1
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Miller AH, Stroud JT, Losos JB. The ecology and evolution of key innovations. Trends Ecol Evol 2023; 38:122-131. [PMID: 36220711 DOI: 10.1016/j.tree.2022.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/05/2022]
Abstract
The idea of 'key innovations' has long been influential in theoretical and empirical approaches to understanding adaptive diversification. Despite originally revolving around traits inducing major ecological shifts, the key innovation concept itself has evolved, conflating lineage diversification with trait-dependent ecological shifts. In this opinion article we synthesize the history of the term, clarify the relationship between key innovations and adaptive radiation, and propose a return to the original concept of key innovations: the evolution of organismal features which permit a species to occupy a previously inaccessible ecological state. Ultimately, we suggest an integrative approach to studying key innovations, necessitating experimental approaches of form and function, natural history studies of resource use, and phylogenetic comparative perspectives.
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Affiliation(s)
- Aryeh H Miller
- Department of Biology, Washington University, St Louis, MO, USA.
| | - James T Stroud
- Department of Biology, Washington University, St Louis, MO, USA.
| | - Jonathan B Losos
- Department of Biology, Washington University, St Louis, MO, USA.
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2
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Choi IS, Cardoso D, de Queiroz LP, de Lima HC, Lee C, Ruhlman TA, Jansen RK, Wojciechowski MF. Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics. FRONTIERS IN PLANT SCIENCE 2022; 13:823190. [PMID: 35283880 PMCID: PMC8905342 DOI: 10.3389/fpls.2022.823190] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/31/2022] [Indexed: 05/31/2023]
Abstract
Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
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Affiliation(s)
- In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Luciano P. de Queiroz
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Haroldo C. de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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3
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Bajić D, Rebolleda-Gómez M, Muñoz MM, Sánchez Á. The Macroevolutionary Consequences of Niche Construction in Microbial Metabolism. Front Microbiol 2021; 12:718082. [PMID: 34671327 PMCID: PMC8522508 DOI: 10.3389/fmicb.2021.718082] [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: 05/31/2021] [Accepted: 08/20/2021] [Indexed: 12/01/2022] Open
Abstract
Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g., horizontal gene transfer or de novo evolution of enzymes and pathways. This process is governed by a combination of environmental factors, selective pressures, and the constraints imposed by the genetic architecture of metabolic networks. In addition, many independent results hint that the process of niche construction, by which organisms actively modify their own and each other’s niches and selective pressures, could play a major role in microbial innovation and diversification. Yet, the general principles by which niche construction shapes microbial macroevolutionary patterns remain largely unexplored. Here, we discuss several new hypotheses and directions, and suggest metabolic modeling methods that could allow us to explore large-scale empirical genotype-phenotype-(G-P)-environment spaces in order to study the macroevolutionary effects of niche construction. We hope that this short piece will further stimulate a systematic and quantitative characterization of macroevolutionary patterns and processes in microbial metabolism.
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Affiliation(s)
- Djordje Bajić
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | - María Rebolleda-Gómez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States.,Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States
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4
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Opell BD, Elmore HM, Hendricks ML. Humidity mediated performance and material properties of orb weaving spider adhesive droplets. Acta Biomater 2021; 131:440-451. [PMID: 34144212 DOI: 10.1016/j.actbio.2021.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 12/01/2022]
Abstract
Capture thread glue droplets retain insects that strike an orb web and are key to the success of over 4,600 described spider species. Each droplet is a self-assembling adhesive system whose emergent biomechanical properties are centered on its viscoelastic, protein core. This bioadhesive is dependent on its surrounding hygroscopic aqueous layer for hydration and chemical conditioning. Consequently, a droplet's water content and adhesive performance track environmental humidity. We tested the hypothesis that natural selection has tuned a droplet's adhesive performance and material properties to a species' foraging humidity. At 55% relative humidity (RH) the adhesive properties of 12 species ranged from that of PEG-based hydrogels to that of silicone rubber, exhibiting a 1088-fold inter-specific difference in stiffness (0.02-21.76 MPa) and a 147-fold difference in toughness (0.14-20.51 MJ/m3). When tested over a 70% RH range, droplet extension lengths per protein core volume peaked at lower humidities in species from exposed, low humidity habitats, and at higher humidities in nocturnal species and those found in humid habitats. However, at the RH's where these species' maximum extension per protein volume indices were observed, the stiffness of most species' adhesive did not differ, documenting that selection has tuned elastic modulus by adjusting droplet hygroscopicity. This inverse relationship between droplet hygroscopicity and a species' foraging humidity ensures optimal adhesive stiffness. By characterizing the humidity responsiveness and properties of orb spider glue droplets, our study also profiles the range of its biomimetic potential. STATEMENT OF SIGNIFICANCE: Over 4,600 described species of orb weaving spider rely on tiny glue droplets in their webs to retain insect that the web intercepts. The aqueous layer that covers each droplet's core allows this adhesive to remain pliable and to stretch as an insect struggles to escape. The aqueous solution also attracts water from the air, causing the glue droplet's performance to change with humidity. By characterizing the droplet extensions and adhesive material properties of twelve species at relative humidities between of 20 and 90%, this study examined how this unique adhesive system responds to its environment and how it is tuned to the humidity of a species' habitat.
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Affiliation(s)
- Brent D Opell
- Department of Biological Sciences, Virginia Tech Blacksburg, VA 24061 United States.
| | - Hannah Mae Elmore
- Department of Biological Sciences, Virginia Tech Blacksburg, VA 24061 United States
| | - Mary L Hendricks
- Department of Biological Sciences, Virginia Tech Blacksburg, VA 24061 United States
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5
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Burress ED, Muñoz MM. Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation. Syst Biol 2021; 71:93-104. [PMID: 33956152 DOI: 10.1093/sysbio/syab031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists ('ecomorphs') evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in stimulating diversification. Here, we assess the proposed "island effect" on anole diversification using Bayesian phylogenetic comparative methods that explicitly incorporate rate heterogeneity across the tree and demonstrate two cases of would-be false positives. We discovered that rates of speciation and morphological evolution of island and mainland anoles are equivalent, implying that islands provide no special context for exceptionally rapid diversification. Likewise, rates of evolution were equivalent between island anoles that arose via in situ versus dispersal-based mechanisms, and we found no evidence for island-specific rates of speciation or morphological evolution. Nonetheless, the origin of Anolis is characterized by a speciation pulse that slowed over time - a classic signature of waning ecological opportunity. Our findings cast doubt on the notion that islands catalyzed the anole adaptive radiation and instead point to a key innovation, adhesive toe pads, which facilitated the exploitation of many arboreal niches sparsely utilized by other iguanian lizards. The selective pressures responsible for arboreal niche diversification differ between islands and the mainland, but the tempo of diversification driven by these discordant processes is indistinguishable.
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Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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6
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Abstract
Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing of some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.
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Affiliation(s)
- Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, 5020 Bergen, Norway;
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA;
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7
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Kono N, Nakamura H, Mori M, Tomita M, Arakawa K. Spidroin profiling of cribellate spiders provides insight into the evolution of spider prey capture strategies. Sci Rep 2020; 10:15721. [PMID: 32973264 PMCID: PMC7515903 DOI: 10.1038/s41598-020-72888-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/08/2020] [Indexed: 01/29/2023] Open
Abstract
Orb-weaving spiders have two main methods of prey capture: cribellate spiders use dry, sticky capture threads, and ecribellate spiders use viscid glue droplets. Predation behaviour is a major evolutionary driving force, and it is important on spider phylogeny whether the cribellate and ecribellate spiders each evolved the orb architecture independently or both strategies were derived from an ancient orb web. These hypotheses have been discussed based on behavioural and morphological characteristics, with little discussion on this subject from the perspective of molecular materials of orb web, since there is little information about cribellate spider-associated spidroin genes. Here, we present in detail a spidroin catalogue of six uloborid species of cribellate orb-weaving spiders, including cribellate and pseudoflagelliform spidroins, with transcriptome assembly complemented with long read sequencing, where silk composition is confirmed by proteomics. Comparative analysis across families (Araneidae and Uloboridae) shows that the gene architecture, repetitive domains, and amino acid frequencies of the orb web constituting silk proteins are similar among orb-weaving spiders regardless of the prey capture strategy. Notably, the fact that there is a difference only in the prey capture thread proteins strongly supports the monophyletic origin of the orb web.
