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Lin RC, Ferreira BT, Yuan YW. The molecular basis of phenotypic evolution: beyond the usual suspects. Trends Genet 2024; 40:668-680. [PMID: 38704304 PMCID: PMC11303103 DOI: 10.1016/j.tig.2024.04.010] [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: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
It has been well documented that mutations in coding DNA or cis-regulatory elements underlie natural phenotypic variation in many organisms. However, the development of sophisticated functional tools in recent years in a wide range of traditionally non-model systems have revealed many 'unusual suspects' in the molecular bases of phenotypic evolution, including upstream open reading frames (uORFs), cryptic splice sites, and small RNAs. Furthermore, large-scale genome sequencing, especially long-read sequencing, has identified a cornucopia of structural variation underlying phenotypic divergence and elucidated the composition of supergenes that control complex multi-trait polymorphisms. In this review article we highlight recent studies that demonstrate this great diversity of molecular mechanisms producing adaptive genetic variation and the panoply of evolutionary paths leading to the 'grandeur of life'.
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Affiliation(s)
- Rong-Chien Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bianca T Ferreira
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
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2
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Gao Q, Luo F, Yu H, Lin Y, Xu R, Li P, Zhang Y, Liu J, Su L, Li Y. U-shaped association between triglyceride-glucose index and all-cause mortality among critically ill pediatrics: a population-based retrospective cohort study. Cardiovasc Diabetol 2024; 23:222. [PMID: 38926737 PMCID: PMC11210025 DOI: 10.1186/s12933-024-02310-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Previous studies have shown that an elevated triglyceride-glucose (TyG) index was associated with all-cause mortality in both general adult individuals and critically ill adult patients. However, the relationship between the TyG index and clinical prognosis in pediatric patients admitted to the intensive care unit (ICU) remains unknown. We aimed to investigate the association of the TyG index with in-hospital all-cause mortality in critically ill pediatric patients. METHODS A total of 5706 patients in the Pediatric Intensive Care database were enrolled in this study. The primary outcome was 30-day in-hospital all-cause mortality, and secondary outcome was 30-day in-ICU all-cause mortality. The restricted cubic spline (RCS) curves and two-piecewise multivariate Cox hazard regression models were performed to explore the relationship between the TyG index and outcomes. RESULTS The median age of the study population was 20.5 [interquartile range (IQR): 4.8, 63.0] months, and 3269 (57.3%) of the patients were male. The mean TyG index level was 8.6 ± 0.7. A total of 244 (4.3%) patients died within 30 days of hospitalization during a median follow-up of 11 [7, 18] days, and 236 (4.1%) patients died in ICU within 30 days of hospitalization during a median follow-up of 6 [3, 11] days. The RCS curves indicated a U-shape association between the TyG index and 30-day in-hospital and in-ICU all-cause mortality (both P values for non-linear < 0.001). The risk of 30-day in-hospital all-cause mortality was negatively correlated with the TyG index until it bottoms out at 8.6 (adjusted hazard ratio [HR], 0.72, 95% confidence interval [CI] 0.55-0.93). However, when the TyG index was higher than 8.6, the risk of primary outcome increased significantly (adjusted HR, 1.51, 95% CI 1.16-1.96]). For 30-day in-ICU all-cause mortality, we also found a similar relationship (TyG < 8.6: adjusted HR, 0.75, 95% CI 0.57-0.98; TyG ≥ 8.6: adjusted HR, 1.42, 95% CI 1.08-1.85). Those results were consistent in subgroups and various sensitivity analysis. CONCLUSIONS Our study showed that the association between the TyG index and 30-day in-hospital and in-ICU all-cause mortality was nonlinear U-shaped, with a cutoff point at the TyG index of 8.6 in critically ill pediatric patients. Our findings suggest that the TyG index may be a novel and important factor for the short-term clinical prognosis in pediatric patients.
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Affiliation(s)
- Qi Gao
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China
| | - Fan Luo
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China
| | - Hongxue Yu
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China
| | - Yuxin Lin
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China
| | - Ruqi Xu
- Division of Nephrology, People's Hospital of Yangjiang Affiliated to Guangdong Medical University, Yangjiang, China
| | - Pingping Li
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China
| | - Yuping Zhang
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China
| | - Jiao Liu
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China
| | - Licong Su
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China.
| | - Yanqin Li
- State Key Laboratory of Organ Failure Research, Division of Nephrology, National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, 1838 N Guangzhou Ave, Guangzhou, 510515, China.
