1
|
Liu S, Zheng J, Li F, Chi M, Cheng S, Jiang W, Liu Y, Gu Z, Zhao J. Chromosome-scale assembly and quantitative trait locus mapping for major economic traits of the Culter alburnus genome using Illumina and PacBio sequencing with Hi-C mapping information. Front Genet 2023; 14:1072506. [PMID: 37303957 PMCID: PMC10248148 DOI: 10.3389/fgene.2023.1072506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Topmouth culter (Culter alburnus) is an economically important freshwater fish with high nutritional value. However, its potential genetic advantages have not been fully exploited. Therefore, we aimed to determine the genome sequence of C. alburnus and examine quantitative trait loci (QTLs) related to major economic traits. The results showed that 24 pseudochromosomes were anchored by 914.74 Mb of the C. alburnus genome sequence. De novo sequencing identified 31,279 protein-coding genes with an average length of 8507 bp and average coding sequ ence of 1115 bp. In addition, a high-density genetic linkage map consisting of 24 linkage groups was constructed based on 353,532 high-quality single nucleotide polymorphisms and 4,710 bin markers. A total of 28 QTLs corresponding to 11 genes, 26 QTLs corresponding to 11 genes, and 12 QTLs corresponding to 5 genes were identified for sex, intermuscular spine number and body weight traits, respectively. In this study, we assembled an accurate and nearly complete genome of C. alburnus by combining Illumina, PacBio, and high-throughput Chromosome conformation capture (Hi-C) technologies. In addition, we identified QTLs that explained variances in intermuscular spine number, body weight, and sex differences in C. alburnus. These genetic markers or candidate genes associated with growth traits provide a basis for marker-assisted selection in C. alburnus.
Collapse
Affiliation(s)
- Shili Liu
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Jianbo Zheng
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Fei Li
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Meili Chi
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shun Cheng
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Wenping Jiang
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Yinuo Liu
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Zhimin Gu
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Jinliang Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
2
|
Abstract
Abstract
Convergent evolution, the evolution of similar phenotypes among distantly related lineages, is often attributed to adaptation in response to similar selective pressures. Here, we assess the prevalence and degree of convergence in functional traits of stream fishes at the microhabitat scale in five zoogeographical regions across the world. We categorized species by microhabitat, water velocity and preference for substrate complexity and calculated the prevalence of convergence, degree of convergence and functional diversity for each category. Among species occupying similar microhabitats of small, low-gradient streams, 34% had combinations of convergent traits. Convergence occurred at higher rates than expected by chance alone, implying that adaptation to similar environmental conditions often resulted in similar evolutionary patterns along multiple niche dimensions. Two of the microhabitat groupings had significantly convergent species represented in all zoogeographical regions. Fishes occupying microhabitats with high water velocity and low structural complexity generally occupied a restricted morphospace and exhibited greater prevalence and higher degrees of convergence. This suggests that water velocity and habitat structural complexity interact, selecting a restricted distribution of trait distributions and higher degrees of convergence in stream fish assemblages. Furthermore, these results suggest that microhabitat features in streams select for fish trait distributions in a fairly predictable and deterministic manner worldwide.
Collapse
Affiliation(s)
- Luke M Bower
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843, USA
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634, USA
| | - David E Saenz
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | - Kirk O Winemiller
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
3
|
Bainbridge HE, Brien MN, Morochz C, Salazar PA, Rastas P, Nadeau NJ. Limited genetic parallels underlie convergent evolution of quantitative pattern variation in mimetic butterflies. J Evol Biol 2020; 33:1516-1529. [DOI: 10.1111/jeb.13704] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/05/2020] [Accepted: 09/04/2020] [Indexed: 01/28/2023]
Affiliation(s)
- Hannah E. Bainbridge
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| | - Melanie N. Brien
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| | - Carlos Morochz
- Biology & Research Department Mashpi Lodge Mashpi Ecuador
| | - Patricio A. Salazar
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| | - Pasi Rastas
- Institute of Biotechnology University of Helsinki Helsinki Finland
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| |
Collapse
|
4
|
Inoue T, Nakata R, Savitzky AH, Yoshinaga N, Mori A, Mori N. Variation in Bufadienolide Composition of Parotoid Gland Secretion From Three Taxa of Japanese Toads. J Chem Ecol 2020; 46:997-1009. [PMID: 32996040 DOI: 10.1007/s10886-020-01217-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/14/2020] [Accepted: 09/06/2020] [Indexed: 11/25/2022]
Abstract
Toads of the genus Bufo synthesize and accumulate bufadienolides (BDs) in their parotoid glands. BDs are cardiotonic steroids that play an important role in defense against the toads' predators. Three bufonid taxa occur in mainland Japan, Bufo japonicus formosus, B. j. japonicus, and B. torrenticola. The chemical structures of BDs isolated from B. j. formosus were studied several decades ago, but there is no further information on the toxic components of Japanese toads and their metabolism. In this study, we analyzed BDs of toads from throughout Japan and compared the BD profiles by liquid chromatography/mass spectrometry (LC/MS) and hierarchical cluster analysis (HCA). We observed BDs in three taxa of Japanese toads, and identified five of the most common BDs by nuclear magnetic resonance (NMR) analyses. Of the five BDs, only bufalin was detected in all individuals. HCA of individual BD profiles divided the three taxa into five primary clusters and several subclusters. This result indicates that BD profiles differ both among and within the taxa. The clustering pattern of BDs is generally concordant with a phylogenetic tree reconstructed from the mitochondrial cytochrome b gene of Japanese toads. Our results suggest that the BDs of Japanese toads have diversified not in response to specific selective pressures, but simply due to population structuring over evolutionary time.
