1
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Li F, Wang W, Cheng H, Li M. Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp ( Opsariichthys bidens). Comput Struct Biotechnol J 2024; 23:2465-2477. [PMID: 38882676 PMCID: PMC11179538 DOI: 10.1016/j.csbj.2024.05.048] [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: 03/07/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
Variations in molecular evolutionary rate have been widely investigated among lineages and genes. However, it remains an open question whether fast rate of molecular evolution is driven by natural selection or random drift, and how the fast rate is linked to metabolic rate. Additionally, previous studies on fast molecular evolution have been largely restricted to concatenated matrix of genes or a few specifically selected genes, but less is known for individual genes at the genome-wide level. Here we addressed these questions using more than 5000 single-copy orthologous (SCO) genes through comparative genomic and phylogenetic analyses among fishes, with a special focus on a newly-sequenced clupeocephalan fish the Chinese hook snout carp Opsariichthys bidens. We showed O. bidens displays significantly higher mean substitution rate and more fast-evolving SCO genes (2172 genes) than most fishes studied here. The rapidly evolving genes are enriched in highly conserved and very basic functions such as translation and ribosome that are critical for biological fitness. We further revealed that ∼25 % of these fast-evolving genes exhibit a constant increase of substitution rate from the common ancestor down to the present, suggesting a neglected but important contribution from ancestral states. Model fitting showed that ∼85 % of fast-evolving genes exclusive to O. bidens and related species follow the adaptive evolutionary model rather than random-drift model, and 7.6 % of fast-evolving genes identified in O. bidens have experienced positive selection, both indicating the reflection of adaptive selection. Finally, metabolic rate was observed to be linked with substitution rate in a gene-specific manner. Overall, our findings reveal fast molecular evolution of SCO genes at genome-wide level in O. bidens, and uncover the evolutionary and ecological contributors to it.
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Affiliation(s)
- Fengbo Li
- Zhejiang Institute of Freshwater Fisheries, 999 Hangchangqiao South Road, Huzhou 313001, China
| | - Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Beijing 100101, China
| | - Haihua Cheng
- Zhejiang Institute of Freshwater Fisheries, 999 Hangchangqiao South Road, Huzhou 313001, China
| | - Ming Li
- Jinhua Fisheries Technology Extension Center, 828 Shuanglong South Street, Jinhua 321013, China
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2
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Fresneau N, Pipoly I, Gigler D, Kosztolányi A, Székely T, Liker A. The evolution of sex roles: The importance of ecology and social environment. Proc Natl Acad Sci U S A 2024; 121:e2321294121. [PMID: 38771872 PMCID: PMC11145285 DOI: 10.1073/pnas.2321294121] [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: 12/04/2023] [Accepted: 03/27/2024] [Indexed: 05/23/2024] Open
Abstract
Males and females often have different roles in reproduction, although the origin of these differences has remained controversial. Explaining the enigmatic reversed sex roles where males sacrifice their mating potential and provide full parental care is a particularly long-standing challenge in evolutionary biology. While most studies focused on ecological factors as the drivers of sex roles, recent research highlights the significance of social factors such as the adult sex ratio. To disentangle these propositions, here, we investigate the additive and interactive effects of several ecological and social factors on sex role variation using shorebirds (sandpipers, plovers, and allies) as model organisms that provide the full spectrum of sex role variation including some of the best-known examples of sex-role reversal. Our results consistently show that social factors play a prominent role in driving sex roles. Importantly, we show that reversed sex roles are associated with both male-skewed adult sex ratios and high breeding densities. Furthermore, phylogenetic path analyses provide general support for sex ratios driving sex role variations rather than being a consequence of sex roles. Together, these important results open future research directions by showing that different mating opportunities of males and females play a major role in generating the evolutionary diversity of sex roles, mating system, and parental care.
