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Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Mol Phylogenet Evol 2021; 163:107263. [PMID: 34273505 DOI: 10.1016/j.ympev.2021.107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.
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Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Yonas Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic.
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Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Mol Phylogenet Evol 2021; 163:107258. [PMID: 34252546 DOI: 10.1016/j.ympev.2021.107258] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level - southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.
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Deshwal A, Phan P, Datta J, Kannan R, Thallapuranam SK. A Meta-Analysis of the Protein Components in Rattlesnake Venom. Toxins (Basel) 2021; 13:toxins13060372. [PMID: 34071038 DOI: 10.3390/toxins13060372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
The specificity and potency of venom components give them a unique advantage in developing various pharmaceutical drugs. Though venom is a cocktail of proteins, rarely are the synergy and association between various venom components studied. Understanding the relationship between various components of venom is critical in medical research. Using meta-analysis, we observed underlying patterns and associations in the appearance of the toxin families. For Crotalus, Dis has the most associations with the following toxins: PDE; BPP; CRL; CRiSP; LAAO; SVMP P-I and LAAO; SVMP P-III and LAAO. In Sistrurus venom, CTL and NGF have the most associations. These associations can predict the presence of proteins in novel venom and understand synergies between venom components for enhanced bioactivity. Using this approach, the need to revisit the classification of proteins as major components or minor components is highlighted. The revised classification of venom components is based on ubiquity, bioactivity, the number of associations, and synergies. The revised classification can be expected to trigger increased research on venom components, such as NGF, which have high biomedical significance. Using hierarchical clustering, we observed that the genera's venom compositions were similar, based on functional characteristics rather than phylogenetic relationships.
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Affiliation(s)
- Anant Deshwal
- Division of Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Phuc Phan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jyotishka Datta
- Department of Statistics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ragupathy Kannan
- Department of Biology, University of Arkansas-Fort Smith, Fort Smith, AR 72913, USA
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Hofmann EP, Rautsaw RM, Mason AJ, Strickland JL, Parkinson CL. Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes. Toxins (Basel) 2021; 13:336. [PMID: 34066626 PMCID: PMC8148590 DOI: 10.3390/toxins13050336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
The venoms of small rear-fanged snakes (RFS) remain largely unexplored, despite increased recognition of their importance in understanding venom evolution more broadly. Sequencing the transcriptome of venom-producing glands has greatly increased the ability of researchers to examine and characterize the toxin repertoire of small taxa with low venom yields. Here, we use RNA-seq to characterize the Duvernoy's gland transcriptome of the Plains Black-headed Snake, Tantilla nigriceps, a small, semi-fossorial colubrid that feeds on a variety of potentially dangerous arthropods including centipedes and spiders. We generated transcriptomes of six individuals from three localities in order to both characterize the toxin expression of this species for the first time, and to look for initial evidence of venom variation in the species. Three toxin families-three-finger neurotoxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)-dominated the transcriptome of T. nigriceps; 3FTx themselves were the dominant toxin family in most individuals, accounting for as much as 86.4% of an individual's toxin expression. Variation in toxin expression between individuals was also noted, with two specimens exhibiting higher relative expression of c-type lectins than any other sample (8.7-11.9% compared to <1%), and another expressed CRISPs higher than any other toxin. This study provides the first Duvernoy's gland transcriptomes of any species of Tantilla, and one of the few transcriptomic studies of RFS not predicated on a single individual. This initial characterization demonstrates the need for further study of toxin expression variation in this species, as well as the need for further exploration of small RFS venoms.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634, USA
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Holding ML, Strickland JL, Rautsaw RM, Hofmann EP, Mason AJ, Hogan MP, Nystrom GS, Ellsworth SA, Colston TJ, Borja M, Castañeda-Gaytán G, Grünwald CI, Jones JM, Freitas-de-Sousa LA, Viala VL, Margres MJ, Hingst-Zaher E, Junqueira-de-Azevedo ILM, Moura-da-Silva AM, Grazziotin FG, Gibbs HL, Rokyta DR, Parkinson CL. Phylogenetically diverse diets favor more complex venoms in North American pitvipers. Proc Natl Acad Sci U S A 2021; 118:e2015579118. [PMID: 33875585 PMCID: PMC8092465 DOI: 10.1073/pnas.2015579118] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates over evolutionary timescales, with apparent increases and decreases in complexity, and yet the causes of this variation are unclear. We tested alternative hypotheses linking venom complexity and ecological sources of selection from diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths. We generated independent transcriptomic and proteomic measures of venom complexity and collated several natural history studies to quantify dietary variation. We then constructed genome-scale phylogenies for these snakes for comparative analyses. Strikingly, prey phylogenetic diversity was more strongly correlated to venom complexity than was overall prey species diversity, specifically implicating prey species' divergence, rather than the number of lineages alone, in the evolution of complexity. Prey phylogenetic diversity further predicted transcriptomic complexity of three of the four largest gene families in viper venom, showing that complexity evolution is a concerted response among many independent gene families. We suggest that the phylogenetic diversity of prey measures functionally relevant divergence in the targets of venom, a claim supported by sequence diversity in the coagulation cascade targets of venom. Our results support the general concept that the diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.
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Affiliation(s)
- Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | - Gamaliel Castañeda-Gaytán
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | | | - Jason M Jones
- HERP.MX A.C., Villa del Álvarez, Colima 28973, Mexico
| | | | - Vincent Louis Viala
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Ana M Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040, Brazil
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo 05503-900, Brazil
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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The Chemosensory Repertoire of the Eastern Diamondback Rattlesnake (Crotalus adamanteus) Reveals Complementary Genetics of Olfactory and Vomeronasal-Type Receptors. J Mol Evol 2021; 89:313-328. [PMID: 33881604 DOI: 10.1007/s00239-021-10007-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/22/2021] [Indexed: 01/14/2023]
Abstract
Pitviper sensory perception incorporates diverse stimuli through the integration of trichromatic color vision, bifocal heat-sensing, and dual-system chemoperception. Chemoperception, or olfaction, is mediated by chemoreceptors in the olfactory bulb and the vomeronasal organ, but the true genomic complexity of the gene families and their relative contributions is unknown. A full genomic accounting of pitviper chemoperception directly complements our current understanding of their venoms by generating a more complete polyphenic representation of their predatory arsenal. To characterize the genetic repertoire of pitviper chemoperception, we analyzed a full-genome assembly for Crotalus adamanteus, the eastern diamondback rattlesnake. We identified hundreds of genes encoding both olfactory receptors (ORs; 362 full-length genes) and type-2 vomeronasal receptors (V2Rs; 430 full-length genes). Many chemoreceptor genes are organized into large tandem repeat arrays. Comparative analysis of V2R orthologs across squamates demonstrates how gene array expansion and contraction underlies the evolution of the chemoreceptor repertoire, which likely reflects shifts in life history traits. Chromosomal assignments of chemosensory genes identified sex chromosome specific chemoreceptor genes, providing gene candidates underlying observed sex-specific chemosensory-based behaviors. We detected widespread episodic evolution in the extracellular, ligand-binding domains of both ORs and V2Rs, suggesting the diversification of chemoreceptors is driven by transient periods of positive selection. We provide a robust genetic framework for studying pitviper chemosensory ecology and evolution.
