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Kristjánsson BK, Combot D, Reilent A, Phillips JS, Leblanc CA. Invertebrate diversity in groundwater-filled lava caves is influenced by both neutral- and niche-based processes. Ecol Evol 2024; 14:e11560. [PMID: 38932944 PMCID: PMC11199188 DOI: 10.1002/ece3.11560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Understanding which factors shape and maintain biodiversity is essential to understand how ecosystems respond to crises. Biodiversity observed in ecological communities is a result of the interaction of various factors which can be classified as either neutral- or niche-based. The importance of these processes has been debated, but many scientists believe that both processes are important. Here, we use unique ecosystems in groundwater-filled lava caves near Lake Mývatn, to examine the importance of neutral- versus niche-based factors for shaping invertebrate communities. We studied diversity in benthic and epibenthic invertebrate communities and related them to ecological variables. We hypothesized that if neutral processes are the main drivers of community structure we would not see any clear relationship between the structure of community within caves and ecological factors. If niche-based processes are important we should see clear relationships between community structure and variation in ecological variables across caves. Both communities were species poor, with low densities of invertebrates, showing the resource limited and oligotrophic nature of these systems. Unusually for Icelandic freshwater ecosystems, the benthic communities were not dominated by Chironomidae (Diptera) larvae, but rather by crustaceans, mainly Cladocera. The epibenthic communities were not shaped by environmental variables, suggesting that they may have been structured primarily by neutral processes. The benthic communities were shaped by the availability of energy, and to some extent pH, suggesting that niche-based processes were important drivers of community structure, although neutral processes may still be relevant. The results suggest that both processes are important for invertebrate communities in freshwater, and research should focus on understanding both of these processes. The ponds we studied are representative of a number of freshwater ecosystems that are extremely vulnerable for human disturbance, making it even more important to understand how their biodiversity is shaped and maintained.
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Affiliation(s)
| | - Doriane Combot
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókurIceland
| | - Anett Reilent
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókurIceland
| | - Joseph S. Phillips
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókurIceland
- Department of BiologyCreighton UniversityOmahaNebraskaUSA
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2
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Jónsdóttir GÓ, von Elm LM, Ingimarsson F, Tersigni S, Snorrason SS, Pálsson A, Steele SE. Diversity in the internal functional feeding elements of sympatric morphs of Arctic charr (Salvelinus alpinus). PLoS One 2024; 19:e0300359. [PMID: 38771821 PMCID: PMC11108142 DOI: 10.1371/journal.pone.0300359] [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: 09/22/2023] [Accepted: 02/23/2024] [Indexed: 05/23/2024] Open
Abstract
The diversity of functional feeding anatomy is particularly impressive in fishes and correlates with various interspecific ecological specializations. Intraspecific polymorphism can manifest in divergent feeding morphology and ecology, often along a benthic-pelagic axis. Arctic charr (Salvelinus alpinus) is a freshwater salmonid known for morphological variation and sympatric polymorphism and in Lake Þingvallavatn, Iceland, four morphs of charr coexist that differ in preferred prey, behaviour, habitat use, and external feeding morphology. We studied variation in six upper and lower jaw bones in adults of these four morphs using geometric morphometrics and univariate statistics. We tested for allometric differences in bone size and shape among morphs, morph effects on bone size and shape, and divergence along the benthic-pelagic axis. We also examined the degree of integration between bone pairs. We found differences in bone size between pelagic and benthic morphs for two bones (dentary and premaxilla). There was clear bone shape divergence along a benthic-pelagic axis in four bones (dentary, articular-angular, premaxilla and maxilla), as well as allometric shape differences between morphs in the dentary. Notably for the dentary, morph explained more shape variation than bone size. Comparatively, benthic morphs possess a compact and taller dentary, with shorter dentary palate, consistent with visible (but less prominent) differences in external morphology. As these morphs emerged in the last 10,000 years, these results indicate rapid functional evolution of specific feeding structures in arctic charr. This sets the stage for studies of the genetics and development of rapid and parallel craniofacial evolution.