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Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan.
| | - Hiroyuki Nakamura
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
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8
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Larouche O, Hodge JR, Alencar LRV, Camper B, Adams DS, Zapfe K, Friedman ST, Wainwright PC, Price SA. Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes. Curr Zool 2020; 66:575-588. [PMID: 33293935 PMCID: PMC7705508 DOI: 10.1093/cz/zoaa048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/26/2020] [Indexed: 12/04/2022] Open
Abstract
Key innovations may allow lineages access to new resources and facilitate the invasion of new adaptive zones, potentially influencing diversification patterns. Many studies have focused on the impact of key innovations on speciation rates, but far less is known about how they influence phenotypic rates and patterns of ecomorphological diversification. We use the repeated evolution of pharyngognathy within acanthomorph fishes, a commonly cited key innovation, as a case study to explore the predictions of key innovation theory. Specifically, we investigate whether transitions to pharyngognathy led to shifts in the rate of phenotypic evolution, as well as shifts and/or expansion in the occupation of morphological and dietary space, using a dataset of 8 morphological traits measured across 3,853 species of Acanthomorpha. Analyzing the 6 evolutionarily independent pharyngognathous clades together, we found no evidence to support pharyngognathy as a key innovation; however, comparisons between individual pharyngognathous lineages and their sister clades did reveal some consistent patterns. In morphospace, most pharyngognathous clades cluster in areas that correspond to deeper-bodied morphologies relative to their sister clades, while occupying greater areas in dietary space that reflects a more diversified diet. Additionally, both Cichlidae and Labridae exhibited higher univariate rates of phenotypic evolution compared with their closest relatives. However, few of these results were exceptional relative to our null models. Our results suggest that transitions to pharyngognathy may only be advantageous when combined with additional ecological or intrinsic factors, illustrating the importance of accounting for lineage-specific effects when testing key innovation hypotheses. Moreover, the challenges we experienced formulating informative comparisons, despite the ideal evolutionary scenario of multiple independent evolutionary origins of pharyngognathous clades, illustrates the complexities involved in quantifying the impact of key innovations. Given the issues of lineage specific effects and rate heterogeneity at macroevolutionary scales we observed, we suggest a reassessment of the expected impacts of key innovations may be warranted.
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Affiliation(s)
- Olivier Larouche
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Jennifer R Hodge
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Laura R V Alencar
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Benjamin Camper
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Danielle S Adams
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Katerina Zapfe
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Sarah T Friedman
- Department of Evolution & Ecology, University of California Davis, Davis, CA, 95616, USA
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California Davis, Davis, CA, 95616, USA
| | - Samantha A Price
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
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9
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Craig HC, Piorkowski D, Nakagawa S, Kasumovic MM, Blamires SJ. Meta-analysis reveals materiomic relationships in major ampullate silk across the spider phylogeny. J R Soc Interface 2020; 17:20200471. [PMID: 32993436 PMCID: PMC7536055 DOI: 10.1098/rsif.2020.0471] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/07/2020] [Indexed: 01/17/2023] Open
Abstract
Spider major ampullate (MA) silk, with its combination of strength and extensibility, outperforms any synthetic equivalents. There is thus much interest in understanding its underlying materiome. While the expression of the different silk proteins (spidroins) appears an integral component of silk performance, our understanding of the nature of the relationship between the spidroins, their constituent amino acids and MA silk mechanics is ambiguous. To provide clarity on these relationships across spider species, we performed a meta-analysis using phylogenetic comparative methods. These showed that glycine and proline, both of which are indicators of differential spidroin expression, had effects on MA silk mechanics across the phylogeny. We also found serine to correlate with silk mechanics, probably via its presence within the carboxyl and amino-terminal domains of the spidroins. From our analyses, we concluded that the spidroin expression shifts across the phylogeny from predominantly MaSp1 in the MA silks of ancestral spiders to predominantly MaSp2 in the more derived spiders' silks. This trend was accompanied by an enhanced ultimate strain and decreased Young's modulus in the silks. Our meta-analysis enabled us to decipher between real and apparent influences on MA silk properties, providing significant insights into spider silk and web coevolution and enhancing our capacity to create spider silk-like materials.
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Affiliation(s)
- Hamish C. Craig
- Evolution and Ecology Research Centre and School of Biological Earth and Environmental Sciences, UNSW, Sydney, Australia
| | | | - Shinichi Nakagawa
- Evolution and Ecology Research Centre and School of Biological Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Michael M. Kasumovic
- Evolution and Ecology Research Centre and School of Biological Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Sean J. Blamires
- Evolution and Ecology Research Centre and School of Biological Earth and Environmental Sciences, UNSW, Sydney, Australia
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10
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Greving I, Terry AE, Holland C, Boulet-Audet M, Grillo I, Vollrath F, Dicko C. Structural Diversity of Native Major Ampullate, Minor Ampullate, Cylindriform, and Flagelliform Silk Proteins in Solution. Biomacromolecules 2020; 21:3387-3393. [PMID: 32551521 PMCID: PMC7421538 DOI: 10.1021/acs.biomac.0c00819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/17/2020] [Indexed: 01/23/2023]
Abstract
The foundations of silk spinning, the structure, storage, and activation of silk proteins, remain highly debated. By combining solution small-angle neutron and X-ray scattering (SANS and SAXS) alongside circular dichroism (CD), we reveal a shape anisotropy of the four principal native spider silk feedstocks from Nephila edulis. We show that these proteins behave in solution like elongated semiflexible polymers with locally rigid sections. We demonstrated that minor ampullate and cylindriform proteins adopt a monomeric conformation, while major ampullate and flagelliform proteins have a preference for dimerization. From an evolutionary perspective, we propose that such dimerization arose to help the processing of disordered silk proteins. Collectively, our results provide insights into the molecular-scale processing of silk, uncovering a degree of evolutionary convergence in protein structures and chemistry that supports the macroscale micellar/pseudo liquid crystalline spinning mechanisms proposed by the community.
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Affiliation(s)
- Imke Greving
- Institute
of Materials Research, Helmholtz Zentrum
Geesthacht, 21502 Geesthacht, Germany
| | - Ann E. Terry
- MAX IV Laboratory, 224 84 Lund, Sweden
- Lund
Institute of Advanced Neutron and X-ray Science, 223 70 Lund, Sweden
| | - Chris Holland
- Department
of Materials Science and Engineering, The
University of Sheffield, Sheffield S1 3JD, United Kingdom
| | | | | | - Fritz Vollrath
- Department
of Zoology, University of Oxford, Mansfield Road, Oxford OX1 3SZ, United
Kingdom
| | - Cedric Dicko
- Pure
and
Applied Biochemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
- Lund
Institute of Advanced Neutron and X-ray Science, 223 70 Lund, Sweden
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11
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Ramírez MJ, Magalhaes ILF, Derkarabetian S, Ledford J, Griswold CE, Wood HM, Hedin M. Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems. Syst Biol 2020; 70:14-20. [PMID: 32497195 DOI: 10.1093/sysbio/syaa043] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/16/2020] [Accepted: 05/27/2020] [Indexed: 12/25/2022] Open
Abstract
The common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse "true spiders" (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of multiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of true spiders. This robust phylogenomic framework was used to conduct maximum likelihood and Bayesian character evolution analyses for respiratory systems, silk glands, and aerial webs, based on a combination of original and published data. Our results indicate that in true spiders, posterior book lungs were transformed into morphologically similar tracheal systems six times independently, after the evolution of novel silk gland systems and the origin of aerial webs. From these comparative data, we put forth a novel hypothesis that early-diverging web-building spiders were faced with new energetic demands for spinning, which prompted the evolution of similar tracheal systems via convergence; we also propose tests of predictions derived from this hypothesis.[Book lungs; discrete character evolution; respiratory systems; silk; spider web evolution; ultraconserved elements.].