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Nachtigall PG, Rautsaw RM, Ellsworth SA, Mason AJ, Rokyta DR, Parkinson CL, Junqueira-de-Azevedo ILM. ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics. Brief Bioinform 2021; 22:6235957. [PMID: 33866357 DOI: 10.1093/bib/bbab095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/15/2021] [Accepted: 03/03/2021] [Indexed: 01/23/2023] Open
Abstract
MOTIVATION Next-generation sequencing has become exceedingly common and has transformed our ability to explore nonmodel systems. In particular, transcriptomics has facilitated the study of venom and evolution of toxins in venomous lineages; however, many challenges remain. Primarily, annotation of toxins in the transcriptome is a laborious and time-consuming task. Current annotation software often fails to predict the correct coding sequence and overestimates the number of toxins present in the transcriptome. Here, we present ToxCodAn, a python script designed to perform precise annotation of snake venom gland transcriptomes. We test ToxCodAn with a set of previously curated transcriptomes and compare the results to other annotators. In addition, we provide a guide for venom gland transcriptomics to facilitate future research and use Bothrops alternatus as a case study for ToxCodAn and our guide. RESULTS Our analysis reveals that ToxCodAn provides precise annotation of toxins present in the transcriptome of venom glands of snakes. Comparison with other annotators demonstrates that ToxCodAn has better performance with regard to run time ($>20x$ faster), coding sequence prediction ($>3x$ more accurate) and the number of toxins predicted (generating $>4x$ less false positives). In this sense, ToxCodAn is a valuable resource for toxin annotation. The ToxCodAn framework can be expanded in the future to work with other venomous lineages and detect novel toxins.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP 05503-900, Brazil
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634, USA
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Nydam ML, Lemmon AR, Cherry JR, Kortyna ML, Clancy DL, Hernandez C, Cohen CS. Phylogenomic and morphological relationships among the botryllid ascidians (Subphylum Tunicata, Class Ascidiacea, Family Styelidae). Sci Rep 2021; 11:8351. [PMID: 33863944 PMCID: PMC8052435 DOI: 10.1038/s41598-021-87255-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/16/2021] [Indexed: 02/02/2023] Open
Abstract
Ascidians (Phylum Chordata, Class Ascidiacea) are a large group of invertebrates which occupy a central role in the ecology of marine benthic communities. Many ascidian species have become successfully introduced around the world via anthropogenic vectors. The botryllid ascidians (Order Stolidobranchia, Family Styelidae) are a group of 53 colonial species, several of which are widespread throughout temperate or tropical and subtropical waters. However, the systematics and biology of this group of ascidians is not well-understood. To provide a systematic framework for this group, we have constructed a well-resolved phylogenomic tree using 200 novel loci and 55 specimens. A Principal Components Analysis of all species described in the literature using 31 taxonomic characteristics revealed that some species occupy a unique morphological space and can be easily identified using characteristics of adult colonies. For other species, additional information such as larval or life history characteristics may be required for taxonomic discrimination. Molecular barcodes are critical for guiding the delineation of morphologically similar species in this group.
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Affiliation(s)
- Marie L Nydam
- Math and Science Program, Soka University of America, 1 University Drive, Aliso Viejo, CA, 92656, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Jesse R Cherry
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - Darragh L Clancy
- Biology Department and Estuarine and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | - Cecilia Hernandez
- Biology Department and Estuarine and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | - C Sarah Cohen
- Biology Department and Estuarine and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
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Abstract
Although oral venom systems are ecologically important characters, how they originated is still unclear. In this study, we show that oral venom systems likely originated from a gene regulatory network conserved across amniotes. This network, which we term the “metavenom network,” comprises over 3,000 housekeeping genes coexpressed with venom and play a role in protein folding and modification. Comparative transcriptomics revealed that the network is conserved between venom glands of snakes and salivary glands of mammals. This suggests that while these tissues have evolved different functions, they share a common regulatory core, that persisted since their common ancestor. We propose several evolutionary mechanisms that can utilize this common regulatory core to give rise to venomous animals from their nonvenomous ancestors. Oral venom systems evolved multiple times in numerous vertebrates enabling the exploitation of unique predatory niches. Yet how and when they evolved remains poorly understood. Up to now, most research on venom evolution has focused strictly on the toxins. However, using toxins present in modern day animals to trace the origin of the venom system is difficult, since they tend to evolve rapidly, show complex patterns of expression, and were incorporated into the venom arsenal relatively recently. Here we focus on gene regulatory networks associated with the production of toxins in snakes, rather than the toxins themselves. We found that overall venom gland gene expression was surprisingly well conserved when compared to salivary glands of other amniotes. We characterized the “metavenom network,” a network of ∼3,000 nonsecreted housekeeping genes that are strongly coexpressed with the toxins, and are primarily involved in protein folding and modification. Conserved across amniotes, this network was coopted for venom evolution by exaptation of existing members and the recruitment of new toxin genes. For instance, starting from this common molecular foundation, Heloderma lizards, shrews, and solenodon, evolved venoms in parallel by overexpression of kallikreins, which were common in ancestral saliva and induce vasodilation when injected, causing circulatory shock. Derived venoms, such as those of snakes, incorporated novel toxins, though still rely on hypotension for prey immobilization. These similarities suggest repeated cooption of shared molecular machinery for the evolution of oral venom in mammals and reptiles, blurring the line between truly venomous animals and their ancestors.
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Warwick AR, Barrow LN, Smith ML, Means DB, Lemmon AR, Lemmon EM. Signatures of north-eastern expansion and multiple refugia: genomic phylogeography of the Pine Barrens tree frog, Hyla andersonii (Anura: Hylidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Range fragmentation poses challenges for species persistence over time and can be caused by both historical and contemporary processes. We combined genomic data, phylogeographical model testing and palaeoclimatic niche modelling to infer the evolutionary history of the Pine Barrens tree frog (Hyla andersonii), a seepage bog specialist, in eastern North America to gain a better understanding of the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species range: Alabama/Florida (AF), the Carolinas (CL) and New Jersey (NJ). Phylogenetic relationships within H. andersonii were consistent between the nuclear species tree and mitochondrial analyses, indicating divergence between AF and CL/NJ (Atlantic clade) ~0.9 Mya and divergence of the NJ clade ~0.15 Mya. Several predictions of north-eastern expansion along the Atlantic coast were supported by phylogeographical analyses. Model testing using genome-wide single nucleotide polymorphism data and species distribution models both provided evidence for multiple disjunct refugia. This comprehensive phylogeographical study of H. andersonii demonstrates a long history of range fragmentation within an endemic coastal plain species and highlights the influence of historical climate change on the current distribution of species and their genetic diversity.
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Affiliation(s)
- Alexa R Warwick
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - D Bruce Means
- Coastal Plains Institute and Land Conservancy, Tallahassee, FL, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
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Scieuzo C, Salvia R, Franco A, Pezzi M, Cozzolino F, Chicca M, Scapoli C, Vogel H, Monti M, Ferracini C, Pucci P, Alma A, Falabella P. An integrated transcriptomic and proteomic approach to identify the main Torymus sinensis venom components. Sci Rep 2021; 11:5032. [PMID: 33658582 PMCID: PMC7930282 DOI: 10.1038/s41598-021-84385-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/22/2020] [Indexed: 01/31/2023] Open
Abstract
During oviposition, ectoparasitoid wasps not only inject their eggs but also a complex mixture of proteins and peptides (venom) in order to regulate the host physiology to benefit their progeny. Although several endoparasitoid venom proteins have been identified, little is known about the components of ectoparasitoid venom. To characterize the protein composition of Torymus sinensis Kamijo (Hymenoptera: Torymidae) venom, we used an integrated transcriptomic and proteomic approach and identified 143 venom proteins. Moreover, focusing on venom gland transcriptome, we selected additional 52 transcripts encoding putative venom proteins. As in other parasitoid venoms, hydrolases, including proteases, phosphatases, esterases, and nucleases, constitute the most abundant families in T. sinensis venom, followed by protease inhibitors. These proteins are potentially involved in the complex parasitic syndrome, with different effects on the immune system, physiological processes and development of the host, and contribute to provide nutrients to the parasitoid progeny. Although additional in vivo studies are needed, initial findings offer important information about venom factors and their putative host effects, which are essential to ensure the success of parasitism.
