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Dong Z, Wang C, Qu Q. WGCCRR: a web-based tool for genome-wide screening of convergent indels and substitutions of amino acids. BIOINFORMATICS ADVANCES 2024; 4:vbae070. [PMID: 38808070 PMCID: PMC11132816 DOI: 10.1093/bioadv/vbae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 04/05/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
Summary Genome-wide analyses of proteincoding gene sequences are being employed to examine the genetic basis of adaptive evolution in many organismal groups. Previous studies have revealed that convergent/parallel adaptive evolution may be caused by convergent/parallel amino acid changes. Similarly, detailed analysis of lineage-specific amino acid changes has shown correlations with certain lineage-specific traits. However, experimental validation remains the ultimate measure of causality. With the increasing availability of genomic data, a streamlined tool for such analyses would facilitate and expedite the screening of genetic loci that hold potential for adaptive evolution, while alleviating the bioinformatic burden for experimental biologists. In this study, we present a user-friendly web-based tool called WGCCRR (Whole Genome Comparative Coding Region Read) designed to screen both convergent/parallel and lineage-specific amino acid changes on a genome-wide scale. Our tool allows users to replicate previous analyses with just a few clicks, and the exported results are straightforward to interpret. In addition, we have also included amino acid indels that are usually neglected in previous work. Our website provides an efficient platform for screening candidate loci for downstream experimental tests. Availability and Implementation The tool is available at: https://fishevo.xmu.edu.cn/.
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Affiliation(s)
- Zheng Dong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xià-Mén, Fú-Jiàn 361102, China
| | - Chen Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xià-Mén, Fú-Jiàn 361102, China
| | - Qingming Qu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xià-Mén, Fú-Jiàn 361102, China
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2
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Pappert FA, Dubin A, Torres GG, Roth O. Navigating sex and sex roles: deciphering sex-biased gene expression in a species with sex-role reversal ( Syngnathus typhle). ROYAL SOCIETY OPEN SCIENCE 2024; 11:rsos.231620. [PMID: 38577217 PMCID: PMC10987989 DOI: 10.1098/rsos.231620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
Sexual dimorphism, the divergence in morphological traits between males and females of the same species, is often accompanied by sex-biased gene expression. However, the majority of research has focused on species with conventional sex roles, where females have the highest energy burden with both egg production and parental care, neglecting the diversity of reproductive roles found in nature. We investigated sex-biased gene expression in Syngnathus typhle, a sex-role reversed species with male pregnancy, allowing us to separate two female traits: egg production and parental care. Using RNA sequencing, we examined gene expression across organs (brain, head kidney and gonads) at various life stages, encompassing differences in age, sex and reproductive status. While some gene groups were more strongly associated with sex roles, such as stress resistance and immune defence, others were driven by biological sex, such as energy and lipid storage regulation in an organ- and age-specific manner. By investigating how genes regulate and are regulated by changing reproductive roles and resource allocation in a model system with an unconventional life-history strategy, we aim to better understand the importance of sex and sex role in regulating gene expression patterns, broadening the scope of this discussion to encompass a wide range of organisms.
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Affiliation(s)
- Freya A. Pappert
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
- Evolutionary Ecology of Marine Fishes, Helmholtz-Centre for Ocean Research Kiel (GEOMAR), Kiel24105, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
| | - Guillermo G. Torres
- Institute of Clinical Molecular Biology (IKMB), University Hospital Schleswig-Holstein, Kiel University, Kiel24105, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
- Evolutionary Ecology of Marine Fishes, Helmholtz-Centre for Ocean Research Kiel (GEOMAR), Kiel24105, Germany
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3
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Qu M, Zhang Y, Gao Z, Zhang Z, Liu Y, Wan S, Wang X, Yu H, Zhang H, Liu Y, Schneider R, Meyer A, Lin Q. The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2317-6. [PMID: 37204606 DOI: 10.1007/s11427-022-2317-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 05/20/2023]
Abstract
The leafy seadragon certainly is among evolution's most "beautiful and wonderful" species aptly named for its extraordinary camouflage mimicking its coastal seaweed habitat. However, limited information is known about the genetic basis of its phenotypes and conspicuous camouflage. Here, we revealed genomic signatures of rapid evolution and positive selection in core genes related to its camouflage, which allowed us to predict population dynamics for this species. Comparative genomic analysis revealed that seadragons have the smallest olfactory repertoires among all ray-finned fishes, suggesting adaptations to the highly specialized habitat. Other positively selected and rapidly evolving genes that serve in bone development and coloration are highly expressed in the leaf-like appendages, supporting a recent adaptive shift in camouflage appendage formation. Knock-out of bmp6 results in dysplastic intermuscular bones with a significantly reduced number in zebrafish, implying its important function in bone formation. Global climate change-induced loss of seagrass beds now severely threatens the continued existence of this enigmatic species. The leafy seadragon has a historically small population size likely due to its specific habitat requirements that further exacerbate its vulnerability to climate change. Therefore, taking climate change-induced range shifts into account while developing future protection strategies.
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Affiliation(s)
- Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingyi Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Guangzhou, 510301, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Yuhong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China
| | - Ralf Schneider
- Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118, Kiel, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany.
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou, 511458, China.
- Sanya Institute of Oceanology, SCSIO, Sanya, 572000, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Brownstein CD. Syngnathoid Evolutionary History and the Conundrum of Fossil Misplacement. Integr Org Biol 2023; 5:obad011. [PMID: 37251781 PMCID: PMC10210065 DOI: 10.1093/iob/obad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/21/2023] [Indexed: 05/31/2023] Open
Abstract
Seahorses, pipefishes, trumpetfishes, shrimpfishes, and allies are a speciose, globally distributed clade of fishes that have evolved a large number of unusual body plans. The clade that includes all these forms, Syngnathoidei, has become a model for the study of life history evolution, population biology, and biogeography. Yet, the timeline of syngnathoid evolution has remained highly contentious. This debate is largely attributable to the nature of the syngnathoid fossil record, which is both poorly described and patchy for several major lineages. Although fossil syngnathoids have been used to calibrate molecular phylogenies, the interrelationships of extinct species and their affinities to major living syngnathoid clades have scarcely been quantitatively tested. Here, I use an expanded morphological dataset to reconstruct the evolutionary relationships and clade ages of fossil and extant syngnathoids. Phylogenies generated using different analytical methodologies are largely congruent with molecular phylogenetic trees of Syngnathoidei but consistently find novel placements for several key taxa used as fossil calibrators in phylogenomic studies. Tip-dating of the syngnathoid phylogeny finds a timeline for their evolution that differs slightly from the one inferred using molecular trees but is generally congruent with a post-Cretaceous diversification event. These results emphasize the importance of quantitatively testing the relationships of fossil species, particularly when they are critical to assessing divergence times.