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Affiliation(s)
- Nolwenn Fresneau
- Evolutionary Ecology Research Group, Hungarian Research Network-University of Pannonia, Veszprém8200, Hungary
- Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém8200, Hungary
| | - Ivett Pipoly
- Evolutionary Ecology Research Group, Hungarian Research Network-University of Pannonia, Veszprém8200, Hungary
- Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém8200, Hungary
| | - Dóra Gigler
- World Wide Fund (WWF) for Nature Hungary Foundation, Budapest1141, Hungary
| | - András Kosztolányi
- Department of Zoology, University of Veterinary Medicine, Budapest1077, Hungary
| | - Tamás Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, BathBA2 7AZ, United Kingdom
- Reproductive Strategies Research Group, Department of Evolutionary Zoology, Hungarian Research Network - University of Debrecen, Debrecen4032, Hungary
- Debrecen Biodiversity Centre, University of Debrecen, Debrecen4032, Hungary
| | - András Liker
- Evolutionary Ecology Research Group, Hungarian Research Network-University of Pannonia, Veszprém8200, Hungary
- Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém8200, Hungary
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3
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Bravo C, Bautista-Sopelana LM, Alonso JC. Revisiting niche divergence hypothesis in sexually dimorphic birds: Is diet overlap correlated with sexual size dimorphism? J Anim Ecol 2024; 93:460-474. [PMID: 38462717 DOI: 10.1111/1365-2656.14058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/04/2024] [Indexed: 03/12/2024]
Abstract
The evolution of sexual size dimorphism (SSD) is a long-standing topic in evolutionary biology, but there is little agreement on the extent to which SSD is driven by the different selective forces. While sexual selection and fecundity selection have traditionally been proposed as the two leading hypotheses, SSD may also result from natural selection through mechanisms such as sexual niche divergence, which might have reduced resource competition between sexes. Here, we revisited the niche divergence hypothesis by testing the relationship between the sexual overlap in diet and SSD of 56 bird species using phylogenetic comparative analyses. We then assessed how SSD variation relates to the three main hypotheses: sexual selection, fecundity selection, and sexual niche divergence using phylogenetic generalized least squares (PGLS). Then, we compared sexual selection, fecundity selection and niche divergence selection as SSD drivers through phylogenetic confirmatory path analyses to disentangle the possible causal evolutionary relationships between SSD and the three hypotheses. Phylogenetic generalized least squares showed that SSD was negatively correlated with diet overlap, that is, the greater the difference in body size between males and females, the less diet overlap. As predicted by sexual selection theory, the difference in body size between sexes was higher in polygynous species. Confirmatory phylogenetic path analyses suggested that the most likely evolutionary path might include the mating system as a main driver in SSD and niche divergence as a result of SSD. We found no evidence of a role of fecundity selection in the evolution of female-biased SSD. Our study provides evidence that sexual selection has likely been the main cause of SSD and that dietary divergence is likely an indirect effect of SSD.
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Affiliation(s)
- Carolina Bravo
- Instituto de Investigación en Recursos Cinegéticos (IREC)-(CSIC-UCLM-JCCM), Ciudad Real, Spain
| | | | - Juan Carlos Alonso
- Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales (MNCN), CSIC, Madrid, Spain
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4
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Thorson JT, Maureaud AA, Frelat R, Mérigot B, Bigman JS, Friedman ST, Palomares MLD, Pinsky ML, Price SA, Wainwright P. Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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5
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Experimental evidence in a poison frog model suggests that tadpole transport on the dorsum may affects warning signal effectiveness in poison frogs. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Skeels A, Bach W, Hagen O, Jetz W, Pellissier L. Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations. Syst Biol 2022:6637530. [PMID: 35809070 DOI: 10.1093/sysbio/syac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/21/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - W Bach
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - O Hagen
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.,Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
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7
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Jeckel AM, Bolton SK, Waters KR, Antoniazzi MM, Jared C, Matsumura K, Nishikawa K, Morimoto Y, Grant T, Saporito RA. Dose-dependent alkaloid sequestration and N-methylation of decahydroquinoline in poison frogs. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2022; 337:537-546. [PMID: 35201668 DOI: 10.1002/jez.2587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/22/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Sequestration of chemical defenses from dietary sources is dependent on the availability of compounds in the environment and the mechanism of sequestration. Previous experiments have shown that sequestration efficiency varies among alkaloids in poison frogs, but little is known about the underlying mechanism. The aim of this study was to quantify the extent to which alkaloid sequestration and modification are dependent on alkaloid availability and/or sequestration mechanism. To do this, we administered different doses of histrionicotoxin (HTX) 235A and decahydroquinoline (DHQ) to captive-bred Adelphobates galactonotus and measured alkaloid quantity in muscle, kidney, liver, and feces. HTX 235A and DHQ were detected in all organs, whereas only DHQ was present in trace amounts in feces. For both liver and skin, the quantity of alkaloid accumulated increased at higher doses for both alkaloids. Accumulation efficiency in the skin increased at higher doses for HTX 235A but remained constant for DHQ. In contrast, the efficiency of HTX 235A accumulation in the liver was inversely related to dose and a similar, albeit statistically nonsignificant, pattern was observed for DHQ. We identified and quantified the N-methylation of DHQ in A. galactonotus, which represents a previously unknown example of alkaloid modification in poison frogs. Our study suggests that variation in alkaloid composition among individuals and species can result from differences in sequestration efficiency related to the type and amount of alkaloids available in the environment.