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Affiliation(s)
- Martín J Ramírez
- Division of Arachnology, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Buenos Aires, Argentina
| | - Ivan L F Magalhaes
- Division of Arachnology, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Buenos Aires, Argentina
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joel Ledford
- Department of Plant Biology, University of California, Davis, CA 95616 USA
| | - Charles E Griswold
- Entomology, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Hannah M Wood
- National Museum of Natural History, Smithsonian Institution, Washington DC 20560-0188, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
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12
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Burress ED, Wainwright PC. A peacock bass (Cichla) functional novelty relaxes a constraint imposed by the classic cichlid pharyngeal jaw innovation. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Abstract
Innovations may provide access to new resources but often result in significant trade-offs. Pharyngognathy is a classic pharyngeal jaw innovation in which the left and right lower pharyngeal jaw (LPJ) bones are united into a single structure, producing a strong bite but reduced gape. Throughout cichlids, pharyngeal suturing occurs along the entire medial border between LPJ bones, except in peacock bass (Cichla), where these bones are connected by ligaments only in their anterior region. We show that this limited attachment permits the jaw bones to spread apart and we link this feature to an increase in pharyngeal gape that is comparable to non-pharyngognathous species. The capacity of the LPJ bones to spread apart is strongest in juveniles and is mostly lost during development. Juvenile Cichla exhibit size-specific pharyngeal gape similar to non-pharyngognathous percomorphs; however, adults exhibit pharyngeal gape on par with other predatory cichlids. Relaxation of pharyngeal suturing offsets a major deleterious consequence of pharyngognathy by reducing gape limitation and we propose this may accelerate the ontogenetic transition to piscivory. Partial reversal of the classic cichlid pharyngeal jaw innovation highlights the functional trade-offs that often accompany innovations and may be a major cause of variation in their macroevolutionary consequences.
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Affiliation(s)
- Edward D Burress
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Peter C Wainwright
- Department of Evolution and Ecology, University of California, Davis, CA, USA
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13
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Barua A, Mikheyev AS. Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates. Proc Biol Sci 2020; 287:20200613. [PMID: 32345154 PMCID: PMC7282918 DOI: 10.1098/rspb.2020.0613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Key innovations provide ecological opportunity by enabling access to new resources, colonization of new environments, and are associated with adaptive radiation. The most well-known pattern associated with adaptive radiation is an early burst of phenotypic diversification. Venoms facilitate prey capture and are widely believed to be key innovations leading to adaptive radiation. However, few studies have estimated their evolutionary rate dynamics. Here, we test for patterns of adaptive evolution in venom gene expression data from 52 venomous snake species. By identifying shifts in tempo and mode of evolution along with models of phenotypic evolution, we show that snake venom exhibits the macroevolutionary dynamics expected of key innovations. Namely, all toxin families undergo shifts in their rates of evolution, likely in response to changes in adaptive optima. Furthermore, we show that rapid-pulsed evolution modelled as a Lévy process better fits snake venom evolution than conventional early burst or Ornstein-Uhlenbeck models. While our results support the idea of snake venom being a key innovation, the innovation of venom chemistry lacks clear mechanisms that would lead to reproductive isolation and thus adaptive radiation. Therefore, the extent to which venom directly influences the diversification process is still a matter of contention.
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Affiliation(s)
- Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa-ken 904-0495, Japan
- Evolutionary genomics group, Australian National University, Canberra ACT 0200, Australia
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14
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Okamura Y, Sato A, Tsuzuki N, Murakami M, Heidel‐Fischer H, Vogel H. Molecular signatures of selection associated with host plant differences in
Pieris
butterflies. Mol Ecol 2019; 28:4958-4970. [DOI: 10.1111/mec.15268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Okamura
- Department of Entomology Max Planck Institute for Chemical Ecology Jena Germany
- Community Ecology Lab Faculty of Science Chiba University Chiba Japan
| | - Ai Sato
- Community Ecology Lab Faculty of Science Chiba University Chiba Japan
| | - Natsumi Tsuzuki
- Community Ecology Lab Faculty of Science Chiba University Chiba Japan
| | - Masashi Murakami
- Community Ecology Lab Faculty of Science Chiba University Chiba Japan
| | - Hanna Heidel‐Fischer
- Department of Entomology Max Planck Institute for Chemical Ecology Jena Germany
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI) Jena Germany
| | - Heiko Vogel
- Department of Entomology Max Planck Institute for Chemical Ecology Jena Germany
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15
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Burress ED, Tan M, Wainwright PC. Head Shape Modulates Diversification of a Classic Cichlid Pharyngeal Jaw Innovation. Am Nat 2019; 194:693-706. [PMID: 31613667 DOI: 10.1086/705392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Functional innovations are often invoked to explain the uneven distribution of ecological diversity. Innovations may provide access to new adaptive zones by expanding available ecological opportunities and may serve as catalysts of adaptive radiation. However, diversity is often unevenly distributed within clades that share a key innovation, highlighting the possibility that the impact of the innovation is mediated by other traits. Pharyngognathy is a widely recognized innovation of the pharyngeal jaws that enhances the ability to process hard and tough prey in several major radiations of fishes, including marine wrasses and freshwater cichlids. We explored diversification of lower pharyngeal jaw shape, a key feature of pharyngognathy, and the extent to which it is influenced by head shape in Neotropical cichlids. While pharyngeal jaw shape was unaffected by either head length or head depth, its disparity declined dramatically with increasing head width. Head width also predicted the rate of pharyngeal jaw evolution such that higher rates were associated with narrow heads. Wide heads are associated with exploiting prey that require intense processing by pharyngeal jaws that have expanded surfaces for the attachment of enlarged muscles. However, we show that a wide head constrains access to adaptive peaks associated with several trophic roles. A constraint on the independent evolution of pharyngeal jaw and head shape may explain the uneven distribution of ecological diversity within a clade that shares a major functional innovation.