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Affiliation(s)
- Carmen Scieuzo
- grid.7367.50000000119391302Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy ,grid.7367.50000000119391302Spinoff XFlies S.R.L, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Rosanna Salvia
- grid.7367.50000000119391302Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy ,grid.7367.50000000119391302Spinoff XFlies S.R.L, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Antonio Franco
- grid.7367.50000000119391302Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy ,grid.7367.50000000119391302Spinoff XFlies S.R.L, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Marco Pezzi
- grid.8484.00000 0004 1757 2064Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy
| | - Flora Cozzolino
- grid.4691.a0000 0001 0790 385XDepartment of Chemical Sciences, University Federico II of Napoli, Via Cinthia 6, 80126 Naples, Italy ,CEINGE Advanced Biotechnology, Via Gaetano Salvatore 486, 80126 Naples, Italy
| | - Milvia Chicca
- grid.8484.00000 0004 1757 2064Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy
| | - Chiara Scapoli
- grid.8484.00000 0004 1757 2064Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy
| | - Heiko Vogel
- grid.418160.a0000 0004 0491 7131Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Maria Monti
- grid.4691.a0000 0001 0790 385XDepartment of Chemical Sciences, University Federico II of Napoli, Via Cinthia 6, 80126 Naples, Italy ,CEINGE Advanced Biotechnology, Via Gaetano Salvatore 486, 80126 Naples, Italy
| | - Chiara Ferracini
- grid.7605.40000 0001 2336 6580Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Pietro Pucci
- grid.4691.a0000 0001 0790 385XDepartment of Chemical Sciences, University Federico II of Napoli, Via Cinthia 6, 80126 Naples, Italy ,CEINGE Advanced Biotechnology, Via Gaetano Salvatore 486, 80126 Naples, Italy
| | - Alberto Alma
- grid.7605.40000 0001 2336 6580Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Patrizia Falabella
- grid.7367.50000000119391302Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy ,grid.7367.50000000119391302Spinoff XFlies S.R.L, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
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62
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Percequillo AR, Prado JRD, Abreu EF, Dalapicolla J, Pavan AC, de Almeida Chiquito E, Brennand P, Steppan SJ, Lemmon AR, Lemmon EM, Wilkinson M. Tempo and mode of evolution of oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): A phylogenomic approach. Mol Phylogenet Evol 2021; 159:107120. [PMID: 33610650 DOI: 10.1016/j.ympev.2021.107120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 11/19/2022]
Abstract
The tribe Oryzomyini is an impressive group of rodents, comprising 30 extant genera and an estimated 147 species. Recent remarkable advances in the understanding of the diversity, taxonomy and systematics of the tribe have mostly derived from analyses of single or few genetic markers. However, the evolutionary history and biogeography of Oryzomyini, its origin and diversification across the Neotropics, remain unrevealed. Here we use a multi-locus dataset (over 400 loci) obtained through anchored phylogenomics to provide a genome-wide phylogenetic hypothesis for Oryzomyini and to investigate the tempo and mode of its evolution. Species tree and supermatrix analyses produced topologies with strong support for most branches, with all genera confirmed as monophyletic, a result that previous studies failed to obtain. Our analyses also corroborated the monophyly and phylogenetic relationship of three main clades of Oryzomyini (B, C and D). The origin of the tribe is estimated to be in the Miocene (8.93-5.38 million years ago). The cladogenetic events leading to the four main clades occurred during the late Miocene and early Pliocene and most speciation events in the Pleistocene. Geographic range estimates suggested an east of Andes origin for the ancestor of oryzomyines, most likely in the Boreal Brazilian region, which includes the north bank of Rio Amazonas and the Guiana Shield. Oryzomyini rodents are an autochthonous South America radiation, that colonized areas and dominions of this continent mainly by dispersal events. The evolutionary history of the tribe is deeply associated with the Andean cordillera and the landscape history of Amazon basin.
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Affiliation(s)
- Alexandre Reis Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK.
| | - Joyce Rodrigues do Prado
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Edson Fiedler Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Jeronymo Dalapicolla
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil; Instituto Tecnológico Vale, Desenvolvimento Sustentável, 66055-090 Belém, PA, Brazil.
| | - Ana Carolina Pavan
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Elisandra de Almeida Chiquito
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil; Laboratório de Mastozoologia e Biogeografia, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, 29075-910 Vitória, ES, Brazil.
| | - Pamella Brennand
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Scott J Steppan
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, 400 Dirac Science Library, Florida State University, Tallahassee, FL 32306, USA.
| | - Emily Moriarty Lemmon
- Department of Scientific Computing, 400 Dirac Science Library, Florida State University, Tallahassee, FL 32306, USA.
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK.
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63
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Bybee SM, Kalkman VJ, Erickson RJ, Frandsen PB, Breinholt JW, Suvorov A, Dijkstra KDB, Cordero-Rivera A, Skevington JH, Abbott JC, Sanchez Herrera M, Lemmon AR, Moriarty Lemmon E, Ware JL. Phylogeny and classification of Odonata using targeted genomics. Mol Phylogenet Evol 2021; 160:107115. [PMID: 33609713 DOI: 10.1016/j.ympev.2021.107115] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Dragonflies and damselflies are a charismatic, medium-sized insect order (~6300 species) with a unique potential to approach comparative research questions. Their taxonomy and many ecological traits for a large fraction of extant species are relatively well understood. However, until now, the lack of a large-scale phylogeny based on high throughput data with the potential to connect both perspectives has precluded comparative evolutionary questions for these insects. Here, we provide an ordinal hypothesis of classification based on anchored hybrid enrichment using a total of 136 species representing 46 of the 48 families or incertae sedis, and a total of 478 target loci. Our analyses recovered the monophyly for all three suborders: Anisoptera, Anisozygoptera and Zygoptera. Although the backbone of the topology was reinforced and showed the highest support values to date, our genomic data was unable to stronglyresolve portions of the topology. In addition, a quartet sampling approach highlights the potential evolutionary scenarios that may have shaped evolutionary phylogeny (e.g., incomplete lineage sorting and introgression) of this taxon. Finally, in light of our phylogenomic reconstruction and previous morphological and molecular information we proposed an updated odonate classification and define five new families (Amanipodagrionidae fam. nov., Mesagrionidae fam. nov., Mesopodagrionidae fam. nov., Priscagrionidae fam. nov., Protolestidae fam. nov.) and reinstate another two (Rhipidolestidae stat. res., Tatocnemididae stat. res.). Additionally, we feature the problematic taxonomic groupings for examination in future studies to improve our current phylogenetic hypothesis.
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Affiliation(s)
- Seth M Bybee
- Department of Biology and Monte L. Bean Museum, Brigham Young University, USA.
| | | | - Robert J Erickson
- Department of Biology and Monte L. Bean Museum, Brigham Young University, USA
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, USA; Data Science Lab, Smithsonian Institution, USA
| | - Jesse W Breinholt
- Intermountain Healthcare, Intermountain Precision Genomics, USA; RAPiD Genomics, USA; McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, USA
| | - Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, USA
| | | | | | - Jeffrey H Skevington
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Canada
| | - John C Abbott
- Alabama Museum of Natural History, Department of Research and Collections, The University of Alabama, USA
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, USA
| | | | - Jessica L Ware
- Division of Invertebrate Zoology, American Museum of Natural History, USA
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64
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Mouchbahani-Constance S, Sharif-Naeini R. Proteomic and Transcriptomic Techniques to Decipher the Molecular Evolution of Venoms. Toxins (Basel) 2021; 13:154. [PMID: 33669432 PMCID: PMC7920473 DOI: 10.3390/toxins13020154] [Citation(s) in RCA: 12] [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: 01/16/2021] [Revised: 02/06/2021] [Accepted: 02/10/2021] [Indexed: 12/24/2022] Open
Abstract
Nature's library of venoms is a vast and untapped resource that has the potential of becoming the source of a wide variety of new drugs and therapeutics. The discovery of these valuable molecules, hidden in diverse collections of different venoms, requires highly specific genetic and proteomic sequencing techniques. These have been used to sequence a variety of venom glands from species ranging from snakes to scorpions, and some marine species. In addition to identifying toxin sequences, these techniques have paved the way for identifying various novel evolutionary links between species that were previously thought to be unrelated. Furthermore, proteomics-based techniques have allowed researchers to discover how specific toxins have evolved within related species, and in the context of environmental pressures. These techniques allow groups to discover novel proteins, identify mutations of interest, and discover new ways to modify toxins for biomimetic purposes and for the development of new therapeutics.
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Affiliation(s)
| | - Reza Sharif-Naeini
- Department of Physiology and Cell Information Systems Group, Alan Edwards Center for Research on Pain, McGill University, Montreal, QC H3A 0G4, Canada;
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65
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Dashevsky D, Rokyta D, Frank N, Nouwens A, Fry BG. Electric Blue: Molecular Evolution of Three-Finger Toxins in the Long-Glanded Coral Snake Species Calliophis bivirgatus. Toxins (Basel) 2021; 13:124. [PMID: 33567660 PMCID: PMC7915963 DOI: 10.3390/toxins13020124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/17/2023] Open
Abstract
The genus Calliophis is the most basal branch of the family Elapidae and several species in it have developed highly elongated venom glands. Recent research has shown that C. bivirgatus has evolved a seemingly unique toxin (calliotoxin) that produces spastic paralysis in their prey by acting on the voltage-gated sodium (NaV) channels. We assembled a transcriptome from C. bivirgatus to investigate the molecular characteristics of these toxins and the venom as a whole. We find strong confirmation that this genus produces the classic elapid eight-cysteine three-finger toxins, that δδ-elapitoxins (toxins that resemble calliotoxin) are responsible for a substantial portion of the venom composition, and that these toxins form a distinct clade within a larger, more diverse clade of C. bivirgatus three-finger toxins. This broader clade of C. bivirgatus toxins also contains the previously named maticotoxins and is somewhat closely related to cytotoxins from other elapids. However, the toxins from this clade that have been characterized are not themselves cytotoxic. No other toxins show clear relationships to toxins of known function from other species.