Collapse
Affiliation(s)
- Takato Inoue
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Kyoto, 606-8502, Japan
| | - Ryu Nakata
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Kyoto, 606-8502, Japan
- Department of Bioscience and Biotechnology, Kyoto University of Advanced Science, 1-1 Nanjo Otani, Sogabe, Kameoka, Kyoto, 621-8555, Japan
| | - Alan H Savitzky
- Department of Biology, Utah State University, Logan, UT, 84322-5305, USA
| | - Naoko Yoshinaga
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Kyoto, 606-8502, Japan
| | - Akira Mori
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakwa, Sakyo, Kyoto, Kyoto, 606-8502, Japan
| | - Naoki Mori
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Kyoto, 606-8502, Japan.
| |
Collapse
|
5
|
Torres-Sánchez M, Wilkinson M, Gower DJ, Creevey CJ, San Mauro D. Insights into the skin of caecilian amphibians from gene expression profiles. BMC Genomics 2020; 21:515. [PMID: 32718305 PMCID: PMC7385959 DOI: 10.1186/s12864-020-06881-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary processes. During vertebrate evolution, the skin has played a crucial role, displaying a wide diversity of essential functions. To unravel the molecular basis of skin specialisations and adaptations, we compared gene expression in the skin with eight other tissues in a phylogenetically and ecologically diverse species sample of one of the most neglected vertebrate groups, the caecilian amphibians (order Gymnophiona). Results The skin of the five studied caecilian species showed a distinct gene expression profile reflecting its developmental origin and showing similarities to other epithelial tissues. We identified 59 sequences with conserved enhanced expression in the skin that might be associated with caecilian dermal specialisations. Some of the up-regulated genes shared expression patterns with human skin and potentially are involved in skin functions across vertebrates. Variation trends in gene expression were detected between mid and posterior body skin suggesting different functions between body regions. Several candidate biologically active peptides were also annotated. Conclusions Our study provides the first atlas of differentially expressed sequences in caecilian tissues and a baseline to explore the molecular basis of the skin functions in caecilian amphibians, and more broadly in vertebrates.
Collapse
Affiliation(s)
- María Torres-Sánchez
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain. .,Present address: Department of Biology, University of Florida, Gainesville, Florida, 32611, USA.
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Christopher J Creevey
- Institute for Global Food Security, Queen's University Belfast, University Road, Belfast, Northern Ireland, BT7 1NN, UK
| | - Diego San Mauro
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain
| |
Collapse
|
6
|
Lüddecke T, von Reumont BM, Förster F, Billion A, Timm T, Lochnit G, Vilcinskas A, Lemke S. An Economic Dilemma Between Molecular Weapon Systems May Explain an Arachno-atypical Venom in Wasp Spiders ( Argiope bruennichi). Biomolecules 2020; 10:E978. [PMID: 32630016 PMCID: PMC7407881 DOI: 10.3390/biom10070978] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Spiders use venom to subdue their prey, but little is known about the diversity of venoms in different spider families. Given the limited data available for orb-weaver spiders (Araneidae), we selected the wasp spider Argiope bruennichi for detailed analysis. Our strategy combined a transcriptomics pipeline based on multiple assemblies with a dual proteomics workflow involving parallel mass spectrometry techniques and electrophoretic profiling. We found that the remarkably simple venom of A. bruennichi has an atypical composition compared to other spider venoms, prominently featuring members of the cysteine-rich secretory protein, antigen 5 and pathogenesis-related protein 1 (CAP) superfamily and other, mostly high-molecular-weight proteins. We also detected a subset of potentially novel toxins similar to neuropeptides. We discuss the potential function of these proteins in the context of the unique hunting behavior of wasp spiders, which rely mostly on silk to trap their prey. We propose that the simplicity of the venom evolved to solve an economic dilemma between two competing yet metabolically expensive weapon systems. This study emphasizes the importance of cutting-edge methods to encompass the lineages of smaller venomous species that have yet to be characterized in detail, allowing us to understand the biology of their venom systems and to mine this prolific resource for translational research.
Collapse
Affiliation(s)
- Tim Lüddecke
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany; (A.B.); (A.V.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
| | - Björn M. von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Frank Förster
- Institute for Bioinformatics and Systems Biology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 58, 35392 Gießen, Germany;
| | - André Billion
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany; (A.B.); (A.V.)
| | - Thomas Timm
- Institute of Biochemistry, Justus-Liebig-University of Gießen, Friedrichstr. 24, 35392 Gießen, Germany; (T.T.); (G.L.)
| | - Günter Lochnit
- Institute of Biochemistry, Justus-Liebig-University of Gießen, Friedrichstr. 24, 35392 Gießen, Germany; (T.T.); (G.L.)
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Gießen, Germany; (A.B.); (A.V.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Sarah Lemke
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; (B.M.v.R.); (S.L.)
- Institute for Insect Biotechnology, Justus-Liebig-University of Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| |
Collapse
|
7
|
Doane MP, Morris MM, Papudeshi B, Allen L, Pande D, Haggerty JM, Johri S, Turnlund AC, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery AJ, Lima LFO, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards RA, Dinsdale EA. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. MICROBIOME 2020; 8:93. [PMID: 32534596 PMCID: PMC7293782 DOI: 10.1186/s40168-020-00840-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/15/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. RESULTS We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. CONCLUSION Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.
Collapse
Affiliation(s)
- Michael P Doane
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Megan M Morris
- Biology Department, San Diego State University, San Diego, CA, USA
- Department Biology, Stanford University, Stanford, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Indiana University, San Diego, Indiana, USA
| | - Lauren Allen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Dnyanada Pande
- Computer Sciences Department, San Diego State University, San Diego, CA, USA
| | - John M Haggerty
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shaili Johri
- Biology Department, San Diego State University, San Diego, CA, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Abigail C Turnlund
- Biology Department, San Diego State University, San Diego, CA, USA
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queens, USA
| | | | - Dovi Kacev
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
| | - Andy Nosal
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA, USA
| | - Deni Ramirez
- Whale Shark Mexico, ConCiencia Mexico AC, La Paz, BC, USA
| | - Kevin Hovel
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Julia Ledbetter
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Alker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Jackeline Avalos
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristi Baker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shruti Bhide
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Emma Billings
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Steven Byrum
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Molly Clemens
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | | | - Oscar Gomez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Omar Gutierrez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Selena Hinton
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Donald Kieu
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Angie Kim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rebeca Loaiza
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | - Jordan McGhee
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristine Nguyen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Sabrina Parlan
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Pham
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rosalyn Price-Waldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert A Edwards
- Biology Department, San Diego State University, San Diego, CA, USA
- Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Elizabeth A Dinsdale
- Biology Department, San Diego State University, San Diego, CA, USA.
