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Cooper WJ, Conith MR, Conith AJ. Surfperches versus Damselfishes: Trophic Evolution in Closely Related Pharyngognath Fishes with Highly Divergent Reproductive Strategies. Integr Org Biol 2024; 6:obae018. [PMID: 38939103 PMCID: PMC11210498 DOI: 10.1093/iob/obae018] [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: 08/06/2023] [Revised: 04/17/2024] [Accepted: 05/26/2024] [Indexed: 06/29/2024] Open
Abstract
Surfperches and damselfishes are very closely related ovalentarians with large reproductive differences. Damselfishes are typical of most Ovalentaria in that they lay demersal eggs that hatch into small, free-feeding larvae. Surfperches are unusual among ovalentarians and most acanthomorphs in having prolonged internal development. They are born at an advanced stage, some as adults, and bypass the need to actively feed throughout an extended period of ontogeny. Damselfishes and surfperches possess the same modifications of the fifth branchial arch that allow them to perform advanced food processing within the pharynx. This condition (pharyngognathy) has large effects on the evolution of feeding mechanics and trophic ecology. Although the evolution of pharyngognaths has received considerable attention, the effects of different reproductive strategies on their diversification have not been examined. We compared head shape evolution in surfperches and damselfishes using geometric morphometrics, principal component analyses, and multiple phylogenetic-comparative techniques. We found that they have similar mean head shapes, that their primary axes of shape variation are comparable and distinguish benthic-feeding and pelagic-feeding forms in each case, and that, despite large differences in crown divergence times, their head shape disparities are not significantly different. Several lines of evidence suggest that evolution has been more constrained in damselfishes: Head shape is evolving faster in surfperches, more anatomical traits have undergone correlated evolution in damselfishes, there is significant phylogenetic signal in damselfish evolution (but not surfperches), and damselfishes exhibit significant allometry in head shape that is not present in surfperches.
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Affiliation(s)
- W J Cooper
- Biology Department, College of Science and Engineering, Western Washington University, Bellingham, WA 98225, USA
- Marine and Coastal Science, Western Washington University, Bellingham, WA 98225, USA
| | - M R Conith
- Biology Department, College of Science and Engineering, Western Washington University, Bellingham, WA 98225, USA
| | - A J Conith
- Department of Biology, DePaul University, Chicago, IL 60604, USA
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2
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Bernardi G, Azzurro E, Bariche M, Jimenez C, Kalogirou S, Kleitou P. Invasion genomics of lionfish in the Mediterranean Sea. Ecol Evol 2024; 14:e11087. [PMID: 38450316 PMCID: PMC10915480 DOI: 10.1002/ece3.11087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
The rate of biological invasions is steadily increasing, with major ecological and economic impacts accounting for billions of dollars in damage as a result. One spectacular example is the western Atlantic invasion by lionfishes. In the Mediterranean Sea, invasions from the Red Sea via the Suez Canal (termed Lessepsian invasions) comprise more than 100 fish species, including a recent invasion by lionfish. In light of the devastating effects of lionfish in the Caribbean Sea, understanding the dynamics of Mediterranean lionfish invasion is crucial. The Lessepsian lionfish invasion started in 2012, and rapidly spread to the central Mediterranean. Here, we used thousands of RAD seq genomic markers to study the population dynamics of this invasion. While we did not find a reduction in genetic diversity between source (Red Sea) and invasive (Mediterranean) populations (i.e., bottleneck effects), we found evidence of population structure within the invasive range in the Mediterranean Sea. We found that loci that are potentially under selection may play an important role in invasion success (in particular, genes involved in osmoregulation and fin spine sizes). Genomic approaches proved powerful in examining the ecological and evolutionary patterns of successful invaders and may be used as tools to understand and potentially mitigate future invasions.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | - Ernesto Azzurro