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16
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Wolff JO, Paterno GB, Liprandi D, Ramírez MJ, Bosia F, Meijden A, Michalik P, Smith HM, Jones BR, Ravelo AM, Pugno N, Herberstein ME. Evolution of aerial spider webs coincided with repeated structural optimization of silk anchorages. Evolution 2019; 73:2122-2134. [DOI: 10.1111/evo.13834] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/11/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jonas O. Wolff
- Department of Biological SciencesMacquarie University Sydney New South Wales 2109 Australia
| | - Gustavo B. Paterno
- Departamento de Ecologia, Centro de BiociênciasUniversidade Federal do Rio Grande do Norte (UFRN) Lagoa Nova 59072–970 Natal Rio Grande do Norte Brazil
- Instituto de Ciências Biológicas, Programa de Pós‐Graduação em EcologiaUniversidade Federal de Juiz de Fora Rua José Lourenço Kelmer 36036–900 Juiz de Fora Minas Gerais Brazil
| | - Daniele Liprandi
- Laboratory of Bio‐Inspired and Graphene Nanomechanics, Department of CivilEnvironmental and Mechanical EngineeringUniversity of Trento Via Masiano 77 I‐38123 Trento Italy
| | - Martín J. Ramírez
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. Ángel Gallardo 470 C1405DJR Buenos Aires Argentina
| | - Federico Bosia
- Department of Physics and Nanostructured Interfaces and Surfaces Interdepartmental CentreUniversità di Torino Via P. Giuria 1 10125 Torino Italy
| | - Arie Meijden
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIOUniversidade do Porto Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde Porto 4485–661 Portugal
| | - Peter Michalik
- Zoologisches Institut und MuseumUniversität Greifswald Loitzer Str. 26 17489 Greifswald Germany
| | - Helen M. Smith
- Australian Museum 1 William St Sydney New South Wales 2010 Australia
| | - Braxton R. Jones
- Department of Biological SciencesMacquarie University Sydney New South Wales 2109 Australia
| | - Alexandra M. Ravelo
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. Ángel Gallardo 470 C1405DJR Buenos Aires Argentina
| | - Nicola Pugno
- Laboratory of Bio‐Inspired and Graphene Nanomechanics, Department of CivilEnvironmental and Mechanical EngineeringUniversity of Trento Via Masiano 77 I‐38123 Trento Italy
- School of Engineering and Materials ScienceQueen Mary University Mile End Rd London E1 4NS UK
- KET Labs, Edoardo Amaldi Foundation Via del Politecnico snc 00133 Rome Italy
| | - Marie E. Herberstein
- Department of Biological SciencesMacquarie University Sydney New South Wales 2109 Australia
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17
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Opell BD, Burba CM, Deva PD, Kin MHY, Rivas MX, Elmore HM, Hendricks ML. Linking properties of an orb-weaving spider's capture thread glycoprotein adhesive and flagelliform fiber components to prey retention time. Ecol Evol 2019; 9:9841-9854. [PMID: 31534698 PMCID: PMC6745672 DOI: 10.1002/ece3.5525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 07/05/2019] [Accepted: 07/16/2019] [Indexed: 11/07/2022] Open
Abstract
An orb web's adhesive capture spiral is responsible for prey retention. This thread is formed of regularly spaced glue droplets supported by two flagelliform axial lines. Each glue droplet features a glycoprotein adhesive core covered by a hygroscopic aqueous layer, which also covers axial lines between the droplets, making the entire thread responsive to environmental humidity.We characterized the effect of relative humidity (RH) on ability of Argiope aurantia and Argiope trifasciata thread arrays to retain houseflies and characterize the effect of humidity on their droplet properties. Using these data and those of Araneus marmoreus from a previous study, we then develop a regression model that correlated glycoprotein and flagelliform fiber properties with prey retention time. The model selection process included newly determined, humidity-specific Young's modulus and toughness values for the three species' glycoproteins.Argiope aurantia droplets are more hygroscopic than A. trifasciata droplets, causing the glycoprotein within A. aurantia droplets to become oversaturated at RH greater than 55% RH and their extension to decrease, whereas A. trifasciata droplet performance increases to 72% RH. This difference is reflected in species' prey retention times, with that of A. aurantia peaking at 55% RH and that of A. trifasciata at 72% RH.Fly retention time was explained by a regression model of five variables: glue droplet distribution, flagelliform fiber work of extension, glycoprotein volume, glycoprotein thickness, and glycoprotein Young's modulus.The material properties of both glycoprotein and flagelliform fibers appear to be phylogenetically constrained, whereas natural selection can more freely act on the amount of each material invested in a thread and on components of the thread's aqueous layer. Thus, it becomes easier to understand how natural selection can tune the performance of viscous capture threads by directing small changes in these components.
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Affiliation(s)
- Brent D. Opell
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
| | | | - Pritesh D. Deva
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
| | | | - Malik X. Rivas
- Department of Biological SciencesVirginia TechBlacksburgVAUSA
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18
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Marki PZ, Kennedy JD, Cooney CR, Rahbek C, Fjeldså J. Adaptive radiation and the evolution of nectarivory in a large songbird clade. Evolution 2019; 73:1226-1240. [DOI: 10.1111/evo.13734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Petter Z. Marki
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen DK‐2100 Denmark
- Natural History MuseumUniversity of Oslo Oslo 0318 Norway
| | - Jonathan D. Kennedy
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen DK‐2100 Denmark
- Department of Animal and Plant SciencesUniversity of Sheffield Sheffield S10 2TN United Kingdom
| | - Christopher R. Cooney
- Department of Animal and Plant SciencesUniversity of Sheffield Sheffield S10 2TN United Kingdom
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen DK‐2100 Denmark
- Department of Life SciencesImperial College London Ascot SL5 7PY United Kingdom
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen DK‐2100 Denmark
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19
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Orb weaver glycoprotein is a smart biological material, capable of repeated adhesion cycles. Naturwissenschaften 2019; 106:10. [DOI: 10.1007/s00114-019-1607-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 12/26/2022]
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20
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Silk genes and silk gene expression in the spider Tengella perfuga (Zoropsidae), including a potential cribellar spidroin (CrSp). PLoS One 2018; 13:e0203563. [PMID: 30235223 PMCID: PMC6147414 DOI: 10.1371/journal.pone.0203563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/27/2018] [Indexed: 12/21/2022] Open
Abstract
Most spiders spin multiple types of silk, including silks for reproduction, prey capture, and draglines. Spiders are a megadiverse group and the majority of spider silks remain uncharacterized. For example, nothing is known about the silk molecules of Tengella perfuga, a spider that spins sheet webs lined with cribellar silk. Cribellar silk is a type of adhesive capture thread composed of numerous fibrils that originate from a specialized plate-like spinning organ called the cribellum. The predominant components of spider silks are spidroins, members of a protein family synthesized in silk glands. Here, we use silk gland RNA-Seq and cDNA libraries to infer T. perfuga silks at the protein level. We show that T. perfuga spiders express 13 silk transcripts representing at least five categories of spider silk proteins (spidroins). One category is a candidate for cribellar silk and is thus named cribellar spidroin (CrSp). Studies of ontogenetic changes in web construction and spigot morphology in T. perfuga have documented that after sexual maturation, T. perfuga females continue to make capture webs but males halt web maintenance and cease spinning cribellar silk. Consistent with these observations, our candidate CrSp was expressed only in females. The other four spidroin categories correspond to paralogs of aciniform, ampullate, pyriform, and tubuliform spidroins. These spidroins are associated with egg sac and web construction. Except for the tubuliform spidroin, the spidroins from T. perfuga contain novel combinations of amino acid sequence motifs that have not been observed before in these spidroin types. Characterization of T. perfuga silk genes, particularly CrSp, expand the diversity of the spidroin family and inspire new structure/function hypotheses.
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21
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Shao L, Li S. Early Cretaceous greenhouse pumped higher taxa diversification in spiders. Mol Phylogenet Evol 2018; 127:146-155. [PMID: 29803949 DOI: 10.1016/j.ympev.2018.05.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 05/14/2018] [Accepted: 05/19/2018] [Indexed: 12/13/2022]
Abstract
The Cretaceous experienced one of the most remarkable greenhouse periods in geological history. During this time, ecosystem reorganization significantly impacted the diversification of many groups of organisms. The rise of angiosperms marked a major biome turnover. Notwithstanding, relatively little remains known about how the Cretaceous global ecosystem impacted the evolution of spiders, which constitute one of the most abundant groups of predators. Herein, we evaluate the transcriptomes of 91 taxa representing more than half of the spider families. We add 23 newly sequenced taxa to the existing database to obtain a robust phylogenomic assessment. Phylogenetic reconstructions using different datasets and methods obtain novel placements of some groups, especially in the Synspermiata and the group having a retrolateral tibial apophysis (RTA). Molecular analyses indicate an expansion of the RTA clade at the Early Cretaceous with a hunting predatory strategy shift. Fossil analyses show a 7-fold increase of diversification rate at the same period, but this likely owes to the first occurrence of spiders in amber deposit. Additional analyses of fossil abundance show an accumulation of spider lineages in the Early Cretaceous. We speculate that the establishment of a warm greenhouse climate pumped the diversification of spiders, in particular among webless forms tracking the abundance of insect prey. Our study offers a new pathway for future investigations of spider phylogeny and diversification.