- Viral Information Institute, San Diego State University, San Diego, CA, USA.
| |
Collapse
|
8
|
Cholecystokinin in the central nervous system of the sea lamprey Petromyzon marinus: precursor identification and neuroanatomical relationships with other neuronal signalling systems. Brain Struct Funct 2019; 225:249-284. [PMID: 31807925 DOI: 10.1007/s00429-019-01999-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/27/2019] [Indexed: 12/23/2022]
Abstract
Cholecystokinin (CCK) is a neuropeptide that modulates processes such as digestion, satiety, and anxiety. CCK-type peptides have been characterized in jawed vertebrates and invertebrates, but little is known about CCK-type signalling in the most ancient group of vertebrates, the agnathans. Here, we have cloned and sequenced a cDNA encoding a sea lamprey (Petromyzon marinus L.) CCK-type precursor (PmCCK), which contains a CCK-type octapeptide sequence (PmCCK-8) that is highly similar to gnathostome CCKs. Using mRNA in situ hybridization, the distribution of PmCCK-expressing neurons was mapped in the CNS of P. marinus. This revealed PmCCK-expressing neurons in the hypothalamus, posterior tubercle, prethalamus, nucleus of the medial longitudinal fasciculus, midbrain tegmentum, isthmus, rhombencephalic reticular formation, and the putative nucleus of the solitary tract. Some PmCCK-expressing neuronal populations were only observed in adults, revealing important differences with larvae. We generated an antiserum to PmCCK-8 to enable immunohistochemical analysis of CCK expression, which revealed that GABA or glutamate, but not serotonin, tyrosine hydroxylase or neuropeptide Y, is co-expressed in some PmCCK-8-immunoreactive (ir) neurons. Importantly, this is the first demonstration of co-localization of GABA and CCK in neurons of a non-mammalian vertebrate. We also characterized extensive cholecystokinergic fibre systems of the CNS, including innervation of habenular subnuclei. A conspicuous PmCCK-8-ir tract ascending in the lateral rhombencephalon selectively innervates a glutamatergic population in the dorsal isthmic grey. Interestingly, this tract is reminiscent of the secondary gustatory/visceral tract of teleosts. In conclusion, this study provides important new information on the evolution of the cholecystokinergic system in vertebrates.
Collapse
|
9
|
A Hylarana latouchii Skin Secretion-Derived Novel Bombesin-Related Pentadecapeptide (Ranatensin-HLa) Evoke Myotropic Effects on the in vitro Rat Smooth Muscles. Toxins (Basel) 2019; 11:toxins11040204. [PMID: 30959738 PMCID: PMC6521075 DOI: 10.3390/toxins11040204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 11/17/2022] Open
Abstract
Amphibians have developed successful defensive strategies for combating predators and invasive microorganisms encountered in their broad range of environments, which involve secretion of complex cocktails of noxious, toxic and diverse bioactive molecules from the skins. In recent years, amphibian skin secretions have been considered as an extraordinary warehouse for the discovery of therapeutic medicines. In this study, through bioactivity screening of the Hylarana latouchii skin secretion-derived fractions, a novel peptide belonging to ranatensin subfamily (ranatensin-HLa) was discovered, and structurally and pharmacologically-characterised. It consists of 15 amino acid residues, pGlu-NGDRAPQWAVGHFM-NH2, and its synthetic replicate was found to exhibit pharmacological activities on increasing the contraction of the in vitro rat bladder and uterus smooth muscles. Corresponding characteristic sigmoidal dose-response curves with EC50 values of 7.1 nM and 5.5 nM were produced, respectively, in bladder and uterus. Moreover, the precursor of ranatensin-HLa showed a high degree of similarity to those of bombesin-like peptides from Odorrana grahami and Odorrana schmackeri. Hylarana latouchii skin continues to serve as a storehouse with diverse lead compounds for the development of therapeutically effective medicines.
Collapse
|
10
|
Torres-Sánchez M, Creevey CJ, Kornobis E, Gower DJ, Wilkinson M, San Mauro D. Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families. DNA Res 2019; 26:13-20. [PMID: 30351380 PMCID: PMC6379020 DOI: 10.1093/dnares/dsy034] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 09/13/2018] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians.
Collapse
Affiliation(s)
- María Torres-Sánchez
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Etienne Kornobis
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Diego San Mauro
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| |
Collapse
|
11
|
Mitchell ML, Shafee T, Papenfuss AT, Norton RS. Evolution of cnidarian
trans
‐defensins: Sequence, structure and exploration of chemical space. Proteins 2019; 87:551-560. [DOI: 10.1002/prot.25679] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/24/2019] [Accepted: 02/19/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Michela L. Mitchell
- Medicinal Chemistry Monash Institute of Pharmaceutical Sciences, Monash University Melbourne Victoria Australia
- Bioinformatics Division Walter & Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Marine Invertebrates, Museum Victoria Melbourne Victoria Australia
- Biodiversity and Geosciences, Queensland Museum South Brisbane Queensland Australia
| | - Thomas Shafee
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria Australia
- Department of Animal Plant, and Soil Sciences, AgriBio, La Trobe University Melbourne Victoria Australia
| | - Anthony T. Papenfuss
- Bioinformatics Division Walter & Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Peter MacCallum Cancer Centre Melbourne Victoria Australia
- Department of Medical Biology University of Melbourne Melbourne Victoria Australia
- Sir Peter MacCallum Department of Oncology University of Melbourne Melbourne Victoria Australia
- Department of Mathematics and Statistics University of Melbourne Melbourne Victoria Australia
| | - Raymond S. Norton
- Medicinal Chemistry Monash Institute of Pharmaceutical Sciences, Monash University Melbourne Victoria Australia
| |
Collapse
|
12
|
Independent evolution of complex development in animals and plants: deep homology and lateral gene transfer. Dev Genes Evol 2019; 229:25-34. [PMID: 30685797 DOI: 10.1007/s00427-019-00626-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/10/2019] [Indexed: 01/25/2023]
Abstract
The evolution of multicellularity is a premier example of phenotypic convergence: simple multicellularity evolved independently many times, and complex multicellular phenotypes are found in several distant groups. Furthermore, both animal and plant lineages have independently reached extreme levels of morphological, functional, and developmental complexity. This study explores the genetic basis for the parallel evolution of complex multicellularity and development in the animal and green plant (i.e., green algae and land plants) lineages. Specifically, the study (i) identifies the SAND domain-a DNA-binding domain with important roles in the regulation of cell proliferation and differentiation, as unique to animals, green algae, and land plants; and (ii) suggests that the parallel deployment of this ancestral domain in similar regulatory roles could have contributed to the independent evolution of complex development in these distant groups. Given the deep animal-green plant divergence, the limited distribution of the SAND domain is best explained by invoking a lateral gene transfer (LGT) event from a green alga to an early metazoan. The presence of a sequence motif specifically shared by a family of SAND-containing transcription factors involved in the evolution of complex multicellularity in volvocine algae and two types of SAND proteins that emerged early in the evolution of animals is consistent with this scenario. Overall, these findings imply that (i) in addition to be involved in the evolution of similar phenotypes, deep homologous sequences can also contribute to shaping parallel evolutionary trajectories in distant lineages, and (ii) LGT could provide an additional source of latent homologous sequences that can be deployed in analogous roles and affect the evolutionary potentials of distantly related groups.