- CNR‐IRBIM, National Research CouncilInstitute of Biological Resources and Marine BiotechnologiesAnconaItaly
- Zoological Station A. DohrnNaplesItaly
| | - Michel Bariche
- Department of BiologyAmerican University of BeirutBeirutLebanon
| | - Carlos Jimenez
- Enalia Physis Environmental Research Centre (ENALIA)NicosiaCyprus
- The Cyprus InstituteEnergy Environment and Water Research CenterNicosiaCyprus
| | - Stefanos Kalogirou
- Hellenic Centre for Marine Research, Institute for Marine Biological Resources and Inland WatersHydrobiological Station of RhodesRhodesGreece
| | - Periklis Kleitou
- Marine & Environmental Research (MER) LabLimassolCyprus
- School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
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3
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Miller EC. Historical biogeography supports Point Conception as the site of turnover between temperate East Pacific ichthyofaunas. PLoS One 2023; 18:e0291776. [PMID: 37725614 PMCID: PMC10508600 DOI: 10.1371/journal.pone.0291776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
The cold temperate and subtropical marine faunas of the Northeastern Pacific meet within California as part of one of the few eastern boundary upwelling ecosystems in the world. Traditionally, it is believed that Point Conception is the precise site of turnover between these two faunas due to sharp changes in oceanographic conditions. However, evidence from intraspecific phylogeography and species range terminals do not support this view, finding stronger biogeographic breaks elsewhere along the coast. Here I develop a new application of historical biogeographic approaches to uncover sites of transition between faunas without needing an a priori hypothesis of where these occur. I used this approach to determine whether the point of transition between northern and southern temperate faunas occurs at Point Conception or elsewhere within California. I also examined expert-vetted latitudinal range data of California fish species from the 1970s and the 2020s to assess how biogeography could change with the backdrop of climate change. The site of turnover was found to occur near Point Conception, in concordance with the traditional view. I suggest that recent species- and population-level processes could be expected to give signals of different events from historical biogeography, possibly explaining the discrepancy across studies. Species richness of California has increased since the 1970s, mostly due to species's ranges expanding northward from Baja California (Mexico). Range shifts under warming conditions seem to be increasing the disparity between northern and southern faunas of California, creating a more divergent biogeography.
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Affiliation(s)
- Elizabeth Christina Miller
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
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4
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Toy JA, Bernardi G. A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage. J Hered 2023; 114:404-409. [PMID: 36790952 PMCID: PMC10287144 DOI: 10.1093/jhered/esad009] [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: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
The surfperches (family Embiotocidae) are a unique group of mostly marine fishes whose phylogenetic position within the Ovalentaria clade (Percomorpha) is still unresolved. As a result of their viviparity and lack of a dispersive larval stage, surfperches are an excellent model for the study of speciation, gene flow, and local adaptation in the ocean. They are also the target of an immensely popular recreational fishery. Very few high-quality molecular resources, however, are available for this group and only for a single species. Here, we describe a highly complete reference genome for the kelp surfperch, Brachyistius frenatus, assembled using a combination of short-read (Illumina, ~47× coverage) and long-read (Oxford Nanopore Technologies, ~27× coverage) sequencing. The 596 Mb assembly has a completeness level of 98.1% (BUSCO), a contig N50 of 2.6 Mb (n = 56), and a contig N90 of 406.6 kb (n = 293). Comparative analysis revealed a high level of synteny between B. frenatus and its close relative, Embiotoca jacksoni. This assembly will serve as a valuable molecular resource upon which future evolutionary dynamics research will build, such as the investigation of local adaptation and the genomic potential for climate adaptation in wild populations.