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5
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Wilson AB, Whittington CM, Meyer A, Scobell SK, Gauthier ME. Prolactin and the evolution of male pregnancy. Gen Comp Endocrinol 2023; 334:114210. [PMID: 36646326 DOI: 10.1016/j.ygcen.2023.114210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 11/04/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Prolactin (PRL) is a multifunctional hormone of broad physiological importance, and is involved in many aspects of fish reproduction, including the regulation of live birth (viviparity) and both male and female parental care. Previous research suggests that PRL also plays an important reproductive role in syngnathid fishes (seahorses, pipefish and seadragons), a group with a highly derived reproductive strategy, male pregnancy - how the PRL axis has come to be co-opted for male pregnancy remains unclear. We investigated the molecular evolution and expression of the genes for prolactin and its receptor (PRLR) in an evolutionarily diverse sampling of syngnathid fishes to explore how the co-option of PRL for male pregnancy has impacted its evolution, and to clarify whether the PRL axis is also involved in regulating reproductive function in species with more rudimentary forms of male pregnancy. In contrast to the majority of teleost fishes, all syngnathid fishes tested carry single copies of PRL and PRLR that cluster genetically within the PRL1 and PRLRa lineages of teleosts, respectively. PRL1 gene expression in seahorses and pipefish is restricted to the pituitary, while PRLRa is expressed in all tissues, including the brood pouch of species with both rudimentary and complex brooding structures. Pituitary PRL1 expression remains stable throughout pregnancy, but PRLRa expression is specifically upregulated in the male brood pouch during pregnancy, consistent with the higher affinity of pouch tissues for PRL hormone during embryonic incubation. Finally, immunohistochemistry of brood pouch tissues reveals that both PRL1 protein and PRLRa and Na+/K+ ATPase-positive cells line the inner pouch epithelium, suggesting that pituitary-derived PRL1 may be involved in brood pouch osmoregulation during pregnancy. Our data provide a unique molecular perspective on the evolution and expression of prolactin and its receptor during male pregnancy, and provide the foundation for further manipulative experiments exploring the role of PRL in this unique form of reproduction.
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Affiliation(s)
- Anthony B Wilson
- Department of Biology, Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, United States; The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, United States; Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Germany.
| | - Camilla M Whittington
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Sydney School of Veterinary Science, University of Sydney, Sydney 2006, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney 2006, Australia
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Germany
| | - Sunny K Scobell
- Department of Biology, Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, United States
| | - Marie-Emilie Gauthier
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
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6
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Shalu K, Thomas L, Ramvilas G, Shabeena KS, Philip S, Sureshkumar S, Raghavan R, Ranjeet K. DNA barcodes for the pipefish genus Corythoichthys (Actinopterygii: Syngnathiformes) from the Indian Ocean provide insights into cryptic diversity. JOURNAL OF FISH BIOLOGY 2023; 102:680-688. [PMID: 36602224 DOI: 10.1111/jfb.15300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
The syngnathiform genus Corythoichthys comprises a group of taxonomically complex, tail-brooding (Syngnathinae) pipefishes widely distributed in the Indo-Pacific region. Due to the presence of overlapping interspecific morphological characters, reliable taxonomic information on Corythoichthys is still lacking. Using 52 CO1 sequences, including seven newly generated, a phylogenetic analysis was carried out to understand the genetic diversity, distribution and 'species groups' within the genus Corythoichthys. Species delimitation using Automatic Barcode Gap Discovery (ABGD) analysis confirmed the presence of 13 species which include 'species-complexes' previously considered as a single taxon. Our results revealed the presence of three species groups, 'C. amplexus', 'C. conspicillatus' and 'C. haematopterus' and four unidentified/undescribed species in the wider Indo-Pacific realm. Interestingly, 60 sequences and a mitogenome identified as Corythoichthys in GenBank are misidentified at the genus level. Based on our findings, we suggest that the taxonomy and systematics of Corythoichthys need to be re-examined and validated using integrative methods, and care should be taken while selecting specimens for genetic studies.
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Affiliation(s)
- Kannan Shalu
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Liju Thomas
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Ghosh Ramvilas
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | | | - Siby Philip
- Department of Zoology, Nirmalagiri College, Kannur, India
| | - Sivanpillai Sureshkumar
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Kutty Ranjeet
- Department of Aquatic Environment Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
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7
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Monteiro N. Mom and dad are not that different after all: Immune modulation as a prerequisite for the evolution of pregnancy. Mol Ecol 2023; 32:753-755. [PMID: 36655908 PMCID: PMC10107839 DOI: 10.1111/mec.16857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
Pregnancy, the post-fertilization period when embryos are incubated within the body, is a dynamic multistage process that has convergently evolved in many vertebrates. To increase independence from environmental fluctuations and protect offspring from predation, challenges had to be initially overcome. The most obvious, when considering such an intimate relationship between the parent and its semi-allogenic offspring, was the pressing need to dodge immunity-associated embryo rejection. In mammals, immunological tolerance was found to be dependent on the active modulation of the immune system. Even though supporting much of the current knowledge on vertebrate pregnancy, mammals lack extant transitional stages that could help reconstruct the evolutionary pathway of this fascinatingly complex reproduction mode. In this issue of Molecular Ecology, Parker et al. selected an untraditional model-the seahorse and pipefish family, whose species evolved male pregnancy across an almost continuous gradient of complexity, from external oviparity to internal gestation. By contrasting gene expression profiles of syngnathids with distinct brooding architectures, this study allowed for the observation of subtle evolutionary adaptations, while confirming the existence of remarkable similarities to "female" pregnancy (e.g., the evolution of male pregnancy in pouched species occurred alongside immune downregulation, and inflammation seems vital during early pregnancy stages). In a world where the debate on sex-roles takes centre stage, Parker et al.'s appeasing results hint at the fact that the strongly convergent evolution of vertebrate pregnancy was seemingly unaffected by which sex carries the burden of gestation.
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Affiliation(s)
- Nuno Monteiro
- CIBIO-InBio, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,IUCN SSC Seahorse, Pipefish and Seadragon Specialist Group
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8
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Liu Y, Qu M, Jiang H, Schneider R, Qin G, Luo W, Yu H, Zhang B, Wang X, Zhang Y, Zhang H, Zhang Z, Wu Y, Zhang Y, Yin J, Zhang S, Venkatesh B, Roth O, Meyer A, Lin Q. Immunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia. Nat Commun 2022; 13:7610. [PMID: 36494371 PMCID: PMC9734139 DOI: 10.1038/s41467-022-35338-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
In the highly derived syngnathid fishes (pipefishes, seadragons & seahorses), the evolution of sex-role reversed brooding behavior culminated in the seahorse lineage's male pregnancy, whose males feature a specialized brood pouch into which females deposit eggs during mating. Then, eggs are intimately engulfed by a placenta-like tissue that facilitates gas and nutrient exchange. As fathers immunologically tolerate allogenic embryos, it was suggested that male pregnancy co-evolved with specific immunological adaptations. Indeed, here we show that a specific amino-acid replacement in the tlx1 transcription factor is associated with seahorses' asplenia (loss of spleen, an organ central in the immune system), as confirmed by a CRISPR-Cas9 experiment using zebrafish. Comparative genomics across the syngnathid phylogeny revealed that the complexity of the immune system gene repertoire decreases as parental care intensity increases. The synchronous evolution of immunogenetic alterations and male pregnancy supports the notion that male pregnancy co-evolved with the immunological tolerance of the embryo.