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Affiliation(s)
- Adriana M Jeckel
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Sarah K Bolton
- Department of Biology, Notre Dame College, South Euclid, Ohio, USA
| | - Katherine R Waters
- Department of Biology, John Carroll University, University Heights, Ohio, USA
| | - Marta M Antoniazzi
- Structural Biology Lab, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Carlos Jared
- Structural Biology Lab, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Kunihiro Matsumura
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Keisuke Nishikawa
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Yoshiki Morimoto
- Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Taran Grant
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ralph A Saporito
- Department of Biology, John Carroll University, University Heights, Ohio, USA
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8
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Song Z, Liker A, Liu Y, Székely T. Evolution of social organization: phylogenetic analyses of ecology and sexual selection in weavers. Am Nat 2022; 200:250-263. [DOI: 10.1086/720270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Ivan J, Moritz C, Potter S, Bragg J, Turakulov R, Hua X. Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks. Evolution 2022; 76:252-261. [PMID: 34486736 DOI: 10.1111/evo.14342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/12/2021] [Accepted: 08/15/2021] [Indexed: 01/21/2023]
Abstract
Temperature differences over time and space have been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs from the Eugongylinae subfamily using regression analyses. Temperature is the strongest, positively correlated predictor of variation in substitution rate across the Australian Eugongylinae. It explains 45% of variation in synonymous substitution rate, and 11% after controlling for all the other factors. Synonymous substitution rate is also negatively associated with body size, with a 6% variation explained by body size after controlling for the effects of temperature. Other factors are not associated with synonymous substitution rate after controlling for temperature. Overall, this study points to temperature as a strong predictor of the molecular evolution rate in the Eugongylinae subfamily, and demonstrates the power of large-scale exonic data to identify correlates of the rate of molecular evolution.
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Affiliation(s)
- Jeremias Ivan
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jason Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Rust Turakulov
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, United States
| | - Xia Hua
- Mathematical Sciences Institute, Australian National University, Canberra, Australian Capital Territory, Australia
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10
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Liker A, Bókony V, Pipoly I, Lemaître JF, Gaillard JM, Székely T, Freckleton RP. Evolution of large males is associated with female-skewed adult sex ratios in amniotes. Evolution 2021; 75:1636-1649. [PMID: 34021590 DOI: 10.1111/evo.14273] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/30/2022]
Abstract
Body size often differs between the sexes (leading to sexual size dimorphism, SSD), as a consequence of differential responses by males and females to selection pressures. Adult sex ratio (ASR, the proportion of males in the adult population) should influence SSD because ASR relates to both the number of competitors and available mates, which shape the intensity of mating competition and thereby promotes SSD evolution. However, whether ASR correlates with SSD variation among species has not been yet tested across a broad range of taxa. Using phylogenetic comparative analyses of 462 amniotes (i.e., reptiles, birds, and mammals), we fill this knowledge gap by showing that male bias in SSD increases with increasingly female-skewed ASRs in both mammals and birds. This relationship is not explained by the higher mortality of the larger sex because SSD is not associated with sex differences in either juvenile or adult mortality. Phylogenetic path analysis indicates that higher mortality in one sex leads to skewed ASR, which in turn may generate selection for SSD biased toward the rare sex. Taken together, our findings provide evidence that skewed ASRs in amniote populations can result in the rarer sex evolving large size to capitalize on enhanced mating opportunities.
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Affiliation(s)
- András Liker
- MTA-PE Evolutionary Ecology Research Group, University of Pannonia, Veszprém, H-8210, Hungary.,Behavioral Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém, H-8210, Hungary
| | - Veronika Bókony
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, H-1022, Hungary
| | - Ivett Pipoly
- MTA-PE Evolutionary Ecology Research Group, University of Pannonia, Veszprém, H-8210, Hungary.,Behavioral Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém, H-8210, Hungary
| | - Jean-Francois Lemaître
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, F-69622, France
| | - Jean-Michel Gaillard
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, F-69622, France
| | - Tamás Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom.,Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Robert P Freckleton
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, S10 2TN, United Kingdom
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11
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Szemán K, Liker A, Székely T. Social organization in ungulates: Revisiting Jarman's hypotheses. J Evol Biol 2021; 34:604-613. [PMID: 33706412 DOI: 10.1111/jeb.13782] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022]
Abstract
Ungulates (antelopes, deer and relatives) have some of the most diverse social systems among mammals. To understand the evolution of ungulate social organization, Jarman (1974) proposed an ecological scenario of how distribution of resources, habitat and feeding style may have influenced social organization. Although Jarman's scenario makes intuitive sense and remains a textbook example of social evolution, it has not been scrutinized using modern phylogenetic comparative methods. Here we use 230 ungulate species from ten families to test Jarman's hypotheses using phylogenetic analyses. Consistent with Jarman's proposition, both habitat and feeding style predict group size, since grazing ungulates typically live in open habitats and form large herds. Group size, in turn, has a knock-on effect on mating systems and sexual size dimorphism, since ungulates that live in large herds exhibit polygamy and extensive sexual size dimorphism. Phylogenetic confirmatory path analyses suggest that evolutionary changes in habitat type, feeding style and body size directly (or indirectly) induce shifts in social organization. Taken together, these phylogenetic comparative analyses confirm Jarman's conjectures, although they also uncover novel relationships between ecology and social organization. Further studies are needed to explore the relevance of Jarman (1974) scenario for mammals beyond ungulates.