Collapse
|
13
|
Hume JB, Wagner M. A death in the family: Sea lamprey ( Petromyzon marinus) avoidance of confamilial alarm cues diminishes with phylogenetic distance. Ecol Evol 2018; 8:3751-3762. [PMID: 29686855 PMCID: PMC5901161 DOI: 10.1002/ece3.3930] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/05/2018] [Accepted: 01/16/2018] [Indexed: 11/25/2022] Open
Abstract
Alarm signals released after predator attack function as reliable public information revealing areas of high risk. The utility of this information can extend beyond species boundaries, benefiting heterospecifics capable of recognizing and responding appropriately to the signal. Nonmutually exclusive hypotheses explaining the acquisition of heterospecific reactivity to cues suggest it could be conserved phylogenetically following its evolution in a common ancestor (a species‐level effect) and/or learned during periods of shared risk (a population‐level effect; e.g., shared predators). Using a laboratory‐based space‐use behavioral assay, we tested the response of sea lamprey (Petromyzon marinus) to the damage‐released alarm cues of five confamilial (sympatric and allopatric) species and two distantly related out‐groups: a sympatric teleost (white sucker Catostomus commersonii) and an allopatric agnathan (Atlantic hagfish Myxine glutinosa). We found that sea lamprey differed in their response to conspecific and heterospecific odors; exhibiting progressively weaker avoidance of cues derived from more phylogenetically distant confamilials regardless of current overlap in distribution. Odors from out‐groups elicited no response. These findings suggest that a damage‐released alarm cue is at least partially conserved within the Petromyzontidae and that sea lamprey perceives predator attacks directed to closely related taxa. These findings are consistent with similar observations from gastropod, amphibian and bony fish taxa, and we discuss this in an eco‐evo context to provide a plausible explanation for the acquisition and maintenance of the response in sea lamprey.
Collapse
Affiliation(s)
- John B Hume
- Department of Fisheries & Wildlife Michigan State University East Lansing MI USA
| | - Michael Wagner
- Department of Fisheries & Wildlife Michigan State University East Lansing MI USA
| |
Collapse
|
14
|
Gao B, Zhu S. Mesobuthus Venom-Derived Antimicrobial Peptides Possess Intrinsic Multifunctionality and Differential Potential as Drugs. Front Microbiol 2018; 9:320. [PMID: 29599756 PMCID: PMC5863496 DOI: 10.3389/fmicb.2018.00320] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/09/2018] [Indexed: 11/15/2022] Open
Abstract
Animal venoms are a mixture of peptides and proteins that serve two basic biological functions: predation and defense against both predators and microbes. Antimicrobial peptides (AMPs) are a common component extensively present in various scorpion venoms (herein abbreviated as svAMPs). However, their roles in predation and defense against predators and potential as drugs are poorly understood. Here, we report five new venom peptides with antimicrobial activity from two Mesobuthus scorpion species. These α-helical linear peptides displayed highly bactericidal activity toward all the Gram-positive bacteria used here but differential activity against Gram-negative bacteria and fungi. In addition to the antibiotic activity, these AMPs displayed lethality to houseflies and hemotoxin-like toxicity on mice by causing hemolysis, tissue damage and inducing inflammatory pain. Unlike AMPs from other origins, these venom-derived AMPs seem to be unsuitable as anti-infective drugs due to their high hemolysis and low serum stability. However, MeuTXKβ1, a known two-domain Mesobuthus AMP, is an exception since it exhibits high activity toward antibiotic resistant Staphylococci clinical isolates with low hemolysis and high serum stability. The findings that the classical AMPs play predatory and defensive roles indicate that the multifunctionality of scorpion venom components is an intrinsic feature likely evolved by natural selection from microbes, prey and predators of scorpions. This definitely provides an excellent system in which one can study how a protein adaptively evolves novel functions in a new environment. Meantimes, new strategies are needed to remove the toxicity of svAMPs on eukaryotic cells when they are used as leads for anti-infective drugs.
Collapse
Affiliation(s)
- Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
15
|
Koludarov I, Jackson TN, Brouw BOD, Dobson J, Dashevsky D, Arbuckle K, Clemente CJ, Stockdale EJ, Cochran C, Debono J, Stephens C, Panagides N, Li B, Manchadi MLR, Violette A, Fourmy R, Hendrikx I, Nouwens A, Clements J, Martelli P, Kwok HF, Fry BG. Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms. Toxins (Basel) 2017; 9:E242. [PMID: 28783084 PMCID: PMC5577576 DOI: 10.3390/toxins9080242] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023] Open
Abstract
While snake venoms have been the subject of intense study, comparatively little work has been done on lizard venoms. In this study, we have examined the structural and functional diversification of anguimorph lizard venoms and associated toxins, and related these results to dentition and predatory ecology. Venom composition was shown to be highly variable across the 20 species of Heloderma, Lanthanotus, and Varanus included in our study. While kallikrein enzymes were ubiquitous, they were also a particularly multifunctional toxin type, with differential activities on enzyme substrates and also ability to degrade alpha or beta chains of fibrinogen that reflects structural variability. Examination of other toxin types also revealed similar variability in their presence and activity levels. The high level of venom chemistry variation in varanid lizards compared to that of helodermatid lizards suggests that venom may be subject to different selection pressures in these two families. These results not only contribute to our understanding of venom evolution but also reveal anguimorph lizard venoms to be rich sources of novel bioactive molecules with potential as drug design and development lead compounds.