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Affiliation(s)
- Yali Liu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Meng Qu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Han Jiang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Ralf Schneider
- grid.9764.c0000 0001 2153 9986Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Geng Qin
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Wei Luo
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Haiyan Yu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Bo Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Xin Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Yanhong Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Huixian Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Zhixin Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.412785.d0000 0001 0695 6482Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Yongli Wu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Yingyi Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Jianping Yin
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Si Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Byrappa Venkatesh
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, 138673 Singapore, Singapore
| | - Olivia Roth
- grid.9764.c0000 0001 2153 9986Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Axel Meyer
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Qiang Lin
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
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9
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Johnson BD, Anderson AP, Small CM, Rose E, Flanagan SP, Hendrickson-Rose C, Jones AG. The evolution of the testis transcriptome in pregnant male pipefishes and seahorses. Evolution 2022; 76:2162-2180. [PMID: 35863060 DOI: 10.1111/evo.14579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
In many animals, sperm competition and sexual conflict are thought to drive the rapid evolution of male-specific genes, especially those expressed in the testes. A potential exception occurs in the male pregnant pipefishes, where females transfer eggs to the males, eliminating testes from participating in these processes. Here, we show that testis-related genes differ dramatically in their rates of molecular evolution and expression patterns in pipefishes and seahorses (Syngnathidae) compared to other fish. Genes involved in testis or sperm function within syngnathids experience weaker selection in comparison to their orthologs in spawning and livebearing fishes. An assessment of gene turnover and expression in the testis transcriptome suggests that syngnathids have lost (or significantly reduced expression of) important classes of genes from their testis transcriptomes compared to other fish. Our results indicate that more than 50 million years of male pregnancy have removed syngnathid testes from the molecular arms race that drives the rapid evolution of male reproductive genes in other taxa.
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Affiliation(s)
| | | | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
| | - Emily Rose
- Department of Biology, Valdosta State University, Valdosta, Georgia, 31698
| | - Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, 8041, New Zealand
| | | | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, 83844
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10
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Dudley J, Paul J, Teh V, Mackenzie T, Butler T, Tolosa J, Smith R, Foley M, Dowland S, Thompson M, Whittington C. Seahorse brood pouch morphology and control of male parturition in Hippocampus abdominalis. Placenta 2022; 127:88-94. [DOI: 10.1016/j.placenta.2022.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/07/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
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11
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Stiller J, Short G, Hamilton H, Saarman N, Longo S, Wainwright P, Rouse GW, Simison WB. Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biol 2022; 20:75. [PMID: 35346180 PMCID: PMC8962102 DOI: 10.1186/s12915-022-01271-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Background Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved. Results Here, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus. In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea. Conclusions Our results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01271-w.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA. .,Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Graham Short
- Ichthyology, Australian Museum, Sydney, Australia.,Ichthyology, California Academy of Sciences, San Francisco, USA.,Ichthyology, Burke Museum of Natural History and Culture, Seattle, USA
| | | | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Sarah Longo
- Department of Biological Science, Towson University, Towson, MD, 21252, USA
| | - Peter Wainwright
- Department of Evolution & Ecology, University of California, Davis, USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, USA
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12
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Harada A, Shiota R, Okubo R, Yorifuji M, Sogabe A, Motomura H, Hiroi J, Yasumasu S, Kawaguchi M. Brood pouch evolution in pipefish and seahorse based on histological observation. Placenta 2022; 120:88-96. [DOI: 10.1016/j.placenta.2022.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/09/2022] [Accepted: 02/20/2022] [Indexed: 12/17/2022]
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13
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Short GA, Trnski T. A New Genus and Species of Pygmy Pipehorse from Taitokerau Northland, Aotearoa New Zealand, with a Redescription of Acentronura Kaup, 1853 and Idiotropiscis Whitley, 1947 (Teleostei, Syngnathidae). ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Graham A. Short
- Department of Ichthyology, California Academy of Sciences, San Francisco, California 94118; . Send reprint requests to this address
| | - Thomas Trnski
- Auckland War Memorial Museum Tāmaki Paenga Hira, Auckland 1142, New Zealand;
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14
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Qu M, Liu Y, Zhang Y, Wan S, Ravi V, Qin G, Jiang H, Wang X, Zhang H, Zhang B, Gao Z, Huysseune A, Zhang Z, Zhang H, Chen Z, Yu H, Wu Y, Tang L, Li C, Zhong J, Ma L, Wang F, Zheng H, Yin J, Witten PE, Meyer A, Venkatesh B, Lin Q. Seadragon genome analysis provides insights into its phenotype and sex determination locus. SCIENCE ADVANCES 2021; 7:eabg5196. [PMID: 34407945 PMCID: PMC8373133 DOI: 10.1126/sciadv.abg5196] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/01/2021] [Indexed: 05/29/2023]
Abstract
The iconic phenotype of seadragons includes leaf-like appendages, a toothless tubular mouth, and male pregnancy involving incubation of fertilized eggs on an open "brood patch." We de novo-sequenced male and female genomes of the common seadragon (Phyllopteryx taeniolatus) and its closely related species, the alligator pipefish (Syngnathoides biaculeatus). Transcription profiles from an evolutionary novelty, the leaf-like appendages, show that a set of genes typically involved in fin development have been co-opted as well as an enrichment of transcripts for potential tissue repair and immune defense genes. The zebrafish mutants for scpp5, which is lost in all syngnathids, were found to lack or have deformed pharyngeal teeth, supporting the hypothesis that the loss of scpp5 has contributed to the loss of teeth in syngnathids. A putative sex-determining locus encoding a male-specific amhr2y gene shared by common seadragon and alligator pipefish was identified.
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Affiliation(s)
- Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Shiming Wan
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology, A*STAR, 138673 Biopolis, Singapore
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Han Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ann Huysseune
- Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Zhixin Zhang
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Hao Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Zelin Chen
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Yongli Wu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Lu Tang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Chunyan Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Jia Zhong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Liming Ma
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Fengling Wang
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Paul Eckhard Witten
- Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany.
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, 138673 Biopolis, Singapore.