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Affiliation(s)
- Jason A Toy
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
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5
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Gold Z, Koch MQ, Schooler NK, Emery KA, Dugan JE, Miller RJ, Page HM, Schroeder DM, Hubbard DM, Madden JR, Whitaker SG, Barber PH. A comparison of biomonitoring methodologies for surf zone fish communities. PLoS One 2023; 18:e0260903. [PMID: 37314989 DOI: 10.1371/journal.pone.0260903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/25/2023] [Indexed: 06/16/2023] Open
Abstract
Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch (Amphistichus argenteus). In contrast, eDNA metabarcoding captured 88.9% (32/36) of all fishes observed in seine and BRUV surveys plus 57 additional species, including 15 that frequent surf zone habitats. On average, eDNA detected over 5 times more species than BRUVs and 8 times more species than seine surveys at a given site. eDNA approaches also showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 31 of the 32 (96.9%) jointly observed species across beaches. The four species detected by BRUV/seines, but not eDNA were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches and Sygnathidae pipefishes). In frequent co-detection of species between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - McKenzie Q Koch
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Nicholas K Schooler
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Kyle A Emery
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jenifer E Dugan
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Robert J Miller
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Henry M Page
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Donna M Schroeder
- Bureau of Ocean Energy Management, Camarillo, CA, United States of America
| | - David M Hubbard
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jessica R Madden
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Stephen G Whitaker
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
- Channel Islands National Park, Ventura, CA, United States of America
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
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Bernardi G, Toy JA, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB. Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage. J Hered 2022; 113:657-664. [PMID: 35809222 PMCID: PMC9709976 DOI: 10.1093/jhered/esac034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Black Surfperch, Embiotoca jacksoni, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on genomic data. The genome of E. jacksoni is typical of marine fishes at less than 1Gb (genome size = 635 Mb), and our assembly is near-chromosome level (contig N50 = 6.5Mb, scaffold N50 = 15.5 Mb, BUSCO = 98.1%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Jason A Toy
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California–Los Angeles, Los Angeles, CA, USA
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7
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Haque R, Das II, Sawant PB, Chadha NK, Sahoo L, Kumar R, Sundaray JK. Tenets in Microbial Endocrinology: A New Vista in Teleost Reproduction. Front Physiol 2022; 13:871045. [PMID: 36035477 PMCID: PMC9411670 DOI: 10.3389/fphys.2022.871045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Climate vulnerability and induced changes in physico-chemical properties of aquatic environment can bring impairment in metabolism, physiology and reproduction in teleost. Variation in environmental stimuli mainly acts on reproduction by interfering with steroidogenesis, gametogenesis and embryogenesis. The control on reproductive function in captivity is essential for the sustainability of aquaculture production. There are more than 3,000 teleost species across the globe having commercial importance; however, adequate quality and quantity of seed production have been the biggest bottleneck. Probiotics are widely used in aquaculture as a growth promoter, stress tolerance, pathogen inhibition, nutrient digestibility and metabolism, reproductive performance and gamete quality. As the gut microbiota exerts various effects on the intestinal milieu which influences distant organs and pathways, therefore it is considered to be a full-fledged endocrine organ. Researches on Gut-Brain-Gonad axis (GBG axis) and its importance on physiology and reproduction have already been highlighted for higher mammals; however, the study on fish physiology and reproduction is limited. While looking into the paucity of information, we have attempted to review the present status of microbiome and its interaction between the brain and gut. This review will address a process of the microbiome physiological mechanism involved in fish reproduction. The gut microbiota influences the BPG axis through a wide variety of compounds, including neuropeptides, neurotransmitter homologs and transmitters. Currently, research is being conducted to determine the precise process by which gut microbial composition influences brain function in fish. The gut-brain bidirectional interaction can influence brain biochemistry such as GABA, serotonin and tryptophan metabolites which play significant roles in CNS regulation. This review summarizes the fact, how microbes from gut, skin and other parts of the body influence fish reproduction through the Gut-Brain-Gonad axis.