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Affiliation(s)
| | - Laura-Marie von Elm
- Institute of Life- and Environmental Science, University of Iceland, Reykjavik, Iceland
| | | | - Samuel Tersigni
- Institute of Life- and Environmental Science, University of Iceland, Reykjavik, Iceland
| | | | - Arnar Pálsson
- Institute of Life- and Environmental Science, University of Iceland, Reykjavik, Iceland
| | - Sarah Elizabeth Steele
- Institute of Life- and Environmental Science, University of Iceland, Reykjavik, Iceland
- Canadian Museum of Nature, Ottawa, Canada
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3
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Judson BJ, Kristjánsson BK, Leblanc CA, Ferguson MM. The role of neutral and adaptive evolutionary processes on patterns of genetic diversity across small cave-dwelling populations of Icelandic Arctic charr ( Salvelinus alpinus). Ecol Evol 2024; 14:e11363. [PMID: 38770124 PMCID: PMC11103641 DOI: 10.1002/ece3.11363] [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: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024] Open
Abstract
Understanding the adaptability of small populations in the face of environmental change is a central problem in evolutionary biology. Solving this problem is challenging because neutral evolutionary processes that operate on historical and contemporary timescales can override the effects of selection in small populations. We assessed the effects of isolation by colonization (IBC), isolation by dispersal limitation (IBDL) as reflected by a pattern of isolation by distance (IBD), and isolation by adaptation (IBA) and the roles of genetic drift and gene flow on patterns of genetic differentiation among 19 cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus). We detected evidence of IBC based on the genetic affinity of nearby cave populations and the genetic relationships between the cave populations and the presumed ancestral population in the lake. A pattern of IBD was evident regardless of whether high-level genetic structuring (IBC) was taken into account. Genetic signatures of bottlenecks and lower genetic diversity in smaller populations indicate the effect of drift. Estimates of gene flow and fish movement suggest that gene flow is limited to nearby populations. In contrast, we found little evidence of IBA as patterns of local ecological and phenotypic variation showed little association with genetic differentiation among populations. Thus, patterns of genetic variation in these small populations likely reflect localized gene flow and genetic drift superimposed onto a larger-scale structure that is largely a result of colonization history. Our simultaneous assessment of the effects of neutral and adaptive processes in a tractable and replicated system has yielded novel insights into the evolution of small populations on both historical and contemporary timescales and over a smaller spatial scale than is typically studied.
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Affiliation(s)
- Braden J. Judson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Moira M. Ferguson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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4
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Leblanc CA, Räsänen K, Morrissey M, Skúlason S, Ferguson M, Kristjánsson BK. Fine scale diversity in the lava: genetic and phenotypic diversity in small populations of Arctic charr Salvelinus alpinus. BMC Ecol Evol 2024; 24:45. [PMID: 38622503 PMCID: PMC11017478 DOI: 10.1186/s12862-024-02232-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND A major goal in evolutionary biology is to understand the processes underlying phenotypic variation in nature. Commonly, studies have focused on large interconnected populations or populations found along strong environmental gradients. However, studies on small fragmented populations can give strong insight into evolutionary processes in relation to discrete ecological factors. Evolution in small populations is believed to be dominated by stochastic processes, but recent work shows that small populations can also display adaptive phenotypic variation, through for example plasticity and rapid adaptive evolution. Such evolution takes place even though there are strong signs of historical bottlenecks and genetic drift. Here we studied 24 small populations of the freshwater fish Arctic charr (Salvelinus alpinus) found in groundwater filled lava caves. Those populations were found within a few km2-area with no apparent water connections between them. We studied the relative contribution of neutral versus non-neutral evolutionary processes in shaping phenotypic divergence, by contrasting patterns of phenotypic and neutral genetic divergence across populations in relation to environmental measurements. This allowed us to model the proportion of phenotypic variance explained by the environment, taking in to account the observed neutral genetic structure. RESULTS These populations originated from the nearby Lake Mývatn, and showed small population sizes with low genetic diversity. Phenotypic variation was mostly correlated with neutral genetic diversity with only a small environmental effect. CONCLUSIONS Phenotypic diversity in these cave populations appears to be largely the product of neutral processes, fitting the classical evolutionary expectations. However, the fact that neutral processes did not explain fully the phenotypic patterns suggests that further studies can increase our understanding on how neutral evolutionary processes can interact with other forces of selection at early stages of divergence. The accessibility of these populations has provided the opportunity for long-term monitoring of individual fish, allowing tracking how the environment can influence phenotypic and genetic divergence for shaping and maintaining diversity in small populations. Such studies are important, especially in freshwater, as habitat alteration is commonly breaking populations into smaller units, which may or may not be viable.
