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Fonseca-González I, Velasquez-Agudelo E, Londoño-Mesa MH, Álvarez JC. De novo transcriptome sequencing and annotation of the Antarctic polychaete Microspio moorei (Spionidae) with its characterization of the heat stress-related proteins (HSP, SOD & CAT). Mar Genomics 2024; 73:101085. [PMID: 38301367 DOI: 10.1016/j.margen.2024.101085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
We present a de novo transcriptome assembly for the non-model Antarctic polychaete worm Microspio moorei (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for Microspio spp. The gene sequences of the spionid worm were annotated from a wide range of functions (i.e., biological, and metabolic processes, catalytic processes, and catalytic activity). HSP70, HSP90 SOD and CAT families were compared to reported annelid transcriptomes and proteomes. The phylogenetic analysis using COI, 16S, and 18S markers effectively clusters the species within the family. However, it also casts uncertainty on the monophyletic nature of the Microspio genera, indicating the necessity for additional data and potentially requiring a reevaluation of its grouping. Within these protein families, 3D model software was used to create one representative of their protein structures. Structural predictions were compared with related reported annelids living at different temperatures and a human X-ray reference. We found structural differences (RMSE >1.8) between the human HSP proteins but no significant differences between the polychaete-predicted proteins (RMSE <1.2). These results encourage further research of heat stress-related proteins, the development of genetic markers for climate change-induced temperature stress, and the study of the underlying mechanisms of the heat response. Moreover, these results motivate the extension of these findings to congeneric species.
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Affiliation(s)
- Idalyd Fonseca-González
- LimnoBasE & Biotamar Research Group, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Esteban Velasquez-Agudelo
- Research Group in Biodiversity, Evolution and Conservation (BEC), EAFIT University, Medellín 050022, Colombia
| | - Mario H Londoño-Mesa
- LimnoBasE & Biotamar Research Group, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Javier C Álvarez
- Research Group in Biodiversity, Evolution and Conservation (BEC), EAFIT University, Medellín 050022, Colombia.
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2
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Hiillos A, Thonig A, Knott KE. Droplet digital PCR as a tool for investigating dynamics of cryptic symbionts. Ecol Evol 2021; 11:17381-17396. [PMID: 34938515 PMCID: PMC8668802 DOI: 10.1002/ece3.8372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions are critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking, which hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected, and high host densities were found to have a lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.
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Affiliation(s)
- Anna‐Lotta Hiillos
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anne Thonig
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Department of Science and EnvironmentRoskilde UniversityRoskildeDenmark
| | - Karelyn Emily Knott
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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3
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Figueroa Á, Brante A, Cárdenas L. RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis. Sci Rep 2021; 11:14997. [PMID: 34294855 PMCID: PMC8298564 DOI: 10.1038/s41598-021-94646-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
Abstract
The polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.
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Affiliation(s)
- Álvaro Figueroa
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.
| | - Antonio Brante
- Facultad de Ciencias, Centro de Investigación en Biodiversidad y Ambientes Sustentables, Universidad Católica de la Ssma, Concepción, Concepción, Chile
- Departamento Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Leyla Cárdenas
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Centro Fondap-IDEAL, Valdivia, Chile
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4
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Tellez-Garcia AA, Álvarez-Martínez R, López-Martínez JM, Arellano-Carbajal F. Transcriptome analysis during early regeneration of Lumbriculus variegatus. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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5
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Ponz-Segrelles G, Ribeiro RP, Bleidorn C, Aguado Molina MT. Sex-specific gene expression differences in reproducing Syllis prolifera and Nudisyllis pulligera (Annelida, Syllidae). Mar Genomics 2020; 54:100772. [DOI: 10.1016/j.margen.2020.100772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/02/2020] [Accepted: 04/02/2020] [Indexed: 01/22/2023]
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6
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Ribeiro RP, Ponz-Segrelles G, Bleidorn C, Aguado MT. Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process. BMC Genomics 2019; 20:855. [PMID: 31726983 PMCID: PMC6854643 DOI: 10.1186/s12864-019-6223-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/24/2019] [Indexed: 02/23/2023] Open
Abstract
Background Annelids exhibit remarkable postembryonic developmental abilities. Most annelids grow during their whole life by adding segments through the action of a segment addition zone (SAZ) located in front of the pygidium. In addition, they show an outstanding ability to regenerate their bodies. Experimental evidence and field observations show that many annelids are able to regenerate their posterior bodies, while anterior regeneration is often limited or absent. Syllidae, for instance, usually show high abilities of posterior regeneration, although anterior regeneration varies across species. Some syllids are able to partially restore the anterior end, while others regenerate all lost anterior body after bisection. Here, we used comparative transcriptomics to detect changes in the gene expression profiles during anterior regeneration, posterior regeneration and regular growth of two syllid species: Sphaerosyllis hystrix and Syllis gracilis; which exhibit limited and complete anterior regeneration, respectively. Results We detected a high number of genes with differential expression: 4771 genes in S. hystrix (limited anterior regeneration) and 1997 genes in S. gracilis (complete anterior regeneration). For both species, the comparative transcriptomic analysis showed that gene expression during posterior regeneration and regular growth was very similar, whereas anterior regeneration was characterized by up-regulation of several genes. Among the up-regulated genes, we identified putative homologs of regeneration-related genes associated to cellular proliferation, nervous system development, establishment of body axis, and stem-cellness; such as rup and JNK (in S. hystrix); and glutamine synthetase, elav, slit, Hox genes, β-catenin and PL10 (in S. gracilis). Conclusions Posterior regeneration and regular growth show no significant differences in gene expression in the herein investigated syllids. However, anterior regeneration is associated with a clear change in terms of gene expression in both species. Our comparative transcriptomic analysis was able to detect differential expression of some regeneration-related genes, suggesting that syllids share some features of the regenerative mechanisms already known for other annelids and invertebrates.