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Affiliation(s)
- Ramjanul Haque
- Division of Aquaculture, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Ipsita Iswari Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | | | - Narinder Kumar Chadha
- Division of Aquaculture, ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Rajesh Kumar
- Aquaculture Production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Jitendra Kumar Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
- *Correspondence: Jitendra Kumar Sundaray,
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8
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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9
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Azzurro E, Nourigat M, Cohn F, Ben Souissi J, Bernardi G. Right out of the gate: the genomics of Lessepsian invaders in the vicinity of the Suez Canal. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractMarine organisms that enter the Mediterranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spatial genetic variation. In this study, by sampling two invasive fishes with different life histories (the rabbitfish Siganus rivulatus and the filefish Stephanolepis diaspros), we looked at evidence of population structure and selection at the boundary between the Red Sea and the Mediterranean (the Suez Canal), using thousands of molecular markers. Results illustrate two divergent patterns of genetic patterns, with little genetic structure in S. rivulatus and strong population structure in S. diaspros, even at such small spatial scale. We discuss differences in ecological characteristics between the two species to account for such differences. In addition, we report that in the face of both high (S. rivulatus) and low (S. diaspros) gene flow, loci under selection were uncovered, and some protein coding genes were identified as being involved with osmoregulation, which seems to be an important feature of individuals crossing the salinity-variable Suez Canal. The presence of genes under selection in populations near the Suez Canal supports the idea that selection may be active and essential for successful invasions right out of the gate.
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10
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Bond ER, Forsgren KL. External reproductive structures of male Surfperches (Embiotocidae): Urogenital papilla. Anat Rec (Hoboken) 2021; 305:1712-1723. [PMID: 34821058 DOI: 10.1002/ar.24836] [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: 07/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/08/2022]
Abstract
Fishes exhibit a dynamic array of reproductive diversity. Among the various forms of reproduction, internal fertilization has evolved at least 13 times and has been observed in 2-3% of teleost species, half of which are marine. Internal fertilization has led to the evolution of male intromittent organs to aid in sperm transfer during copulation. The intromittent organs of poeciliids have been widely investigated, but little research has focused on the intromittent organs of marine fishes. The surfperches are internally fertilizing, viviparous fishes with a ventrally located papilla. In this article, the external morphology of 19 Embiotocidae species was examined. Additionally, paraffin histology was used to investigate the walleye surfperch (Hyperprosopon argenteum), black perch (Embiotoca jacksoni), and dwarf perch (Micrometrus minimus) papilla to aid in the identification of tissue composition to determine its function. External morphology was documented via macro photography and males were dissected to observe the relationship between the testes, spermatic duct, and papilla. We provide histological evidence that the urogenital papilla is directly connected to the spermatic duct and testis and likely involved in spermatozeugmata transfer. Our research also determined that the papillae were composed of both urinary and reproductive tissues, thus we propose the papilla be referred to as a urogenital papilla. Our study contributes to an overall understanding of intromittent organs of marine fishes, particularly in the surfperches, which has not been previously documented.
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Affiliation(s)
- Evelyn Ruelas Bond
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - Kristy L Forsgren
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
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11
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McCord CL, Nash CM, Cooper WJ, Westneat MW. Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology. PLoS One 2021; 16:e0258889. [PMID: 34705840 PMCID: PMC8550381 DOI: 10.1371/journal.pone.0258889] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.
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Affiliation(s)
- Charlene L. McCord
- College of Natural and Behavioral Sciences, California State University Dominguez Hills, Carson, California, United States of America
| | - Chloe M. Nash
- Department of Organismal Biology and Anatomy, and Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Division of Fishes, Field Museum of Natural History, Chicago, Illinois, United States of America
| | - W. James Cooper
- Department of Biology and Program in Marine and Coastal Science, Western Washington University, Bellingham, Washington, United States of America
| | - Mark W. Westneat
- Department of Organismal Biology and Anatomy, and Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Division of Fishes, Field Museum of Natural History, Chicago, Illinois, United States of America
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12
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Love MS, Bizzarro JJ, Cornthwaite AM, Frable BW, Maslenikov KP. Checklist of marine and estuarine fishes from the AlaskaYukon Border, Beaufort Sea, to Cabo San Lucas, Mexico. Zootaxa 2021; 5053:1-285. [PMID: 34810850 DOI: 10.11646/zootaxa.5053.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Indexed: 11/04/2022]
Abstract
This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.
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Affiliation(s)
- Milton S Love
- Marine Science Institute, University of California, Santa Barbara, CA 93106.
| | - Joseph J Bizzarro
- Cooperative Institute for Marine Ecosystems and Climate, University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060. .
| | - A Maria Cornthwaite
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada .