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
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15
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Fuiten AM, Cresko WA. Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays. Dev Genes Evol 2021; 231:57-71. [PMID: 34003345 DOI: 10.1007/s00427-021-00676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
Hoxa2 genes provide critical patterning signals during development, and their regulation and function have been extensively studied. We report a previously uncharacterized significant sequence divergence of a highly conserved hindbrain hoxa2b enhancer element in the family syngnathidae (pipefishes, seahorses, pipehorses, seadragons). We compared the hox cis-regulatory element variation in the Gulf pipefish and two species of seahorse against eight other species of fish, as well as human and mouse. We annotated the hoxa2b enhancer element binding sites across three species of seahorse, four species of pipefish, and one species of ghost pipefish. Finally, we performed in situ hybridization analysis of hoxa2b expression in Gulf pipefish embryos. We found that all syngnathid fish examined share a modified rhombomere 4 hoxa2b enhancer element, despite the fact that this element has been found to be highly conserved across all vertebrates examined previously. Binding element sequence motifs and spacing between binding elements have been modified for the hoxa2b enhancer in several species of pipefish and seahorse, and that the loss of the Prep/Meis binding site and further space shortening happened after ghost pipefish split from the rest of the syngnathid clade. We showed that expression of this gene in rhombomere 4 is lower relative to the surrounding rhombomeres in developing Gulf pipefish embryos, reflecting previously published functional tests for this enhancer. Our findings highlight the benefits of studying highly derived, diverse taxa for understanding of gene regulatory evolution and support the hypothesis that natural mutations can occur in deeply conserved pathways in ways potentially related to phenotypic diversity.
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Affiliation(s)
- Allison M Fuiten
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
- Present address: Department of Dermatology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
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16
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Abstract
Abstract
Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are seahorses (Hippocampus spp.: 14/42 species, with an additional 17 that are Data Deficient) or freshwater pipefishes of the genus Microphis (2/18 species, with seven additional that are Data Deficient). Two species are Near Threatened. Nearly one-third of syngnathiformes (97 species) are Data Deficient and could potentially be threatened, requiring further field research and evaluation. Most species (61%) were, however, evaluated as Least Concern. Primary threats to syngnathids are (1) overexploitation, primarily by non-selective fisheries, for which most assessments were determined by criterion A (Hippocampus) and/or (2) habitat loss and degradation, for which assessments were determined by criterion B (Microphis and some Hippocampus). Threatened species occurred in most regions but more are found in East and South-east Asia and in South African estuaries. Vital conservation action for syngnathids, including constraining fisheries, particularly non-selective extraction, and habitat protection and rehabilitation, will benefit many other aquatic species.
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17
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Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade. DIVERSITY 2021. [DOI: 10.3390/d13050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.
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18
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Santaquiteria A, Siqueira AC, Duarte-Ribeiro E, Carnevale G, White W, Pogonoski J, Baldwin CC, Ortí G, Arcila D, Betancur RR. Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences. Syst Biol 2021; 70:1145-1162. [PMID: 33892493 DOI: 10.1093/sysbio/syab028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/14/2022] Open
Abstract
The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.
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Affiliation(s)
- Aintzane Santaquiteria
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Emanuell Duarte-Ribeiro
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10125, Torino, Italy
| | - William White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - John Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - Guillermo Ortí
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA.,Department of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.,Sam Noble Oklahoma Museum of Natural History, 2401 Chautauqua Ave, Norman, OK 73072, USA
| | - Ricardo R Betancur
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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19
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Li C, Olave M, Hou Y, Qin G, Schneider RF, Gao Z, Tu X, Wang X, Qi F, Nater A, Kautt AF, Wan S, Zhang Y, Liu Y, Zhang H, Zhang B, Zhang H, Qu M, Liu S, Chen Z, Zhong J, Zhang H, Meng L, Wang K, Yin J, Huang L, Venkatesh B, Meyer A, Lu X, Lin Q. Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution. Nat Commun 2021; 12:1094. [PMID: 33597547 PMCID: PMC7889852 DOI: 10.1038/s41467-021-21379-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses' worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring "bony spines" adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.
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Affiliation(s)
- Chunyan Li
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China ,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Melisa Olave
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,grid.423606.50000 0001 1945 2152Present Address: Argentine Dryland Research Institute, National Council for Scientific and Technical Research (IADIZA-CONICET), Mendoza, Argentina
| | - Yali Hou
- grid.464209.d0000 0004 0644 6935Beijing Institute of Genomics, Chinese Academy of Sciences; China National Center for Bioinformation, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Geng Qin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ralf F. Schneider
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,Marine Ecology, Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Zexia Gao
- grid.35155.370000 0004 1790 4137College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | | | - Xin Wang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Furong Qi
- grid.464209.d0000 0004 0644 6935Beijing Institute of Genomics, Chinese Academy of Sciences; China National Center for Bioinformation, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Alexander Nater
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F. Kautt
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany ,grid.38142.3c000000041936754XPresent Address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Shiming Wan
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yanhong Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yali Liu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Huixian Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Bo Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Zhang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Meng Qu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Shuaishuai Liu
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Zeyu Chen
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.419010.d0000 0004 1792 7072State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jia Zhong
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Kai Wang
- grid.443651.1School of Agriculture, Ludong University, Yantai, China
| | - Jianping Yin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Liangmin Huang
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Byrappa Venkatesh
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Axel Meyer
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Xuemei Lu
- grid.419010.d0000 0004 1792 7072State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Qiang Lin
- grid.458498.c0000 0004 1798 9724CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China ,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China ,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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20
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Planas M, Piñeiro-Corbeira C, Bouza C, Castejón-Silvo I, Vera M, Regueira M, Ochoa V, Bárbara I, Terrados J, Chamorro A, Barreiro R, Hernández-Urcera J, Alejo I, Nombela M, García ME, Pardo BG, Peña V, Díaz-Tapia P, Cremades J, Morales-Nin B. A multidisciplinary approach to identify priority areas for the monitoring of a vulnerable family of fishes in Spanish Marine National Parks. BMC Ecol Evol 2021; 21:4. [PMID: 33514312 PMCID: PMC7853308 DOI: 10.1186/s12862-020-01743-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Syngnathid fishes (Actinopterygii, Syngnathidae) are flagship species strongly associated with seaweed and seagrass habitats. Seahorses and pipefishes are highly vulnerable to anthropogenic and environmental disturbances, but most species are currently Data Deficient according to the IUCN (2019), requiring more biological and ecological research. This study provides the first insights into syngnathid populations in the two marine Spanish National Parks (PNIA—Atlantic- and PNAC—Mediterranean). Fishes were collected periodically, marked, morphologically identified, analysed for size, weight, sex and sexual maturity, and sampled for stable isotope and genetic identification. Due the scarcity of previous information, habitat characteristics were also assessed in PNIA. Results Syngnathid diversity and abundance were low, with two species identified in PNIA (Hippocampus guttulatus and Syngnathus acus) and four in PNAC (S. abaster, S. acus, S. typhle and Nerophis maculatus). Syngnathids from both National Parks (NP) differed isotopically, with much lower δ15N in PNAC than in PNIA. The dominant species were S. abaster in PNAC and S. acus in PNIA. Syngnathids preferred less exposed sites in macroalgal assemblages in PNIA and Cymodocea meadows in PNAC. The occurrence of very large specimens, the absence of small-medium sizes and the isotopic comparison with a nearby population suggest that the population of Syngnathus acus (the dominant syngnathid in PNIA) mainly comprised breeders that migrate seasonally. Mitochondrial cytochrome b sequence variants were detected for H. guttulatus, S. acus, and S. abaster, and a novel 16S rDNA haplotype was obtained in N. maculatus. Our data suggest the presence of a cryptic divergent mitochondrial lineage of Syngnathus abaster species in PNAC. Conclusions This is the first multidisciplinary approach to the study of syngnathids in Spanish marine NPs. Habitat preferences and population characteristics in both NPs differed. Further studies are needed to assess the occurrence of a species complex for S. abaster, discarding potential misidentifications of genus Syngnathus in PNAC, and evaluate migratory events in PNIA. We propose several preferential sites in both NPs for future monitoring of syngnathid populations and some recommendations for their conservation.