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Affiliation(s)
- Lili Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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22
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Hochberg ME, Marquet PA, Boyd R, Wagner A. Innovation: an emerging focus from cells to societies. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0414. [PMID: 29061887 DOI: 10.1098/rstb.2016.0414] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability.This article is part of the theme issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- Michael E Hochberg
- Institut des Sciences de l'Evolution, Université de Montpellier, 34095 Montpellier, France .,Santa Fe Institute, Santa Fe, NM 87501, USA.,Institute for Advanced Study in Toulouse, 31015 Toulouse, France
| | - Pablo A Marquet
- Santa Fe Institute, Santa Fe, NM 87501, USA.,Departamento de Ecologı́a, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Instituto de Ecología y Biodiversidad (IEB), Casilla 653, Santiago, Chile.,Instituto de Sistemas Complejos de Valparaíso (ISCV), Artillería 4780, Valparaíso, Chile
| | - Robert Boyd
- Santa Fe Institute, Santa Fe, NM 87501, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
| | - Andreas Wagner
- Santa Fe Institute, Santa Fe, NM 87501, USA.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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23
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Rabosky DL. Phylogenetic tests for evolutionary innovation: the problematic link between key innovations and exceptional diversification. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0417. [PMID: 29061890 DOI: 10.1098/rstb.2016.0417] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2017] [Indexed: 11/12/2022] Open
Abstract
Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. 'Key innovations' are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches. Under traditional interpretations of the macroevolutionary 'adaptive zone', we should not necessarily expect key innovations to confer faster diversification rates upon lineages that possess them relative to their extant sister clades. I suggest that a key innovation is a trait that allows a lineage to interact with the environment in a fundamentally different way and which, as a result, increases the total diversification-but not necessarily the diversification rate-of the parent clade. Considered alone, branching patterns in phylogenetic trees are poorly suited to the inference of evolutionary innovation due to their inherently low information content with respect to the processes that produce them. However, phylogenies may be important for identifying transformational shifts in ecological and morphological space that are characteristic of innovation at the macroevolutionary scale.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1079, USA
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24
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Fernández R, Kallal RJ, Dimitrov D, Ballesteros JA, Arnedo MA, Giribet G, Hormiga G. Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life. Curr Biol 2018; 28:1489-1497.e5. [PMID: 29706520 DOI: 10.1016/j.cub.2018.03.064] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.
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Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
| | - Dimitar Dimitrov
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jesús A Ballesteros
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
| | - Miquel A Arnedo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research Institute (IRBio) Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
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25
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Cheng DQ, Piel WH. The origins of the Psechridae: Web-building lycosoid spiders. Mol Phylogenet Evol 2018; 125:213-219. [PMID: 29635024 DOI: 10.1016/j.ympev.2018.03.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/21/2018] [Accepted: 03/30/2018] [Indexed: 01/09/2023]
Abstract
Psechrids are an enigmatic family of S.E. Asian spiders. This small family builds sheet webs and even orb webs, yet unlike other orb weavers, its putative relatives are largely cursorial lycosoids - a superfamily of approximately seven spider families related to wolf spiders. The orb web was invented at least twice: first in a very ancient event, and then second, within this clade of wolf-like spiders that reinvented this ability. Exactly how the spiders modified their silks, anatomy, and behaviors to accomplish this transition requires that we identify their precise evolutionary origins - yet, thus far, molecular phylogenies show poor support and considerable disagreement. Using phylogenomic methods based on whole body transcriptomes for psechrids and their putative relatives, we have recovered a well-supported phylogeny that places the Psechridae sister to the Ctenidae - a family of mostly cursorial habits but that, as with all psechrids, retains some cribellate species. Although this position reinforces the prevailing view that orb weaving in psechrids is largely a consequence of convergence, it is still possible that some components of this behavior are retained or resurrected in common with more distant true orb weaving ancestors.
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Affiliation(s)
- Dong-Qiang Cheng
- Yale-NUS College, 10 College Avenue West #01-101, Singapore 138609, Singapore
| | - William H Piel
- Yale-NUS College, 10 College Avenue West #01-101, Singapore 138609, Singapore; National University of Singapore, Department of Biological Sciences, Singapore.
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26
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Opell BD, Jain D, Dhinojwala A, Blackledge TA. Tuning orb spider glycoprotein glue performance to habitat humidity. J Exp Biol 2018; 221:221/6/jeb161539. [DOI: 10.1242/jeb.161539] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
ABSTRACT
Orb-weaving spiders use adhesive threads to delay the escape of insects from their webs until the spiders can locate and subdue the insects. These viscous threads are spun as paired flagelliform axial fibers coated by a cylinder of solution derived from the aggregate glands. As low molecular mass compounds (LMMCs) in the aggregate solution attract atmospheric moisture, the enlarging cylinder becomes unstable and divides into droplets. Within each droplet an adhesive glycoprotein core condenses. The plasticity and axial line extensibility of the glycoproteins are maintained by hygroscopic LMMCs. These compounds cause droplet volume to track changes in humidity and glycoprotein viscosity to vary approximately 1000-fold over the course of a day. Natural selection has tuned the performance of glycoprotein cores to the humidity of a species' foraging environment by altering the composition of its LMMCs. Thus, species from low-humidity habits have more hygroscopic threads than those from humid forests. However, at their respective foraging humidities, these species' glycoproteins have remarkably similar viscosities, ensuring optimal droplet adhesion by balancing glycoprotein adhesion and cohesion. Optimal viscosity is also essential for integrating the adhesion force of multiple droplets. As force is transferred to a thread's support line, extending droplets draw it into a parabolic configuration, implementing a suspension bridge mechanism that sums the adhesive force generated over the thread span. Thus, viscous capture threads extend an orb spider's phenotype as a highly integrated complex of large proteins and small molecules that function as a self-assembling, highly tuned, environmentally responsive, adhesive biomaterial. Understanding the synergistic role of chemistry and design in spider adhesives, particularly the ability to stick in wet conditions, provides insight in designing synthetic adhesives for biomedical applications.
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Affiliation(s)
- Brent D. Opell
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Dharamdeep Jain
- Department of Polymer Science, Integrated Bioscience Program, The University of Akron, Akron, OH 44325, USA
| | - Ali Dhinojwala
- Department of Polymer Science, Integrated Bioscience Program, The University of Akron, Akron, OH 44325, USA
| | - Todd A. Blackledge
- Department of Biology, Integrated Bioscience Program, The University of Akron, Akron, OH 44325, USA
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27
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Alfaro RE, Griswold CE, Miller KB. -Comparative spigot ontogeny across the spider tree of life. PeerJ 2018; 6:e4233. [PMID: 29362692 PMCID: PMC5772386 DOI: 10.7717/peerj.4233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Spiders are well known for their silk and its varying use across taxa. Very few studies have examined the silk spigot ontogeny of the entire spinning field of a spider. Historically the spider phylogeny was based on morphological data and behavioral data associated with silk. Recent phylogenomics studies have shifted major paradigms in our understanding of silk use evolution, reordering phylogenetic relationships that were once thought to be monophyletic. Considering this, we explored spigot ontogeny in 22 species, including Dolomedes tenebrosus and Hogna carolinensis, reported here for the first time. This is the first study of its kind and the first to incorporate the Araneae Tree of Life. After rigorous testing for phylogenetic signal and model fit, we performed 60 phylogenetic generalized least squares analyses on adult female and second instar spigot morphology. Six analyses had significant correlation coefficients, suggesting that instar, strategy, and spigot variety are good predictors of spigot number in spiders, after correcting for bias of shared evolutionary history. We performed ancestral character estimation of singular, fiber producing spigots on the posterior lateral spinneret whose potential homology has long been debated. We found that the ancestral root of our phylogram of 22 species, with the addition of five additional cribellate and ecribellate lineages, was more likely to have either none or a modified spigot rather than a pseudoflagelliform gland spigot or a flagelliform spigot. This spigot ontogeny approach is novel and we can build on our efforts from this study by growing the dataset to include deeper taxon sampling and working towards the capability to incorporate full ontogeny in the analysis.