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Affiliation(s)
- Camille A Leblanc
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland.
| | - Katja Räsänen
- Department of Biology and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | | | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
- Icelandic Museum of Natural History, Reykjavik, Iceland
| | - Moira Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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5
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Fenton S, Jacobs A, Bean CW, Adams CE, Elmer KR. Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs. Mol Ecol 2024; 33:e17305. [PMID: 38421099 DOI: 10.1111/mec.17305] [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: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head- and body-shape-associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.
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Affiliation(s)
- Sam Fenton
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Arne Jacobs
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- NatureScot, Clydebank, UK
| | - Colin E Adams
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
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6
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Dȩbicki IT, Mittell EA, Kristjánsson BK, Leblanc CA, Morrissey MB, Terzić K. Re-identification of individuals from images using spot constellations: a case study in Arctic charr ( Salvelinus alpinus). ROYAL SOCIETY OPEN SCIENCE 2021; 8:201768. [PMID: 34295512 PMCID: PMC8292754 DOI: 10.1098/rsos.201768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
The ability to re-identify individuals is fundamental to the individual-based studies that are required to estimate many important ecological and evolutionary parameters in wild populations. Traditional methods of marking individuals and tracking them through time can be invasive and imperfect, which can affect these estimates and create uncertainties for population management. Here we present a photographic re-identification method that uses spot constellations in images to match specimens through time. Photographs of Arctic charr (Salvelinus alpinus) were used as a case study. Classical computer vision techniques were compared with new deep-learning techniques for masks and spot extraction. We found that a U-Net approach trained on a small set of human-annotated photographs performed substantially better than a baseline feature engineering approach. For matching the spot constellations, two algorithms were adapted, and, depending on whether a fully or semi-automated set-up is preferred, we show how either one or a combination of these algorithms can be implemented. Within our case study, our pipeline both successfully identified unmarked individuals from photographs alone and re-identified individuals that had lost tags, resulting in an approximately 4% increase in our estimate of survival rate. Overall, our multi-step pipeline involves little human supervision and could be applied to many organisms.
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Affiliation(s)
- Ignacy T. Dȩbicki
- School of Computer Science, University of St Andrews, St Andrews, UK
| | - Elizabeth A. Mittell
- School of Biology, University of St Andrews, St Andrews, UK
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
| | | | - Camille A. Leblanc
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
| | | | - Kasim Terzić
- School of Computer Science, University of St Andrews, St Andrews, UK
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7
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Guðbrandsson J, Kapralova KH, Franzdóttir SR, Bergsveinsdóttir ÞM, Hafstað V, Jónsson ZO, Snorrason SS, Pálsson A. Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs. Ecol Evol 2019; 9:10964-10983. [PMID: 31641448 PMCID: PMC6802010 DOI: 10.1002/ece3.5516] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment, and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly, well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL), and piscivorous (PI) charr differ in many regards, including size, form, and life history traits. To investigate relatedness and genomic differentiation between morphs, we identified variable sites from RNA-sequencing data from three of those morphs and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis, and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Marine and Freshwater Research InstituteReykjavikIceland
| | - Kalina H. Kapralova
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Sigríður R. Franzdóttir
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Völundur Hafstað
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Zophonías O. Jónsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Arnar Pálsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
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8
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Skúlason S, Parsons KJ, Svanbäck R, Räsänen K, Ferguson MM, Adams CE, Amundsen P, Bartels P, Bean CW, Boughman JW, Englund G, Guðbrandsson J, Hooker OE, Hudson AG, Kahilainen KK, Knudsen R, Kristjánsson BK, Leblanc CA, Jónsson Z, Öhlund G, Smith C, Snorrason SS. A way forward with eco evo devo: an extended theory of resource polymorphism with postglacial fishes as model systems. Biol Rev Camb Philos Soc 2019; 94:1786-1808. [PMID: 31215138 PMCID: PMC6852119 DOI: 10.1111/brv.12534] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/12/2019] [Accepted: 05/20/2019] [Indexed: 12/16/2022]
Abstract
A major goal of evolutionary science is to understand how biological diversity is generated and altered. Despite considerable advances, we still have limited insight into how phenotypic variation arises and is sorted by natural selection. Here we argue that an integrated view, which merges ecology, evolution and developmental biology (eco evo devo) on an equal footing, is needed to understand the multifaceted role of the environment in simultaneously determining the development of the phenotype and the nature of the selective environment, and how organisms in turn affect the environment through eco evo and eco devo feedbacks. To illustrate the usefulness of an integrated eco evo devo perspective, we connect it with the theory of resource polymorphism (i.e. the phenotypic and genetic diversification that occurs in response to variation in available resources). In so doing, we highlight fishes from recently glaciated freshwater systems as exceptionally well-suited model systems for testing predictions of an eco evo devo framework in studies of diversification. Studies on these fishes show that intraspecific diversity can evolve rapidly, and that this process is jointly facilitated by (i) the availability of diverse environments promoting divergent natural selection; (ii) dynamic developmental processes sensitive to environmental and genetic signals; and (iii) eco evo and eco devo feedbacks influencing the selective and developmental environments of the phenotype. We highlight empirical examples and present a conceptual model for the generation of resource polymorphism - emphasizing eco evo devo, and identify current gaps in knowledge.
