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Speirs ZC, Loynes CA, Mathiessen H, Elks PM, Renshaw SA, Jørgensen LVG. What can we learn about fish neutrophil and macrophage response to immune challenge from studies in zebrafish. FISH & SHELLFISH IMMUNOLOGY 2024; 148:109490. [PMID: 38471626 DOI: 10.1016/j.fsi.2024.109490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/06/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Fish rely, to a high degree, on the innate immune system to protect them against the constant exposure to potential pathogenic invasion from the surrounding water during homeostasis and injury. Zebrafish larvae have emerged as an outstanding model organism for immunity. The cellular component of zebrafish innate immunity is similar to the mammalian innate immune system and has a high degree of sophistication due to the needs of living in an aquatic environment from early embryonic stages of life. Innate immune cells (leukocytes), including neutrophils and macrophages, have major roles in protecting zebrafish against pathogens, as well as being essential for proper wound healing and regeneration. Zebrafish larvae are visually transparent, with unprecedented in vivo microscopy opportunities that, in combination with transgenic immune reporter lines, have permitted visualisation of the functions of these cells when zebrafish are exposed to bacterial, viral and parasitic infections, as well as during injury and healing. Recent findings indicate that leukocytes are even more complex than previously anticipated and are essential for inflammation, infection control, and subsequent wound healing and regeneration.
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Affiliation(s)
- Zoë C Speirs
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Catherine A Loynes
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Heidi Mathiessen
- Laboratory of Experimental Fish Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Philip M Elks
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Stephen A Renshaw
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Louise von Gersdorff Jørgensen
- Laboratory of Experimental Fish Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark.
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2
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Díaz-Arce N, Gagnaire PA, Richardson DE, Walter JF, Arnaud-Haond S, Fromentin JM, Brophy D, Lutcavage M, Addis P, Alemany F, Allman R, Deguara S, Fraile I, Goñi N, Hanke AR, Karakulak FS, Pacicco A, Quattro JM, Rooker JR, Arrizabalaga H, Rodríguez-Ezpeleta N. Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna. Mol Ecol 2024; 33:e17188. [PMID: 37921120 DOI: 10.1111/mec.17188] [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: 06/21/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.
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Affiliation(s)
- Natalia Díaz-Arce
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - David E Richardson
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Narragansett, Rhode Island, USA
| | - John F Walter
- Southeast Fisheries Sciences Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, Florida, USA
| | | | | | - Deirdre Brophy
- Marine and Freshwater Research Center, Atlantic Technological University (ATU), Galway City, Ireland
| | - Molly Lutcavage
- Large Pelagics Research Center, School for the Environment, University of Massachusetts Boston, Gloucester, Massachusetts, USA
| | - Piero Addis
- Department of Environmental and Life Science, University of Cagliari, Cagliari, Italy
| | - Francisco Alemany
- International Commission for the Conservation of Atlantic Tunas, GBYP, Madrid, Spain
| | - Robert Allman
- National Marine Fisheries Service, Southeast Fisheries Science Center, Panama City Laboratory, Panama City, Florida, USA
| | | | - Igaratza Fraile
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Nicolas Goñi
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Alex R Hanke
- St Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, New Brunswick, Canada
| | | | - Ashley Pacicco
- Cooperative Institute for Marine and Atmospheric Studies Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
| | - Joseph M Quattro
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Jay R Rooker
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Haritz Arrizabalaga
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
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3
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Muschick M, Jemmi E, Lengacher N, Hänsch S, Wales N, Kishe MA, Mwaiko S, Dieleman J, Lever MA, Salzburger W, Verschuren D, Seehausen O. Ancient DNA is preserved in fish fossils from tropical lake sediments. Mol Ecol 2023; 32:5913-5931. [PMID: 37830773 DOI: 10.1111/mec.17159] [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: 04/18/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.