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Affiliation(s)
- Karola Szemán
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
| | - András Liker
- MTA-PE Evolutionary Ecology Research Group, University of Pannonia, Veszprém, Hungary.,Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém, Hungary
| | - Tamás Székely
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary.,Milner Centre for Evolution, University of Bath, Bath, UK
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12
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Mortz M, Levivier A, Lartillot N, Dufresne F, Blier PU. Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates. Front Mol Biosci 2021; 8:626042. [PMID: 33791336 PMCID: PMC8005583 DOI: 10.3389/fmolb.2021.626042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/28/2021] [Indexed: 01/21/2023] Open
Abstract
Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1–2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates.
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Affiliation(s)
- Mathieu Mortz
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Aurore Levivier
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Nicolas Lartillot
- Laboratoire De Biométrie et Biologie Evolutive, UMR CNRS, Université Lyon 1, Villeurbanne, France
| | - France Dufresne
- Laboratoire D'écologie Moléculaire, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada.,Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Pierre U Blier
- Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
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13
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May JA, Feng Z, Orton MG, Adamowicz SJ. The Effects of Ecological Traits on the Rate of Molecular Evolution in Ray-Finned Fishes: A Multivariable Approach. J Mol Evol 2020; 88:689-702. [PMID: 33009923 DOI: 10.1007/s00239-020-09967-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 09/22/2020] [Indexed: 11/25/2022]
Abstract
Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.
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Affiliation(s)
- Jacqueline A May
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Matthew G Orton
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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14
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Shafir A, Azouri D, Goldberg EE, Mayrose I. Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates. Evolution 2020; 74:1620-1639. [PMID: 32510165 DOI: 10.1111/evo.14036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/17/2020] [Indexed: 12/01/2022]
Abstract
As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel.,School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | | | - Itay Mayrose
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
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15
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Ancona S, Liker A, Carmona‐Isunza MC, Székely T. Sex differences in age-to-maturation relate to sexual selection and adult sex ratios in birds. Evol Lett 2020; 4:44-53. [PMID: 32055410 PMCID: PMC7006465 DOI: 10.1002/evl3.156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 11/26/2022] Open
Abstract
Maturation (the age when organisms are physiologically capable of breeding) is one of the major life history traits that have pervasive implications for reproductive strategies, fitness, and population growth. Sex differences in maturation are common in nature, although the causes of such differences are not understood. Fisher and Lack proposed that delayed maturation in males is expected when males are under intense sexual selection, but their proposition has never been tested across a wide range of taxa. By using phylogenetic comparative analyses and the most comprehensive dataset to date, including 201 species from 59 avian families, we show that intense sexual selection on males (as indicated by polygamous mating and male-skewed sexual size dimorphism) correlates with delayed maturation. We also show that the adult sex ratio (ASR), an indicator of the social environment, is associated with sex-specific maturation because in species with a female-skewed ASR, males experience later maturation. Phylogenetic path analyses suggest that adult sex ratio drives interspecific changes in the intensity of sexual selection which, in turn, influences maturation. These results are robust to alternative phylogenetic hypotheses and to potential life-history confounds, and they provide the first comprehensive support of Fisher's and Lack's propositions. Importantly, our work suggests that both social environment and mate competition influence the evolution of a major life history trait, maturation.
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Affiliation(s)
- Sergio Ancona
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
| | - András Liker
- MTA‐PE Evolutionary Ecology Research GroupUniversity of PannoniaPO Box 158Veszprém8201Hungary
- Department of LimnologyUniversity of PannoniaPO Box 158Veszprém8201Hungary
| | - M. Cristina Carmona‐Isunza
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
| | - Tamás Székely
- Milner Centre for Evolution, Department of Biology & BiochemistryUniversity of BathBathBA2 7AYUK
- Department of Evolutionary Zoology and Human BiologyUniversity of DebrecenH‐4010DebrecenEgyetem tér 1Hungary
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16
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Sanchez E, Rodríguez A, Grau JH, Lötters S, Künzel S, Saporito RA, Ringler E, Schulz S, Wollenberg Valero KC, Vences M. Transcriptomic Signatures of Experimental Alkaloid Consumption in a Poison Frog. Genes (Basel) 2019; 10:genes10100733. [PMID: 31546679 PMCID: PMC6827147 DOI: 10.3390/genes10100733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/14/2019] [Accepted: 09/17/2019] [Indexed: 01/19/2023] Open
Abstract
In the anuran family Dendrobatidae, aposematic species obtain their toxic or unpalatable alkaloids from dietary sources, a process known as sequestering. To understand how toxicity evolved in this family, it is paramount to elucidate the pathways of alkaloid processing (absorption, metabolism, and sequestering). Here, we used an exploratory skin gene expression experiment in which captive-bred dendrobatids were fed alkaloids. Most of these experiments were performed with Dendrobates tinctorius, but some trials were performed with D. auratus, D. leucomelas and Allobates femoralis to explore whether other dendrobatids would show similar patterns of gene expression. We found a consistent pattern of up-regulation of genes related to muscle and mitochondrial processes, probably due to the lack of mutations related to alkaloid resistance in these species. Considering conserved pathways of drug metabolism in vertebrates, we hypothesize alkaloid degradation is a physiological mechanism of resistance, which was evidenced by a strong upregulation of the immune system in D. tinctorius, and of complement C2 across the four species sampled. Probably related to this strong immune response, we found several skin keratins downregulated, which might be linked to a reduction of the cornified layer of the epidermis. Although not conclusive, our results offer candidate genes and testable hypotheses to elucidate alkaloid processing in poison frogs.