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Affiliation(s)
- Daniel Dashevsky
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia;
- Australian National Insect Collection, Commonwealth Science and Industry Research Organization, Canberra, ACT 2601, Australia
| | - Darin Rokyta
- Department of Biological Sciences, Florida State University, Tallahassee, FL 24105, USA;
| | - Nathaniel Frank
- MToxins Venom Lab, 717 Oregon Street, Oshkosh, WI 54902, USA;
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia;
| | - Bryan G. Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia;
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66
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Margres MJ, Rautsaw RM, Strickland JL, Mason AJ, Schramer TD, Hofmann EP, Stiers E, Ellsworth SA, Nystrom GS, Hogan MP, Bartlett DA, Colston TJ, Gilbert DM, Rokyta DR, Parkinson CL. The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proc Natl Acad Sci U S A 2021; 118:e2014634118. [PMID: 33468678 PMCID: PMC7848695 DOI: 10.1073/pnas.2014634118] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Variation in gene regulation is ubiquitous, yet identifying the mechanisms producing such variation, especially for complex traits, is challenging. Snake venoms provide a model system for studying the phenotypic impacts of regulatory variation in complex traits because of their genetic tractability. Here, we sequence the genome of the Tiger Rattlesnake, which possesses the simplest and most toxic venom of any rattlesnake species, to determine whether the simple venom phenotype is the result of a simple genotype through gene loss or a complex genotype mediated through regulatory mechanisms. We generate the most contiguous snake-genome assembly to date and use this genome to show that gene loss, chromatin accessibility, and methylation levels all contribute to the production of the simplest, most toxic rattlesnake venom. We provide the most complete characterization of the venom gene-regulatory network to date and identify key mechanisms mediating phenotypic variation across a polygenic regulatory network.
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Affiliation(s)
- Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Biology, University of South Alabama, Mobile, AL 36688
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Tristan D Schramer
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erin Stiers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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67
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Hurt C, Hultgren K, Anker A, Lemmon AR, Moriarty Lemmon E, Bracken-Grissom H. First worldwide molecular phylogeny of the morphologically and ecologically hyperdiversified snapping shrimp genus Alpheus (Malacostraca: Decapoda). Mol Phylogenet Evol 2021; 158:107080. [PMID: 33482381 DOI: 10.1016/j.ympev.2021.107080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 11/26/2022]
Abstract
Hyperdiverse animal groups raise intriguing questions regarding the factors that generate and maintain their diversity. The snapping shrimp genus Alpheus (with >300 described species) is a spectacularly diversified group of decapod crustaceans that serves as an exemplary system for addressing evolutionary questions regarding morphological adaptations, symbiosis, cryptic diversity and molecular divergence. A lack of information regarding evolutionary relationships among species has limited investigations into the mechanisms that drive the diversification of Alpheus. Previous phylogenetic studies of Alpheus have been restricted in scope, while molecular datasets used for phylogenetic reconstructions have been based solely on mitochondrial and a handful of nuclear markers. Here we use an anchored hybrid enrichment (AHE) approach to resolve phylogenetic relationships among species of Alpheus. The AHE method generated sequence data for 240 loci (>72,000 bp) for 65 terminal species that span the geographic, ecological and taxonomic diversity of Alpheus. Our resulting, well-supported phylogeny demonstrates a lack of monophyly for five out of seven morphologically defined species groups that have traditionally been used as a framework in Alpheus taxonomy. Our results also suggest that symbiotic associations with a variety of other animals have evolved independently in at least seven lineages in this genus. Our AHE phylogeny represents the most comprehensive phylogenetic treatment of Alpheus to date and will provide a useful evolutionary framework to further investigate questions, such as various modifications of the snapping claw and the role of habitat specialization and symbiosis in promoting speciation. Running head: PHYLOGENY OF THE SNAPPING SHRIMP GENUS ALPHEUS.
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Affiliation(s)
- Carla Hurt
- Department of Biology, Tennessee Tech University, Cookeville, TN 38505, United States.
| | - Kristin Hultgren
- Department of Biology, Seattle University, Seattle, WA 98122, United States.
| | - Arthur Anker
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiás, Brazil
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306-4120, United States; Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306-4120, United States; Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, United States
| | - Heather Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL 33181, United States
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68
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Mikula O, Nicolas V, Šumbera R, Konečný A, Denys C, Verheyen E, Bryjová A, Lemmon AR, Moriarty Lemmon E, Bryja J. Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Mol Phylogenet Evol 2021; 157:107069. [PMID: 33421615 DOI: 10.1016/j.ympev.2021.107069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 01/09/2023]
Abstract
The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.
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Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.
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69
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Banker SE, Lemmon AR, Hassinger AB, Dye M, Holland SD, Kortyna ML, Ospina OE, Ralicki H, Lemmon EM. Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris). Syst Biol 2021; 69:756-773. [PMID: 31886503 PMCID: PMC7302053 DOI: 10.1093/sysbio/syz074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.].
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Affiliation(s)
- Sarah E Banker
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Integrative Biology, University of California, Berkeley, #3160 Berkeley, CA 94720-3160, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
| | - Mysia Dye
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Oscar E Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Hannah Ralicki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Biological Science, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06268, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
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70
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Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, Kunte K, Ron SR, Das S, Gaitonde N, Green DM, Labisko J, Che J, Weisrock DW. Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Syst Biol 2021; 70:49-66. [PMID: 32359157 PMCID: PMC7823230 DOI: 10.1093/sysbio/syaa034] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/30/2022] Open
Abstract
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].
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Affiliation(s)
- Paul M Hime
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Elizabeth Prendini
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Justin D Kratovil
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Pedro L V Peloso
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, 66075-750, Brazil
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Stephen C Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | | | - Christopher J Raxworthy
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sandeep Das
- Forest Ecology and Biodiversity Conservation Division, Kerala Forest Research Institute, Peechi, Kerala 680653, India
| | - Nikhil Gaitonde
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - David M Green
- Redpath Museum, McGill University, Montreal, Quebec H3A 0C4, Canada
| | - Jim Labisko
- The Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, The University of Kent, Canterbury, Kent, CT2 7NR, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, PO Box 1348, Anse Royale, Mahé, Seychelles
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
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71
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Bayona-Serrano JD, Viala VL, Rautsaw RM, Schramer TD, Barros-Carvalho GA, Nishiyama MY, Freitas-de-Sousa LA, Moura-da-Silva AM, Parkinson CL, Grazziotin FG, Junqueira-de-Azevedo ILM. Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes. Mol Biol Evol 2020; 37:3563-3575. [PMID: 32722789 PMCID: PMC8525196 DOI: 10.1093/molbev/msaa192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an "SVMP-like" function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.
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Affiliation(s)
| | - Vincent Louis Viala
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC
| | | | | | - Milton Yutaka Nishiyama
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | | | - Ana Maria Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
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72
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Freitas-de-Sousa LA, Nachtigall PG, Portes-Junior JA, Holding ML, Nystrom GS, Ellsworth SA, Guimarães NC, Tioyama E, Ortiz F, Silva BR, Kunz TS, Junqueira-de-Azevedo ILM, Grazziotin FG, Rokyta DR, Moura-da-Silva AM. Size Matters: An Evaluation of the Molecular Basis of Ontogenetic Modifications in the Composition of Bothrops jararacussu Snake Venom. Toxins (Basel) 2020; 12:toxins12120791. [PMID: 33322460 PMCID: PMC7763748 DOI: 10.3390/toxins12120791] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Ontogenetic changes in venom composition have been described in Bothrops snakes, but only a few studies have attempted to identify the targeted paralogues or the molecular mechanisms involved in modifications of gene expression during ontogeny. In this study, we decoded B. jararacussu venom gland transcripts from six specimens of varying sizes and analyzed the variability in the composition of independent venom proteomes from 19 individuals. We identified 125 distinct putative toxin transcripts, and of these, 73 were detected in venom proteomes and only 10 were involved in the ontogenetic changes. Ontogenetic variability was linearly related to snake size and did not correspond to the maturation of the reproductive stage. Changes in the transcriptome were highly predictive of changes in the venom proteome. The basic myotoxic phospholipases A2 (PLA2s) were the most abundant components in larger snakes, while in venoms from smaller snakes, PIII-class SVMPs were the major components. The snake venom metalloproteinases (SVMPs) identified corresponded to novel sequences and conferred higher pro-coagulant and hemorrhagic functions to the venom of small snakes. The mechanisms modulating venom variability are predominantly related to transcriptional events and may consist of an advantage of higher hematotoxicity and more efficient predatory function in the venom from small snakes.
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Affiliation(s)
- Luciana A. Freitas-de-Sousa
- Programa de Pós-Graduação em Ciências-Toxinologia, Laboratório de Imunopatologia, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (N.C.G.); (E.T.)