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0244, USA. .
| | - Katherine P Maslenikov
- University of Washington Fish Collection, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture, 1122 NE Boat St., Seattle, WA 98105.
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13
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Bowen BW, Forsman ZH, Whitney JL, Faucci A, Hoban M, Canfield SJ, Johnston EC, Coleman RR, Copus JM, Vicente J, Toonen RJ. Species Radiations in the Sea: What the Flock? J Hered 2021; 111:70-83. [PMID: 31943081 DOI: 10.1093/jhered/esz075] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Species flocks are proliferations of closely-related species, usually after colonization of depauperate habitat. These radiations are abundant on oceanic islands and in ancient freshwater lakes, but rare in marine habitats. This contrast is well documented in the Hawaiian Archipelago, where terrestrial examples include the speciose silverswords (sunflower family Asteraceae), Drosophila fruit flies, and honeycreepers (passerine birds), all derived from one or a few ancestral lineages. The marine fauna of Hawai'i is also the product of rare colonization events, but these colonizations usually yield only one species. Dispersal ability is key to understanding this evolutionary inequity. While terrestrial fauna rarely colonize between oceanic islands, marine fauna with pelagic larvae can make this leap in every generation. An informative exception is the marine fauna that lack a pelagic larval stage. These low-dispersal species emulate a "terrestrial" mode of reproduction (brooding, viviparity, crawl-away larvae), yielding marine species flocks in scattered locations around the world. Elsewhere, aquatic species flocks are concentrated in specific geographic settings, including the ancient lakes of Baikal (Siberia) and Tanganyika (eastern Africa), and Antarctica. These locations host multiple species flocks across a broad taxonomic spectrum, indicating a unifying evolutionary phenomenon. Hence marine species flocks can be singular cases that arise due to restricted dispersal or other intrinsic features, or they can be geographically clustered, promoted by extrinsic ecological circumstances. Here, we review and contrast intrinsic cases of species flocks in individual taxa, and extrinsic cases of geological/ecological opportunity, to elucidate the processes of species radiations.
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Affiliation(s)
- Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Jonathan L Whitney
- Joint Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI
| | - Anuschka Faucci
- Math & Sciences Division, Leeward Community College, University of Hawai'i, Pearl City, HI
| | - Mykle Hoban
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | | | - Erika C Johnston
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Richard R Coleman
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Jan Vicente
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
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14
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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15
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Evolutionary origin of the Atlantic Cabo Verde nibbler (Girella stuebeli), a member of a primarily Pacific Ocean family of antitropical herbivorous reef fishes. Mol Phylogenet Evol 2020; 156:107021. [PMID: 33248204 DOI: 10.1016/j.ympev.2020.107021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/21/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022]
Abstract
Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa. Based on thousands of genomic markers (RAD sequences), we identified the closest relatives of G. stuebeli as being a clade of three species endemic to the northwestern Pacific, restricted to the Sea of Japan and vicinity. This clade diverged from G. stuebeli approximately 2.2 Mya. Two alternative potential routes of migration may explain this affinity: a western route, from the Tropical Eastern Pacific and the Tropical Western Atlantic, and an eastern route via the Indian Ocean and Southern Africa. The geological history and oceanography of the regions combined with molecular data presented here, suggest that the eastern route of invasion (via the Indian Ocean and Southern Africa) is a more likely scenario.