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Affiliation(s)
- Eugenia Sanchez
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Ariel Rodríguez
- Institut fur Zoologie, Tierärztliche Hochschule Hannover, 30559 Hannover, Germany.
| | - Jose H Grau
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany.
| | - Stefan Lötters
- Biogeography Department, Trier University, 54296 Trier, Germany.
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.
| | - Ralph A Saporito
- Department of Biology, John Carroll University, University Heights, OH 44118, USA.
| | - Eva Ringler
- Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna, and University of Vienna, A-1210 Vienna, Austria.
- Department of Integrative Zoology, University of Vienna, A-1090 Vienna, Austria.
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | | | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
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17
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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18
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Lin G, Huang Z, Wang L, Chen Z, Zhang T, Gillman LN, Zhao F. Evolutionary Rates of Bumblebee Genomes Are Faster at Lower Elevations. Mol Biol Evol 2019; 36:1215-1219. [PMID: 30865278 PMCID: PMC6526908 DOI: 10.1093/molbev/msz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The importance of climate in determining biodiversity patterns has been well documented. However, the relationship between climate and rates of genetic evolution remains controversial. Latitude and elevation have been associated with rates of change in genetic markers such as cytochrome b. What is not known, however, is the strength of such associations and whether patterns found among these genes apply across entire genomes. Here, using bumblebee genetic data from seven subgenera of Bombus, we demonstrate that all species occupying warmer elevations have undergone faster genome-wide evolution than those in the same subgenera occupying cooler elevations. Our findings point to a critical biogeographic role in the relative rates of whole species evolution, potentially influencing global biodiversity patterns.
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Affiliation(s)
- Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhenhua Chen
- Qinghai-CAS Institute of Apicultural Research, Xining, Qinghai, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Lennard N Gillman
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Fang Zhao
- School of Life Sciences, Jinggangshan University, Ji'an, China
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19
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Eliason CM, Clarke JA. Metabolic physiology explains macroevolutionary trends in the melanic colour system across amniotes. Proc Biol Sci 2018; 285:20182014. [PMID: 30963907 PMCID: PMC6304050 DOI: 10.1098/rspb.2018.2014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/21/2018] [Indexed: 11/12/2022] Open
Abstract
Metabolism links organisms to their environment through its effects on thermoregulation, feeding behaviour and energetics. Genes involved in metabolic processes have known pleiotropic effects on some melanic colour traits. Understanding links between physiology and melanic colour is critical for understanding the role of, and potential constraints on, colour production. Despite considerable variation in metabolic rates and presumed ancestral melanic coloration in vertebrates, few studies have looked at a potential relationship between these two systems in a comparative framework. Here, we test the hypothesis that changes in melanosome shape in integumentary structures track metabolic rate variation across amniotes. Using multivariate comparative analyses and incorporating both extant and fossil taxa, we find significantly faster rates of melanosome shape evolution in taxa with high metabolic rates, as well as both colour- and clade-specific differences in the relationship between metabolic rate and melanosome shape. Phylogenetic tests recover an expansion in melanosome morphospace in maniraptoran dinosaurs, as well as rate shifts within birds (in songbirds) and mammals. These findings indicate another core phenotype influenced by metabolic changes in vertebrates. They also provide a framework for testing clade-specific gene expression patterns in the melanocortin system and may improve colour reconstructions in extinct taxa.