Collapse
Affiliation(s)
- Ivan Koludarov
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Timothy Nw Jackson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
- Australian Venom Research Unit, School of Biomedical Sciences, Level 2 Medical Building, University of Melbourne, Victoria 3010, Australia.
| | - Bianca Op den Brouw
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - James Dobson
- 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.
| | - Kevin Arbuckle
- Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Christofer J Clemente
- University of the Sunshine Coast, School of Science and Engineering, Sippy Downs, Queensland 4558, Australia.
| | | | - Chip Cochran
- Department of Earth and Biological Sciences, Loma Linda University, Loma Linda, CA 92350, USA.
| | - Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Carson Stephens
- School of Biomedical Sciences, Queensland University of Technology, Brisbane QLD 4001, Australia.
| | - Nadya Panagides
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Bin Li
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.
| | | | - Aude Violette
- Alphabiotoxine Laboratory sprl, Barberie 15, 7911 Montroeul-au-bois, Belgium.
| | - Rudy Fourmy
- Alphabiotoxine Laboratory sprl, Barberie 15, 7911 Montroeul-au-bois, Belgium.
| | - Iwan Hendrikx
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| | - Amanda Nouwens
- School of Chemistry and Molecular Biology, University of Queenslnd, St. Lucia QLD 4072, Australia.
| | - Judith Clements
- School of Biomedical Sciences, Queensland University of Technology, Brisbane QLD 4001, Australia.
| | | | - Hang Fai Kwok
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia QLD 4072, Australia.
| |
Collapse
|
16
|
Verdonck R, De Haes W, Cardoen D, Menschaert G, Huhn T, Landuyt B, Baggerman G, Boonen K, Wenseleers T, Schoofs L. Fast and Reliable Quantitative Peptidomics with labelpepmatch. J Proteome Res 2016; 15:1080-9. [DOI: 10.1021/acs.jproteome.5b00845] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Gerben Menschaert
- Research
Group of Bio-informatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Thomas Huhn
- Chemistry
Department, University of Konstanz, Konstanz, Germany
| | | | - Geert Baggerman
- CFP/CeProMa, Antwerp University, Antwerp, Belgium
- Applied Bio & Molecular Systems, Vito, Mol, Belgium
| | - Kurt Boonen
- Biology
Department, KU Leuven, Leuven, Belgium
| | | | | |
Collapse
|
17
|
Shigeri Y, Horie M, Yoshida T, Hagihara Y, Imura T, Inagaki H, Haramoto Y, Ito Y, Asashima M. Physicochemical and biological characterizations of Pxt peptides from amphibian (Xenopus tropicalis) skin. J Biochem 2016; 159:619-29. [PMID: 26802742 DOI: 10.1093/jb/mvw003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/15/2015] [Indexed: 01/27/2023] Open
Abstract
Pxt peptides (Pxt-1 through Pxt-12) have been isolated from amphibian, Xenopus tropicalis Pxt-related peptides (Pxt-2, Pxt-5, Pxt-12, reverse Pxt-2, reverse Pxt-5 and reverse Pxt-12) with significant foaming properties were further characterized. In the physicochemical experiments, all Pxt-related peptides formed significant amphiphilic α-helices in 50% 2,2,2-trifluoroethanol by circular dichroism measurements. Among Pxt-related peptides, both Pxt-5 and reverse Pxt-5 were the most effective in reducing their surface tensions. Moreover, Pxt-2, Pxt-5 and reverse Pxt-5 produced constant surface tensions above their critical association concentrations, suggesting the micelle-like assemblies. In the biological experiments, Pxt-5 possessed the most potent hemolytic activity, while reverse Pxt-5 exhibited the most remarkable gene expression of interleukin 8 and heme oxygenase 1 and the most potent cytotoxicity in HaCaT cells. In contrast, Pxt-12 and reverse Pxt-12 were much weaker in antimicrobial assays for Gram-negative bacteria, Gram-positive bacteria and yeasts, as well as in hemolytic, cell viability and cytotoxicity assays in HaCaT cells. All Pxt-related peptides exhibited about 20-50% of the total cellular histamine release at 10(-5) M, as well as mastoparan and melittin in mast cells. Real-time polymerase chain reaction analysis confirmed the gene expressions of Pxt-5 in testis and Pxt-12 in muscle, in addition to skin, while Pxt-2 was only in skin.
Collapse
Affiliation(s)
- Yasushi Shigeri
- Health Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan;
| | - Masanori Horie
- Health Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Tsuyoshi Yoshida
- Health Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yoshihisa Hagihara
- Health Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Tomohiro Imura
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5-2, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Hidetoshi Inagaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan; and
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Makoto Asashima
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| |
Collapse
|
18
|
König E, Bininda-Emonds ORP, Shaw C. The diversity and evolution of anuran skin peptides. Peptides 2015; 63:96-117. [PMID: 25464160 DOI: 10.1016/j.peptides.2014.11.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 02/06/2023]
Abstract
Amphibians exhibit various, characteristic adaptations related to their "incomplete" shift from the aquatic to the terrestrial habitat. In particular, the integument was subject to a number of specialized modifications during the evolution of these animals. In this review, we place special emphasis on endogenous host-defence skin peptides from the cuteanous granular glands anuran amphibians (frogs and toads). The overview on the two broad groups of neuroactive and antimicrobial peptides (AMPs) goes beyond a simple itemization in that we provide a new perspective into the evolution and function of anuran AMPs. Briefly, these cationic, amphipathic and α-helical peptides are traditionally viewed as being part of the innate immune system, protecting the moist skin against invading microorganisms through their cytolytic action. However, the complete record of anuran species investigated to date suggests that AMPs are distributed sporadically (i.e., non-universally) across Anura. Together with the intriguing observation that virtually all anurans known to produce neuropeptides in their granular glands also co-secrete cytolytic peptides, we call the traditional role for AMPs as being purely antimicrobial into question and present an alternative scenario. We hypothesize AMPs to assist neuroactive peptides in their antipredator role through their cytolytic action increasing the delivery of the latter to the endocrine and nervous system of the predator. Thus, AMPs are more accurately viewed as cytolysins and their contribution to the immune system is better regarded as an accessory benefit.