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16
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Izumiyama M, Awata S, Crow K. Evaluating Reproductive Strategies and Female Bateman Gradients in Ditrema temminckii: Is the Number of Fathers a Good Approximation for the Number of Mates? COPEIA 2020. [DOI: 10.1643/ce-19-271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Michael Izumiyama
- San Francisco State University, 1600 Holloway Avenue, San Francisco, California 94132; (MI) . Send reprint requests to MI
| | - Satoshi Awata
- Osaka City University 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Karen Crow
- San Francisco State University, 1600 Holloway Avenue, San Francisco, California 94132; (MI) . Send reprint requests to MI
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17
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Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
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Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
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18
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Izumiyama M, Westphal MF, Crow KD. In the surf zone: Reproductive strategy of the calico surfperch (Amphistichus koelzi) in a comparative context. JOURNAL OF FISH BIOLOGY 2020; 96:939-949. [PMID: 32048298 DOI: 10.1111/jfb.14283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/08/2020] [Indexed: 06/10/2023]
Abstract
We examined the reproductive life history of calico surfperch (Amphistichus koelzi), including mating season, pregnancy, gestation and multiple paternity utilizing restriction site-associated DNA sequencing. Furthermore, we compared the mating season of calico with barred (Amphistichus argenteus), walleye (Hyperprosopon argenteum) and silver (Hyperprosopon ellipticum) surfperches to determine if the timing of reproduction is divergent within and between the genera. In calico surfperch, the mating season occurs from October to November, and females gestate from December to May. All broods exhibit multiple paternity with a range of four to seven sires per brood. The mating season of calico overlaps completely with barred surfperch; however, barred surfperches have a protracted mating season which extends until the beginning of December, which may be due to differences in reproductive strategy such as size at first reproduction. In the genus, the Hyperprosopon mating season begins earlier than Amphistichus, with divergence in the onset of mating between Hyperprosopon congeners of approximately 1 month.
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Affiliation(s)
- Michael Izumiyama
- Department of Biology, San Francisco State University, San Francisco, California, USA
| | - Michael F Westphal
- Bureau of Land Management, California Coastal National Monument, Marina, California, USA
| | - Karen D Crow
- Department of Biology, San Francisco State University, San Francisco, California, USA
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19
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Garcia E, Simison WB, Bernardi G. Patterns of Genomic Divergence and Signals of Selection in Sympatric and Allopatric Northeastern Pacific and Sea of Cortez Populations of the Sargo (Anisotremus davidsonii) and Longjaw Mudsucker (Gillichthys mirabilis). J Hered 2020; 111:57-69. [DOI: 10.1093/jhered/esz071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractStudying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.
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Affiliation(s)
- Eric Garcia
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
- Department of Biological Sciences, Old Dominion University, Norfolk, VA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - Giacomo Bernardi
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
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20
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Baliga VB, Mehta RS. Morphology, Ecology, and Biogeography of Independent Origins of Cleaning Behavior Around the World. Integr Comp Biol 2019; 59:625-637. [DOI: 10.1093/icb/icz030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Members of an ecological guild may be anticipated to show morphological convergence, as similar functional demands exert similar selective pressures on phenotypes. Nature is rife with examples, however, where such taxa instead exhibit ‘incomplete’ convergence or even divergence. Incorporating factors such as character displacement by other guild members or variation in ecological specialization itself may therefore be necessary to gain a more complete understanding of what constrains or promotes diversity. Cleaning, a behavior in which species remove and consume ectoparasites from “clientele,” has been shown to exhibit variation in specialization and has evolved in a variety of marine habitats around the globe. To determine the extent to which specialization in this tropic strategy has affected phenotypic evolution, we examined the evolution of cleaning behavior in five marine fish families: Labridae, Gobiidae, Pomacanthidae, Pomacentridae, and Embiotocidae. We used a comparative framework to determine patterns of convergence and divergence in body shape and size across non-cleaning and cleaning members within these five clades. Highly specialized obligate cleaning, found in the Indo-Pacific and the Caribbean, evolved in the Labridae and Gobiidae at strikingly similar times. In these two regions, obligate cleaning evolves early, shows convergence on an elongate body shape, and is restricted to species of small body size. Facultative cleaning, shown either throughout ontogeny or predominately in the juvenile phase, exhibits a much more varied phenotype, especially in geographic regions where obligate cleaning occurs. Collectively, our results are consistent with varying extents of an ecological specialization constraining or spurring morphological evolution in recurrent ways across regions.