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Affiliation(s)
- Chad M. Eliason
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - Julia A. Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
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20
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Orton MG, May JA, Ly W, Lee DJ, Adamowicz SJ. Is molecular evolution faster in the tropics? Heredity (Edinb) 2018; 122:513-524. [PMID: 30202084 PMCID: PMC6461915 DOI: 10.1038/s41437-018-0141-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 11/30/2022] Open
Abstract
The evolutionary speed hypothesis (ESH) suggests that molecular evolutionary rates are higher among species inhabiting warmer environments. Previously, the ESH has been investigated using small numbers of latitudinally-separated sister lineages; in animals, these studies typically focused on subsets of Chordata and yielded mixed support for the ESH. This study analyzed public DNA barcode sequences from the cytochrome c oxidase subunit I (COI) gene for six of the largest animal phyla (Arthropoda, Chordata, Mollusca, Annelida, Echinodermata, and Cnidaria) and paired latitudinally-separated taxa together informatically. Of 8037 lineage pairs, just over half (51.6%) displayed a higher molecular rate in the lineage inhabiting latitudes closer to the equator, while the remainder (48.4%) displayed a higher rate in the higher-latitude lineage. To date, this study represents the most comprehensive analysis of latitude-related molecular rate differences across animals. While a statistically-significant pattern was detected from our large sample size, our findings suggest that the EHS may not serve as a strong universal mechanism underlying the latitudinal diversity gradient and that COI molecular clocks may generally be applied across latitudes. This study also highlights the merits of using automation to analyze large DNA barcode datasets.
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Affiliation(s)
- Matthew G Orton
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,School of Biological Sciences and Applied Chemistry, Seneca College, 1750 Finch Ave E, North York, ON, M2J 2X5, Canada
| | - Jacqueline A May
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Winfield Ly
- School of Biological Sciences and Applied Chemistry, Seneca College, 1750 Finch Ave E, North York, ON, M2J 2X5, Canada
| | - David J Lee
- School of Biological Sciences and Applied Chemistry, Seneca College, 1750 Finch Ave E, North York, ON, M2J 2X5, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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21
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Oliveira BF, São-Pedro VA, Santos-Barrera G, Penone C, Costa GC. AmphiBIO, a global database for amphibian ecological traits. Sci Data 2017; 4:170123. [PMID: 28872632 PMCID: PMC5584397 DOI: 10.1038/sdata.2017.123] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022] Open
Abstract
Current ecological and evolutionary research are increasingly moving from species- to trait-based approaches because traits provide a stronger link to organism's function and fitness. Trait databases covering a large number of species are becoming available, but such data remains scarce for certain groups. Amphibians are among the most diverse vertebrate groups on Earth, and constitute an abundant component of major terrestrial and freshwater ecosystems. They are also facing rapid population declines worldwide, which is likely to affect trait composition in local communities, thereby impacting ecosystem processes and services. In this context, we introduce AmphiBIO, a comprehensive database of natural history traits for amphibians worldwide. The database releases information on 17 traits related to ecology, morphology and reproduction features of amphibians. We compiled data from more than 1,500 literature sources, and for more than 6,500 species of all orders (Anura, Caudata and Gymnophiona), 61 families and 531 genera. This database has the potential to allow unprecedented large-scale analyses in ecology, evolution, and conservation of amphibians.
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Affiliation(s)
- Brunno Freire Oliveira
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Lagoa Nova, Natal, RN 59072-970, Brazil
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611-0430, USA
| | - Vinícius Avelar São-Pedro
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Lagoa Nova, Natal, RN 59072-970, Brazil
| | - Georgina Santos-Barrera
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria 04510, México
| | - Caterina Penone
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Lagoa Nova, Natal, RN 59072-970, Brazil
| | - Gabriel C. Costa
- Department of Biology, Auburn University at Montgomery, Montgomery, AL 36117, USA
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22
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Tarvin RD, Powell EA, Santos JC, Ron SR, Cannatella DC. The birth of aposematism: High phenotypic divergence and low genetic diversity in a young clade of poison frogs. Mol Phylogenet Evol 2017; 109:283-295. [PMID: 28089841 DOI: 10.1016/j.ympev.2016.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/30/2016] [Accepted: 12/28/2016] [Indexed: 01/01/2023]
Abstract
Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence. We found low genetic divergence (2.6% in the 16S gene) despite substantial differences in color and acoustic signals. While chemical defense is inferred to have evolved in the ancestor of Epipedobates, aposematic coloration evolved at least twice or was lost once in Epipedobates, suggesting that it is evolutionarily labile. We inferred at least one event of introgression between two cryptically colored species with adjacent ranges (E. boulengeri and E. machalilla). We also find evidence for peripheral isolation resulting in phenotypic divergence and potential speciation of the aposematic E. tricolor from the non-aposematic E. machalilla. However, we were unable to estimate a well-supported species tree or delimit species using multispecies coalescent models. We attribute this failure to factors associated with recent speciation including mitochondrial introgression, incomplete lineage sorting, and too few informative molecular characters. We suggest that species delimitation within young aposematic lineages such as Epipedobates will require genome-level molecular studies. We caution against relying solely on DNA barcoding for species delimitation or identification and highlight the value of phenotypic divergence and natural history in delimiting species.