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Affiliation(s)
- Skúli Skúlason
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókur, 551Iceland
- Icelandic Museum of Natural History, Brynjólfsgata 5ReykjavíkIS‐107Iceland
| | - Kevin J. Parsons
- Institute of Biodiversity, Animal Health & Comparative MedicineUniversity of GlasgowGlasgow, G12 8QQU.K.
| | - Richard Svanbäck
- Animal Ecology, Department of Ecology and Genetics, Science for Life LaboratoryUppsala University, Norbyvägen 18DUppsala, SE‐752 36Sweden
| | - Katja Räsänen
- Department of Aquatic EcologyEAWAG, Swiss Federal Institute of Aquatic Science and Technology, and Institute of Integrative Biology, ETH‐Zurich, Ueberlandstrasse 133CH‐8600DübendorfSwitzerland
| | - Moira M. Ferguson
- Department of Integrative BiologyUniversity of GuelphGuelph, Ontario N1G 2W1Canada
| | - Colin E. Adams
- Scottish Centre for Ecology and the Natural Environment, IBAHCMUniversity of GlasgowGlasgow G12 8QQU.K.
| | - Per‐Arne Amundsen
- Freshwater Ecology Group, Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and EconomicsUniversity of TromsöTromsö, N‐9037Norway
| | - Pia Bartels
- Department of Ecology and Environmental ScienceUmeå UniversityUmeå, SE‐90187Sweden
| | - Colin W. Bean
- Scottish Natural Heritage, Caspian House, Mariner Court, Clydebank Business ParkClydebank, G81 2NRU.K.
| | - Janette W. Boughman
- Department of Integrative BiologyMichigan State UniversityEast Lansing, MI 48824U.S.A.
| | - Göran Englund
- Department of Ecology and Environmental ScienceUmeå UniversityUmeå, SE‐90187Sweden
| | - Jóhannes Guðbrandsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavik, 101Iceland
| | | | - Alan G. Hudson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeå, SE‐90187Sweden
| | - Kimmo K. Kahilainen
- Inland Norway University of Applied Sciences, Department of Forestry and Wildlife Management, Campus Evenstad, Anne Evenstadvei 80Koppang, NO‐2480Norway
| | - Rune Knudsen
- Freshwater Ecology Group, Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and EconomicsUniversity of TromsöTromsö, N‐9037Norway
| | | | - Camille A‐L. Leblanc
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókur, 551Iceland
| | - Zophonías Jónsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavik, 101Iceland
| | - Gunnar Öhlund
- Department of Ecology and Environmental ScienceUmeå UniversityUmeå, SE‐90187Sweden
| | - Carl Smith
- School of BiologyUniversity of St Andrews, St. AndrewsFife, KY16 9AJU.K.