Collapse
Affiliation(s)
- Enrico König
- AG Systematik und Evolutionsbiologie, IBU - Fakultät V, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Strasse 9-11, 26129 Oldenburg, Germany.
| | - Olaf R P Bininda-Emonds
- AG Systematik und Evolutionsbiologie, IBU - Fakultät V, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Strasse 9-11, 26129 Oldenburg, Germany
| | - Chris Shaw
- School of Pharmacy, Medical Biology Center, Queen's University, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, UK
| |
Collapse
|
19
|
MS approaches to select peptides with post-translational modifications from amphibian defense secretions prior to full sequence elucidation. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
20
|
Shigeri Y, Yasuda A, Hagihara Y, Nishi K, Watanabe K, Imura T, Inagaki H, Haramoto Y, Ito Y, Asashima M. Identification of novel peptides from amphibian (Xenopus tropicalis) skin by direct tissue MALDI-MS analysis. FEBS J 2014; 282:102-13. [PMID: 25312021 DOI: 10.1111/febs.13107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/01/2014] [Accepted: 10/08/2014] [Indexed: 01/08/2023]
Abstract
Twelve novel peptides (Pxt-1 to Pxt-12) were isolated from the skin of Xenopus tropicalis, diploid frogs, using topological MS analysis. Among them, Pxt-8, Pxt-9, and Pxt-10 were the N terminus of Pxt-1, N terminus of Pxt-3 and C terminus of Pxt-11, respectively. The Pxt-3 and Pxt-11 peptides shared significant sequence homologies with magainins 1, -2 and levitide, respectively, which all isolated from X. laevis. Pxt-12 was identical to the X. tropicalis XT-6-like precursor previously isolated by ESI-MS/MS. None of the Pxt peptides contained any Cys, Asp, Tyr or Trp, although Leu and Lys were frequently found as typical frog-skin peptides. RT-PCR analysis confirmed the gene expressions of Pxt-2, Pxt-3, Pxt-4, Pxt-5, Pxt-7 and Pxt-11 in X. tropicalis skin. Several ion peaks corresponding to all identified Pxt peptides were observed with MALDI-MS analysis of X. tropicalis secretory fluids, collected after in vivo stimulation, which suggested that Pxt peptides were definitely secretory molecules. CD studies and Schiffer-Edmundson helical wheel projections suggested that Pxt-5, as well as mastoparan, at least, could form a typical amphiphilic α helix without a phospholipid or a membrane-mimetic solvent (trifluoroethanol). Moreover, Pxt-2 and Pxt-5 showed growth inhibitory effects on both Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive). Measurements of dynamic light scattering and the surface tensions of Pxt peptides solutions suggested that both Pxt-2 and Pxt-5 could form associations as micelles and behave like a general surfactant. Moreover, the remarkable foaming properties of Pxt-2 and Pxt-5 were observed, as well as those of the secretory fluids of X. tropicalis.
Collapse
Affiliation(s)
- Yasushi Shigeri
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Osaka, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Identification and localization of gastrointestinal hormones in the skin of the bullfrog Rana catesbeiana during periods of activity and hibernation. Acta Histochem 2014; 116:1418-26. [PMID: 25440532 DOI: 10.1016/j.acthis.2014.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/11/2014] [Accepted: 09/18/2014] [Indexed: 11/23/2022]
Abstract
Amphibian skin and its secretions contain a wide variety of biogenic amines and biologically active peptides, some of which are either identical or highly homologous to gastrointestinal hormones (GHs) of higher vertebrates. This study investigated the distribution density and immunoreactive (IR) intensity of 5-hydroxytryptamine (5-HT), gastrin (GAS), somatostatin (SS), pancreatic polypeptide (PP), neuropeptide Y (NPY) and glucagon (GLU) IR cells in the skin of the bullfrog Rana catesbeiana during periods of activity and hibernation. The results indicated that the six types of GHs were all present in the bullfrog skin and were most predominant in the epidermis and mucous glands. In dorsal skin, the density of the GHs-IR cells in mucous glands was higher than that in epidermis except for GAS-IR cells. In ventral skin, the density of 5-HT, PP and NPY-IR cells in mucous glands was also higher than that in the epidermis. During hibernation, the density of the six types of GHs-IR cells and the IR intensity of GAS, SS, NPY and GLU-IR cells in the epidermis of dorsal skin increased significantly. The IR intensity of SS, PP and NPY-IR cells in granular glands of ventral skin also increased significantly during hibernation. These results suggested that multiple types of GHs-IR cells present in the skin of R. catesbeiana, may play important roles in the regulation of the physiological functions of skin. Also, adaptive changes in the density and IR intensity of GHs-IR cells occurred during hibernation.
Collapse
|
22
|
Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat Commun 2014; 5:4471. [PMID: 25034666 DOI: 10.1038/ncomms5471] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/19/2014] [Indexed: 01/29/2023] Open
Abstract
Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms arose early in fungal evolution and became dominant independently in multiple clades, most likely via parallel diversification of Zn-cluster transcription factors, a fungal-specific family involved in regulating yeast-filamentous switches. Our results imply that convergent evolution can happen by the repeated deployment of a conserved genetic toolkit for the same function in distinct clades via regulatory evolution. We suggest that this mechanism might be a common source of evolutionary convergence even at large time scales.