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Affiliation(s)
- Rebecca D Tarvin
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States.
| | - Emily A Powell
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States; Department of Biology, University of Miami, Miami, FL, United States
| | - Juan C Santos
- Department of Biology, Brigham Young University, Provo, UT, United States; Department of Biological Sciences, St. John's University, Queens, NY, United States
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States
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23
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Mohlhenrich ER, Mueller RL. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 2016; 70:2865-2878. [DOI: 10.1111/evo.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/25/2022]
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24
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Fujisawa T, Vogler AP, Barraclough TG. Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles. Proc Biol Sci 2015; 282:20142476. [PMID: 25621335 DOI: 10.1098/rspb.2014.2476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.
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25
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Hua X, Cowman P, Warren D, Bromham L. Longevity Is Linked to Mitochondrial Mutation Rates in Rockfish: A Test Using Poisson Regression. Mol Biol Evol 2015; 32:2633-45. [PMID: 26048547 DOI: 10.1093/molbev/msv137] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: That the rate of mitochondrial mutations is negatively correlated with longevity. Comparative studies face three challenges in detecting correlates of mutation rate: Covariation of mutation rates between species due to ancestry, covariation between life-history traits, and difficulty obtaining accurate estimates of mutation rate. We address these challenges using a novel Poisson regression method to examine the link between mutation rate and lifespan in rockfish (Sebastes). This method has better performance than traditional sister-species comparisons when sister species are too recently diverged to give reliable estimates of mutation rate. Rockfish are an ideal model system: They have long life spans with indeterminate growth and little evidence of senescence, which minimizes the confounding tradeoffs between lifespan and fecundity. We show that lifespan in rockfish is negatively correlated to rate of mitochondrial mutation, but not the rate of nuclear mutation. The life history of rockfish allows us to conclude that this relationship is unlikely to be driven by the tradeoffs between longevity and fecundity, or by the frequency of DNA replications in the germline. Instead, the relationship is compatible with the hypothesis that mutation rates are reduced by selection in long-lived taxa to reduce the chance of mitochondrial damage over its lifespan, consistent with the mitochondrial theory of ageing.
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Affiliation(s)
- Xia Hua
- Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Peter Cowman
- Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia Department of Ecology and Evolutionary Biology, Yale University
| | - Dan Warren
- Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia Department of Biology, Macquarie University, North Ryde, NSW, Australia
| | - Lindell Bromham
- Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
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26
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Rodríguez A, Börner M, Pabijan M, Gehara M, Haddad CFB, Vences M. Genetic divergence in tropical anurans: deeper phylogeographic structure in forest specialists and in topographically complex regions. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9774-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Glazier DS. Is metabolic rate a universal ‘pacemaker’ for biological processes? Biol Rev Camb Philos Soc 2014; 90:377-407. [DOI: 10.1111/brv.12115] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 12/11/2022]
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28
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Scombroid Fishes Provide Novel Insights into the Trait/Rate Associations of Molecular Evolution. J Mol Evol 2014; 78:338-48. [DOI: 10.1007/s00239-014-9621-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 04/19/2014] [Indexed: 12/25/2022]
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29
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Chong RA, Mueller RL. Evolution along the mutation gradient in the dynamic mitochondrial genome of salamanders. Genome Biol Evol 2014; 5:1652-60. [PMID: 23918809 PMCID: PMC3787671 DOI: 10.1093/gbe/evt119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.
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Patterns of Evolutionary Speed: In Search of a Causal Mechanism. DIVERSITY-BASEL 2013. [DOI: 10.3390/d5040811] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Affiliation(s)
- Shane D. Wright
- School of Biological Sciences; University of Auckland; 22 Princes St; Auckland; 1010; New Zealand
| | - Klaus Rohde
- School of Environmental and Rural Sciences; University of New England; Elm Avenue; Armidale; NSW; 2351; Australia
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Taller plants have lower rates of molecular evolution. Nat Commun 2013; 4:1879. [DOI: 10.1038/ncomms2836] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 04/05/2013] [Indexed: 01/20/2023] Open
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Genetic diversity, phylogeny and evolution of alkaloid sequestering in Cuban miniaturized frogs of the Eleutherodactylus limbatus group. Mol Phylogenet Evol 2013; 68:541-54. [PMID: 23665040 DOI: 10.1016/j.ympev.2013.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/02/2013] [Accepted: 04/22/2013] [Indexed: 11/22/2022]
Abstract