| | - Sigurður S. Snorrason
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavik, 101Iceland
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9
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Abecia JED, Luiz OJ, King AJ. Intraspecific morphological and reproductive trait variation in mouth almighty Glossamia aprion (Apogonidae) across different flow environments. JOURNAL OF FISH BIOLOGY 2018; 93:961-971. [PMID: 30267413 DOI: 10.1111/jfb.13821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
Intraspecific variability, although comparably less studied than interspecific variation, is an important tool in understanding population responses to environmental gradients. This study investigated intraspecific trait variation across three contrasting aquatic flow habitat types (intermittent creek, billabong and river) in a common mouth-brooding freshwater fish in northern Australia, the mouth almighty Glossamia aprion. Samples of G. aprion were collected at various sites, within the Daly River catchment. It was predicted that a number of morphological and reproductive traits would vary among individuals across the contrasting habitats. Five out of the nine morphological and reproductive traits studied significantly varied across flow habitat types. Significant intraspecific variation in functional traits related to foraging and reproduction, such as relative eye size, eye vertical position and relative maxillary length in males suggest that the inherent characteristics of each flow habitat type could be exerting selective pressure on the morphology of G. aprion. Interestingly, traits related to swimming performance (body lateral shape) and manoeuvrability (pectoral fin ventral position) differed between flow habitat types but showed inconsistent responses to predictions. Whilst this study was temporally and spatially limited, it highlights that intraspecific variability in morphological traits can occur among flow habitat types over relatively small spatial scales.
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Affiliation(s)
- Janine E D Abecia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Australia
| | - Osmar J Luiz
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Australia
| | - Alison J King
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Australia
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10
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Chavarie L, Howland KL, Harris LN, Hansen MJ, Harford WJ, Gallagher CP, Baillie SM, Malley B, Tonn WM, Muir AM, Krueger CC. From top to bottom: Do Lake Trout diversify along a depth gradient in Great Bear Lake, NT, Canada? PLoS One 2018; 13:e0193925. [PMID: 29566015 PMCID: PMC5863968 DOI: 10.1371/journal.pone.0193925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/21/2018] [Indexed: 11/19/2022] Open
Abstract
Depth is usually considered the main driver of Lake Trout intraspecific diversity across lakes in North America. Given that Great Bear Lake is one of the largest and deepest freshwater systems in North America, we predicted that Lake Trout intraspecific diversity to be organized along a depth axis within this system. Thus, we investigated whether a deep-water morph of Lake Trout co-existed with four shallow-water morphs previously described in Great Bear Lake. Morphology, neutral genetic variation, isotopic niches, and life-history traits of Lake Trout across depths (0-150 m) were compared among morphs. Due to the propensity of Lake Trout with high levels of morphological diversity to occupy multiple habitat niches, a novel multivariate grouping method using a suite of composite variables was applied in addition to two other commonly used grouping methods to classify individuals. Depth alone did not explain Lake Trout diversity in Great Bear Lake; a distinct fifth deep-water morph was not found. Rather, Lake Trout diversity followed an ecological continuum, with some evidence for adaptation to local conditions in deep-water habitat. Overall, trout caught from deep-water showed low levels of genetic and phenotypic differentiation from shallow-water trout, and displayed higher lipid content (C:N ratio) and occupied a higher trophic level that suggested an potential increase of piscivory (including cannibalism) than the previously described four morphs. Why phenotypic divergence between shallow- and deep-water Lake Trout was low is unknown, especially when the potential for phenotypic variation should be high in deep and large Great Bear Lake. Given that variation in complexity of freshwater environments has dramatic consequences for divergence, variation in the complexity in Great Bear Lake (i.e., shallow being more complex than deep), may explain the observed dichotomy in the expression of intraspecific phenotypic diversity between shallow- vs. deep-water habitats. The ambiguity surrounding mechanisms driving divergence of Lake Trout in Great Bear Lake should be seen as reflective of the highly variable nature of ecological opportunity and divergent natural selection itself.