- Correspondence: (L.A.F.-d.-S.); (A.M.M.-d.-S.); Tel.: +55-11-2627-9779 (A.M.M.-d.-S.)
| | - Pedro G. Nachtigall
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (P.G.N.); (I.L.M.J.-d.-A.)
| | - José A. Portes-Junior
- Laboratório de Coleções Zoológicas, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (J.A.P.-J.); (F.O.); (B.R.S.); (T.S.K.); (F.G.G.)
| | - Matthew L. Holding
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; (M.L.H.); (G.S.N.); (S.A.E.); (D.R.R.)
| | - Gunnar S. Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; (M.L.H.); (G.S.N.); (S.A.E.); (D.R.R.)
| | - Schyler A. Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; (M.L.H.); (G.S.N.); (S.A.E.); (D.R.R.)
| | - Noranathan C. Guimarães
- Programa de Pós-Graduação em Ciências-Toxinologia, Laboratório de Imunopatologia, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (N.C.G.); (E.T.)
| | - Emilly Tioyama
- Programa de Pós-Graduação em Ciências-Toxinologia, Laboratório de Imunopatologia, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (N.C.G.); (E.T.)
| | - Flora Ortiz
- Laboratório de Coleções Zoológicas, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (J.A.P.-J.); (F.O.); (B.R.S.); (T.S.K.); (F.G.G.)
| | - Bruno R. Silva
- Laboratório de Coleções Zoológicas, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (J.A.P.-J.); (F.O.); (B.R.S.); (T.S.K.); (F.G.G.)
| | - Tobias S. Kunz
- Laboratório de Coleções Zoológicas, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (J.A.P.-J.); (F.O.); (B.R.S.); (T.S.K.); (F.G.G.)
| | | | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (J.A.P.-J.); (F.O.); (B.R.S.); (T.S.K.); (F.G.G.)
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; (M.L.H.); (G.S.N.); (S.A.E.); (D.R.R.)
| | - Ana M. Moura-da-Silva
- Programa de Pós-Graduação em Ciências-Toxinologia, Laboratório de Imunopatologia, Instituto Butantan, 05503-900 São Paulo, SP, Brazil; (N.C.G.); (E.T.)
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, 69040-000 Manaus, AM, Brazil
- Correspondence: (L.A.F.-d.-S.); (A.M.M.-d.-S.); Tel.: +55-11-2627-9779 (A.M.M.-d.-S.)
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73
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Ospina OE, Tieu L, Apodaca JJ, Lemmon EM. Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States. COPEIA 2020. [DOI: 10.1643/ch2020009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Oscar E. Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Lynee Tieu
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Joseph J. Apodaca
- Tangled Bank Conservation, 128 Bingham Road, Suite 1150, Asheville, North Carolina 28806;
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
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74
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Sharanowski BJ, Ridenbaugh RD, Piekarski PK, Broad GR, Burke GR, Deans AR, Lemmon AR, Moriarty Lemmon EC, Diehl GJ, Whitfield JB, Hines HM. Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization. Mol Phylogenet Evol 2020; 156:107023. [PMID: 33253830 DOI: 10.1016/j.ympev.2020.107023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 12/26/2022]
Abstract
Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.
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Affiliation(s)
| | - Ryan D Ridenbaugh
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Patrick K Piekarski
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA; Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Gavin R Broad
- Department of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30606, USA
| | - Andrew R Deans
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Gloria J Diehl
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - James B Whitfield
- Department of Entomology, University of Illinois, Urbana, IL 61801, USA
| | - Heather M Hines
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802; Department of Biology, Pennsylvania State University, University Park, PA, 16802
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75
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Cai L, Xi Z, Lemmon EM, Lemmon AR, Mast A, Buddenhagen CE, Liu L, Davis CC. The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales. Syst Biol 2020; 70:491-507. [PMID: 33169797 DOI: 10.1093/sysbio/syaa083] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022] Open
Abstract
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0$\%$, 34.8$\%$, and 21.4$\%$ of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution. [Coalescent; concatenation; flanking region; hybrid enrichment, introgression; phylogenomics; rapid radiation, triplet frequency.].
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Affiliation(s)
- Liming Cai
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Austin Mast
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher E Buddenhagen
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
- AgResearch, 10 Bisley Road, Hamilton 3214, New Zealand
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
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76
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Smith CF, Mackessy SP. Asymmetrical expression of toxins between the left and right venom glands of an individual prairie rattlesnake (Crotalus viridis viridis). Toxicon 2020; 186:105-108. [PMID: 32777251 DOI: 10.1016/j.toxicon.2020.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/01/2020] [Accepted: 08/05/2020] [Indexed: 10/23/2022]
Abstract
It is assumed that toxin expression is equivalent between left and right glands of a single snake. In the current study, we report venoms that differ in enzyme functionality and overall composition between the left and right gland of a single snake. The right gland produced venom of comparable composition to venom previously extracted from the same individual; however, the left gland produced venom with overall lower protein content and considerably less enzyme activity.
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Affiliation(s)
- Cara Francesca Smith
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639-0017, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639-0017, USA.
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77
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Perry BW, Schield DR, Westfall AK, Mackessy SP, Castoe TA. Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands. Sci Rep 2020; 10:18083. [PMID: 33093509 PMCID: PMC7582160 DOI: 10.1038/s41598-020-75048-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/09/2020] [Indexed: 01/30/2023] Open
Abstract
Despite the extensive body of research on snake venom, many facets of snake venom systems, such as the physiology and regulation of the venom gland itself, remain virtually unstudied. Here, we use time series gene expression analyses of the rattlesnake venom gland in comparison with several non-venom tissues to characterize physiological and cellular processes associated with venom production and to highlight key distinctions of venom gland cellular and physiological function. We find consistent evidence for activation of stress response pathways in the venom gland, suggesting that mitigation of cellular stress is a crucial component of venom production. Additionally, we demonstrate evidence for an unappreciated degree of cellular and secretory activity in the steady state venom gland relative to other secretory tissues and identify vacuolar ATPases as the likely mechanisms driving acidification of the venom gland lumen during venom production and storage.
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Affiliation(s)
- Blair W Perry
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Aundrea K Westfall
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA.
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78
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Pereira LDM, Messias EA, Sorroche BP, Oliveira ADN, Arantes LMRB, de Carvalho AC, Tanaka-Azevedo AM, Grego KF, Carvalho AL, Melendez ME. In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland. J Venom Anim Toxins Incl Trop Dis 2020; 26:e20190058. [PMID: 33149734 PMCID: PMC7579844 DOI: 10.1590/1678-9199-jvatitd-2019-0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background: Lack of complete genomic data of Bothrops jararaca impedes molecular biology research focusing on biotechnological applications of venom gland components. Identification of full-length coding regions of genes is crucial for the correct molecular cloning design. Methods: RNA was extracted from the venom gland of one adult female specimen of Bothrops jararaca. Deep sequencing of the mRNA library was performed using Illumina NextSeq 500 platform. De novo assembly of B. jararaca transcriptome was done using Trinity. Annotation was performed using Blast2GO. All predicted proteins after clustering step were blasted against non-redundant protein database of NCBI using BLASTP. Metabolic pathways present in the transcriptome were annotated using the KAAS-KEGG Automatic Annotation Server. Toxins were identified in the B. jararaca predicted proteome using BLASTP against all protein sequences obtained from Animal Toxin Annotation Project from Uniprot KB/Swiss-Pro database. Figures and data visualization were performed using ggplot2 package in R language environment. Results: We described the in-depth transcriptome analysis of B. jararaca venom gland, in which 76,765 de novo assembled isoforms, 96,044 transcribed genes and 41,196 unique proteins were identified. The most abundant transcript was the zinc metalloproteinase-disintegrin-like jararhagin. Moreover, we identified 78 distinct functional classes of proteins, including toxins, inhibitors and tumor suppressors. Other venom proteins identified were the hemolytic lethal factors stonustoxin and verrucotoxin. Conclusion: It is believed that the application of deep sequencing to the analysis of snake venom transcriptomes may represent invaluable insight on their biotechnological potential focusing on candidate molecules.