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Affiliation(s)
- Miquel Planas
- Department of Ecology and Marine Resources, Instituto de Investigaciones Marinas (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain.
| | | | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Facultade de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, Avenida Carballo Calero S/N, 27002, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain
| | - Inés Castejón-Silvo
- Mediterranean Institute for Advanced Studies (CSIC-UIB), 07190, Esporles, Spain
| | - Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, Facultade de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, Avenida Carballo Calero S/N, 27002, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain
| | - Marcos Regueira
- Department of Ecology and Marine Resources, Instituto de Investigaciones Marinas (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Verónica Ochoa
- Department of Ecology and Marine Resources, Instituto de Investigaciones Marinas (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Ignacio Bárbara
- BioCost Research Group, Facultad de Ciencias and CICA, Universidade da Coruña, 15071, Coruña, Spain
| | - Jorge Terrados
- Mediterranean Institute for Advanced Studies (CSIC-UIB), 07190, Esporles, Spain
| | - Alexandro Chamorro
- Department of Ecology and Marine Resources, Instituto de Investigaciones Marinas (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Rodolfo Barreiro
- BioCost Research Group, Facultad de Ciencias and CICA, Universidade da Coruña, 15071, Coruña, Spain
| | - Jorge Hernández-Urcera
- Department of Ecology and Marine Resources, Instituto de Investigaciones Marinas (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Irene Alejo
- Department of Marine Geosciences and Territorial Planning, Marine Sciences Faculty, University of Vigo, 36310, Vigo, Spain
| | - Miguel Nombela
- Department of Marine Geosciences and Territorial Planning, Marine Sciences Faculty, University of Vigo, 36310, Vigo, Spain
| | - Manuel Enrique García
- Department of Ecology and Marine Resources, Instituto de Investigaciones Marinas (IIM-CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Belén G Pardo
- Department of Zoology, Genetics and Physical Anthropology, Facultade de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, Avenida Carballo Calero S/N, 27002, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain
| | - Viviana Peña
- BioCost Research Group, Facultad de Ciencias and CICA, Universidade da Coruña, 15071, Coruña, Spain
| | - Pilar Díaz-Tapia
- BioCost Research Group, Facultad de Ciencias and CICA, Universidade da Coruña, 15071, Coruña, Spain
| | - Javier Cremades
- BioCost Research Group, Facultad de Ciencias and CICA, Universidade da Coruña, 15071, Coruña, Spain
| | - Beatriz Morales-Nin
- Mediterranean Institute for Advanced Studies (CSIC-UIB), 07190, Esporles, Spain
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21
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Short G, Trevor-Jones A. Stigmatopora harastii, a new species of pipefish in facultative associations with finger sponges and red algae from New South Wales, Australia (Teleostei, Syngnathidae). Zookeys 2020; 994:105-123. [PMID: 33273883 PMCID: PMC7686221 DOI: 10.3897/zookeys.994.57160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/20/2020] [Indexed: 11/12/2022] Open
Abstract
A new species of pipefish, Stigmatopora harastii sp. nov., is described based on the male holotype and two female paratypes, 136.3-145.5 mm SL, collected from red algae (sp.?) at 12 meters depth in Botany Bay, New South Wales (NSW), Australia. The new taxon shares morphological synapomorphies with the previously described members of Stigmatopora, including principle body ridges, fin placement, slender tail, and absence of a caudal fin. It is morphologically and meristically similar to Stigmatopora nigra, including snout length and shape, dorsal-fin origin on 6th-7th trunk ring, and lateral trunk ridge terminating on the first tail ring. Stigmatopora harastii sp. nov. is distinguished from its congeners, however, by characters of the head and first trunk ring, distinct sexual dimorphic markings on sides and venter of anterior trunk rings, and red background coloration in life. The new taxon can be further differentiated by genetic divergence in the mitochondrial COI gene (uncorrected p-distances of 9.8%, 10.1%, 10.7%, and 14.6%, from S. argus, S. macropterygia, S. narinosa, and S. nigra, respectively). The type locality is characterised by semi-exposed deep-water sandy areas interspersed with boulders, flat reefs, and an absence of seagrass beds, in which S. harastii has been observed living in facultative associations with a finger sponge and red algae at depths of 10-25 meters, compared to the shallow coastal and estuarine habitats preferred by the fucoid algae and seagrass-associating members of Stigmatopora. Stigmatopora harastii sp. nov. represents the fourth species of Stigmatopora recorded in temperate southern Australia.
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Affiliation(s)
- Graham Short
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney NSW 2010, Australia Australian Museum Sydney Australia.,California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA California Academy of Sciences San Francisco United States of America.,Burke Museum of Natural History and Culture, 4300 15th Ave NE, Seattle, WA 98105, USA Burke Museum of Natural History and Culture Seattle United States of America.,IUCN Seahorse, Pipefish & Seadragon Specialist Group (SPS SG), Institute for the Oceans and Fisheries, The University of British Columbia 2202 Main Mall, Vancouver BC V6T 1Z4, Canada University of British Columbia Vancouver Canada
| | - Andrew Trevor-Jones
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney NSW 2010, Australia Australian Museum Sydney Australia
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22
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Skalkos ZMG, Van Dyke JU, Whittington CM. Paternal nutrient provisioning during male pregnancy in the seahorse Hippocampus abdominalis. J Comp Physiol B 2020; 190:547-556. [PMID: 32617716 DOI: 10.1007/s00360-020-01289-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/22/2020] [Accepted: 06/18/2020] [Indexed: 02/06/2023]
Abstract
Vertebrates that incubate embryos on or within the body cavity exhibit diverse strategies to provide nutrients to developing embryos, ranging from lecithotrophy (solely yolk-provided nutrition) to substantial matrotrophy (supplemental nutrients from the mother before birth). Syngnathid fishes (seahorses, pipefishes and sea dragons) are the only vertebrates to exhibit male pregnancy. Therefore, they provide a unique opportunity for comparative evolutionary research, in examining pregnancy independent of the female reproductive tract. Here, we tested the hypothesis that the most complex form of syngnathid pregnancy involves nutrient transport from father to offspring. We compared the dry masses of newly fertilised Hippocampus abdominalis eggs with those of fully developed neonates to derive a patrotrophy index. The patrotrophy index of H. abdominalis was 1, indicating paternal nutrient supplementation to embryos during gestation. We also measured the lipid content of newly fertilised eggs and neonates and found that there was no significant decrease in lipid mass during embryonic development. Since lipids are likely to be the main source of energy during embryonic development, our results suggest that lipid yolk reserves being depleted by embryonic metabolism are replaced by the brooding father. The results of our study support the hypothesis that nutrient transport occurs in the most advanced form of male pregnancy in vertebrates.