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Xu R, Gao Q, Zhang Y, Lin Y, Li Y, Su L, Zhou S, Cao Y, Gao P, Li P, Luo F, Chen R, Zhang X, Nie S, Xu X. Associations between Different Antivirals and Hospital-Acquired Acute Kidney Injury in Adults with Herpes Zoster. Clin J Am Soc Nephrol 2024; 19:694-703. [PMID: 38527975 PMCID: PMC11168829 DOI: 10.2215/cjn.0000000000000452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
Abstract
Key Points Among intravenous antivirals, acyclovir was associated with the highest risk of hospital-acquired AKI, followed by penciclovir/ganciclovir and foscarnet. The risk of hospital-acquired AKI was dose dependent for intravenous nucleoside analogs. Background To examine the association of use of different antivirals with hospital-acquired AKI among Chinese adults with herpes zoster. Methods This study selected 3273 adult patients who received antiviral therapy for herpes zoster during hospitalization from the China Renal Data System. We identified and staged AKI using patient-level serum creatinine data according to the Kidney Disease Improving Global Outcomes criteria. We compared the relative risks of hospital-acquired AKI among patients treated with different antivirals using Cox proportional hazards models. Results Among 3273 patients, 1480 (45%), 681 (21%), 489 (15%), and 623 (19%) were treated with acyclovir/valacyclovir, ganciclovir, penciclovir/famciclovir, and foscarnet, respectively. During the follow-up period, a total of 111 cases of hospital-acquired AKI occurred, predominantly classified as AKI stage 1. The cumulative incidences of hospital-acquired AKI were 5%, 3%, 3%, and 1% in the patients receiving acyclovir/valacyclovir, ganciclovir, penciclovir/famciclovir, and foscarnet, respectively. Compared with acyclovir/valacyclovir, penciclovir/famciclovir/ganciclovir and foscarnet were associated with a lower risk of hospital-acquired AKI, with an adjusted hazard ratio of 0.59 (95% confidence interval [CI], 0.37 to 0.94) and 0.27 (95% CI, 0.11 to 0.63), respectively. Compared with intravenous acyclovir, intravenous penciclovir/ganciclovir and foscarnet were associated with a lower risk of hospital-acquired AKI with an adjusted hazard ratio of 0.53 (95% CI, 0.29 to 0.98) and 0.31 (95% CI, 0.12 to 0.76), respectively. The associations were consistent across various subgroups and sensitivity analyses. Conclusions Among antiviral therapies for herpes zoster, we found different risks of hospital-acquired AKI among the patients receiving different antivirals, in particular, those administered intravenously. Among intravenous antivirals, acyclovir was associated with the highest risk of hospital-acquired AKI, followed by penciclovir/ganciclovir and foscarnet. Confirmation studies with large samples from other populations are warranted.
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Affiliation(s)
- Ruqi Xu
- Division of Nephrology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Renal Failure Research, National Clinical Research Center for Kidney Disease, Guangdong Provincial Institute of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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4
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Scarparo G, Palanchon M, Brelsford A, Purcell J. Social antagonism facilitates supergene expansion in ants. Curr Biol 2023; 33:5085-5095.e4. [PMID: 37979579 DOI: 10.1016/j.cub.2023.10.049] [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: 04/26/2023] [Revised: 08/07/2023] [Accepted: 10/25/2023] [Indexed: 11/20/2023]
Abstract
Antagonistic selection has long been considered a major driver of the formation and expansion of sex chromosomes. For example, sexually antagonistic variation on an autosome can select for suppressed recombination between that autosome and the sex chromosome, leading to a neo-sex chromosome. Autosomal supergenes, chromosomal regions containing tightly linked variants affecting the same complex trait, share similarities with sex chromosomes, raising the possibility that sex chromosome evolution models can explain the evolution of genome structure and recombination in other contexts. We tested this premise in a Formica ant species, wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. We discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is in strong linkage disequilibrium with one chromosome 3 haplotype (P2) found in multi-queen (polygyne) colonies. We suggest that queen miniaturization is strongly disfavored in the single-queen (monogyne) background and is thus socially antagonistic. As such, divergent selection experienced by ants living in alternative social "environments" (monogyne and polygyne) may have contributed to the emergence of a genetic polymorphism on chromosome 9 and associated queen-size dimorphism. Consequently, an ancestral polygyne-associated haplotype may have expanded to include the polymorphism on chromosome 9, resulting in a larger region of suppressed recombination spanning two chromosomes. This process is analogous to the formation of neo-sex chromosomes and consistent with models of expanding regions of suppressed recombination. We propose that miniaturized queens, 16%-20% smaller than queens without 9r, could be incipient intraspecific social parasites.
