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Burden DJ, Bartley DJ, Besier RB, Claerebout E, Elliott TP, Höglund J, Rehbein S, Torres-Acosta JFJ, Van Wyk JA, Yazwinski T. World Association for the Advancement of Veterinary Parasitology (W.A.A.V.P.): Third edition of the guideline for evaluating efficacy of anthelmintics in ruminants (bovine, ovine, caprine). Vet Parasitol 2024; 329:110187. [PMID: 38728835 DOI: 10.1016/j.vetpar.2024.110187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024]
Abstract
This guideline is aimed at those who are involved in the assessment of anthelmintic efficacy in ruminant livestock species (bovine, ovine and caprine). The intent is to provide a framework that can be adopted worldwide for the testing of anthelmintics in ruminants, such that studies carried out in different countries can be compared and thereby unnecessary duplication can be reduced. Recommendations are made for the selection, housing and feeding of study animals, the type of studies required, the method used to conduct those studies, the assessment of results and the standards for defining anthelmintic efficacy.
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Affiliation(s)
- D J Burden
- Duilio Veterinary Parasitology, The Vicarage, Church Lane, Churcham, Gloucester, UK.
| | - D J Bartley
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - R B Besier
- College of Environmental and Life Sciences, Murdoch University, Perth, WA, Australia
| | - E Claerebout
- Laboratory for Parasitology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - T P Elliott
- Centre for Animal Research and Teaching, University of New England, Armidale, NSW, Australia
| | - J Höglund
- Section for Parasitology, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - S Rehbein
- Boehringer Ingelheim Vetmedica GmbH, Kathrinenhof Research Center, Rohrdorf, Germany
| | - J F J Torres-Acosta
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - J A Van Wyk
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - T Yazwinski
- University of Arkansas, Fayetteville, AR, USA
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2
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Höglund J, Dias G, Olsen RA, Soares A, Bunikis I, Talla V, Backström N. A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern. Genome Biol Evol 2024; 16:evae031. [PMID: 38368625 PMCID: PMC10901555 DOI: 10.1093/gbe/evae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024] Open
Abstract
The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.
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Affiliation(s)
- Jacob Höglund
- Animal Ecology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
| | - Guilherme Dias
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala 752 37, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna 17165, Sweden
| | - André Soares
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala 752 37, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 752 37, Sweden
| | - Venkat Talla
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala SE-752 36, Sweden
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3
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Chondrelli N, Kuehn E, Meurling S, Cortázar-Chinarro M, Laurila A, Höglund J. Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo). Sci Rep 2024; 14:2495. [PMID: 38291226 PMCID: PMC10828426 DOI: 10.1038/s41598-024-52975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/25/2024] [Indexed: 02/01/2024] Open
Abstract
Batrachochytrium dendrobatidis (Bd) is a fungal pathogen that has decimated amphibian populations worldwide for several decades. We examined the changes in gene expression in response to Bd infection in two populations of the common toad, Bufo bufo, in a laboratory experiment. We collected B. bufo eggs in southern and northern Sweden, and infected the laboratory-raised metamorphs with two strains of the global panzoonotic lineage Bd-GPL. Differential expression analysis showed significant differences between infected and control individuals in both liver and skin. The skin samples showed no discernible differences in gene expression between the two strains used, while liver samples were differentiated by strain, with one of the strains eliciting no immune response from infected toads. Immune system genes were overexpressed in skin samples from surviving infected individuals, while in liver samples the pattern was more diffuse. Splitting samples by population revealed a stronger immune response in northern individuals. Differences in transcriptional regulation between populations are particularly relevant to study in Swedish amphibians, which may have experienced varying exposure to Bd. Earlier exposure to this pathogen and subsequent adaptation or selection pressure may contribute to the survival of some populations over others, while standing genetic diversity in different populations may also affect the infection outcome.
