Simulations of Biological Data. Evol Biol 2023. [DOI: 10.1007/s11692-023-09600-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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45
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Rhoda DP, Haber A, Angielczyk KD. Diversification of the ruminant skull along an evolutionary line of least resistance. SCIENCE ADVANCES 2023; 9:eade8929. [PMID: 36857459 PMCID: PMC9977183 DOI: 10.1126/sciadv.ade8929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/30/2023] [Indexed: 05/28/2023]
Abstract
Clarifying how microevolutionary processes scale to macroevolutionary patterns is a fundamental goal in evolutionary biology, but these analyses, requiring comparative datasets of population-level variation, are limited. By analyzing a previously published dataset of 2859 ruminant crania, we find that variation within and between ruminant species is biased by a highly conserved mammalian-wide allometric pattern, CREA (craniofacial evolutionary allometry), where larger species have proportionally longer faces. Species with higher morphological integration and species more biased toward CREA have diverged farther from their ancestors, and Ruminantia as a clade diversified farther than expected in the direction of CREA. Our analyses indicate that CREA acts as an evolutionary "line of least resistance" and facilitates morphological diversification due to its alignment with the browser-grazer continuum. Together, our results demonstrate that constraints at the population level can produce highly directional patterns of phenotypic evolution at the macroevolutionary scale. Further research is needed to explore how CREA has been exploited in other mammalian clades.
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Affiliation(s)
- Daniel P. Rhoda
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Chicago, IL 60637, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S. DuSable Lake Shore Dr., Chicago, IL 60605, USA
| | - Annat Haber
- The Jackson Laboratory, Farmington, CT 06032, USA
| | - Kenneth D. Angielczyk
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Chicago, IL 60637, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S. DuSable Lake Shore Dr., Chicago, IL 60605, USA
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46
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Mathou A, Bonnet X, Daoues K, Ksas R, Herrel A. Evolutionary convergence of muscle architecture in relation to locomotor ecology in snakes. J Anat 2023; 242:862-871. [PMID: 36732067 PMCID: PMC10093152 DOI: 10.1111/joa.13823] [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: 08/24/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 02/04/2023] Open
Abstract
The epaxial muscles in snakes are responsible for locomotion and as such can be expected to show adaptations in species living in different environments. Here, we tested whether the structural units that comprise the superficial epaxial muscles (semispinalis-spinalis, SSP; longissimus dorsi, LD; iliocostalis, IC) were different in animals occupying similar habitats. To do so, we analyzed and compared the muscle architecture (mass, fiber length, and physiological cross-sectional area) of the superficial epaxial muscle segments in snakes that differ in their habitat use (e.g., arboreal, terrestrial, and aquatic). Our results showed that arboreal species have on average longer muscles and tendons spanning more segments likely important during gap bridging. Moreover, aquatic snakes show relatively heavier semispinalis-spinalis muscles with a greater cross-sectional area. The longissimus dorsi muscles also showed a greater cross-sectional area compared with terrestrial and especially arboreal snakes. Whereas the more strongly developed muscles in aquatic snakes are likely associated with the dense and viscous environment through which they move, the lighter muscles in arboreal snakes may provide an advantage when climbing. Future studies comparing other ecologies (e.g., burrowing snakes) and additional muscle units (e.g., multifidus; hypaxial muscles) are needed to better understand the structural features driving variation in locomotor performance and efficiency in snakes.
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Affiliation(s)
- Adrien Mathou
- Département Adaptations du Vivant, Bâtiment d'Anatomie Comparée, UMR 7179 C.N.R.S/M.N.H.N., Paris, France
| | - Xavier Bonnet
- CEBC, UMR-7372, CNRS-Université de La Rochelle, Villiers en Bois, France
| | | | - Rémi Ksas
- Venomworld, Saint-Thibault-des-vignes, France
| | - Anthony Herrel
- Département Adaptations du Vivant, Bâtiment d'Anatomie Comparée, UMR 7179 C.N.R.S/M.N.H.N., Paris, France
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47
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Rothier PS, Fabre AC, Clavel J, Benson RBJ, Herrel A. Mammalian forelimb evolution is driven by uneven proximal-to-distal morphological diversity. eLife 2023; 12:81492. [PMID: 36700542 PMCID: PMC9908075 DOI: 10.7554/elife.81492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
Vertebrate limb morphology often reflects the environment due to variation in locomotor requirements. However, proximal and distal limb segments may evolve differently from one another, reflecting an anatomical gradient of functional specialization that has been suggested to be impacted by the timing of development. Here, we explore whether the temporal sequence of bone condensation predicts variation in the capacity of evolution to generate morphological diversity in proximal and distal forelimb segments across more than 600 species of mammals. Distal elements not only exhibit greater shape diversity, but also show stronger within-element integration and, on average, faster evolutionary responses than intermediate and upper limb segments. Results are consistent with the hypothesis that late developing distal bones display greater morphological variation than more proximal limb elements. However, the higher integration observed within the autopod deviates from such developmental predictions, suggesting that functional specialization plays an important role in driving within-element covariation. Proximal and distal limb segments also show different macroevolutionary patterns, albeit not showing a perfect proximo-distal gradient. The high disparity of the mammalian autopod, reported here, is consistent with the higher potential of development to generate variation in more distal limb structures, as well as functional specialization of the distal elements.