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Affiliation(s)
- Giulia Scarparo
- Department of Entomology, University of California, Riverside, 165 Entomology Bldg. Citrus Drive, Riverside, CA 92521, USA.
| | - Marie Palanchon
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, 2710 Life Science Bldg., Riverside, CA 92521, USA
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, 2710 Life Science Bldg., Riverside, CA 92521, USA
| | - Jessica Purcell
- Department of Entomology, University of California, Riverside, 165 Entomology Bldg. Citrus Drive, Riverside, CA 92521, USA.
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5
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Tigano A, Russello MA. The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid. Mol Ecol 2022; 31:6588-6604. [PMID: 36208020 DOI: 10.1111/mec.16724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.
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Affiliation(s)
- Anna Tigano
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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Morris CJ, Nguyen KQ, Green JM. Comparison of lethal and non-lethal age-based growth estimation methodologies to assess an endemic bay population of Atlantic cod (Gadus morhua). J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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7
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Hamed-Mohamed D, AbouelFadl KY, Younis AM, Mohammed-Geba K. Preliminary analysis for genetic structure and interspecific relationships within genus Chrysichthys in Lake Nasser, Egypt. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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8
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Jeong H, Baran NM, Sun D, Chatterjee P, Layman TS, Balakrishnan CN, Maney DL, Yi SV. Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows. eLife 2022; 11:79387. [PMID: 36040313 PMCID: PMC9427109 DOI: 10.7554/elife.79387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/17/2022] [Indexed: 12/11/2022] Open
Abstract
In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of 'supergenes.' Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2m chromosomes in this species. We found that features of ZAL2m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.
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Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Nicole M Baran
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Psychology, Emory University, Atlanta, United States.,Department of Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Dan Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Paramita Chatterjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Thomas S Layman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | | | - Donna L Maney
- Department of Psychology, Emory University, Atlanta, United States
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
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9
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Jay P, Leroy M, Le Poul Y, Whibley A, Arias M, Chouteau M, Joron M. Association mapping of colour variation in a butterfly provides evidence that a supergene locks together a cluster of adaptive loci. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210193. [PMID: 35694756 PMCID: PMC9189503 DOI: 10.1098/rstb.2021.0193] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Supergenes are genetic architectures associated with discrete and concerted variation in multiple traits. It has long been suggested that supergenes control these complex polymorphisms by suppressing recombination between sets of coadapted genes. However, because recombination suppression hinders the dissociation of the individual effects of genes within supergenes, there is still little evidence that supergenes evolve by tightening linkage between coadapted genes. Here, combining a landmark-free phenotyping algorithm with multivariate genome-wide association studies, we dissected the genetic basis of wing pattern variation in the butterfly Heliconius numata. We show that the supergene controlling the striking wing pattern polymorphism displayed by this species contains several independent loci associated with different features of wing patterns. The three chromosomal inversions of this supergene suppress recombination between these loci, supporting the hypothesis that they may have evolved because they captured beneficial combinations of alleles. Some of these loci are, however, associated with colour variations only in a subset of morphs where the phenotype is controlled by derived inversion forms, indicating that they were recruited after the formation of the inversions. Our study shows that supergenes and clusters of adaptive loci in general may form via the evolution of chromosomal rearrangements suppressing recombination between co-adapted loci but also via the subsequent recruitment of linked adaptive mutations. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Paul Jay
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Manon Leroy
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Yann Le Poul
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Mónica Arias
- CIRAD, UMR PHIM, F-34398 Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, CEDEX 5, 34398 Montpellier, France
| | - Mathieu Chouteau
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France.,LEEISA, USR 63456, Université de Guyane, CNRS, IFREMER, 275 route de Montabo, 797334 Cayenne, French Guiana
| | - Mathieu Joron
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