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Affiliation(s)
- Niki Chondrelli
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - Emily Kuehn
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Sara Meurling
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- MEMEG/Department of Biology, Faculty of Science, Lund University, Lund, Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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4
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Meurling S, Siljestam M, Cortazar-Chinarro M, Åhlen D, Rödin-Mörch P, Ågren E, Höglund J, Laurila A. Body size mediates latitudinal population differences in the response to chytrid fungus infection in two amphibians. Oecologia 2024; 204:71-81. [PMID: 38097779 PMCID: PMC10830819 DOI: 10.1007/s00442-023-05489-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/14/2023] [Indexed: 02/02/2024]
Abstract
Factors behind intraspecific variation in sensitivity to pathogens remain poorly understood. We investigated how geographical origin in two North European amphibians affects tolerance to infection by the chytrid fungus Batrachochytrium dendrobatidis (Bd), a generalist pathogen which has caused amphibian population declines worldwide. We exposed newly metamorphosed individuals of moor frog Rana arvalis and common toad Bufo bufo from two latitudinal regions to two different BdGPL strains. We measured survival and growth as infections may cause sub-lethal effects in fitness components even in the absence of mortality. Infection loads were higher in B. bufo than in R. arvalis, and smaller individuals had generally higher infection loads. B. bufo had high mortality in response to Bd infection, whereas there was little mortality in R. arvalis. Bd-mediated mortality was size-dependent and high-latitude individuals were smaller leading to high mortality in the northern B. bufo. Bd exposure led to sub-lethal effects in terms of reduced growth suggesting that individuals surviving the infection may have reduced fitness mediated by smaller body size. In both host species, the Swedish Bd strain caused stronger sublethal effects than the British strain. We suggest that high-latitude populations can be more vulnerable to chytrids than those from lower latitudes and discuss the possible mechanisms how body size and host geographical origin contribute to the present results.
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Affiliation(s)
- Sara Meurling
- Animal Ecology/ Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Mattias Siljestam
- Animal Ecology/ Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Maria Cortazar-Chinarro
- Animal Ecology/ Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- MEMEG/Department of Biology, Lund University, Lund, Sweden
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - David Åhlen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Uppsala, Sweden
| | - Patrik Rödin-Mörch
- Animal Ecology/ Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Erik Ågren
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/ Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Anssi Laurila
- Animal Ecology/ Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
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5
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Cortazar-Chinarro M, Richter-Boix A, Rödin-Mörch P, Halvarsson P, Logue JB, Laurila A, Höglund J. Association between the skin microbiome and MHC class II diversity in an amphibian. Mol Ecol 2024; 33:e17198. [PMID: 37933583 DOI: 10.1111/mec.17198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.
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Affiliation(s)
- M Cortazar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- MEMEG/Department of Biology, Lund University, Lund, Sweden
- Department of Earth Ocean and Atmospheric Sciences, Faculty of Science 2020-2207, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Richter-Boix
- Department of Political and Social Science, Pompeu Fabra University, Barcelona, Spain
| | - P Rödin-Mörch
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - P Halvarsson
- Parasitology/Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J B Logue
- Aquatic Ecology/Department of Biology, Lund University, Lund, Sweden
- SLU University Library, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - J Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Jing CL, Lou YQ, Liu H, Song K, Fang Y, Höglund J, Halvarsson P, Sun YH. Avian malaria parasite infections do not affect personality in the chestnut thrush ( Turdus rubrocanus) on the Qinghai-Tibet Plateau. Heliyon 2023; 9:e20082. [PMID: 37809652 PMCID: PMC10559808 DOI: 10.1016/j.heliyon.2023.e20082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Personality traits, the consistent individual behavioral differences, are currently gaining much attention in studies of natural bird populations. However, associations between personality traits and parasite infections are not often investigated. Even less attention has been given to studies of birds in the high-elevation region such as the Tibetan plateau. This research aims to examine the relationship between avian malaria parasites and two personality traits in a population of the Chestnut Thrush (Turdus rubrocanus) breed in the Tibetan plateau. Our results revealed no evidence of sex bias in malaria parasite prevalence. Furthermore, we found no effect of infection status on two personality scores: activity and boldness. Additionally, no effects on the activity level or boldness were observed for different parasite lineages of Haemoproteus, Leucocytozoon, the sex of the birds, or their interactions. Similarly, we did not find any relationship between activity level and boldness with nestling numbers, sex, or their interactions. Notably, individuals with a larger number of offspring tended to display greater boldness. Our findings indicate that blood parasite infections are common in this population but do not significantly impact the personality of the birds.
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Affiliation(s)
- Chun-lei Jing
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Qiang Lou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huan Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Song
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Peter Halvarsson
- Unit of Parasitology, Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 75007, Uppsala, Sweden
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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Squires TE, Rödin-Mörch P, Formenti G, Tracey A, Abueg L, Brajuka N, Jarvis E, Halapi EC, Melsted P, Höglund J, Magnússon KP. A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta). G3 (Bethesda) 2023:7152384. [PMID: 37141262 DOI: 10.1093/g3journal/jkad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were, 33605, 394, and 4265 bp respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes).