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Affiliation(s)
- Louise Chavarie
- Department of Fisheries and Wildlife, Center for Systems Integration and Sustainability, Michigan State University, East Lansing, MI, United States of America
- * E-mail:
| | - Kimberly L. Howland
- Fisheries and Oceans Canada, Winnipeg, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | | | - Michael J. Hansen
- U.S. Geological Survey, Hammond Bay Biological Station, Millersburg, MI, United States of America
| | - William J. Harford
- Cooperative Institute of Marine & Atmospheric Studies, University of Miami, Miami, FL, United States of America
| | | | | | | | - William M. Tonn
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Andrew M. Muir
- Great Lakes Fishery Commission, Ann Arbor, MI, United States of America
| | - Charles C. Krueger
- Department of Fisheries and Wildlife, Center for Systems Integration and Sustainability, Michigan State University, East Lansing, MI, United States of America
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11
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Guðbrandsson J, Franzdóttir SR, Kristjánsson BK, Ahi EP, Maier VH, Kapralova KH, Snorrason SS, Jónsson ZO, Pálsson A. Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs. PeerJ 2018; 6:e4345. [PMID: 29441236 PMCID: PMC5807978 DOI: 10.7717/peerj.4345] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/19/2018] [Indexed: 02/06/2023] Open
Abstract
Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3'-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and translin (tsn). The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Freshwater Division, Marine and Freshwater Research Institute, Reykjavík, Iceland
| | - Sigríður Rut Franzdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | - Ehsan Pashay Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Karl-Franzens-Universität, Graz, Austria
| | - Valerie Helene Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | | | - Zophonías Oddur Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
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12
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Kristjánsson BK, Leblanc CA. Variation in the magnitude of morphological and dietary differences between individuals among populations of small benthic Arctic charr in relation to ecological factors. Ecol Evol 2018; 8:1573-1581. [PMID: 29435233 PMCID: PMC5792579 DOI: 10.1002/ece3.3761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/14/2017] [Accepted: 12/06/2017] [Indexed: 11/17/2022] Open
Abstract
The early stages of intraspecific diversity are important for the evolution of diversification and speciation. Early stages of diversification can be seen in individual specialization, where individuals consume only a portion of the diet of the population as a whole, and how such specialization is related to phenotypic diversity within populations. Here, we study the strength of the relationship between morphological and dietary distances among individuals in eighteen populations of Icelandic small benthic charr. We furthermore studied if the strength of the relationship could be related to variation in local ecological factors these populations inhabit. In all the populations studied, there was a clear relationship between morphological and dietary distances, indicating that fish that had similar morphology were at the same time-consuming similar food items. Our findings show a systematic variation in the relationship between morphology and diet at early stages of diversification in a highly specialized small benthic charr morph. The results show the importance of fine scale comparisons within populations and furthermore the value that systematic comparisons among populations under parallel evolution can contribute toward our increased understanding of evolutionary and ecological processes.
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13
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Oke KB, Rolshausen G, LeBlond C, Hendry AP. How Parallel Is Parallel Evolution? A Comparative Analysis in Fishes. Am Nat 2017; 190:1-16. [DOI: 10.1086/691989] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Chavarie L, Muir AM, Zimmerman MS, Baillie SM, Hansen MJ, Nate NA, Yule DL, Middel T, Bentzen P, Krueger CC. Challenge to the model of lake charr evolution: shallow- and deep-water morphs exist within a small postglacial lake. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Louise Chavarie
- Center for Systems Integration and Sustainability; Michigan State University; 115 Manly Miles Building, 1405 South Harrison Road East Lansing Michigan USA
| | - Andrew M. Muir
- Great Lakes Fishery Commission; 2100 Commonwealth Blvd. Suite 100 Ann Arbor Michigan USA
| | - Mara S. Zimmerman
- Washington Department of Fish and Wildlife; 600 Capitol Way N. Olympia Washington USA
| | - Shauna M. Baillie
- Department of Biology; Dalhousie University; 1355 Oxford St. Halifax Nova Scotia Canada
| | - Michael J. Hansen
- United States Geological Survey; Hammond Bay Biological Station; 11188 Ray Road Millersburg Michigan USA
| | - Nancy A. Nate
- Center for Systems Integration and Sustainability; Michigan State University; 115 Manly Miles Building, 1405 South Harrison Road East Lansing Michigan USA
| | - Daniel L. Yule
- United States Geological Survey; Lake Superior Biological Station; 2800 Lakeshore Drive Ashland Wisconsin USA
| | - Trevor Middel
- Harkness Laboratory of Fisheries Research; Ontario Ministry of Natural Resources and Forestry; Trent University; 2140 East Bank Drive Peterborough Ontario Canada
| | - Paul Bentzen
- Department of Biology; Dalhousie University; 1355 Oxford St. Halifax Nova Scotia Canada
| | - Charles C. Krueger
- Center for Systems Integration and Sustainability; Michigan State University; 115 Manly Miles Building, 1405 South Harrison Road East Lansing Michigan USA
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15
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Lostrom S, Evans JP, Grierson PF, Collin SP, Davies PM, Kelley JL. Linking stream ecology with morphological variability in a native freshwater fish from semi-arid Australia. Ecol Evol 2015; 5:3272-87. [PMID: 26380663 PMCID: PMC4569025 DOI: 10.1002/ece3.1590] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/21/2015] [Accepted: 06/10/2015] [Indexed: 11/11/2022] Open