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Jeffery NW, Lehnert SJ, Kess T, Layton KKS, Wringe BF, Stanley RR. Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy. Front Genet 2022; 13:886494. [PMID: 35812740 PMCID: PMC9257101 DOI: 10.3389/fgene.2022.886494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and ecosystem function, and ultimately support the blue economy strategy by balancing ocean use with conservation. New “big data” omics approaches, including genomics and transcriptomics, are becoming essential tools for the development and maintenance of MPA networks. Current molecular omics techniques, including population-scale genome sequencing, have direct applications for assessing population connectivity and for evaluating how genetic variation is represented within and among MPAs. Effective baseline characterization and long-term, scalable, and comprehensive monitoring are essential for successful MPA management, and omics approaches hold great promise to characterize the full range of marine life, spanning the microbiome to megafauna across a range of environmental conditions (shallow sea to the deep ocean). Omics tools, such as eDNA metabarcoding can provide a cost-effective basis for biodiversity monitoring in large and remote conservation areas. Here we provide an overview of current omics applications for conservation planning and monitoring, with a focus on metabarcoding, metagenomics, and population genomics. Emerging approaches, including whole-genome sequencing, characterization of genomic architecture, epigenomics, and genomic vulnerability to climate change are also reviewed. We demonstrate that the operationalization of omics tools can enhance the design, monitoring, and management of MPAs and thus will play an important role in a modern and comprehensive blue economy strategy.
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Affiliation(s)
- Nicholas W. Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
- *Correspondence: Nicholas W. Jeffery,
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Kara K. S. Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Brendan F. Wringe
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
| | - Ryan R.E. Stanley
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
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11
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Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish. Proc Natl Acad Sci U S A 2022; 119:e2121469119. [PMID: 35658077 DOI: 10.1073/pnas.2121469119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species of Takifugu fish that compose an important model for the study of genomics and sex determination. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.
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12
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Thorstensen MJ, Vandervelde CA, Bugg WS, Michaleski S, Vo L, Mackey TE, Lawrence MJ, Jeffries KM. Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish. Front Genet 2022; 13:795355. [PMID: 35547248 PMCID: PMC9081360 DOI: 10.3389/fgene.2022.795355] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.
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Affiliation(s)
- Matt J. Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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13
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Munsch SH, Greene CM, Mantua NJ, Satterthwaite WH. One hundred-seventy years of stressors erode salmon fishery climate resilience in California's warming landscape. GLOBAL CHANGE BIOLOGY 2022; 28:2183-2201. [PMID: 35075737 DOI: 10.1111/gcb.16029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 11/12/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
People seek reliable natural resources despite climate change. Diverse habitats and biologies stabilize productivity against disturbances like climate, prompting arguments to promote climate-resilient resources by prioritizing complex, less-modified ecosystems. These arguments hinge on the hypothesis that simplifying and degrading ecosystems will reduce resources' climate resilience, a process liable to be cryptically evolving across landscapes and human generations, but rarely documented. Here, we examined the industrial era (post 1848) of California's Central Valley, chronicling the decline of a diversified, functional portfolio of salmon habitats and life histories and investigating for empirical evidence of lost climate resilience in its fishery. Present perspectives indicate that California's dynamic, warming climate overlaid onto its truncated, degraded habitat mosaic severely constrains its salmon fishery. We indeed found substantial climate constraints on today's fishery, but this reflected a shifted ecological baseline. During the early stages of a stressor legacy that transformed the landscape and -- often consequently -- compressed salmon life history expression, the fishery diffused impacts of dry years across a greater number of fishing years and depended less on cool spring-summer transitions. The latter are important given today's salmon habitats, salmon life histories, and resource management practices, but are vanishing with climate change while year-to-year variation in fishery performance is rising. These findings give empirical weight to the idea that human legacies influence ecosystems' climate resilience across landscapes and boundaries (e.g., land/sea). They also raise the question of whether some contemporary climate effects are recent and attributable not only to increasing climate stress, but to past and present human actions that erode resilience. In general, it is thus worth considering that management approaches that prioritize complex, less-modified ecosystems may stabilize productivity despite increasing climate stress and such protective actions may be required for some ecological services to persist into uncertain climate futures.