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Affiliation(s)
- Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Eliane Jemmi
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Nicholas Lengacher
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Stephanie Hänsch
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nathan Wales
- Department of Archaeology, University of York, York, UK
| | - Mary A Kishe
- Tanzania Fisheries Research Institute, Dar es Salaam, Tanzania
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Jorunn Dieleman
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
| | | | - Dirk Verschuren
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
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4
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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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5
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Scarsbrook L, Mitchell KJ, Mcgee MD, Closs GP, Rawlence NJ. Ancient DNA from the extinct New Zealand grayling ( Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in New Zealand (NZ), including their relationship to the Australian grayling, is poorly understood. The NZ grayling (Prototroctes oxyrhynchus) is the only known fish in NZ to have gone extinct since human arrival there. Despite its historical abundance, only 23 wet and dried, formalin-fixed specimens exist in museums. We used high-throughput DNA sequencing to generate mitogenomes from formalin-fixed P. oxyrhynchus specimens, and analysed these in a temporal phylogenetic framework of retropinnids and osmerids. We recovered a strong sister-relationship between NZ and Australian grayling (P. mareana), with a common ancestor ~13.8 Mya [95% highest posterior density (HPD): 6.1–23.2 Mya], after the height of Oligocene marine inundation in NZ. Our temporal phylogenetic analysis suggests a single marine dispersal between NZ and Australia, although the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. This study provides further insights into the possible extinction drivers of the NZ grayling, informs discussion regarding reintroduction of Prototroctes to NZ and highlights how advances in palaeogenetics can be used to test evolutionary hypotheses in fish, which, until relatively recently, have been comparatively neglected in ancient-DNA research.
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Affiliation(s)
- Lachie Scarsbrook
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford , Oxford , UK
| | - Kieren J Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Matthew D Mcgee
- Behavioural Studies Group, School of Biological Sciences, Monash University , Melbourne, Victoria , Australia
| | - Gerard P Closs
- Department of Zoology, University of Otago , Dunedin , New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago , Dunedin , New Zealand
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6
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Reid BN, Pinsky ML. Simulation-Based Evaluation of Methods, Data Types, and Temporal Sampling Schemes for Detecting Recent Population Declines. Integr Comp Biol 2022; 62:1849-1863. [PMID: 36104155 PMCID: PMC9801984 DOI: 10.1093/icb/icac144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 01/05/2023] Open
Abstract
Understanding recent population trends is critical to quantifying species vulnerability and implementing effective management strategies. To evaluate the accuracy of genomic methods for quantifying recent declines (beginning <120 generations ago), we simulated genomic data using forward-time methods (SLiM) coupled with coalescent simulations (msprime) under a number of demographic scenarios. We evaluated both site frequency spectrum (SFS)-based methods (momi2, Stairway Plot) and methods that employ linkage disequilibrium information (NeEstimator, GONE) with a range of sampling schemes (contemporary-only samples, sampling two time points, and serial sampling) and data types (RAD-like data and whole-genome sequencing). GONE and momi2 performed best overall, with >80% power to detect severe declines with large sample sizes. Two-sample and serial sampling schemes could accurately reconstruct changes in population size, and serial sampling was particularly valuable for making accurate inferences when genotyping errors or minor allele frequency cutoffs distort the SFS or under model mis-specification. However, sampling only contemporary individuals provided reliable inferences about contemporary size and size change using either site frequency or linkage-based methods, especially when large sample sizes or whole genomes from contemporary populations were available. These findings provide a guide for researchers designing genomics studies to evaluate recent demographic declines.
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Affiliation(s)
| | - Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
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7
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Ancient DNA reveals phenological diversity of Coast Salish herring harvests over multiple centuries. Sci Rep 2022; 12:13512. [PMID: 35933511 PMCID: PMC9357025 DOI: 10.1038/s41598-022-17656-4] [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: 01/03/2022] [Accepted: 07/28/2022] [Indexed: 11/08/2022] Open
Abstract
Phenological diversity in food resources prolongs foraging opportunities for consumers and buffers them against environmental disturbances. Such diversity is particularly important in forage fish such as Pacific herring (Clupea pallasii), which are foundational to coastal food webs and fisheries. While the importance of phenological diversity is well-known from contemporary studies, the extent to which different populations contribute to fisheries over long time scales is mostly unknown. In this study, we investigated the relative contributions of genetically and phenologically distinct herring populations to Indigenous Peoples' food systems over multiple centuries, using ancient DNA extracted from archaeological herring bones. These bones were excavated from two Coast Salish archaeological sites (Burton Acres Shell Midden and Bay Street Shell Midden) in the Puget Sound region, USA. Using genetic stock identification from seven nuclear DNA markers, we showed that catches at the two sites in central Puget Sound were dominated by January-February and March-April spawners, which are the contemporary spawning groups in the vicinity of the sites. However, May spawners were detected in the older Burton Acres assemblage (dated to 910-685 cal BP), and a mixed stock analysis indicated that catches at this site consisted of multiple populations. These results suggest that Coast Salish ancestors used a portfolio of herring populations and benefited from the ecological resource wave created by different spawning groups of herring. This study of ancient DNA allowed us to glimpse into Indigenous traditional food and management systems, and it enabled us to investigate long-term patterns of biodiversity in an ecologically important forage fish species.