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Affiliation(s)
- Priscila S Rothier
- Département Adaptations du Vivant, Muséum National d'Histoire NaturelleParisFrance
| | - Anne-Claire Fabre
- Naturhistorisches Museum BernBernSwitzerland
- Institute of Ecology and Evolution, University of BernBernSwitzerland
- Life Sciences Department, Vertebrates Division, Natural History MuseumLondonUnited Kingdom
| | - Julien Clavel
- Life Sciences Department, Vertebrates Division, Natural History MuseumLondonUnited Kingdom
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023VilleurbanneFrance
| | - Roger BJ Benson
- Department of Earth Sciences, University of OxfordOxfordUnited Kingdom
| | - Anthony Herrel
- Département Adaptations du Vivant, Muséum National d'Histoire NaturelleParisFrance
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48
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Bai K, Zhou X, Lv S, Wei S, Deng L, Tan Y. Biogeochemical niche conservatism relates to plant species diversification and life form evolution in a subtropical montane evergreen broad‐leaved forest. Ecol Evol 2022; 12:e9587. [DOI: 10.1002/ece3.9587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/05/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Kundong Bai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education Guiling China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Guangxi Normal University Guiling China
- Guangxi Lijiangyuan Forest Ecosystem Research Station Nanning China
| | - Xuewen Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education Guiling China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Guangxi Normal University Guiling China
| | - Shihong Lv
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Institute of Botany Guiling China
| | - Shiguang Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education Guiling China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Guangxi Normal University Guiling China
| | - Lili Deng
- Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Institute of Botany Guiling China
| | - Yibo Tan
- Xing'an Guilin Lijiangyuan Forest Ecosystem Observation and Research Station of Guangxi Nanning China
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49
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Law CJ, Blackwell EA, Curtis AA, Dickinson E, Hartstone-Rose A, Santana SE. Decoupled evolution of the cranium and mandible in carnivoran mammals. Evolution 2022; 76:2959-2974. [PMID: 35875871 DOI: 10.1111/evo.14578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/06/2022] [Accepted: 06/17/2022] [Indexed: 01/22/2023]
Abstract
The relationship between skull morphology and diet is a prime example of adaptive evolution. In mammals, the skull consists of the cranium and the mandible. Although the mandible is expected to evolve more directly in response to dietary changes, dietary regimes may have less influence on the cranium because additional sensory and brain-protection functions may impose constraints on its morphological evolution. Here, we tested this hypothesis by comparing the evolutionary patterns of cranium and mandible shape and size across 100+ species of carnivoran mammals with distinct feeding ecologies. Our results show decoupled modes of evolution in cranial and mandibular shape; cranial shape follows clade-based evolutionary shifts, whereas mandibular shape evolution is linked to broad dietary regimes. These results are consistent with previous hypotheses regarding hierarchical morphological evolution in carnivorans and greater evolutionary lability of the mandible with respect to diet. Furthermore, in hypercarnivores, the evolution of both cranial and mandibular size is associated with relative prey size. This demonstrates that dietary diversity can be loosely structured by craniomandibular size within some guilds. Our results suggest that mammal skull morphological evolution is shaped by mechanisms beyond dietary adaptation alone.
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Affiliation(s)
- Chris J Law
- Department of Integrative Biology, University of Texas, Austin, Texas, 78712.,Department of Biology, University of Washington, Seattle, Washington, 98105.,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98105.,Richard Gilder Graduate School, American Museum of Natural History, New York, New York, 10024.,Department of Mammalogy, American Museum of Natural History, New York, New York, 10024.,Division of Paleontology, American Museum of Natural History, New York, New York, 10024
| | - Emily A Blackwell
- Richard Gilder Graduate School, American Museum of Natural History, New York, New York, 10024.,Department of Mammalogy, American Museum of Natural History, New York, New York, 10024.,Division of Paleontology, American Museum of Natural History, New York, New York, 10024.,Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063
| | - Abigail A Curtis
- Department of Biology, University of Washington, Seattle, Washington, 98105.,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98105
| | - Edwin Dickinson
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695.,Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, New York, New York, 11545
| | - Adam Hartstone-Rose
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695
| | - Sharlene E Santana
- Department of Biology, University of Washington, Seattle, Washington, 98105.,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98105
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50
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Fertilization mode differentially impacts the evolution of vertebrate sperm components. Nat Commun 2022; 13:6809. [PMID: 36357384 PMCID: PMC9649735 DOI: 10.1038/s41467-022-34609-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/31/2022] [Indexed: 11/12/2022] Open
Abstract
Environmental change frequently drives morphological diversification, including at the cellular level. Transitions in the environment where fertilization occurs (i.e., fertilization mode) are hypothesized to be a driver of the extreme diversity in sperm morphology observed in animals. Yet how fertilization mode impacts the evolution of sperm components-head, midpiece, and flagellum-each with different functional roles that must act as an integrated unit remains unclear. Here, we test this hypothesis by examining the evolution of sperm component lengths across 1103 species of vertebrates varying in fertilization mode (external vs. internal fertilization). Sperm component length is explained in part by fertilization mode across vertebrates, but how fertilization mode influences sperm evolution varies among sperm components and vertebrate clades. We also identify evolutionary responses not influenced by fertilization mode: midpieces evolve rapidly in both external and internal fertilizers. Fertilization mode thus influences vertebrate sperm evolution through complex component- and clade-specific evolutionary responses.
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