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Affiliation(s)
- Leandro de Mattos Pereira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Laboratory of Molecular Microbial Ecology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Elisa Alves Messias
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | | | | | | | | | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Pelé Little Prince Research Institute, Curitiba, PR, Brazil.,Little Prince College, Curitiba, PR, Brazil
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79
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Wang B, Wang Q, Wang C, Wang B, Qiu L, Zou S, Zhang F, Liu G, Zhang L. A comparative analysis of the proteomes and biological activities of the venoms from two sea snakes, Hydrophis curtus and Hydrophis cyanocinctus, from Hainan, China. Toxicon 2020; 187:35-46. [PMID: 32871160 DOI: 10.1016/j.toxicon.2020.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/05/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022]
Abstract
We characterized and compared the venom protein profiles of Hydrophis curtus (synonyms: Lapemis hardwickii, Lapemis curtus and Hydrophis hardwickii) and Hydrophis cyanocinctus, the two representatives of medically important venomous sea snakes in Chinese waters using proteomic approaches. A total of 47 and 38 putative toxins were identified in H. curtus venom (HcuV) and H. cyanocinctus venom (HcyV), respectively, and these toxins could be grouped into 15 functional categories, mainly proteinases, phospholipases, three-finger toxins (3FTxs), lectins, protease inhibitors, ion channel inhibitors, cysteine-rich venom proteins (CRVPs) and snake venom metalloproteases (SVMPs). The constituent ratio of each toxin category varied between HcuV and HcyV with 3FTx (54% in HcuV/69% in HcyV) and PLA2 (38% in HcuV/22% in HcyV) unanimously ranked as the top two most abundant families. Both HcuV and HcyV exhibited relatively high lethality (LD50 values in mice of 0.34 μg/g and 0.24 μg/g, respectively), specific PLA2 activity and hemolytic activity. On the basis of several previous reports of HcuV and HcyV collected from other areas, these findings greatly expand our understanding of geographical variation and interspecies diversity of the two sea snake venoms and can provide a scientific basis for the development of specific sea snake antivenom in the future.
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Affiliation(s)
- Bo Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Qianqian Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Chao Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Beilei Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Leilei Qiu
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Shuaijun Zou
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Fuhai Zhang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China
| | - Guoyan Liu
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China.
| | - Liming Zhang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Shanghai, 200433, China.
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80
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Bénard-Valle M, Neri-Castro E, Yañez-Mendoza MF, Lomonte B, Olvera A, Zamudio F, Restano-Cassulini R, Possani LD, Jiménez-Ferrer E, Alagón A. Functional, proteomic and transcriptomic characterization of the venom from Micrurus browni browni: Identification of the first lethal multimeric neurotoxin in coral snake venom. J Proteomics 2020; 225:103863. [DOI: 10.1016/j.jprot.2020.103863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 10/24/2022]
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81
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Ochoa A, Broe M, Moriarty Lemmon E, Lemmon AR, Rokyta DR, Gibbs HL. Drift, selection and adaptive variation in small populations of a threatened rattlesnake. Mol Ecol 2020; 29:2612-2625. [PMID: 32557885 DOI: 10.1111/mec.15517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/09/2020] [Accepted: 05/21/2020] [Indexed: 01/22/2023]
Abstract
An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long- and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre-date the effects of recent drift, and that functional variation in these loci persists despite small short-term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of "drift debt," a nonequilibrium state where present-day levels of variation overestimate the amount of functional genetic diversity present in future populations.
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Affiliation(s)
- Alexander Ochoa
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Michael Broe
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - H Lisle Gibbs
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
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82
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Rose JP, Toledo CAP, Lemmon EM, Lemmon AR, Sytsma KJ. Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal. Syst Biol 2020; 70:162-180. [PMID: 32617587 DOI: 10.1093/sysbio/syaa049] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.].
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Affiliation(s)
- Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
| | - Cassio A P Toledo
- Programa de Pós-Graduação em Biologia Vegetal, Instituto de Biolgia, Universidade Estadual de Campinas-UNICAMP, Rua Monteiro Lobato, 255, Campinas, SP. CEP: 13083-862, Brazil
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
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83
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Modahl CM, Roointan A, Rogers J, Currier K, Mackessy SP. Interspecific and intraspecific venom enzymatic variation among cobras (Naja sp. and Ophiophagus hannah). Comp Biochem Physiol C Toxicol Pharmacol 2020; 232:108743. [PMID: 32194156 DOI: 10.1016/j.cbpc.2020.108743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/28/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023]
Abstract
The genera Ophiophagus and Naja comprise part of a clade of snakes referred to as cobras, dangerously venomous front-fanged snakes in the family Elapidae responsible for significant human mortality and morbidity throughout Asia and Africa. We evaluated venom enzyme variation for eleven cobra species and three N. kaouthia populations using SDS-PAGE venom fingerprinting and numerous enzyme assays. Acetylcholinesterase and PLA2 activities were the most variable between species, and PLA2 activity was significantly different between Malaysian and Thailand N. kaouthia populations. Venom metalloproteinase activity was low and significantly different among most species, but levels were identical for N. kaouthia populations; minor variation in venom L-amino acid oxidase and phosphodiesterase activities were seen between cobra species. Naja siamensis venom lacked the α-fibrinogenolytic activity common to other cobra venoms. In addition, venom from N. siamensis had no detectable metalloproteinase activity and exhibited an SDS-PAGE profile with reduced abundance of higher mass proteins. Venom profiles from spitting cobras (N. siamensis, N. pallida, and N. mossambica) exhibited similar reductions in higher mass proteins, suggesting the evolution of venoms of reduced complexity and decreased enzymatic activity among spitting cobras. Generally, the venom proteomes of cobras show highly abundant three-finger toxin diversity, followed by large quantities of PLA2s. However, PLA2 bands and activity were very reduced for N. haje, N. annulifera and N. nivea. Venom compositionalenzy analysis provides insight into the evolution, diversification and distribution of different venom phenotypes that complements venomic data, and this information is critical for the development of effective antivenoms and snakebite treatment.
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Affiliation(s)
- Cassandra M Modahl
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Amir Roointan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore; Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jessica Rogers
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA
| | - Katelyn Currier
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th St., Greeley, CO 80639-0017, USA.
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84
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Venom gland transcriptome from Heloderma horridum horridum by high-throughput sequencing. Toxicon 2020; 180:62-78. [PMID: 32283106 DOI: 10.1016/j.toxicon.2020.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/24/2020] [Accepted: 04/03/2020] [Indexed: 02/01/2023]
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85
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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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86
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Crowl AA, Manos PS, McVay JD, Lemmon AR, Lemmon EM, Hipp AL. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). THE NEW PHYTOLOGIST 2020; 226:1158-1170. [PMID: 30963585 DOI: 10.1111/nph.15842] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/29/2019] [Indexed: 05/10/2023]
Abstract
Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci. Concatenation, species-tree and network analyses were carried out in an attempt to uncover the genomic signal of ancient introgression and infer the divergent phylogenetic topology for the white oak clade. Locus and site-level likelihood comparisons were then conducted to further explore the introgressed signal within our dataset. Historical, intersectional gene flow is suggested to have occurred between an ancestor of the Eurasian Roburoid lineage and Quercus pontica and North American Dumosae and Prinoideae lineages. Despite extensive time past, our approach proved successful in detecting the genomic signature of ancient introgression. Our results, however, highlight the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history.
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Affiliation(s)
- Andrew A Crowl
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Paul S Manos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - John D McVay
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32317, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 89 Chieftan Way, Tallahassee, FL, 32317, USA
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
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87
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Pyron RA, O'Connell KA, Lemmon EM, Lemmon AR, Beamer DA. Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus). Mol Phylogenet Evol 2020; 146:106751. [DOI: 10.1016/j.ympev.2020.106751] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 01/02/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
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88
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Novikova PY, Brennan IG, Booker W, Mahony M, Doughty P, Lemmon AR, Moriarty Lemmon E, Roberts JD, Yant L, Van de Peer Y, Keogh JS, Donnellan SC. Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLoS Genet 2020; 16:e1008769. [PMID: 32392206 PMCID: PMC7259803 DOI: 10.1371/journal.pgen.1008769] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/29/2020] [Accepted: 04/08/2020] [Indexed: 01/13/2023] Open
Abstract
Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.