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Affiliation(s)
- Stuart H Munsch
- Ocean Associates Inc., Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, USA
| | - Correigh M Greene
- Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, USA
| | - Nathan J Mantua
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA
| | - William H Satterthwaite
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA
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14
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Matschiner M, Barth JMI, Tørresen OK, Star B, Baalsrud HT, Brieuc MSO, Pampoulie C, Bradbury I, Jakobsen KS, Jentoft S. Supergene origin and maintenance in Atlantic cod. Nat Ecol Evol 2022; 6:469-481. [PMID: 35177802 PMCID: PMC8986531 DOI: 10.1038/s41559-022-01661-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation. Atlantic cod carries four supergenes linked to migratory lifestyle and environmental adaptations. Using whole-genome sequencing, the authors show that the genome inversions that underlie the supergenes originated at different times and show gene flux between supergene haplotypes.
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Affiliation(s)
- Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. .,Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland. .,Natural History Museum, University of Oslo, Oslo, Norway.
| | - Julia Maria Isis Barth
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Ole Kristian Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Helle Tessand Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marine Servane Ono Brieuc
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Ian Bradbury
- Fisheries and Oceans Canada, St John's, Newfoundland and Labrador, Canada
| | - Kjetill Sigurd Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
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15
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Evolutionary genetics: Inversions — Do not quail but go big! Curr Biol 2022; 32:R76-R78. [DOI: 10.1016/j.cub.2021.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Thomson AI, Archer FI, Coleman MA, Gajardo G, Goodall‐Copestake WP, Hoban S, Laikre L, Miller AD, O’Brien D, Pérez‐Espona S, Segelbacher G, Serrão EA, Sjøtun K, Stanley MS. Charting a course for genetic diversity in the UN Decade of Ocean Science. Evol Appl 2021; 14:1497-1518. [PMID: 34178100 PMCID: PMC8210796 DOI: 10.1111/eva.13224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.
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Affiliation(s)
| | | | - Melinda A. Coleman
- New South Wales FisheriesNational Marine Science CentreCoffs HarbourNSWAustralia
- National Marine Science CentreSouthern Cross UniversityCoffs HarbourNSWAustralia
- Oceans Institute and School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Gonzalo Gajardo
- Laboratory of Genetics, Aquaculture & BiodiversityUniversidad de Los LagosOsornoChile
| | | | - Sean Hoban
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
| | - Linda Laikre
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
- The Wildlife Analysis UnitThe Swedish Environmental Protection AgencyStockholmSweden
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | | | - Sílvia Pérez‐Espona
- The Royal (Dick) School of Veterinary Studies and The Roslin InstituteMidlothianUK
| | - Gernot Segelbacher
- Chair of Wildlife Ecology and ManagementUniversity FreiburgFreiburgGermany
| | - Ester A. Serrão
- CCMARCentre of Marine SciencesFaculty of Sciences and TechnologyUniversity of AlgarveFaroPortugal
| | - Kjersti Sjøtun
- Department of Biological SciencesUniversity of BergenBergenNorway
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17
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Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic. Proc Natl Acad Sci U S A 2021; 118:2025453118. [PMID: 33827928 PMCID: PMC8054022 DOI: 10.1073/pnas.2025453118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.
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18
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Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms. Nat Genet 2021; 53:288-293. [PMID: 33495598 DOI: 10.1038/s41588-020-00771-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Chromosomal inversions are ubiquitous in genomes and often coordinate complex phenotypes, such as the covariation of behavior and morphology in many birds, fishes, insects or mammals1-11. However, why and how inversions become associated with polymorphic traits remains obscure. Here we show that despite a strong selective advantage when they form, inversions accumulate recessive deleterious mutations that generate frequency-dependent selection and promote their maintenance at intermediate frequency. Combining genomics and in vivo fitness analyses in a model butterfly for wing-pattern polymorphism, Heliconius numata, we reveal that three ecologically advantageous inversions have built up a heavy mutational load from the sequential accumulation of deleterious mutations and transposable elements. Inversions associate with sharply reduced viability when homozygous, which prevents them from replacing ancestral chromosome arrangements. Our results suggest that other complex polymorphisms, rather than representing adaptations to competing ecological optima, could evolve because chromosomal rearrangements are intrinsically prone to carrying recessive harmful mutations.