Collapse
|
23
|
Matthijs S, Ye L, Stijlemans B, Cornelis P, Bossuyt F, Roelants K. Low structural variation in the host-defense peptide repertoire of the dwarf clawed frog Hymenochirus boettgeri (Pipidae). PLoS One 2014; 9:e86339. [PMID: 24466037 PMCID: PMC3899252 DOI: 10.1371/journal.pone.0086339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/06/2013] [Indexed: 02/05/2023] Open
Abstract
THE skin secretion of many amphibians contains peptides that are able to kill a broad range of microorganisms (antimicrobial peptides: AMPs) and potentially play a role in innate immune defense. Similar to the toxin arsenals of various animals, amphibian AMP repertoires typically show major structural variation, and previous studies have suggested that this may be the result of diversifying selection in adaptation to a diverse spectrum of pathogens. Here we report on transcriptome analyses that indicate a very different pattern in the dwarf clawed frog H. boettgeri. Our analyses reveal a diverse set of transcripts containing two to six tandem repeats, together encoding 14 distinct peptides. Five of these have recently been identified as AMPs, while three more are shown here to potently inhibit the growth of gram-negative bacteria, including multi-drug resistant strains of the medically important Pseudomonas aeruginosa. Although the number of predicted peptides is similar to the numbers of related AMPs in Xenopus and Silurana frog species, they show significantly lower structural variation. Selection analyses confirm that, in contrast to the AMPs of other amphibians, the H. boettgeri peptides did not evolve under diversifying selection. Instead, the low sequence variation among tandem repeats resulted from purifying selection, recent duplication and/or concerted gene evolution. Our study demonstrates that defense peptide repertoires of closely related taxa, after diverging from each other, may evolve under differential selective regimes, leading to contrasting patterns of structural diversity.
Collapse
Affiliation(s)
- Severine Matthijs
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lumeng Ye
- Department of Bioengineering Sciences, Research Group of Microbiology and Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, Brussels, Belgium
| | - Benoit Stijlemans
- Unit of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Pierre Cornelis
- Department of Bioengineering Sciences, Research Group of Microbiology and Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, Brussels, Belgium
| | - Franky Bossuyt
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kim Roelants
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
- * E-mail:
| |
Collapse
|
24
|
Zhu S, Gao B. Nematode-derived drosomycin-type antifungal peptides provide evidence for plant-to-ecdysozoan horizontal transfer of a disease resistance gene. Nat Commun 2014; 5:3154. [DOI: 10.1038/ncomms4154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 12/19/2013] [Indexed: 11/09/2022] Open
|
25
|
Origin and functional diversification of an amphibian defense peptide arsenal. PLoS Genet 2013; 9:e1003662. [PMID: 23935531 PMCID: PMC3731216 DOI: 10.1371/journal.pgen.1003662] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 06/05/2013] [Indexed: 11/19/2022] Open
Abstract
The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones. Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones.
Collapse
|
26
|
Martin A, Orgogozo V. The Loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation. Evolution 2013; 67:1235-50. [PMID: 23617905 DOI: 10.1111/evo.12081] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/26/2013] [Indexed: 12/11/2022]
Abstract
What is the nature of the genetic changes underlying phenotypic evolution? We have catalogued 1008 alleles described in the literature that cause phenotypic differences among animals, plants, and yeasts. Surprisingly, evolution of similar traits in distinct lineages often involves mutations in the same gene ("gene reuse"). This compilation yields three important qualitative implications about repeated evolution. First, the apparent evolution of similar traits by gene reuse can be traced back to two alternatives, either several independent causative mutations or a single original mutational event followed by sorting processes. Second, hotspots of evolution-defined as the repeated occurrence of de novo mutations at orthologous loci and causing similar phenotypic variation-are omnipresent in the literature with more than 100 examples covering various levels of analysis, including numerous gain-of-function events. Finally, several alleles of large effect have been shown to result from the aggregation of multiple small-effect mutations at the same hotspot locus, thus reconciling micromutationist theories of adaptation with the empirical observation of large-effect variants. Although data heterogeneity and experimental biases prevented us from extracting quantitative trends, our synthesis highlights the existence of genetic paths of least resistance leading to viable evolutionary change.
Collapse
Affiliation(s)
- Arnaud Martin
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, 215 Tower Road, Ithaca, New York, 14853, USA.
| | | |
Collapse
|
27
|
Antimicrobial peptides and alytesin are co-secreted from the venom of the Midwife toad, Alytes maurus (Alytidae, Anura): Implications for the evolution of frog skin defensive secretions. Toxicon 2012; 60:967-81. [DOI: 10.1016/j.toxicon.2012.06.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/20/2012] [Accepted: 06/28/2012] [Indexed: 11/20/2022]
|
28
|
Conte GL, Arnegard ME, Peichel CL, Schluter D. The probability of genetic parallelism and convergence in natural populations. Proc Biol Sci 2012; 279:5039-47. [PMID: 23075840 PMCID: PMC3497250 DOI: 10.1098/rspb.2012.2146] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.
Collapse
Affiliation(s)
- Gina L Conte
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada.
| | | | | | | |
Collapse
|
29
|
Wong ES, Belov K. Venom evolution through gene duplications. Gene 2012; 496:1-7. [DOI: 10.1016/j.gene.2012.01.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 01/10/2012] [Accepted: 01/10/2012] [Indexed: 12/30/2022]
|
30
|
Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. Heredity (Edinb) 2011; 108:480-9. [PMID: 22167055 DOI: 10.1038/hdy.2011.119] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Recent findings of sequence convergence in the Prestin gene among some bats and cetaceans suggest that parallel adaptations for high-frequency hearing have taken place during the evolution of echolocation. To determine if this gene is an exception, or instead similar processes have occurred in other hearing genes, we have examined Tmc1 and Pjvk, both of which are associated with non-syndromic hearing loss in mammals. These genes were amplified and sequenced from a number of mammalian species, including echolocating and non-echolocating bats and whales, and were analysed together with published sequences. Sections of both genes showed phylogenetic signals that conflicted with accepted species relationships, with coding regions uniting laryngeal echolocating bats in a monophyletic clade. Bayesian estimates of posterior probabilities of convergent and divergent substitutions provided more direct evidence of sequence convergence between the two groups of laryngeal echolocating bats as well as between echolocating bats and dolphins. We found strong evidence of positive selection acting on some echolocating bat species and echolocating cetaceans, contrasting with purifying selection on non-echolocating bats. Signatures of sequence convergence and molecular adaptation in two additional hearing genes suggest that the acquisition of high-frequency hearing has involved multiple loci.