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Affiliation(s)
- Zoe M G Skalkos
- School of Life and Environmental Sciences, The University of Sydney, Heydon-Laurence A08, Camperdown, NSW, 2006, Australia
| | - James U Van Dyke
- School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Wodonga, VIC, Australia
| | - Camilla M Whittington
- School of Life and Environmental Sciences, The University of Sydney, Heydon-Laurence A08, Camperdown, NSW, 2006, Australia.
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23
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Short G, Claassens L, Smith R, De Brauwer M, Hamilton H, Stat M, Harasti D. Hippocampus nalu, a new species of pygmy seahorse from South Africa, and the first record of a pygmy seahorse from the Indian Ocean (Teleostei, Syngnathidae). Zookeys 2020; 934:141-156. [PMID: 32508498 PMCID: PMC7253503 DOI: 10.3897/zookeys.934.50924] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/12/2020] [Indexed: 11/12/2022] Open
Abstract
A new species and the first confirmed record of a true pygmy seahorse from Africa, Hippocampus nalu sp. nov., is herein described on the basis of two specimens, 18.9-22 mm SL, collected from flat sandy coral reef at 14-17 meters depth from Sodwana Bay, South Africa. The new taxon shares morphological synapomorphies with the previously described central Indo-Pacific pygmy seahorses, H. colemani, H. japapigu, H. pontohi, and H. satomiae, and H. waleananus, including diminutive size, twelve trunk rings, prominent cleithral ring and supracleithrum, spines on the fifth and twelfth superior and lateral trunk ridges, respectively, and prominent wing-like protrusions present on the first and/or second superior trunk rings posterior to the head. Hippocampus nalu sp. nov. is primarily distinguished from its pygmy seahorse congeners by highly distinct spine morphology along the anterior segments of the superior trunk ridge. Comparative molecular analysis reveals that the new species demonstrates significant genetic divergence in the mitochondrial COI gene from the morphologically similar H. japapigu and H. pontohi (estimated uncorrected p-distances of 16.3% and 15.2%, respectively). Hippocampus nalu sp. nov. represents the eighth member of the pygmy seahorse clade to be described from the Indo-Pacific, the first confirmed record from the African continent and the Indian Ocean, and an extension of more than 8000 km beyond the previously known range of pygmy seahorses from the Central and Western Indo-Pacific.
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Affiliation(s)
- Graham Short
- Research Associate, Ichthyology, Australian Museum Research Institute, Sydney, Australia Australian Museum Research Institute Sydney Australia.,Research Associate, Ichthyology, California Academy of Sciences, San Francisco, USA Ichthyology, California Academy of Sciences San Francisco United States of America.,Research Associate, Ichthyology, Burke Museum, Seattle, USA Burke Museum Seattle United States of America
| | - Louw Claassens
- IUCN Seahorse, Pipefish Stickleback Specialist Group, University of British Columbia, Vancouver, Canada University of British Columbia Vancouver Canada.,Rhodes University, Grahamstown, South Africa Rhodes University Grahamstown South Africa.,Knysna Basin Project, Knysna, South Africa Knysna Basin Project Knysna South Africa
| | - Richard Smith
- IUCN Seahorse, Pipefish Stickleback Specialist Group, University of British Columbia, Vancouver, Canada University of British Columbia Vancouver Canada
| | | | - Healy Hamilton
- IUCN Seahorse, Pipefish Stickleback Specialist Group, University of British Columbia, Vancouver, Canada University of British Columbia Vancouver Canada.,NatureServe, Arlington, Virginia, USA NatureServe Arlington United States of America
| | - Michael Stat
- University of Newcastle, Callaghan, NSW, Australia University of Newcastle Callaghan Australia
| | - David Harasti
- IUCN Seahorse, Pipefish Stickleback Specialist Group, University of British Columbia, Vancouver, Canada University of British Columbia Vancouver Canada.,Port Stephens Fisheries Institute, NSW, Australia Port Stephens Fisheries Institute Anna Bay Australia
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24
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Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc 2020; 95:1252-1272. [PMID: 32372478 DOI: 10.1111/brv.12607] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 12/24/2022]
Abstract
The seahorses, pipefishes and seadragons (Syngnathidae) are among the few vertebrates in which pregnant males incubate developing embryos. Syngnathids are popular in studies of sexual selection, sex-role reversal, and reproductive trade-offs, and are now emerging as valuable comparative models for the study of the biology and evolution of reproductive complexity. These fish offer the opportunity to examine the physiology, behavioural implications, and evolutionary origins of embryo incubation, independent of the female reproductive tract and female hormonal milieu. Such studies allow us to examine flexibility in regulatory systems, by determining whether the pathways underpinning female pregnancy are also co-opted in incubating males, or whether novel pathways have evolved in response to the common challenges imposed by incubating developing embryos and releasing live young. The Syngnathidae are also ideal for studies of the evolution of reproductive complexity, because they exhibit multiple parallel origins of complex reproductive phenotypes. Here we assay the taxonomic distribution of syngnathid parity mode, examine the selective pressures that may have led to the emergence of male pregnancy, describe the biology of syngnathid reproduction, and highlight pressing areas for future research. Experimental tests of a range of hypotheses, including many generated with genomic tools, are required to inform overarching theories about the fitness implications of pregnancy and the evolution of male pregnancy. Such information will be widely applicable to our understanding of fundamental reproductive and evolutionary processes in animals.
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Affiliation(s)
- Camilla M Whittington
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, 2006, Australia.,The University of Sydney, Sydney School of Veterinary Science, Sydney, New South Wales, 2006, Australia
| | - Christopher R Friesen
- The University of Wollongong, School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, Wollongong, New South Wales, 2522, Australia.,Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales, 2522, Australia
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25
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Zhang YH, Ravi V, Qin G, Dai H, Zhang HX, Han FM, Wang X, Liu YH, Yin JP, Huang LM, Venkatesh B, Lin Q. Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals. Natl Sci Rev 2020; 7:964-977. [PMID: 34692118 PMCID: PMC8289055 DOI: 10.1093/nsr/nwaa002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/31/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.