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Affiliation(s)
- Rannyele Passos Ribeiro
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
| | - Guillermo Ponz-Segrelles
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Christoph Bleidorn
- Animal Evolution & Biodiversity, Georg-August-Universität Göttingen, 37073, Göttingen, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Maria Teresa Aguado
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain. .,Animal Evolution & Biodiversity, Georg-August-Universität Göttingen, 37073, Göttingen, Germany. .,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, España.
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7
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Johnson LK, Alexander H, Brown CT. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience 2019; 8:giy158. [PMID: 30544207 PMCID: PMC6481552 DOI: 10.1093/gigascience/giy158] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/18/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines," on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. RESULTS New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. CONCLUSIONS Given current bioinformatics approaches, there is no single "best" reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
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Affiliation(s)
- Lisa K Johnson
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Harriet Alexander
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - C Titus Brown
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Genome Center, University of California Davis, 451 Health Sciences Dr, Davis, CA 95616, USA
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Álvarez-Campos P, Kenny NJ, Verdes A, Fernández R, Novo M, Giribet G, Riesgo A. Delegating Sex: Differential Gene Expression in Stolonizing Syllids Uncovers the Hormonal Control of Reproduction. Genome Biol Evol 2019; 11:295-318. [PMID: 30535381 PMCID: PMC6350857 DOI: 10.1093/gbe/evy265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2018] [Indexed: 12/31/2022] Open
Abstract
Stolonization in syllid annelids is a unique mode of reproduction among animals. During the breeding season, a structure resembling the adult but containing only gametes, called stolon, is formed generally at the posterior end of the animal. When stolons mature, they detach from the adult and gametes are released into the water column. The process is synchronized within each species, and it has been reported to be under environmental and endogenous control, probably via endocrine regulation. To further understand reproduction in syllids and to elucidate the molecular toolkit underlying stolonization, we generated Illumina RNA-seq data from different tissues of reproductive and nonreproductive individuals of Syllis magdalena and characterized gene expression during the stolonization process. Several genes involved in gametogenesis (ovochymase, vitellogenin, testis-specific serine/threonine-kinase), immune response (complement receptor 2), neuronal development (tyrosine-protein kinase Src42A), cell proliferation (alpha-1D adrenergic receptor), and steroid metabolism (hydroxysteroid dehydrogenase 2) were found differentially expressed in the different tissues and conditions analyzed. In addition, our findings suggest that several neurohormones, such as methyl farnesoate, dopamine, and serotonin, might trigger stolon formation, the correct maturation of gametes and the detachment of stolons when gametogenesis ends. The process seems to be under circadian control, as indicated by the expression patterns of r-opsins. Overall, our results shed light into the genes that orchestrate the onset of gamete formation and improve our understanding of how some hormones, previously reported to be involved in reproduction and metamorphosis processes in other invertebrates, seem to also regulate reproduction via stolonization.