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Affiliation(s)
- Rachael E. Alfaro
- Museum of Southwestern Biology, Division of Arthropods, University of New Mexico, Albuquerque, NM, United States of America
| | - Charles E. Griswold
- Entomology, California Academy of Sciences, San Francisco, CA, United States of America
| | - Kelly B. Miller
- Museum of Southwestern Biology, Division of Arthropods, University of New Mexico, Albuquerque, NM, United States of America
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Mammola S, Michalik P, Hebets EA, Isaia M. Record breaking achievements by spiders and the scientists who study them. PeerJ 2017; 5:e3972. [PMID: 29104823 PMCID: PMC5668680 DOI: 10.7717/peerj.3972] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022] Open
Abstract
Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students-as well as scientists themselves-into the biology of spiders, we compiled a list of 99 record breaking achievements by spiders (the "Spider World Records"). We chose a world-record style format, as this is known to be an effective way to intrigue readers of all ages. We highlighted, for example, the largest and smallest spiders, the largest prey eaten, the fastest runners, the highest fliers, the species with the longest sperm, the most venomous species, and many more. We hope that our compilation will inspire science educators to embrace the biology of spiders as a resource that engages students in science learning. By making these achievements accessible to non-arachnologists and arachnologists alike, we suggest that they could be used: (i) by educators to draw in students for science education, (ii) to highlight gaps in current organismal knowledge, and (iii) to suggest novel avenues for future research efforts. Our contribution is not meant to be comprehensive, but aims to raise public awareness on spiders, while also providing an initial database of their record breaking achievements.
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Affiliation(s)
- Stefano Mammola
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- IUCN SSC Spider and Scorpion Specialist Group, Torino, Italy
| | - Peter Michalik
- Zoologisches Institut und Museum, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Eileen A. Hebets
- School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Marco Isaia
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- IUCN SSC Spider and Scorpion Specialist Group, Torino, Italy
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Affiliation(s)
- Julia D Sigwart
- Marine Laboratory, Queen’s University Belfast, Portaferry, Northern Ireland, UK
- Museum of Paleontology, University of California, Berkeley, Berkeley, CA, USA
| | - Mark D Sutton
- Department of Earth Sciences and Engineering, Imperial College London, London, UK
| | - K D Bennett
- Marine Laboratory, Queen’s University Belfast, Portaferry, Northern Ireland, UK
- Department of Geography & Sustainable Development, University of St Andrews, St Andrews, Fife, UK
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Evolutionary shifts in gene expression decoupled from gene duplication across functionally distinct spider silk glands. Sci Rep 2017; 7:8393. [PMID: 28827773 PMCID: PMC5566633 DOI: 10.1038/s41598-017-07388-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/28/2017] [Indexed: 11/08/2022] Open
Abstract
Spider silk synthesis is an emerging model for the evolution of tissue-specific gene expression and the role of gene duplication in functional novelty, but its potential has not been fully realized. Accordingly, we quantified transcript (mRNA) abundance in seven silk gland types and three non-silk gland tissues for three cobweb-weaving spider species. Evolutionary analyses based on expression levels of thousands of homologous transcripts and phylogenetic reconstruction of 605 gene families demonstrated conservation of expression for each gland type among species. Despite serial homology of all silk glands, the expression profiles of the glue-forming aggregate glands were divergent from fiber-forming glands. Also surprising was our finding that shifts in gene expression among silk gland types were not necessarily coupled with gene duplication, even though silk-specific genes belong to multi-paralog gene families. Our results challenge widely accepted models of tissue specialization and significantly advance efforts to replicate silk-based high-performance biomaterials.
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Piorkowski D, Blackledge TA. Punctuated evolution of viscid silk in spider orb webs supported by mechanical behavior of wet cribellate silk. Naturwissenschaften 2017; 104:67. [DOI: 10.1007/s00114-017-1489-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 01/09/2023]
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Paleo-López R, Quintero-Galvis JF, Solano-Iguaran JJ, Sanchez-Salazar AM, Gaitan-Espitia JD, Nespolo RF. A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts. Ecol Evol 2016; 6:3851-61. [PMID: 27516851 PMCID: PMC4972215 DOI: 10.1002/ece3.2097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 02/06/2023] Open
Abstract
When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow‐down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the “early burst” prediction on species diversification and also on traits of putative ecological relevance (cell‐size and fermentation versatility). We found that speciation rates are constant during the time‐range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell‐size), suggesting that lineages resemble each other in trait‐values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell‐size. We also found a significant phylogenetic regression between cell‐size and fermentation versatility (R2 = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common‐garden conditions combined with comparative analyses are warranted.
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Affiliation(s)
- Rocío Paleo-López
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Jaiber J Solano-Iguaran
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Angela M Sanchez-Salazar
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile
| | - Juan D Gaitan-Espitia
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile; CSIRO Oceans & Atmosphere GPO Box 1538 Hobart 7001 Tasmania Australia
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia 5090000 Chile; Center of Applied Ecology and Sustainability (CAPES) Facultad de Ciencias Biológicas Universidad Católica de Chile Santiago 6513677 Chile
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Garrison NL, Rodriguez J, Agnarsson I, Coddington JA, Griswold CE, Hamilton CA, Hedin M, Kocot KM, Ledford JM, Bond JE. Spider phylogenomics: untangling the Spider Tree of Life. PeerJ 2016; 4:e1719. [PMID: 26925338 PMCID: PMC4768681 DOI: 10.7717/peerj.1719] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/31/2016] [Indexed: 12/12/2022] Open
Abstract
Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the "usual suspect" genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125-90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.
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Affiliation(s)
- Nicole L. Garrison
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, United States
| | - Juanita Rodriguez
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, United States
| | - Ingi Agnarsson
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Jonathan A. Coddington
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washingtion, DC, United States
| | - Charles E. Griswold
- Arachnology, California Academy of Sciences, San Francisco, CA, United States
| | - Christopher A. Hamilton
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, United States
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Kevin M. Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Joel M. Ledford
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Jason E. Bond
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, United States
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Affiliation(s)
- Robin M. Andrews
- Department of Biological SciencesVirginia TechBlacksburgVirginia
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Clarke TH, Garb JE, Hayashi CY, Arensburger P, Ayoub NA. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution. Genome Biol Evol 2015; 7:1856-70. [PMID: 26058392 PMCID: PMC4524477 DOI: 10.1093/gbe/evv110] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae).
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Affiliation(s)
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts, Lowell
| | | | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona
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36
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Biomaterial evolution parallels behavioral innovation in the origin of orb-like spider webs. Sci Rep 2012; 2:833. [PMID: 23150784 PMCID: PMC3495280 DOI: 10.1038/srep00833] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/25/2012] [Indexed: 01/10/2023] Open
Abstract
Correlated evolution of traits can act synergistically to facilitate organism function. But, what happens when constraints exist on the evolvability of some traits, but not others? The orb web was a key innovation in the origin of >12,000 species of spiders. Orb evolution hinged upon the origin of novel spinning behaviors and innovations in silk material properties. In particular, a new major ampullate spidroin protein (MaSp2) increased silk extensibility and toughness, playing a critical role in how orb webs stop flying insects. Here, we show convergence between pseudo-orb-weaving Fecenia and true orb spiders. As in the origin of true orbs, Fecenia dragline silk improved significantly compared to relatives. But, Fecenia silk lacks the high compliance and extensibility found in true orb spiders, likely due in part to the absence of MaSp2. Our results suggest how constraints limit convergent evolution and provide insight into the evolution of nature's toughest fibers.