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Affiliation(s)
- Theodore E Squires
- University of Akureyri, Faculty of Natural Resource Sciences, Borgir við Norðurslóð, Akureyri 600 ICELAND
- Uppsala University, Faculty of Animal Ecology, Centre for Evolution and Genomics, Norbyvägen 18D, Uppsala 75236 Sweden
| | - Patrik Rödin-Mörch
- University of Akureyri, Faculty of Natural Resource Sciences, Borgir við Norðurslóð, Akureyri 600 ICELAND
- Uppsala University, Faculty of Animal Ecology, Centre for Evolution and Genomics, Norbyvägen 18D, Uppsala 75236 Sweden
| | - Giulio Formenti
- The Rockefeller University, Center for Genomics and Systems Biology, 1230 York Ave, New York, NY 10065 United States of America
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA United Kingdom
| | - Linelle Abueg
- The Rockefeller University, Center for Genomics and Systems Biology, 1230 York Ave, New York, NY 10065 United States of America
| | - Nadolina Brajuka
- The Rockefeller University, Center for Genomics and Systems Biology, 1230 York Ave, New York, NY 10065 United States of America
| | - Erich Jarvis
- The Rockefeller University, Center for Genomics and Systems Biology, 1230 York Ave, New York, NY 10065 United States of America
| | - Eva C Halapi
- University of Akureyri, Faculty of Natural Resource Sciences, Borgir við Norðurslóð, Akureyri 600 Iceland
| | - Páll Melsted
- University of Iceland, Department of Computer Science, Sæmundargata 2, Reykjavík 102 Iceland
- University of Iceland Biomedical Center, Medical Park, Vatnsmýrarvegur 16, Reykjavík 101 Iceland
| | - Jacob Höglund
- Uppsala University, Faculty of Animal Ecology, Centre for Evolution and Genomics, Norbyvägen 18D, Uppsala 75236 Sweden
| | - Kristinn Pétur Magnússon
- University of Akureyri, Faculty of Natural Resource Sciences, Borgir við Norðurslóð, Akureyri 600 Iceland
- University of Iceland Biomedical Center, Medical Park, Vatnsmýrarvegur 16, Reykjavík 101 Iceland
- Icelandic Institute of Natural History, Borgir við Norðurslóð, Akureyri 600 Iceland
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9
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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Cortazar-Chinarro M, Meurling S, Schroyens L, Siljestam M, Richter-Boix A, Laurila A, Höglund J. Major Histocompatibility Complex Variation and Haplotype Associated Survival in Response to Experimental Infection of Two Bd-GPL Strains Along a Latitudinal Gradient. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.915271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While both innate and adaptive immune system mechanisms have been implicated in resistance against the chytrid fungus Batrachochytrium dendrobatidis (Bd), studies on the role of specific MHC haplotypes on Bd infection are rare. Here, we studied variation in MHC Class IIB loci in the common toad Bufo bufo along a latitudinal gradient across Sweden. In general, Swedish toad populations had few MHC Class IIB haplotypes and MHC diversity declined from south (13 haplotypes) to the north (four haplotypes). The low diversity may compromise the ability of northern populations to fight emerging disease, such as Bd. In a laboratory experiment, we infected newly metamorphosed toads with two strains of the Global Pandemic Lineage of the fungus (Bd-GPL) and compared survival with sham controls. Bd-infected toads had lower survival compared to controls. Moreover, survival was dependent on the Bd-strain and northern toads had lower Bd-mediated survival than southern individuals. MHC diversity was lower in northern toads. All northern experimental animals were monomorphic for a single MHC haplotype, whereas we found seven different haplotypes in southern experimental animals. In southern toads, survival was dependent on both Bd-strain and MHC haplotype suggesting differential infection dynamics depending on both Bd-strain and host immune system characteristics.
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11
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Yazwinski T, Höglund J, Permin A, Gauly M, Tucker C. World Association for the Advancement of Veterinary Parasitology (WAAVP): second edition of guidelines for evaluating the efficacy of anthelmintics in poultry. Vet Parasitol 2022; 305:109711. [DOI: 10.1016/j.vetpar.2022.109711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 01/12/2023]
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Song K, Gao B, Halvarsson P, Fang Y, Klaus S, Jiang YX, Swenson JE, Han ZM, Sun YH, Höglund J. Conservation genomics of sibling grouse in boreal forests reveals introgression and adaptive population differentiation in genes controlling epigenetic variation. Zool Res 2022; 43:184-187. [PMID: 35001567 PMCID: PMC8920849 DOI: 10.24272/j.issn.2095-8137.2021.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Kai Song
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala 75236, Sweden
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peter Halvarsson
- Unit of Parasitology, Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ying-Xin Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jon E Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås NO-1432, Norway
| | - Zhi-Ming Han
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. E-mail:
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala 75236, Sweden. E-mail:
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13
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Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M. The era of reference genomes in conservation genomics. Trends Ecol Evol 2022; 37:197-202. [PMID: 35086739 DOI: 10.1016/j.tree.2021.11.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 02/08/2023]
Abstract
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
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Affiliation(s)
- Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environmental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Iliana Bista
- University of Cambridge, Department of Genetics, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, CB10 1SA, Hinxton, UK
| | | | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI) 50019, Italy
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - José A Godoy
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Jacob Höglund
- Dept. of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Sweden
| | | | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Belgium
| | - Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747, AG, Groningen, the Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5, 220 Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Belgium
| | | | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Germany
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark, Build 3, Universitetsparken 15, Copenhagen 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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14
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Song K, Gao B, Halvarsson P, Fang Y, Klaus S, Jiang YX, Swenson JE, Sun YH, Höglund J. Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change. BMC Ecol Evol 2021; 21:194. [PMID: 34689746 PMCID: PMC8543876 DOI: 10.1186/s12862-021-01921-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01921-7.