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Affiliation(s)
- Yan-Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Vydianathan Ravi
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR 138673, Singapore
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hui-Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Feng-Ming Han
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yu-Hong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jian-Ping Yin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Liang-Min Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Byrappa Venkatesh
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR 138673, Singapore
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Wu Y, Wang X, Liu S, Luo H, Lin Q. Population genetic structure and phylogenetic analysis of gray's pipefish, Halicampus grayi in the South China Sea. Genes Genomics 2019; 42:155-164. [PMID: 31797312 DOI: 10.1007/s13258-019-00893-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and they were recognized as flagship species for marine conservation. Genus Halicampus is an important branch of syngnathid fishes that has not received the attention it deserves. OBJECTIVE To sequence the mitochondrial genome of Halicampus grayi, and investage the genetic structure of its populations. METHODS Degenerate primers were designed to amplify the entire mitochondrial genome of H. grayi. The phylogenetic relationship between H. grayi and other syngnathids were conducted using maximum-likelihood method. Population genetic structure of three geographic population of H. grayi were determined using median-joining haplotype network based on COI and Cytb sequences. RESULTS The complete mitochondrial genome of Halicampus grayi was assembled into a 17,059 bp circular sequence, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 D-loop region. The overall base composition of H. grayi is 29.93% A, 29.31% T, 16.23% G and 24.54% C, with a slight A + T rich feature (59.24%). Phylogenetic analysis indicated that H. grayi has a close relationship with Trachyrhamphus serratus. Population genetic analysis revealed a relatively high genetic diversity across different geographic populations of H. grayi, and the results of median-joining haplotype network indicated a lack of structure in populations of H. grayi. CONCLUSION The mitogenome of H. grayi will provided important information about the origin and evolution issues of syngnathid fishes, and the high-level genetic diversity detected in their populations will provide insight into the gene flow pattern of marine fishes.
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Affiliation(s)
- Yingying Wu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, People's Republic of China. .,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| | - Shuaishuai Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Hao Luo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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27
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Abstract
Abstract
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
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Affiliation(s)
- Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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28
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Zhang X, Zhang X, Song N, Gao T, Zhao L. Study on population genetics of Sillago aeolus (Perciformes: Sillaginidae) in the Coast of China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:825-834. [PMID: 31571512 DOI: 10.1080/24701394.2019.1670820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Sillago aeolus is a species from Sillaginidae, which is a widely distributed species with important scientific and economic value in the coast of China. Its population genetics have not been studied. This study investigated the population genetics of S. aeolus in the eastern and southern coast of China based on the mitochondrial control region markers obtained from 248 individuals of 9 locations. The population was characterized by a high population diversity with a low nucleotide diversity. There were no branches corresponding to the sampling sites according to the haplotype network and NJ tree. Recent asymmetric gene flow exchanges and significant genetic differences were detected between the Haikou population and the other populations. AMOVA result indicated slight genetic structures with homogeneity suggested. The neutral test and the mismatch distribution revealed a recent population expansion event. Historical geographic events may be the reason for the homogeneity within the population.
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Affiliation(s)
- Xiaomeng Zhang
- Fisheries College, Ocean University of China, Qingdao, China
| | - Xiumei Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, China.,Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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Garcia E, Rice CA, Eernisse DJ, Forsgren KL, Quimbayo JP, Rouse GW. Systematic relationships of sympatric pipefishes (Syngnathus spp.): A mismatch between morphological and molecular variation. JOURNAL OF FISH BIOLOGY 2019; 95:999-1012. [PMID: 31192446 DOI: 10.1111/jfb.14073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Analyses of mitochondrial DNA and morphological variation were performed on specimens of all five currently recognised Syngnathus pipefish species from the eastern Pacific Ocean with type localities currently considered to lie within the Californian marine biogeographic province: kelp pipefish Syngnathus californiensis, bay pipefish S. leptorhynchus, barred pipefish S. auliscus, barcheek pipefish S. exilis and chocolate pipefish S. euchrous. Results consistently differentiate S. auliscus from the other species and fail to distinguish all other specimens as distinct species, as indicated by extensive morphological overlap as well as incomplete lineage sorting and considerably low genetic divergence for 16s and coI genes(<1%). This study presents a taxonomic revision of eastern Pacific Syngnathus spp. and proposes the synonymy of S. leptorhynchus, S. euchrous and S. exilis, under the senior synonym, S. californiensis. There is still a need to study populations of Syngnathus spp. from north and south of the Californian province to assess whether these too are synonyms of the two-species recognised here.
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Affiliation(s)
- Eric Garcia
- Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Cristy A Rice
- Department of Biological Science, California State University, Fullerton, California, USA
| | - Douglas J Eernisse
- Department of Biological Science, California State University, Fullerton, California, USA
| | - Kristy L Forsgren
- Department of Biological Science, California State University, Fullerton, California, USA
| | - Juan P Quimbayo
- Center for Marine Biology, University of São Paulo, São Paulo, Brazil
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California, San Diego, California, USA
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Wang X, Zhang Y, Zhang H, Qin G, Lin Q. Complete mitochondrial genomes of eight seahorses and pipefishes (Syngnathiformes: Syngnathidae): insight into the adaptive radiation of syngnathid fishes. BMC Evol Biol 2019; 19:119. [PMID: 31185889 PMCID: PMC6560779 DOI: 10.1186/s12862-019-1430-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/30/2019] [Indexed: 11/17/2022] Open
Abstract
Background The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and their specialized life history traits make syngnathid species excellent model species for many issues in biological evolution. However, the origin of syngnathids and the evolutionary divergence time of different syngnathid species remain poorly resolved. Comprehensive phylogenetic studies of the Syngnathidae will provide critical evidence to elucidate their origin, evolution, and dispersal patterns. Results We sequenced the mitochondrial genomes of eight syngnathid species in this study, and the estimated divergence times suggested that syngnathids diverged from other teleosts approximately 48.8 Mya during the Eocene period. Selection analysis showed that many mitochondrial genes of syngnathids exhibited significantly lower Ka/Ks values than those of other teleosts. The two most frequently used codons in syngnathid fishes were different from those in other teleosts, and a greater proportion of the mitochondrial simple sequence repeats (SSRs) were distributed in non-coding sequences in syngnathids compared with other teleosts. Conclusions Our study indicated that syngnathid fishes experienced an adaptive radiation process during the early explosion of species. Syngnathid mitochondrial OXPHOS genes appear to exhibit depressed Ka/Ks ratios compared with those of other teleosts, and this may suggest that their mitogenomes have experienced strong selective constraints to eliminate deleterious mutations. Electronic supplementary material The online version of this article (10.1186/s12862-019-1430-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, People's Republic of China. .,University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Short G, Harasti D, Hamilton H. Hippocampuswhitei Bleeker, 1855, a senior synonym of the southern Queensland seahorse H.procerus Kuiter, 2001: molecular and morphological evidence (Teleostei, Syngnathidae). Zookeys 2019:109-133. [PMID: 30814902 PMCID: PMC6389870 DOI: 10.3897/zookeys.824.30921] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/29/2019] [Indexed: 11/12/2022] Open
Abstract
The taxonomic status of the seahorse Hippocampusprocerus Kuiter, 2001, type locality Hervey Bay, QLD, Australia, was re-examined based on its strong morphological similarity and geographical proximity to its congener H.whitei Bleeker, 1855, a species recorded in ten estuaries of New South Wales, Australia. Kuiter (2001) distinguished H.procerus from H.whitei by a taller coronet, marginally lower meristics, and spinier physiognomy. Meristic, morphometric, and key diagnostic morphological character comparisons from vouchered specimens of the two purported species collected from Sydney Harbour, Nelson Bay, Port Stephens, NSW and Hervey Bay, Bundaberg, and Moreton Bay, QLD did not show diagnostic differences to support species-level classification of H.procerus. Furthermore, partial mitochondrial COI sequence data from specimens sampled from known geographical distributions in NSW and Southport, QLD failed to discriminate between populations as a result of shared haplotypes, and revealed an average intraspecific divergence of 0.002%. Hippocampusprocerus is hereby placed in the synonymy of H.whitei; a redescription is provided, with a revised record of its range across eastern Australia.