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Agnarsson I, Gregorič M, Blackledge TA, Kuntner M. The phylogenetic placement of Psechridae within Entelegynae and the convergent origin of orb-like spider webs. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/jzs.12007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ingi Agnarsson
- Department of Biology; University of Vermont; Burlington VT USA
- National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Matjaž Gregorič
- Institute of Biology; Scientific Research Centre; Slovenian Academy of Sciences and Arts; Ljubljana Slovenia
| | - Todd A. Blackledge
- Department of Biology and Integrated Bioscience Program; University of Akron; Akron OH USA
| | - Matjaž Kuntner
- National Museum of Natural History; Smithsonian Institution; Washington DC USA
- Institute of Biology; Scientific Research Centre; Slovenian Academy of Sciences and Arts; Ljubljana Slovenia
- College of Life Sciences; Hubei University; Wuhan Hubei China
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Tarakanova A, Buehler MJ. The role of capture spiral silk properties in the diversification of orb webs. J R Soc Interface 2012; 9:3240-8. [PMID: 22896566 DOI: 10.1098/rsif.2012.0473] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Among a myriad of spider web geometries, the orb web presents a fascinating, exquisite example in architecture and evolution. Orb webs can be divided into two categories according to the capture silk used in construction: cribellate orb webs (composed of pseudoflagelliform silk) coated with dry cribellate threads and ecribellate orb webs (composed of flagelliform silk fibres) coated by adhesive glue droplets. Cribellate capture silk is generally stronger but less-extensible than viscid capture silk, and a body of phylogenic evidence suggests that cribellate capture silk is more closely related to the ancestral form of capture spiral silk. Here, we use a coarse-grained web model to investigate how the mechanical properties of spiral capture silk affect the behaviour of the whole web, illustrating that more elastic capture spiral silk yields a decrease in web system energy absorption, suggesting that the function of the capture spiral shifted from prey capture to other structural roles. Additionally, we observe that in webs with more extensible capture silk, the effect of thread strength on web performance is reduced, indicating that thread elasticity is a dominant driving factor in web diversification.
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Affiliation(s)
- Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Dimitrov D, Lopardo L, Giribet G, Arnedo MA, Alvarez-Padilla F, Hormiga G. Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling. Proc Biol Sci 2012; 279:1341-50. [PMID: 22048955 PMCID: PMC3282380 DOI: 10.1098/rspb.2011.2011] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 10/11/2011] [Indexed: 11/12/2022] Open
Abstract
In order to study the tempo and the mode of spider orb web evolution and diversification, we conducted a phylogenetic analysis using six genetic markers along with a comprehensive taxon sample. The present analyses are the first to recover the monophyly of orb-weaving spiders based solely on DNA sequence data and an extensive taxon sample. We present the first dated orb weaver phylogeny. Our results suggest that orb weavers appeared by the Middle Triassic and underwent a rapid diversification during the end of the Triassic and Early Jurassic. By the second half of the Jurassic, most of the extant orb-weaving families and web designs were already present. The processes that may have given origin to this diversification of lineages and web architectures are discussed. A combination of biotic factors, such as key innovations in web design and silk composition, as well as abiotic environmental changes, may have played important roles in the diversification of orb weavers. Our analyses also show that increased taxon sampling density in both ingroups and outgroups greatly improves phylogenetic accuracy even when extensive data are missing. This effect is particularly important when addition of character data improves gene overlap.
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Affiliation(s)
- Dimitar Dimitrov
- Center for Macroecology, Evolution and Climate, Zoological Museum, University of Copenhagen, Copenhagen, Denmark.
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Pekár S, Coddington JA, Blackledge TA. Evolution of stenophagy in spiders (Araneae): evidence based on the comparative analysis of spider diets. Evolution 2011; 66:776-806. [PMID: 22380440 DOI: 10.1111/j.1558-5646.2011.01471.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Stenophagy (narrow diet breadth) represents an extreme of trophic specialization in carnivores, but little is known about the forces driving its evolution. We used spiders, the most diversified group of terrestrial predators, to investigate whether stenophagy (1) promoted diversification; (2) was phylogenetically conserved and evolutionarily derived state; and (3) was determined either by geographical distribution and foraging guild. We used published data on the prey of almost 600 species. Six categories of stenophagy were found: myrmecophagy, araneophagy, lepidopterophagy, termitophagy, dipterophagy, and crustaceophagy. We found that the species diversity of euryphagous genera and families was similar to stenophagous genera and families. At the family level, stenophagy evolved repeatedly and independently. Within families, the basal condition was oligophagy or euryphagy. Most types of stenophagy were clearly derived: myrmecophagy in Zodariidae; lepidopterophagy in Araneidae; dipterophagy in Theridiidae. In contrast, araneophagy was confined to basal and intermediate lineages, suggesting its ancestral condition. The diet breadth of species from the tropics and subtropics was less diverse than species from the temperate zone. Diet breadth was lower in cursorial spiders compared to web-building species. Thus, the evolution of stenophagy in spiders appears to be complex and governed by phylogeny as well as by ecological determinants.
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Affiliation(s)
- Stano Pekár
- Department of Botany and Zoology, Faculty of Sciences, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic E-mail: National Museum of Natural History, P.O. Box 37012, Washington, DC 20013-7012Department of Biology and Integrated Bioscience Program, University of Akron, Akron, Ohio 44325-3908
| | - Jonathan A Coddington
- Department of Botany and Zoology, Faculty of Sciences, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic E-mail: National Museum of Natural History, P.O. Box 37012, Washington, DC 20013-7012Department of Biology and Integrated Bioscience Program, University of Akron, Akron, Ohio 44325-3908
| | - Todd A Blackledge
- Department of Botany and Zoology, Faculty of Sciences, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic E-mail: National Museum of Natural History, P.O. Box 37012, Washington, DC 20013-7012Department of Biology and Integrated Bioscience Program, University of Akron, Akron, Ohio 44325-3908
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Aldous DJ, Krikun MA, Popovic L. Five statistical questions about the tree of life. Syst Biol 2011; 60:318-28. [PMID: 21386112 DOI: 10.1093/sysbio/syr008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Stochastic modeling of phylogenies raises five questions that have received varying levels of attention from quantitatively inclined biologists. 1) How large do we expect (from the model) the ratio of maximum historical diversity to current diversity to be? 2) From a correct phylogeny of the extant species of a clade, what can we deduce about past speciation and extinction rates? 3) What proportion of extant species are in fact descendants of still-extant ancestral species, and how does this compare with predictions of models? 4) When one moves from trees on species to trees on sets of species (whether traditional higher order taxa or clades within PhyloCode), does one expect trees to become more unbalanced as a purely logical consequence of tree structure, without signifying any real biological phenomenon? 5) How do we expect that fluctuation rates for counts of higher order taxa should compare with fluctuation rates for number of species? We present a mathematician's view based on an oversimplified modeling framework in which all these questions can be studied coherently.
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Affiliation(s)
- David J Aldous
- Department of Statistics, University of California, Berkeley, 367 Evans Hall # 3860, Berkeley, CA 94720-3860, USA.
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42
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Abstract
The dynamics of species diversification rates are a key component of macroevolutionary patterns. Although not absolutely necessary, the use of divergence times inferred from sequence data has led to development of more powerful methods for inferring diversification rates. However, it is unclear what impact uncertainty in age estimates have on diversification rate inferences. Here, we quantify these effects using both Bayesian and frequentist methodology. Through simulation, we demonstrate that adding sequence data results in more precise estimates of internal node ages, but a reasonable approximation of these node ages is often sufficient to approach the theoretical minimum variance in speciation rate estimates. We also find that even crude estimates of divergence times increase the power of tests of diversification rate differences between sister clades. Finally, because Bayesian and frequentist methods provided similar assessments of error, novel Bayesian approaches may provide a useful framework for tests of diversification rates in more complex contexts than are addressed here.