Abstract
Environmental variation is a potent force affecting phenotypic expression. While freshwater fishes have provided a compelling example of the link between the environment and phenotypic diversity, few studies have been conducted with arid-zone fishes, particularly those that occur in geographically isolated regions where species typically inhabit intermittent and ephemeral creeks. We investigated morphological variation of a freshwater fish (the western rainbowfish, Melanotaenia australis) inhabiting creeks in the Pilbara region of northwest Australia to determine whether body shape variation correlated with local environmental characteristics, including water velocity, habitat complexity, predator presence, and food availability. We expected that the geographic isolation of creeks within this arid region would result in habitat-specific morphological specializations. We used landmark-based geometric morphometrics to quantify the level of morphological variability in fish captured from 14 locations within three distinct subcatchments of a major river system. Western rainbowfish exhibited a range of morphologies, with variation in body depth accounting for a significant proportion (>42%) of the total variance in shape. Sexual dimorphism was also apparent, with males displaying deeper bodies than females. While the measured local habitat characteristics explained little of the observed morphological variation, fish displayed significant morphological differentiation at the level of the subcatchment. Local adaptation may partly explain the geographic patterns of body shape variation, but fine-scale genetic studies are required to disentangle the effects of genetic differentiation from environmentally determined phenotypic plasticity in body shape. Developing a better understanding of environment-phenotype relationships in species from arid regions will provide important insights into ecological and evolutionary processes in these unique and understudied habitats.
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Affiliation(s)
- Samantha Lostrom
- School of Animal Biology (M092), The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia ; Ecosystems Research Group and West Australian Biogeochemistry Centre, School of Plant Biology, The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Jonathan P Evans
- School of Animal Biology (M092), The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Pauline F Grierson
- Ecosystems Research Group and West Australian Biogeochemistry Centre, School of Plant Biology, The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Shaun P Collin
- School of Animal Biology (M092), The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia ; UWA Oceans Institute (M470), The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Peter M Davies
- Centre of Excellence in Natural Resource Management, The University of Western Australia Albany, Western Australia, Australia
| | - Jennifer L Kelley
- School of Animal Biology (M092), The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia ; Ecosystems Research Group and West Australian Biogeochemistry Centre, School of Plant Biology, The University of Western Australia 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
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16
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Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs. F1000Res 2015; 4:136. [PMID: 27635217 PMCID: PMC5007756 DOI: 10.12688/f1000research.6402.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charrSalvelinus alpinuspopulations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr.The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, includinglysozymeandnatterin-likewhich was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr.The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.
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17
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Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs. F1000Res 2015; 4:136. [PMID: 27635217 PMCID: PMC5007756 DOI: 10.12688/f1000research.6402.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr
Salvelinus alpinus populations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr. The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, including
lysozyme and
natterin-like which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr. The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.
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Affiliation(s)
- Johannes Gudbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Ehsan P Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Sigridur R Franzdottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Kalina H Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | | | - S Sophie Steinhaeuser
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Valerie H Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Isak M Johannesson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Sigurdur S Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Zophonias O Jonsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Arnar Palsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
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18
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Chavarie L, Howland K, Harris L, Tonn W. Polymorphism in lake trout in Great Bear Lake: intra-lake morphological diversification at two spatial scales. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12398] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Louise Chavarie
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
| | - Kimberly Howland
- Fisheries and Oceans Canada; 501 University Crescent Winnipeg MB R3T 2N6 Canada
| | - Les Harris
- Fisheries and Oceans Canada; 501 University Crescent Winnipeg MB R3T 2N6 Canada
| | - William Tonn
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
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