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19
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Longo GC, Lam L, Basnett B, Samhouri J, Hamilton S, Andrews K, Williams G, Goetz G, McClure M, Nichols KM. Strong population differentiation in lingcod ( Ophiodon elongatus) is driven by a small portion of the genome. Evol Appl 2020; 13:2536-2554. [PMID: 33294007 PMCID: PMC7691466 DOI: 10.1111/eva.13037] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod (Ophiodon elongatus), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site-associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F-statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low FST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome-level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management.
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Affiliation(s)
- Gary C. Longo
- NRC Research Associateship ProgramNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Laurel Lam
- Pacific States Marine Fisheries CommissionUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
- Moss Landing Marine LaboratoriesMoss LandingCAUSA
| | | | - Jameal Samhouri
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | | | - Kelly Andrews
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Greg Williams
- Pacific States Marine Fisheries CommissionUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Giles Goetz
- UWJISAOUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Michelle McClure
- Fisheries Resource Analysis and Monitoring DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
- Pacific Marine Environmental LaboratoryNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Krista M. Nichols
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
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20
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Thompson NF, Anderson EC, Clemento AJ, Campbell MA, Pearse DE, Hearsey JW, Kinziger AP, Garza JC. A complex phenotype in salmon controlled by a simple change in migratory timing. Science 2020; 370:609-613. [DOI: 10.1126/science.aba9059] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Neil F. Thompson
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
| | - Eric C. Anderson
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Anthony J. Clemento
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
| | - Matthew A. Campbell
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Devon E. Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - James W. Hearsey
- Department of Fisheries Biology, Humboldt State University, Arcata, CA 95521, USA
| | - Andrew P. Kinziger
- Department of Fisheries Biology, Humboldt State University, Arcata, CA 95521, USA
| | - John Carlos Garza
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
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21
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Nowling RJ, Manke KR, Emrich SJ. Detecting inversions with PCA in the presence of population structure. PLoS One 2020; 15:e0240429. [PMID: 33119626 PMCID: PMC7595445 DOI: 10.1371/journal.pone.0240429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI
| | - Krystal R. Manke
- Physics and Chemistry, Milwaukee School of Engineering, Milwaukee, WI
| | - Scott J. Emrich
- Electrical Engineering and Computer Science, University of Tennessee–Knoxville, Knoxville, TN
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22
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Stange M, Barrett RDH, Hendry AP. The importance of genomic variation for biodiversity, ecosystems and people. Nat Rev Genet 2020; 22:89-105. [PMID: 33067582 DOI: 10.1038/s41576-020-00288-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 11/09/2022]
Abstract
The 2019 United Nations Global assessment report on biodiversity and ecosystem services estimated that approximately 1 million species are at risk of extinction. This primarily human-driven loss of biodiversity has unprecedented negative consequences for ecosystems and people. Classic and emerging approaches in genetics and genomics have the potential to dramatically improve these outcomes. In particular, the study of interactions among genetic loci within and between species will play a critical role in understanding the adaptive potential of species and communities, and hence their direct and indirect effects on biodiversity, ecosystems and people. We explore these population and community genomic contexts in the hope of finding solutions for maintaining and improving ecosystem services and nature's contributions to people.