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Affiliation(s)
- Joel O Wertheim
- Department of Pathology, University of California, San Diego, California 92103, USA.
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43
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Key Innovations: Further Remarks on the Importance of Morphology in Elucidating Systematic Relationships and Adaptive Radiations. Evol Biol 2010. [DOI: 10.1007/s11692-010-9098-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Harmer AMT, Blackledge TA, Madin JS, Herberstein ME. High-performance spider webs: integrating biomechanics, ecology and behaviour. J R Soc Interface 2010; 8:457-71. [PMID: 21036911 DOI: 10.1098/rsif.2010.0454] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Spider silks exhibit remarkable properties, surpassing most natural and synthetic materials in both strength and toughness. Orb-web spider dragline silk is the focus of intense research by material scientists attempting to mimic these naturally produced fibres. However, biomechanical research on spider silks is often removed from the context of web ecology and spider foraging behaviour. Similarly, evolutionary and ecological research on spiders rarely considers the significance of silk properties. Here, we highlight the critical need to integrate biomechanical and ecological perspectives on spider silks to generate a better understanding of (i) how silk biomechanics and web architectures interacted to influence spider web evolution along different structural pathways, and (ii) how silks function in an ecological context, which may identify novel silk applications. An integrative, mechanistic approach to understanding silk and web function, as well as the selective pressures driving their evolution, will help uncover the potential impacts of environmental change and species invasions (of both spiders and prey) on spider success. Integrating these fields will also allow us to take advantage of the remarkable properties of spider silks, expanding the range of possible silk applications from single threads to two- and three-dimensional thread networks.
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Affiliation(s)
- Aaron M T Harmer
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia.
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Marazzi B, Sanderson MJ. LARGE-SCALE PATTERNS OF DIVERSIFICATION IN THE WIDESPREAD LEGUME GENUS SENNA AND THE EVOLUTIONARY ROLE OF EXTRAFLORAL NECTARIES. Evolution 2010; 64:3570-92. [DOI: 10.1111/j.1558-5646.2010.01086.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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KUNTNER MATJAŽ, KRALJ-FIŠER SIMONA, GREGORIČ MATJAŽ. Ladder webs in orb-web spiders: ontogenetic and evolutionary patterns in Nephilidae. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01414.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cooper WJ, Steppan SJ. Developmental constraint on the evolution of marsupial forelimb morphology. AUST J ZOOL 2010. [DOI: 10.1071/zo09102] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Compared with the placental mammals, marsupials are born at an almost embryonic stage, but nearly all of these neonates immediately climb or crawl to one of their mother’s teats using precociously developed forelimbs. Marsupial adults also exhibit limited forelimb shape diversity relative to the members of their sister group. That the functional requirements of this natal climb have imposed a developmental constraint on marsupial forelimb evolution represents a compelling and widely accepted hypothesis, yet its resulting predictions for the comparative patterns of mammal limb shape diversity have never been tested. In order to perform such tests we conducted extensive taxonomic sampling of mammal limb morphology (including fossil specimens), and then examined these data using morphometric methods, non-parametric analyses of anatomical disparity, and phylogenetic comparative analyses of evolutionary rates. Our results strongly support the constraint hypothesis, and indicate that the highly significant differences between marsupial and placental forelimb shape diversity has been strongly influenced by different rates of morphological evolution among the distal forelimb elements in these two important mammal lineages.
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Olson ME, Arroyo-Santos A. Thinking in continua: beyond the âadaptive radiationâ metaphor. Bioessays 2009; 31:1337-46. [DOI: 10.1002/bies.200900102] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Blackledge TA, Coddington JA, Agnarsson I. Fecundity increase supports adaptive radiation hypothesis in spider web evolution. Commun Integr Biol 2009; 2:459-63. [PMID: 20195450 PMCID: PMC2829819 DOI: 10.4161/cib.2.6.8855] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 04/28/2009] [Indexed: 11/19/2022] Open
Abstract
Identifying the mechanisms driving adaptive radiations is key to explaining the diversity of life. The extreme reliance of spiders upon silk for survival provides an exceptional system in which to link patterns of diversification to adaptive changes in silk use. Most of the world's 41,000 species of spiders belong to two apical lineages of spiders that exhibit quite different silk ecologies, distinct from their ancestors. Orb spiders spin highly stereotyped webs that are suspended in air and utilize a chemical glue to make them adhesive. RTA clade spiders mostly abandoned silk capture webs altogether. We recently proposed that these two clades present very different evolutionary routes of achieving the same key innovation-escape from the constraints imposed by spinning webs that contain a relatively costly type of physically adhesive cribellate silk. Here, we test the prediction that orb and RTA clade spiders are not only more diverse, but also have higher fecundity than other spiders. We show that RTA clade spiders average 23% higher fecundity and orb spiders average 123% higher fecundity than their ancestors. This supports a functional link between the adaptive escape from cribellate silk and increased resource allocation to reproduction in spiders.
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Affiliation(s)
- Todd A Blackledge
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH, USA.
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Blackledge TA, Boutry C, Wong SC, Baji A, Dhinojwala A, Sahni V, Agnarsson I. How super is supercontraction? Persistent versus cyclic responses to humidity in spider dragline silk. J Exp Biol 2009; 212:1981-9. [DOI: 10.1242/jeb.028944] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
Spider dragline silk has enormous potential for the development of biomimetic fibers that combine strength and elasticity in low density polymers. These applications necessitate understanding how silk reacts to different environmental conditions. For instance, spider dragline silk`supercontracts' in high humidity. During supercontraction, unrestrained dragline silk contracts up to 50% of its original length and restrained fibers generate substantial stress. Here we characterize the response of dragline silk to changes in humidity before, during and after supercontraction. Our findings demonstrate that dragline silk exhibits two qualitatively different responses to humidity. First, silk undergoes a previously unknown cyclic relaxation–contraction response to wetting and drying. The direction and magnitude of this cyclic response is identical both before and after supercontraction. By contrast, supercontraction is a `permanent' tensioning of restrained silk in response to high humidity. Here, water induces stress,rather than relaxation and the uptake of water molecules results in a permanent change in molecular composition of the silk, as demonstrated by thermogravimetric analysis (TGA). Even after drying, silk mass increased by∼1% after supercontraction. By contrast, the cyclic response to humidity involves a reversible uptake of water. Dried, post-supercontraction silk also differs mechanically from virgin silk. Post-supercontraction silk exhibits reduced stiffness and stress at yield, as well as changes in dynamic energy storage and dissipation. In addition to advancing understanding supercontraction, our findings open up new applications for synthetic silk analogs. For example, dragline silk emerges as a model for a biomimetic muscle, the contraction of which is precisely controlled by humidity alone.
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Affiliation(s)
| | - Cecilia Boutry
- Department of Biology, University of Akron, Akron, OH 44325, USA
| | - Shing-Chung Wong
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325,USA
| | - Avinash Baji
- Department of Mechanical Engineering, University of Akron, Akron, OH 44325,USA
| | - Ali Dhinojwala
- Department of Polymer Science, Integrated Bioscience Program, University of Akron, Akron, OH 44325, USA
| | - Vasav Sahni
- Department of Polymer Science, Integrated Bioscience Program, University of Akron, Akron, OH 44325, USA
| | - Ingi Agnarsson
- Department of Biology, University of Akron, Akron, OH 44325, USA
- Department of Biology, University of Puerto Rico, PO Box 23360, San Juan, PR 00931, USA
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