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Affiliation(s)
- Polina Yu. Novikova
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - William Booker
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Michael Mahony
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Paul Doughty
- Western Australian Museum, Welshpool, Perth, Australia
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, United States of America
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - J. Dale Roberts
- School of Biological Sciences, and, Centre for Evolutionary Biology, University of Western Australia, Albany, Western Australia, Australia
| | - Levi Yant
- School of Life Sciences and Future Food Beacon, University of Nottingham, Nottingham, United Kingdom
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Stephen C. Donnellan
- South Australian Museum, North Terrace, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, Australia
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89
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Hempel BF, Damm M, Mrinalini, Göçmen B, Karış M, Nalbantsoy A, Kini RM, Süssmuth RD. Extended Snake Venomics by Top-Down In-Source Decay: Investigating the Newly Discovered Anatolian Meadow Viper Subspecies, Vipera anatolica senliki. J Proteome Res 2020; 19:1731-1749. [PMID: 32073270 DOI: 10.1021/acs.jproteome.9b00869] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomics analyses, were applied to fully characterize the venom of V. a. senliki. Furthermore, the classical top-down venomics approach was extended to elucidate the venom proteome by an alternative in-source decay (ISD) proteomics workflow using the reducing matrix 1,5-diaminonaphthalene. Top-down ISD proteomics allows for disulfide bond counting and effective de novo sequencing-based identification of high-molecular-weight venom constituents, both of which are difficult to achieve by commonly established top-down approaches. Venom gland transcriptome analysis identified 96 toxin transcript annotations from 18 toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (42.9%) as the most abundant protein family, followed by several less dominant toxin families. Online mass profiling and top-down venomics provide a detailed insight into the venom proteome of V. a. senliki and facilitate a comparative analysis of venom variability for the closely related subspecies, Vipera anatolica anatolica.
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Affiliation(s)
- Benjamin-Florian Hempel
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Maik Damm
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Mrinalini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Bayram Göçmen
- Department of Biology, Faculty of Science, Ege University, 35100 Bornova, 35100 Izmir, Turkey
| | - Mert Karış
- Department of Biology, Faculty of Science, Ege University, 35100 Bornova, 35100 Izmir, Turkey
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Izmir, Bornova, Turkey
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16, Medical Drive, Singapore 117600
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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90
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Mason AJ, Margres MJ, Strickland JL, Rokyta DR, Sasa M, Parkinson CL. Trait differentiation and modular toxin expression in palm-pitvipers. BMC Genomics 2020; 21:147. [PMID: 32046632 PMCID: PMC7014597 DOI: 10.1186/s12864-020-6545-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular systems that exhibit extreme diversification even across very short time scales. One well-studied venom phenotype dichotomy is a trade-off between neurotoxicity versus hemotoxicity that occurs through the high expression of a heterodimeric neurotoxic phospholipase A2 (PLA2) or snake venom metalloproteinases (SVMPs). We tested whether the variation in these venom phenotypes could occur via variation in regulatory sub-modules through comparative venom gland transcriptomics of representative Black-Speckled Palm-Pitvipers (Bothriechis nigroviridis) and Talamancan Palm-Pitvipers (B. nubestris). Results We assembled 1517 coding sequences, including 43 toxins for B. nigroviridis and 1787 coding sequences including 42 toxins for B. nubestris. The venom gland transcriptomes were extremely divergent between these two species with one B. nigroviridis exhibiting a primarily neurotoxic pattern of expression, both B. nubestris expressing primarily hemorrhagic toxins, and a second B. nigroviridis exhibiting a mixed expression phenotype. Weighted gene coexpression analyses identified six submodules of transcript expression variation, one of which was highly associated with SVMPs and a second which contained both subunits of the neurotoxic PLA2 complex. The sub-module association of these toxins suggest common regulatory pathways underlie the variation in their expression and is consistent with known patterns of inheritance of similar haplotypes in other species. We also find evidence that module associated toxin families show fewer gene duplications and transcript losses between species, but module association did not appear to affect sequence diversification. Conclusion Sub-modular regulation of expression likely contributes to the diversification of venom phenotypes within and among species and underscores the role of modularity in facilitating rapid evolution of complex traits.
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Affiliation(s)
- Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Darin R Rokyta
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 24105, USA
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA. .,Department of Forestry, and Environmental Conservation, Clemson University, Clemson, SC, USA.
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91
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Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12020070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.
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92
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Granados Mendoza C, Jost M, Hágsater E, Magallón S, van den Berg C, Lemmon EM, Lemmon AR, Salazar GA, Wanke S. Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum. FRONTIERS IN PLANT SCIENCE 2020; 10:1761. [PMID: 32063915 PMCID: PMC7000662 DOI: 10.3389/fpls.2019.01761] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/16/2019] [Indexed: 05/12/2023]
Abstract
Universal angiosperm enrichment probe sets designed to enrich hundreds of putatively orthologous nuclear single-copy loci are increasingly being applied to infer phylogenetic relationships of different lineages of angiosperms at a range of evolutionary depths. Studies applying such probe sets have focused on testing the universality and performance of the target nuclear loci, but they have not taken advantage of off-target data from other genome compartments generated alongside the nuclear loci. Here we do so to infer phylogenetic relationships in the orchid genus Epidendrum and closely related genera of subtribe Laeliinae. Our aims are to: 1) test the technical viability of applying the plant anchored hybrid enrichment (AHE) method (Angiosperm v.1 probe kit) to our focal group, 2) mine plastid protein coding genes from off-target reads; and 3) evaluate the performance of the target nuclear and off-target plastid loci in resolving and supporting phylogenetic relationships along a range of taxonomical depths. Phylogenetic relationships were inferred from the nuclear data set through coalescent summary and site-based methods, whereas plastid loci were analyzed in a concatenated partitioned matrix under maximum likelihood. The usefulness of target and flanking non-target nuclear regions and plastid loci was assessed through the estimation of their phylogenetic informativeness. Our study successfully applied the plant AHE probe kit to Epidendrum, supporting the universality of this kit in angiosperms. Moreover, it demonstrated the feasibility of mining plastome loci from off-target reads generated with the Angiosperm v.1 probe kit to obtain additional, uniparentally inherited sequence data at no extra sequencing cost. Our analyses detected some strongly supported incongruences between nuclear and plastid data sets at shallow divergences, an indication of potential lineage sorting, hybridization, or introgression events in the group. Lastly, we found that the per site phylogenetic informativeness of the ycf1 plastid gene surpasses that of all other plastid genes and several nuclear loci, making it an excellent candidate for assessing phylogenetic relationships at medium to low taxonomic levels in orchids.
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Affiliation(s)
- Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Eric Hágsater
- Herbario AMO, Instituto Chinoin, A.C., Mexico City, Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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93
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Phillips AJ, Dornburg A, Zapfe KL, Anderson FE, James SW, Erséus C, Moriarty Lemmon E, Lemmon AR, Williams BW. Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution. Genome Biol Evol 2020; 11:3082-3093. [PMID: 31214691 PMCID: PMC6598468 DOI: 10.1093/gbe/evz120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2019] [Indexed: 12/17/2022] Open
Abstract
Leeches (Hirudinida) comprise a charismatic, yet often maligned group of worms. Despite their ecological, economic, and medical importance, a general consensus on the phylogenetic relationships of major hirudinidan lineages is lacking. This absence of a consistent, robust phylogeny of early-diverging lineages has hindered our understanding of the underlying processes that enabled evolutionary diversification of this clade. Here, we used an anchored hybrid enrichment-based phylogenomic approach, capturing hundreds of loci to investigate phylogenetic relationships among major hirudinidan lineages and their closest living relatives. We recovered Branchiobdellida as sister to a clade that includes all major lineages of hirudinidans and Acanthobdella, casting doubt on the utility of Acanthobdella as a “missing link” between hirudinidans and the clitellate group formerly known as Oligochaeta. Further, our results corroborate the reciprocal monophyly of jawed and proboscis-bearing leeches. Our phylogenomic resolution of early-diverging leeches provides a useful framework for illuminating the evolution of key adaptations and host–symbiont associations that have allowed leeches to colonize a wide diversity of habitats worldwide.
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Affiliation(s)
- Anna J Phillips
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Research Laboratory, Raleigh, North Carolina
| | - Katerina L Zapfe
- North Carolina Museum of Natural Sciences, Research Laboratory, Raleigh, North Carolina.,Department of Biological Sciences, Clemson University
| | | | | | - Christer Erséus
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University
| | - Bronwyn W Williams
- North Carolina Museum of Natural Sciences, Research Laboratory, Raleigh, North Carolina
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94
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Barua A, Mikheyev AS. Many Options, Few Solutions: Over 60 My Snakes Converged on a Few Optimal Venom Formulations. Mol Biol Evol 2020; 36:1964-1974. [PMID: 31220860 PMCID: PMC6736290 DOI: 10.1093/molbev/msz125] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantified and mapped to a distinct genomic locus and traced for millions of years. Using a phylogenetic generalized linear mixed model, we analyzed expression data of toxin genes from 52 snake species spanning the 3 venomous snake families and estimated phylogenetic covariance, which acts as a measure of evolutionary constraint. We find that evolution of toxin combinations is not constrained. However, although all combinations are in principle possible, the actual dimensionality of phylomorphic space is low, with envenomation strategies focused around only four major toxin families: metalloproteases, three-finger toxins, serine proteases, and phospholipases A2. Although most extant snakes prioritize either a single or a combination of major toxin families, they are repeatedly recruited and lost. We find that over macroevolutionary timescales, the venom phenotypes were not shaped by phylogenetic constraints, which include important microevolutionary constraints such as epistasis and pleiotropy, but more likely by ecological filtering that permits a small number of optimal solutions. As a result, phenotypic optima were repeatedly attained by distantly related species. These results indicate that venoms evolve by selection on biochemistry of prey envenomation, which permit diversity through parallelism, and impose strong limits, since only a few of the theoretically possible strategies seem to work well and are observed in extant snakes.