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Affiliation(s)
- Vikram B Baliga
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Rita S Mehta
- Department of Ecology and Evolutionary Biology, Long Marine Laboratory, University of California, Santa Cruz, CA 95060, USA
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21
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Crotti M, Barratt CD, Loader SP, Gower DJ, Streicher JW. Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus
). ZOOL SCR 2019. [DOI: 10.1111/zsc.12335] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Marco Crotti
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; London UK
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Glasgow UK
| | - Christopher D. Barratt
- Department of Environmental Sciences; University of Basel; Basel Switzerland
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Simon P. Loader
- Department of Life Sciences; The Natural History Museum; London UK
- Department of Environmental Sciences; University of Basel; Basel Switzerland
| | - David J. Gower
- Department of Life Sciences; The Natural History Museum; London UK
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22
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Gajdzik L, Bernardi G, Lepoint G, Frédérich B. Genetic diversity mirrors trophic ecology in coral reef fish feeding guilds. Mol Ecol 2018; 27:5004-5018. [DOI: 10.1111/mec.14936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Laura Gajdzik
- Laboratory of Functional and Evolutionary Morphology FOCUS, University of Liège Liège Belgium
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz California
| | - Gilles Lepoint
- Laboratory of Oceanology FOCUS, University of Liège Liège Belgium
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology FOCUS, University of Liège Liège Belgium
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23
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Worldwide phylogeny of three-spined sticklebacks. Mol Phylogenet Evol 2018; 127:613-625. [DOI: 10.1016/j.ympev.2018.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/16/2018] [Accepted: 06/04/2018] [Indexed: 11/23/2022]
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24
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Bernardi G, Nelson P, Paddack M, Rulmal J, Crane N. Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes. Ecol Evol 2018; 8:8676-8685. [PMID: 30271536 PMCID: PMC6157655 DOI: 10.1002/ece3.4417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/15/2022] Open
Abstract
The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
| | | | | | - John Rulmal
- Ulithi Falalop Community Action ProgramYapFederated States of Micronesia
| | - Nicole Crane
- Department of BiologyCabrillo CollegeAptosCalifornia
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25
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Kuang T, Tornabene L, Li J, Jiang J, Chakrabarty P, Sparks JS, Naylor GJP, Li C. Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness. Mol Phylogenet Evol 2018; 128:192-202. [PMID: 30036699 DOI: 10.1016/j.ympev.2018.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 07/11/2018] [Accepted: 07/17/2018] [Indexed: 11/30/2022]
Abstract
The use of genome-scale data to infer phylogenetic relationships has gained in popularity in recent years due to the progress made in target-gene capture and sequencing techniques. Data filtering, the approach of excluding data inconsistent with the model from analyses, presumably could alleviate problems caused by systematic errors in phylogenetic inference. Different data filtering criteria, such as those based on evolutionary rate and molecular clocklikeness as well as others have been proposed for selecting useful phylogenetic markers, yet few studies have tested these criteria using phylogenomic data. We developed a novel set of single-copy nuclear coding markers to capture thousands of target genes in gobioid fishes, a species-rich lineages of vertebrates, and tested the effects of data-filtering methods based on substitution rate and molecular clocklikeness while attempting to control for the compounding effects of missing data and variation in locus length. We found that molecular clocklikeness was a better predictor than overall substitution rate for phylogenetic usefulness of molecular markers in our study. In addition, when the 100 best ranked loci for our predictors were concatenated and analyzed using maximum likelihood, or combined in a coalescent-based species-tree analysis, the resulting trees showed a well-resolved topology of Gobioidei that mostly agrees with previous studies. However, trees generated from the 100 least clocklike frequently recovered conflicting, and in some cases clearly erroneous topologies with strong support, thus indicating strong systematic biases in those datasets. Collectively these results suggest that data filtering has the potential improve the performance of phylogenetic inference when using both a concatenation approach as well as methods that rely on input from individual gene trees (i.e. coalescent species-tree approaches), which may be preferred in scenarios where incomplete lineage sorting is likely to be an issue.
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Affiliation(s)
- Ting Kuang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Jingyan Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Prosanta Chakrabarty
- Louisiana State University, Museum of Natural Science, Department of Biological Sciences, Baton Rouge, LA 70803, USA
| | - John S Sparks
- American Museum of Natural History, Central Park West at 79th Street, NY, NY 10024, USA
| | | | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China.