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8
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Levin B, Simonov E, Gabrielyan BK, Mayden RL, Rastorguev SM, Roubenyan HR, Sharko FS, Nedoluzhko AV. Caucasian treasure: Genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock. Mol Phylogenet Evol 2021; 167:107346. [PMID: 34763069 DOI: 10.1016/j.ympev.2021.107346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022]
Abstract
Five ecologically and phenotypically divergent ecomorphs of the genus Salmo are known from a landlocked alpine lake in the Caucasus, Lake Sevan. It is an example of sympatric diversification within a species-rich lineage with predominate mode of speciation being allopatric. The diversification of Sevan trouts was accompanied by spawning resource partitioning. Four lacustrine ecomorphs with different temporal-spatial spawning strategies and divergent morphology and coloration evolved along with a fifth ecomorph, brook trout, inhabiting the tributaries. Unfortunately, the Sevan trout diversity was almost destroyed by human activity, with two ecomorphs becoming extinct in the 1980s. We performed reconstruction of the evolutionary history of Sevan trouts based on high-throughput sequencing of both contemporary and historical DNA (∼ 50 y.o.) of all Sevan trout ecomorphs. Our study of complete mitogenomes along with genome-wide SNP data revealed the monophyly of four lacustrine ecomorphs and local brook trout, all derived from the anadromous form Caspian salmon, S. caspius. The species tree suggests a scenario of stepwise evolution from riverine to lacustrine spawning. Three genomic clusters were revealed, of which two refer to the riverine and lacustrine spawners within the flock of Sevan trouts (with FST value = 0.069). A few SNP outliers under selection were discovered that could be responsible for assortative mating based on visual recognition. The Holocene climatic oscillations and the desiccation of tributaries could have played an important role in the origin of lacustrine spawning. The relationships between lacustrine ecomorphs were not yet fully resolved. This radiation warrants further investigation.
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Affiliation(s)
- Boris Levin
- Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia; Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences - Borok, Russia; Cherepovets State University, Cherepovets, Russia.
| | | | - Bardukh K Gabrielyan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences of Republic of Armenia, Yerevan, Armenia
| | - Richard L Mayden
- Department of Biology, Saint Louis University, St. Louis, MO USA
| | | | - Haikaz R Roubenyan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences of Republic of Armenia, Yerevan, Armenia
| | - Fedor S Sharko
- National Research Centre "Kurchatov Institute", Moscow, Russia
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9
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Andrews AJ, Puncher GN, Bernal-Casasola D, Di Natale A, Massari F, Onar V, Toker NY, Hanke A, Pavey SA, Savojardo C, Martelli PL, Casadio R, Cilli E, Morales-Muñiz A, Mantovani B, Tinti F, Cariani A. Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean. Sci Rep 2021; 11:20744. [PMID: 34671077 PMCID: PMC8528830 DOI: 10.1038/s41598-021-99708-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/25/2021] [Indexed: 11/10/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
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Affiliation(s)
- Adam J Andrews
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
| | - Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada.
| | - Darío Bernal-Casasola
- Department of History, Geography and Philosophy, Faculty of Philosophy and Letters, University of Cádiz, Cádiz, Spain
| | | | - Francesco Massari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Vedat Onar
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Nezir Yaşar Toker
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Alex Hanke
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada
| | | | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | | | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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10
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Giammona FF. Form and function of the caudal fin throughout the phylogeny of fishes. Integr Comp Biol 2021; 61:550-572. [PMID: 34114010 DOI: 10.1093/icb/icab127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
Fishes are the longest persisting living vertebrates and as such, display an incredible array of diversity. Variation in the tail, or caudal fin, is often a reflection of a fish's environment, and affects movement, predation, defense, and reproduction. Previous literature has discussed many aspects of caudal fin form and function in particular taxonomic groups; however, no previous work has synthesized these studies in order to detail how the caudal fin is structured, and what purpose this structure serves, throughout the phylogeny of fishes. This review examines the caudal fin throughout the main lineages of fish evolution, and highlights where changes in shape and usage have occurred. Such novelties in form and function tend to have far-reaching evolutionary consequences. Through integration of past and present work, this review creates a coherent picture of caudal fin evolution. Patterns and outliers that demonstrate how form and function of this appendage are intertwined can further inform hypotheses that fill critical gaps in knowledge concerning the caudal fin.