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Affiliation(s)
- Agneesh Barua
- Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University, Onna, Japan.,Evolutionary Genomics Research Group, Ecology and Evolution Unit, Australian National University, Canberra, Australia
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95
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Antimicrobial Activity of Protein Fraction from Naja ashei Venom Against Staphylococcus epidermidis. Molecules 2020; 25:molecules25020293. [PMID: 31936872 PMCID: PMC7024148 DOI: 10.3390/molecules25020293] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/04/2020] [Accepted: 01/08/2020] [Indexed: 01/10/2023] Open
Abstract
One of the key problems of modern infectious disease medicine is the growing number of drug-resistant and multi-drug-resistant bacterial strains. For this reason, many studies are devoted to the search for highly active antimicrobial substances that could be used in therapy against bacterial infections. As it turns out, snake venoms are a rich source of proteins that exert a strong antibacterial effect, and therefore they have become an interesting research material. We analyzed Naja ashei venom for such antibacterial properties, and we found that a specific composition of proteins can act to eliminate individual bacterial cells, as well as the entire biofilm of Staphylococcus epidermidis. In general, we used ion exchange chromatography (IEX) to obtain 10 protein fractions with different levels of complexity, which were then tested against certified and clinical strains of S. epidermidis. One of the fractions (F2) showed exceptional antimicrobial effects both alone and in combination with antibiotics. The protein composition of the obtained fractions was determined using mass spectrometry techniques, indicating a high proportion of phospholipases A2, three-finger toxins, and L-amino acids oxidases in F2 fraction, which are most likely responsible for the unique properties of this fraction. Moreover, we were able to identify a new group of low abundant proteins containing the Ig-like domain that have not been previously described in snake venoms.
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96
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Debono J, Dashevsky D, Nouwens A, Fry BG. The sweet side of venom: Glycosylated prothrombin activating metalloproteases from Dispholidus typus (boomslang) and Thelotornis mossambicanus (twig snake). Comp Biochem Physiol C Toxicol Pharmacol 2020; 227:108625. [PMID: 31634575 DOI: 10.1016/j.cbpc.2019.108625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022]
Abstract
Dispholidus typus and Thelotornis mossambicanus are closely related rear-fanged colubrid snakes that both possess strongly procoagulant venoms. However, despite similarities in overall venom biochemistry and resulting clinical manifestations, the underlying venom composition differs significantly between the two species. As a result, the only available antivenom-which is a monovalent antivenom for D. typus-has minimal cross reactivity with T. mossambicanus and is not a clinically viable option. It was hypothesised that this lack of cross reactivity is due to the additional large metalloprotease protein within T. mossambicanus venom, which may also be responsible for faster coagulation times. In this study, we found that T. mossambicanus venom is a more powerful activator of prothrombin than that of D. typus and that the SVMP transcripts from T. mossambicanus form a clade with those from D. typus. The sequences from D. typus and T. mossambicanus were highly similar in length, with the calculated molecular weights of the T. mossambicanus transcripts being significantly less than the molecular weights of some isoforms on the 1D SDS-PAGE gels. Analyses utilising degylcosylating enzymes revealed that T. mossambicanus SVMPs are glycosylated during post-translational modification, but that this does not lead to the different molecular weight bands observed in 1D SDS-PAGE gels. However, differences in glycosylation patterns may still explain some of the difference between the enzymatic activities and neutralization by antivenom that have been observed in these venoms. The results of this study provide new information regarding the treatment options for patients envenomated by T. mossambicanus as well as the evolution of these dangerous snakes.
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Affiliation(s)
- Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Daniel Dashevsky
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
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97
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Natusch DJ, Esquerré D, Lyons JA, Hamidy A, Lemmon AR, Moriarty Lemmon E, Riyanto A, Keogh JS, Donnellan S. Species delimitation and systematics of the green pythons (Morelia viridis complex) of melanesia and Australia. Mol Phylogenet Evol 2020; 142:106640. [DOI: 10.1016/j.ympev.2019.106640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/30/2019] [Accepted: 10/05/2019] [Indexed: 02/01/2023]
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98
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Chow CY, Chin YKY, Walker AA, Guo S, Blomster LV, Ward MJ, Herzig V, Rokyta DR, King GF. Venom Peptides with Dual Modulatory Activity on the Voltage-Gated Sodium Channel Na V1.1 Provide Novel Leads for Development of Antiepileptic Drugs. ACS Pharmacol Transl Sci 2019; 3:119-134. [PMID: 32259093 DOI: 10.1021/acsptsci.9b00079] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Indexed: 01/14/2023]
Abstract
Voltage-gated sodium (NaV) channels play a fundamental role in normal neurological function, especially via the initiation and propagation of action potentials. The NaV1.1 subtype is found in inhibitory interneurons of the brain and it is essential for maintaining a balance between excitation and inhibition in neuronal networks. Heterozygous loss-of-function mutations of SCN1A, the gene encoding NaV1.1, underlie Dravet syndrome (DS), a severe pediatric epilepsy. We recently demonstrated that selective inhibition of NaV1.1 inactivation prevents seizures and premature death in a mouse model of DS. Thus, selective modulators of NaV1.1 might be useful therapeutics for treatment of DS as they target the underlying molecular deficit. Numerous scorpion-venom peptides have been shown to modulate the activity of NaV channels, but little is known about their activity at NaV1.1. Here we report the isolation, sequence, three-dimensional structure, recombinant production, and functional characterization of two peptidic modulators of NaV1.1 from venom of the buthid scorpion Hottentotta jayakari. These peptides, Hj1a and Hj2a, are potent agonists of NaV1.1 (EC50 of 17 and 32 nM, respectively), and they present dual α/β activity by modifying both the activation and inactivation properties of the channel. NMR studies of rHj1a indicate that it adopts a cystine-stabilized αβ fold similar to known scorpion toxins. Although Hj1a and Hj2a have only limited selectivity for NaV1.1, their unusual dual mode of action provides an alternative approach to the development of selective NaV1.1 modulators for the treatment of DS.
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Affiliation(s)
- Chun Yuen Chow
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew A Walker
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shaodong Guo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Linda V Blomster
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, United States
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, United States
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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99
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Modahl CM, Brahma RK, Koh CY, Shioi N, Kini RM. Omics Technologies for Profiling Toxin Diversity and Evolution in Snake Venom: Impacts on the Discovery of Therapeutic and Diagnostic Agents. Annu Rev Anim Biosci 2019; 8:91-116. [PMID: 31702940 DOI: 10.1146/annurev-animal-021419-083626] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Snake venoms are primarily composed of proteins and peptides, and these toxins have developed high selectivity to their biological targets. This makes venoms interesting for exploration into protein evolution and structure-function relationships. A single venom protein superfamily can exhibit a variety of pharmacological effects; these variations in activity originate from differences in functional sites, domains, posttranslational modifications, and the formations of toxin complexes. In this review, we discuss examples of how the major venom protein superfamilies have diversified, as well as how newer technologies in the omics fields, such as genomics, transcriptomics, and proteomics, can be used to characterize both known and unknown toxins.Because toxins are bioactive molecules with a rich diversity of activities, they can be useful as therapeutic and diagnostic agents, and successful examples of toxin applications in these areas are also reviewed. With the current rapid pace of technology, snake venom research and its applications will only continue to expand.
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Affiliation(s)
- Cassandra M Modahl
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
| | - Rajeev Kungur Brahma
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
| | - Cho Yeow Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077;
| | - Narumi Shioi
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , , .,Department of Chemistry, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan;
| | - R Manjunatha Kini
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
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100
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Nystrom GS, Ward MJ, Ellsworth SA, Rokyta DR. Sex-based venom variation in the eastern bark centipede (Hemiscolopendra marginata). Toxicon 2019; 169:45-58. [DOI: 10.1016/j.toxicon.2019.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/25/2019] [Accepted: 08/08/2019] [Indexed: 11/15/2022]
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