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Affiliation(s)
- Madlen Stange
- Redpath Museum, McGill University, Montreal, QC, Canada
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23
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Pitchford SC, Smith BE, McBride RS. A real-time PCR assay to detect predation by spiny dogfish on Atlantic cod in the western North Atlantic Ocean. Ecol Evol 2020; 10:11022-11030. [PMID: 33144945 PMCID: PMC7593176 DOI: 10.1002/ece3.6694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/18/2022] Open
Abstract
Conventional observations show spiny dogfish (Squalus acanthius Linnaeus) rarely eat Atlantic cod (Gadus morhua Linnaeus; 0.02% of stomachs) in the northwestern Atlantic Ocean. Critics express concern that digestion may limit species-level prey identification, and with recovery from overfishing, dogfish populations may be suppressing cod by competition or predation. This study applied a real-time PCR TaqMan assay to identify cod in dogfish stomachs collected by cooperating fishing boats during normal trawling operations (May 2014-May 2015; Gulf of Maine, Georges Bank). Conventional methods observed 51 different prey taxa and nearly 1,600 individual prey items, but no cod were observed. Cod DNA was detected in 31 (10.5%) of the dogfish stomachs, with a higher percentage of these from the homogenate of amorphous, well-digested prey and stomach fluids (20 stomachs or 65%) than from discrete animal tissues (11 stomachs or 35%). Re-examination of photographs of these 11 tissue samples revealed one whole, partially digested fish that could be recognized in hindsight as cod. Cod DNA was observed in dogfish stomachs year round: in January (1 of 1 trip), February (1 of 1), May (1 of 3), June (0 of 1), July (3 of 4), August (1 of 2), and October (3 of 3). Although these data suggest higher interaction rates between dogfish and cod than previously observed, addressing the population consequences of this predator-prey relationship requires a robust sampling design, estimates of digestion rates by dogfish to account for complete degradation of DNA sequences, and consideration for dogfish scavenging during fishing operations.
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Affiliation(s)
| | - Brian E. Smith
- Northeast Fisheries Science CenterNOAA FisheriesWoods HoleMassachusettsUSA
| | - Richard S. McBride
- Northeast Fisheries Science CenterNOAA FisheriesWoods HoleMassachusettsUSA
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24
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A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea. G3-GENES GENOMES GENETICS 2020; 10:2903-2910. [PMID: 32641450 PMCID: PMC7466986 DOI: 10.1534/g3.120.401423] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a 'southern' cod population which is complementary to the existing 'northern' population based genome assemblies and represents the first step toward developing pan-genomic resources for Atlantic cod.
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25
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Oomen RA, Kuparinen A, Hutchings JA. Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change. J Hered 2020; 111:319-332. [PMID: 32620014 PMCID: PMC7423069 DOI: 10.1093/jhered/esaa020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Anna Kuparinen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Jeffrey A Hutchings
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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26
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Kess T, Bentzen P, Lehnert SJ, Sylvester EVA, Lien S, Kent MP, Sinclair‐Waters M, Morris C, Wringe B, Fairweather R, Bradbury IR. Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish. Ecol Evol 2020; 10:638-653. [PMID: 32015832 PMCID: PMC6988541 DOI: 10.1002/ece3.5828] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
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Affiliation(s)
- Tony Kess
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Sarah J. Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Emma V. A. Sylvester
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Sigbjørn Lien
- Department of Animal and Aquacultural SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Matthew P. Kent
- Department of Animal and Aquacultural SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Marion Sinclair‐Waters
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | - Corey Morris
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Brendan Wringe
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | | | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
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27
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Clucas GV, Lou RN, Therkildsen NO, Kovach AI. Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole-genome sequencing. Evol Appl 2019; 12:1971-1987. [PMID: 31700539 PMCID: PMC6824067 DOI: 10.1111/eva.12861] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 06/14/2019] [Accepted: 07/12/2019] [Indexed: 12/21/2022] Open
Abstract
Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome-wide patterns of variation, we used low-coverage sequencing to perform a region-wide, whole-genome analysis of fine-scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole-genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter- and spring-spawning populations revealed highly elevated relative (FST ) and absolute (dxy ) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain-pituitary-gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high-resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome-scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.
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Affiliation(s)
- Gemma V. Clucas
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - R. Nicolas Lou
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
| | | | - Adrienne I. Kovach
- Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
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Lennox RJ, Paukert CP, Aarestrup K, Auger-Méthé M, Baumgartner L, Birnie-Gauvin K, Bøe K, Brink K, Brownscombe JW, Chen Y, Davidsen JG, Eliason EJ, Filous A, Gillanders BM, Helland IP, Horodysky AZ, Januchowski-Hartley SR, Lowerre-Barbieri SK, Lucas MC, Martins EG, Murchie KJ, Pompeu PS, Power M, Raghavan R, Rahel FJ, Secor D, Thiem JD, Thorstad EB, Ueda H, Whoriskey FG, Cooke SJ. One Hundred Pressing Questions on the Future of Global Fish Migration Science, Conservation, and Policy. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00286] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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