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Affiliation(s)
- Graham Short
- California Academy of Sciences, San Francisco, USA California Academy of Sciences San Francisco United States of America
| | - David Harasti
- Fisheries Research, Port Stephens Fisheries Institute, New South Wales, Australia Fisheries Research, Port Stephens Fisheries Institute Port Stephens Australia
| | - Healy Hamilton
- NatureServe, Arlington, Virginia, USA NatureServe Arlington United States of America
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Short G, Smith R, Motomura H, Harasti D, Hamilton H. Hippocampusjapapigu, a new species of pygmy seahorse from Japan, with a redescription of H.pontohi (Teleostei, Syngnathidae). Zookeys 2018:27-49. [PMID: 30166895 PMCID: PMC6110155 DOI: 10.3897/zookeys.779.24799] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/08/2018] [Indexed: 11/24/2022] Open
Abstract
The pygmy seahorse Hippocampusjapapigusp. n. is described based on three specimens, 13.9–16.3 mm SL, collected from a mixed soft coral and algae reef at 11 m depth at Hachijo-jima Island, Izu Islands, Japan. The new taxon shares morphological synapomorphies with the previously described central Indo-Pacific pygmy seahorses, H.colemani, H.pontohi, H.satomiae, and H.waleananus, including extremely small size, 12 trunk rings, strongly raised continuous cleithral ring, snout spine, large spine on the eighth lateral and fifth and 12 superior trunk ridges, respectively, and unusual wing-like-protrusions immediately posterior to the head. Hippocampusjapapigusp. n. can be distinguished from all congeners by the following combination of features in the anterodorsal area of the trunk: bilaterally paired wing-like protrusions formed by a single pair of large, truncate spines projecting dorsolaterad on the first superior trunk ridge, followed by a unique elevated dorsal ridge formed by triangular bony mounds dorsally on the second to fourth superior trunk ridges. In contrast, H.pontohi possesses a pair of large truncate spines projecting strongly laterad on both the first and second superior trunk ridges followed by flat surfaces dorsally on the third and fourth superior trunk rings. The new species can be further differentiated by genetic divergence from H.pontohi (an uncorrected p-distance of 10.1% in the mitochondrial COI gene) and a striking reticulated white and brown lattice pattern on the head, trunk, and tail. Hippocampusjapapigusp. n. represents the fifth species of pygmy seahorse recorded in Japan.
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Affiliation(s)
- Graham Short
- California Academy of Sciences, San Francisco, United States of America California Academy of Sciences San Francisco United States of America
| | - Richard Smith
- iSeahorse, IUCN Seahorse, Pipefish Stickleback Specialist Group, London U.K. Pipefish Stickleback Specialist Group London United Kingdom
| | - Hiroyuki Motomura
- Kagoshima University Museum, Japan Kagoshima University Museum Kagoshima Japan
| | - David Harasti
- Port Stephens Fisheries Institute, NSW, Australia Port Stephens Fisheries Institute Nelson Bay Australia
| | - Healy Hamilton
- Kagoshima University Museum, Japan Kagoshima University Museum Kagoshima Japan
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Siqueira AC, Quimbayo JP, Cantor M, Silveira RB, Daura-Jorge FG. Estimating population parameters of longsnout seahorses, Hippocampus reidi (Teleostei: Syngnathidae) through mark-recapture. NEOTROPICAL ICHTHYOLOGY 2017. [DOI: 10.1590/1982-0224-20170067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Estimating population parameters is essential for understanding the ecology of species, which ultimately helps to assess their conservation status. The seahorse Hippocampus reidi is directly exposed to anthropogenic threats along the Brazilian coast, but the species still figures as Data Deficient (DD) at IUCN’s Red List. To provide better information on the ecology of this species, we studied how population parameters vary over time in a natural subtropical environment. By combing mark-recapture models for open and closed populations, we estimated abundance, survival rate, emigration probability, and capture probability. We marked 111 individuals, which showed a 1:1 sex ratio, and an average size of 10.5 cm. The population showed high survival rate, low temporary emigration probability and variable capture probability and abundance. Our models considering relevant biological criteria illuminate the relatively poorly known population ecology and life history of seahorses. It is our hope that this study inspires the use of mark-recapture methods in other populations of H. reidi in a collective effort to properly assess their conservation status.
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Affiliation(s)
| | - Juan P. Quimbayo
- Universidade Federal de Santa Catarina, Brazil; Universidad del Valle, Colombia
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Porter MM, Ravikumar N. 3D-printing a 'family' of biomimetic models to explain armored grasping in syngnathid fishes. BIOINSPIRATION & BIOMIMETICS 2017; 12:066007. [PMID: 28749372 DOI: 10.1088/1748-3190/aa8294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Seahorses and pipehorses evolved at least two independent strategies for tail grasping, despite being armored with a heavy body plating. To help explain mechanical trade-offs associated with the different designs, we created a 'family' of 3D-printed models that mimic variations in the presence and size of their armored plates. We measured the performance of the biomimetic proxies across several mechanical metrics, representative of their protective and prehensile capacities. Our results show that the models mimicking the tails of seahorses are the best all-around performers, while those of the distal-most, prehensile region of pipehorses are more flexible, but less protected. The comparison also reveals that different adaptive strategies provide different task-specific performance advantages, which could be leveraged for the design of armored manipulators or other bio-inspired technologies.
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Affiliation(s)
- Michael M Porter
- Department of Mechanical Engineering, Clemson University, Clemson, SC 29634, United States of America. Zucker Family Graduate Education Center, Clemson University, North Charleston, SC 29405, United States of America
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35
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Pregnant pipefish with a simple brooding surface loose less weight when carrying heavier eggs: evidence of compensation for low oocyte quality? Acta Ethol 2017. [DOI: 10.1007/s10211-017-0268-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Mol Phylogenet Evol 2017; 113:33-48. [PMID: 28487262 DOI: 10.1016/j.ympev.2017.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/23/2022]
Abstract
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.
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37
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Berglund A, Sundin J, Rosenqvist G. Baltic pipefish females need twice as many males as they get. Behav Ecol 2017. [DOI: 10.1093/beheco/arx046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol 2016; 17:258. [PMID: 27993155 PMCID: PMC5168715 DOI: 10.1186/s13059-016-1126-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. Results We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. Conclusions The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1126-6) contains supplementary material, which is available to authorized users.
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