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26
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Crane NL, Tariel J, Caselle JE, Friedlander AM, Robertson DR, Bernardi G. Clipperton Atoll as a model to study small marine populations: Endemism and the genomic consequences of small population size. PLoS One 2018; 13:e0198901. [PMID: 29949612 PMCID: PMC6021044 DOI: 10.1371/journal.pone.0198901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/29/2018] [Indexed: 01/05/2023] Open
Abstract
Estimating population sizes and genetic diversity are key factors to understand and predict population dynamics. Marine species have been a difficult challenge in that respect, due to the difficulty in assessing population sizes and the open nature of such populations. Small, isolated islands with endemic species offer an opportunity to groundtruth population size estimates with empirical data and investigate the genetic consequences of such small populations. Here we focus on two endemic species of reef fish, the Clipperton damselfish, Stegastes baldwini, and the Clipperton angelfish, Holacanthus limbaughi, on Clipperton Atoll, tropical eastern Pacific. Visual surveys, performed over almost two decades and four expeditions, and genetic surveys based on genomic RAD sequences, allowed us to estimate kinship and genetic diversity, as well as to compare population size estimates based on visual surveys with effective population sizes based on genetics. We found that genetic and visual estimates of population numbers were remarkably similar. S. baldwini and H. limbaughi had population sizes of approximately 800,000 and 60,000, respectively. Relatively small population sizes resulted in low genetic diversity and the presence of apparent kinship. This study emphasizes the importance of small isolated islands as models to study population dynamics of marine organisms.
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Affiliation(s)
- Nicole L. Crane
- Department of Biology, Cabrillo College, Aptos, CA, United States of America
| | - Juliette Tariel
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennifer E. Caselle
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, United States of America
| | - Alan M. Friedlander
- Pristine Seas, National Geographic Society, Washington, DC, United States of America
- Fisheries Ecology Research Lab, Department of Biology, University of Hawaii, Honolulu, HI, United States of America
| | | | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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27
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Bernardi G, Longo GC, Quiros TEAL. Altrichthys alelia, a new brooding damselfish (Teleostei, Perciformes, Pomacentridae) from Busuanga Island, Philippines. Zookeys 2017:45-55. [PMID: 28769678 PMCID: PMC5523885 DOI: 10.3897/zookeys.675.12061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/24/2017] [Indexed: 11/12/2022] Open
Abstract
A new species of damselfish, Altrichthysaleliasp. n. is described from specimens collected in shallow water (1–8m depth) off Busuanga Island, Palawan Province, Philippines. It differs from the other two species in the genus, A.curatus and A.azurelineatus, in various features including having golden upper body lacking dark edges of dorsal and caudal fins, higher modal number of tubed lateral line scales, as well as differences in two mitochondrial markers, one nuclear marker, and RAD markers.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
| | - Gary C Longo
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA.,Current address: Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - T E Angela L Quiros
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
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28
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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29
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Longo GC, O'Connell B, Green RE, Bernardi G. The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae). Mar Genomics 2016; 28:107-112. [DOI: 10.1016/j.margen.2016.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/11/2016] [Accepted: 03/12/2016] [Indexed: 11/25/2022]
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30
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Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers. Mol Phylogenet Evol 2016; 98:84-8. [DOI: 10.1016/j.ympev.2016.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
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31
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Takahashi T, Sota T. A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol 2016; 100:234-242. [PMID: 27068840 DOI: 10.1016/j.ympev.2016.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/16/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022]
Abstract
The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.
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Affiliation(s)
- Tetsumi Takahashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; National Institute of Genetics, Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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Paun O, Turner B, Trucchi E, Munzinger J, Chase MW, Samuel R. Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot. Syst Biol 2015; 65:212-27. [PMID: 26430059 PMCID: PMC4748748 DOI: 10.1093/sysbio/syv076] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/25/2015] [Indexed: 11/12/2022] Open
Abstract
Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.
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Affiliation(s)
- Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | - Barbara Turner
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria;
| | - Emiliano Trucchi
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | | | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3AB Surrey, UK; and School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
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