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Affiliation(s)
- Patricia Álvarez-Campos
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Spain
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
- Department of Biological & Medical Sciences, Oxford Brookes University, Headington Campus, Gipsy Lane, Oxford, United Kingdom
| | - Nathan J Kenny
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
| | - Aida Verdes
- Facultad de Ciencias, Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Spain
- Department of Biology, The Graduate Center, City University of New York
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Rosa Fernández
- Bioinformatics & Genomics Unit, Center for Genomic Regulation, Barcelona, Spain
| | - Marta Novo
- Facultad de Biología, Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Ana Riesgo
- Department of Biology, The Graduate Center, City University of New York
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Ponz‐Segrelles G, Bleidorn C, Aguado MT. Expression of
vasa
,
piwi
, and
nanos
during gametogenesis in
Typosyllis antoni
(Annelida, Syllidae). Evol Dev 2018; 20:132-145. [DOI: 10.1111/ede.12263] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Guillermo Ponz‐Segrelles
- Departamento de BiologíaFacultad de CienciasUniversidad Autónoma de MadridCantoblancoMadridSpain
| | - Christoph Bleidorn
- Animal Evolution and BiodiversityGeorg‐August‐University GöttingenGöttingenGermany
| | - M. Teresa Aguado
- Departamento de BiologíaFacultad de CienciasUniversidad Autónoma de MadridCantoblancoMadridSpain
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10
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Brugler MR, Aguado MT, Tessler M, Siddall ME. The transcriptome of the Bermuda fireworm Odontosyllis enopla (Annelida: Syllidae): A unique luciferase gene family and putative epitoky-related genes. PLoS One 2018; 13:e0200944. [PMID: 30089107 PMCID: PMC6082529 DOI: 10.1371/journal.pone.0200944] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 07/05/2018] [Indexed: 12/02/2022] Open
Abstract
The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopla during a bioluminescent swarm in Ferry Reach, Bermuda. Using the well-characterized luciferase gene of the Japanese syllid Odontosyllis undecimdonta as a reference, a complete best-matching luciferase open reading frame (329 amino acids in length) was found in all three individuals analyzed in addition to numerous other paralogous sequences in this new gene family. No photoproteins were detected. We also recovered a predicted homolog of 4-coumarate-CoA ligase (268 amino acids in length) that best matched luciferase of the firefly Luciola with the best predicted template being the crystal structure of luciferase for Photinus pyralis, the common eastern firefly. A wide variety of genes associated with periodicity were recovered including predicted homologs of clock, bmal1, period, and timeless. Several genes corresponding to putative epitoky-related changes of the eyes were recovered including predicted homologs of a phototransduction gene, a retinol dehydrogenase and carotenoid isomerooxygenase as well as a visual perception related retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase. Genes correlating to putative epitoky-related changes of the nephridia included predicted homologs of nephrocystin-3 and an egg-release sex peptide receptor.
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Affiliation(s)
- Mercer R. Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Biological Sciences Department, NYC College of Technology, City University of New York, Brooklyn, New York, United States of America
| | - M. Teresa Aguado
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Michael Tessler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Mark E. Siddall
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
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Thonig A, Banta GT, Hansen BW, Knott KE. Seasonal genetic variation associated with population dynamics of a poecilogonous polychaete worm. Ecol Evol 2017; 7:10005-10017. [PMID: 29238532 PMCID: PMC5723597 DOI: 10.1002/ece3.3518] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/05/2017] [Accepted: 09/28/2017] [Indexed: 12/13/2022] Open
Abstract
Poecilogonous species show variation in developmental mode, with larvae that differ both morphologically and ecologically. The spionid polychaete Pygospio elegans shows variation in developmental mode not only between populations, but also seasonally within populations. We investigated the consequences of this developmental polymorphism on the spatial and seasonal genetic structure of P. elegans at four sites in the Danish Isefjord-Roskilde-Fjord estuary at six time points, from March 2014 until February 2015. We found genetic differentiation between our sampling sites as well as seasonal differentiation at two of the sites. The seasonal genetic shift correlated with the appearance of new size cohorts in the populations. Additionally, we found that the genetic composition of reproductive individuals did not always reflect the genetic composition of the entire sample, indicating that variance in reproductive success among individuals is a likely explanation for the patterns of chaotic genetic patchiness observed during this and previous studies. The heterogeneous, unpredictable character of the estuary might maintain poecilogony in P. elegans as a bet-hedging strategy in the Isefjord-Roskilde-Fjord complex in comparison with other sites where P. elegans are expected to be fixed to a certain mode of development.
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Affiliation(s)
- Anne Thonig
- Department of Science and EnvironmentRoskilde UniversityRoskildeDenmark
- Department of Biological & Environmental ScienceUniversity of JyvaskylaUniversity of JyvaskylaFinland
| | - Gary Thomas Banta
- Department of Science and EnvironmentRoskilde UniversityRoskildeDenmark
| | | | - K. Emily Knott
- Department of Biological & Environmental ScienceUniversity of JyvaskylaUniversity of JyvaskylaFinland
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