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11
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Martínez-García L, Ferrari G, Oosting T, Ballantyne R, van der Jagt I, Ystgaard I, Harland J, Nicholson R, Hamilton-Dyer S, Baalsrud HT, Brieuc MSO, Atmore LM, Burns F, Schmölcke U, Jakobsen KS, Jentoft S, Orton D, Hufthammer AK, Barrett JH, Star B. Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.671281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
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12
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Kirch M, Romundset A, Gilbert MTP, Jones FC, Foote AD. Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Curr Biol 2021; 31:2027-2036.e8. [PMID: 33705715 DOI: 10.1016/j.cub.2021.02.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 10/21/2022]
Abstract
Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.1 To address this, we applied a paleogenomics approach2 to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes3 and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.4 The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.
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Affiliation(s)
- Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, DK-1353 Copenhagen, Denmark; Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway; Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, UK.
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Papa Y, Oosting T, Valenza-Troubat N, Wellenreuther M, Ritchie PA. Genetic stock structure of New Zealand fish and the use of genomics in fisheries management: an overview and outlook. NEW ZEALAND JOURNAL OF ZOOLOGY 2020. [DOI: 10.1080/03014223.2020.1788612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Tom Oosting
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Noemie Valenza-Troubat
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
| | - Maren Wellenreuther
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Peter A. Ritchie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Guiry E, Royle TCA, Matson RG, Ward H, Weir T, Waber N, Brown TJ, Hunt BPV, Price MHH, Finney BP, Kaeriyama M, Qin Y, Yang DY, Szpak P. Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications. PLoS One 2020; 15:e0232180. [PMID: 32343728 PMCID: PMC7188214 DOI: 10.1371/journal.pone.0232180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/08/2020] [Indexed: 02/02/2023] Open
Abstract
The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.
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Affiliation(s)
- Eric Guiry
- Department of Anthropology, Trent University, Peterborough, Ontario, Canada
- School of Archaeology and Ancient History, University of Leicester, Leicester, United Kingdom
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas C. A. Royle
- Department of Archaeology, Ancient DNA Laboratory, Simon Fraser University, Burnaby, British Columbia, Canada
| | - R. G. Matson
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hillary Ward
- Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, Penticton, British Columbia, Canada
| | - Tyler Weir
- Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, Penticton, British Columbia, Canada
| | - Nicholas Waber
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas J. Brown
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian P. V. Hunt
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Michael H. H. Price
- Department of Biological Sciences, Earth to Ocean Research Group, Simon Fraser University, British Columbia, Canada
| | - Bruce P. Finney
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
- Department of Geosciences, Idaho State University, Pocatello, Idaho, United States of America
| | | | - Yuxue Qin
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, Liaoning, China
| | - Dongya Y. Yang
- Department of Archaeology, Ancient DNA Laboratory, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, Ontario, Canada
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Rauf HT, Lali MIU, Zahoor S, Shah SZH, Rehman AU, Bukhari SAC. Visual features based automated identification of fish species using deep convolutional neural networks. COMPUTERS AND ELECTRONICS IN AGRICULTURE 2019; 167:105075. [DOI: 10.1016/j.compag.2019.105075] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Pálsdóttir AH, Bläuer A, Rannamäe E, Boessenkool S, Hallsson JH. Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191059. [PMID: 31824712 PMCID: PMC6837180 DOI: 10.1098/rsos.191059] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/09/2019] [Indexed: 05/04/2023]
Abstract
With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.
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Affiliation(s)
- Albína Hulda Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
- Author for correspondence: Albína Hulda Pálsdóttir e-mail:
| | - Auli Bläuer
- Natural Resources Institute Finland (Luke), Itäinen Pitkäkatu 4 A, 20520 Turku, Finland
- University of Turku, Archaeology, Akatemiankatu 1, FI-20500 Turku, Finland
| | - Eve Rannamäe
- Natural Resources Institute Finland (Luke), Itäinen Pitkäkatu 4 A, 20520 Turku, Finland
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Jón Hallsteinn Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
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