The miniaturized frogs of the Eleutherodactylus limbatus group, endemic to Cuba, have recently been shown to contain alkaloids in their skin, representing the fifth independent evolutionary origin of alkaloid sequestering in anurans. Based on a comprehensive sampling of all known species of the group we here assess their range-wide phylogeography using DNA sequences of the mitochondrial cytochrome b and the nuclear Rag-1 gene. We found E. etheridgei, E. cubanus, and E. orientalis to be genetically highly distinct, with uncorrected pair-wise distances >12% in the cytochrome b gene and >5% in the 16S rRNA gene, and without haplotype sharing in the Rag-1 gene. On the contrary, E. iberia, E. jaumei, E. limbatus, and one unnamed lineage from Gran Piedra mountains had lower mitochondrial divergences to each other (<6% in cytochrome b; <3% in 16S) and extensive Rag-1 haplotype sharing, suggesting that their species status requires careful revision. All species and lineages of the group occur in the mountain areas of eastern Cuba and only one of them, E. limbatus, colonized central and western Cuba. Populations of this latter lineage are only weakly genetically differentiated, and its range expansion to western Cuba is probably Pleistocenic, demonstrating that also miniaturized frog species are able of considerable range expansions (over hundreds of kilometers) in short time spans. A phylogeny based on about 5 kb of mitochondrial and nuclear genes places, with maximum support, E. etheridgei basalmost in the group, followed by E. cubanus, E. orientalis, and the E. iberia-jaumei-limbatus clade. The screening of skin alkaloids revealed the presence of alkaloids in all lineages of the group, but alkaloids known to be sequestered by other anurans were not found in the basalmost E. etheridgei. Furthermore, individuals of the derived lineages of the E. iberia-jaumei-limbatus clade had a much larger variety of different alkaloid compounds (3-18) than the other three species (0-4). Traces of alkaloids were found in other species only remotely related to the E. limbatus group, i.e., E. caspari, E. goini, E. ricordii, and E. tetajulia. According to these findings, it can be hypothesized that the capacity to sequester dietary alkaloids into the skin evolved first in an ancestral, litter-dwelling and small-sized Cuban Eleutherodactylus, followed by evolution of miniaturization and diurnality in the early representatives of the E. limbatus group, and eventually by increased brightness of color with probable aposematic function and a highly efficient mechanism of alkaloid sequestering.
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Chong RA, Mueller RL. Low metabolic rates in salamanders are correlated with weak selective constraints on mitochondrial genes. Evolution 2012; 67:894-9. [PMID: 23461338 DOI: 10.1111/j.1558-5646.2012.01830.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondria are the site for the citric acid cycle and oxidative phosphorylation (OXPHOS), the final steps of ATP synthesis via cellular respiration. Each mitochondrion contains its own genome; in vertebrates, this is a small, circular DNA molecule that encodes 13 subunits of the multiprotein OXPHOS electron transport complexes. Vertebrate lineages vary dramatically in metabolic rates; thus, functional constraints on mitochondrial-encoded proteins likely differ, potentially impacting mitochondrial genome evolution. Here, we examine mitochondrial genome evolution in salamanders, which have the lowest metabolic requirements among tetrapods. We show that salamanders experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, we find no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that different aspects of mitochondrial genome evolution (i.e., nucleotide substitution, accumulation of noncoding sequences) are differently affected by metabolic variation across tetrapod lineages.
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Affiliation(s)
- Rebecca A Chong
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523-1878, USA.
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Irisarri I, San Mauro D, Abascal F, Ohler A, Vences M, Zardoya R. The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates. BMC Genomics 2012; 13:626. [PMID: 23153022 PMCID: PMC3551647 DOI: 10.1186/1471-2164-13-626] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/04/2012] [Indexed: 01/20/2023] Open
Abstract
Background Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians. Results We reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia. Conclusions Through the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.
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Affiliation(s)
- Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
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Pabijan M, Wollenberg KC, Vences M. Small body size increases the regional differentiation of populations of tropical mantellid frogs (Anura: Mantellidae). J Evol Biol 2012; 25:2310-24. [DOI: 10.1111/j.1420-9101.2012.02613.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/25/2012] [Accepted: 08/05/2012] [Indexed: 10/27/2022]
Affiliation(s)
| | | | - M. Vences
- Division of Evolutionary Biology; Zoological Institute; Technical University of Braunschweig; Braunschweig; Germany
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Morris Goodman's hominoid rate slowdown: the importance of being neutral. Mol Phylogenet Evol 2012; 66:569-74. [PMID: 22902941 DOI: 10.1016/j.ympev.2012.07.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 07/09/2012] [Accepted: 07/26/2012] [Indexed: 12/30/2022]
Abstract
Half a century ago, when the field of molecular evolution did not even exist, Morris Goodman analyzed profiles of immunological interactions between species and reached the following two remarkable conclusions: first, protein evolution slowed down in the human lineage compared to other primate lineages; second, this slowdown was more pronounced for proteins whose functions were likely to be neutral. It took several decades of research to fully grasp these ideas and document the pattern of hominoid rate slowdown. Along the way, studies of hominoid rate slowdown led to major progresses in understanding determinants of neutral molecular evolution, which in turn is used to calibrate rates of adaptive evolution. Furthermore, the growing knowledge on the origin of mutations provides a basis for understanding differential evolutionary rates between sex chromosomes and autosomes, which has deep implications for inferring human evolutionary histories, and other aspects of molecular evolution. Primate genomics in particular stand to provide critical information in these pursuits, due to the abundance of genomic data, relatively rich documentation of life history traits, and several model systems, including our own species.
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