Collapse
|
31
|
Wong ESW, Papenfuss AT, Whittington CM, Warren WC, Belov K. A limited role for gene duplications in the evolution of platypus venom. Mol Biol Evol 2011; 29:167-77. [PMID: 21816864 DOI: 10.1093/molbev/msr180] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gene duplication followed by adaptive selection is believed to be the primary driver of venom evolution. However, to date, no studies have evaluated the importance of gene duplications for venom evolution using a genomic approach. The availability of a sequenced genome and a venom gland transcriptome for the enigmatic platypus provides a unique opportunity to explore the role that gene duplication plays in venom evolution. Here, we identify gene duplication events and correlate them with expressed transcripts in an in-season venom gland. Gene duplicates (1,508) were identified. These duplicated pairs (421), including genes that have undergone multiple rounds of gene duplications, were expressed in the venom gland. The majority of these genes are involved in metabolism and protein synthesis not toxin functions. Twelve secretory genes including serine proteases, metalloproteinases, and protease inhibitors likely to produce symptoms of envenomation such as vasodilation and pain were detected. Only 16 of 107 platypus genes with high similarity to known toxins evolved through gene duplication. Platypus venom C-type natriuretic peptides and nerve growth factor do not possess lineage-specific gene duplicates. Extensive duplications, believed to increase the potency of toxic content and promote toxin diversification, were not found. This is the first study to take a genome-wide approach in order to examine the impact of gene duplication on venom evolution. Our findings support the idea that adaptive selection acts on gene duplicates to drive the independent evolution and functional diversification of similar venom genes in venomous species. However, gene duplications alone do not explain the "venome" of the platypus. Other mechanisms, such as alternative splicing and mutation, may be important in venom innovation.
Collapse
Affiliation(s)
- Emily S W Wong
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia.
| | | | | | | | | |
Collapse
|
32
|
Zahid OK, Mechkarska M, Ojo OO, Abdel-Wahab YHA, Flatt PR, Meetani MA, Conlon JM. Caerulein-and xenopsin-related peptides with insulin-releasing activities from skin secretions of the clawed frogs, Xenopus borealis and Xenopus amieti (Pipidae). Gen Comp Endocrinol 2011; 172:314-20. [PMID: 21458457 DOI: 10.1016/j.ygcen.2011.03.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Revised: 03/19/2011] [Accepted: 03/23/2011] [Indexed: 11/27/2022]
Abstract
Caerulein-related peptides were identified in norepinephrine-stimulated skin secretions of the tetraploid frog Xenopus borealis and the octoploid frog Xenopus amieti using negative ion electrospray mass spectrometry and their primary structures determined by positive ion tandem (MS/MS) mass spectrometry. X. borealis caerulein-B1 (pGlu-Gln-Asp-Tyr(SO(3))-Gly-Thr-Gly-Trp-Met-Asp-Phe.NH2) contains an additional Gly(5) residue compared with X. laevis caerulein and caerulein-B2 (pGlu-Asp-Tyr(SO(3))-Thr-Gly-Trp-Met-Asp-Phe.NH2) contains a Gln(2) deletion. X. amieti caerulein was identical to the X. laevis peptide. In addition, xenopsin, identical to the peptide from X. laevis, together with xenopsin-AM2 (pGlu-Gly-Arg-Arg-Pro-Trp-Ile- Leu) that contains the substitution Lys(3)→Arg were isolated from X. amieti secretions. X. borealis caerulein-B1, and X. amieti xenopsin and xenopsin-AM2 produced significant (P<0.05) and concentration-dependent stimulations of insulin release from the rat BRIN-BD11 clonal β cell line at concentrations ⩾30nM. The peptides did not stimulate the release of lactate dehydrogenase at concentrations up to 3μM demonstrating that the integrity of the plasma membrane had been preserved. While their precise biological role is unclear, the caerulein- and xenopsin-related peptides may constitute a component of the animal's chemical defenses against predators.
Collapse
Affiliation(s)
- Osama K Zahid
- Departmentof Chemistry, Faculty of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
| | | | | | | | | | | | | |
Collapse
|
33
|
Abstract
Convergent evolution of similar phenotypic features in similar environmental contexts has long been taken as evidence of adaptation. Nonetheless, recent conceptual and empirical developments in many fields have led to a proliferation of ideas about the relationship between convergence and adaptation. Despite criticism from some systematically minded biologists, I reaffirm that convergence in taxa occupying similar selective environments often is the result of natural selection. However, convergent evolution of a trait in a particular environment can occur for reasons other than selection on that trait in that environment, and species can respond to similar selective pressures by evolving nonconvergent adaptations. For these reasons, studies of convergence should be coupled with other methods-such as direct measurements of selection or investigations of the functional correlates of trait evolution-to test hypotheses of adaptation. The independent acquisition of similar phenotypes by the same genetic or developmental pathway has been suggested as evidence of constraints on adaptation, a view widely repeated as genomic studies have documented phenotypic convergence resulting from change in the same genes, sometimes even by the same mutation. Contrary to some claims, convergence by changes in the same genes is not necessarily evidence of constraint, but rather suggests hypotheses that can test the relative roles of constraint and selection in directing phenotypic evolution.
Collapse
Affiliation(s)
- Jonathan B Losos
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA.
| |
Collapse
|
34
|
Current world literature. Curr Opin Endocrinol Diabetes Obes 2011; 18:83-98. [PMID: 21178692 DOI: 10.1097/med.0b013e3283432fa7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
35
|
Knowledge-based computational methods for identifying or designing novel, non-homologous antimicrobial peptides. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:371-85. [DOI: 10.1007/s00249-011-0674-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 12/16/2010] [Accepted: 01/04/2011] [Indexed: 02/07/2023]
|
36
|
Nadeau NJ, Jiggins CD. A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations. Trends Genet 2010; 26:484-92. [DOI: 10.1016/j.tig.2010.08.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/16/2010] [Accepted: 08/18/2010] [Indexed: 12/20/2022]
|
37
|
|