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Affiliation(s)
- Kai Song
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden. .,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Peter Halvarsson
- Unit of Parasitology, Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 75007, Uppsala, Sweden
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | | | - Ying-Xin Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Jon E Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, 1432, Ås, Norway
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
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15
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Gowri Shankar P, Swamy P, Williams RC, Ganesh SR, Moss M, Höglund J, Das I, Sahoo G, Vijayakumar SP, Shanker K, Wüster W, Dutta SK. King or royal family? Testing for species boundaries in the King Cobra, Ophiophagus hannah (Cantor, 1836), using morphology and multilocus DNA analyses. Mol Phylogenet Evol 2021; 165:107300. [PMID: 34474153 DOI: 10.1016/j.ympev.2021.107300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 01/15/2023]
Abstract
In widespread species, the diverse ecological conditions in which the populations occur, and the presence of many potential geographical barriers through their range are expected to have created ample opportunities for the evolution of distinct, often cryptic lineages. In this work, we tested for species boundaries in one such widespread species, the king cobra, Ophiophagus hannah (Cantor, 1836), a largely tropical elapid snake distributed across the Oriental realm. Based on extensive geographical sampling across most of the range of the species, we initially tested for candidate species (CS) using Maximum-Likelihood analysis of mitochondrial genes. We then tested the resulting CS using both morphological data and sequences of three single-copy nuclear genes. We used snapclust to determine the optimal number of clusters in the nuclear dataset, and Bayesian Phylogenetics and Phylogeography (BPP) to test for likely species status. We used non-metric multidimensional scaling (nMDS) analysis for discerning morphological separation. We recovered four independently evolving, geographically separated lineages that we consider Confirmed Candidate Species: (1) Western Ghats lineage; (2) Indo-Chinese lineage (3) Indo-Malayan lineage; (4) Luzon Island lineage, in the Philippine Archipelago. We discuss patterns of lineage divergence, particularly in the context of low morphological divergence, and the conservation implications of recognizing several endemic king cobra lineages.
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Affiliation(s)
- P Gowri Shankar
- Maharaja Shrirama Chandra Bhanja Deo University, Baripada, Takatpur, Odisha, India; CES, Indian Institute of Science, Bangalore, India; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden; Kālinga Foundation, Agumbe, Karnataka, India.
| | | | - Rhiannon C Williams
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - S R Ganesh
- Chennai Snake Park, Raj Bhavan Post, Chennai, India
| | - Matt Moss
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Malaysia
| | | | | | | | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Sushil K Dutta
- Maharaja Shrirama Chandra Bhanja Deo University, Baripada, Takatpur, Odisha, India; Department of Zoology, Assam Don Bosco University, Tapesia, Assam, India
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16
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Jensen A, Lillie M, Bergström K, Larsson P, Höglund J. Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish. Heredity (Edinb) 2021; 127:79-91. [PMID: 33963302 PMCID: PMC8249479 DOI: 10.1038/s41437-021-00438-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 02/03/2023] Open
Abstract
The use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.
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Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Mette Lillie
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden.
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Kristofer Bergström
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Per Larsson
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
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17
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Tarbiat B, Enweji N, Baltrusis P, Halvarsson P, Osterman-Lind E, Jansson DS, Höglund J. A novel duplex ddPCR assay for detection and differential diagnosis of Ascaridia galli and Heterakis gallinarum eggs from chickens feces. Vet Parasitol 2021; 296:109499. [PMID: 34144378 DOI: 10.1016/j.vetpar.2021.109499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022]
Abstract
Since the EU ban on battery cages, many studies have listed Ascaridia galli and Heterakis gallinarum as the most common roundworms in the European laying hen population. A complicating factor is that the eggs of these parasites are almost identical. Thus, lack of molecular diagnostic approaches has driven epidemiological studies to take on necropsy for species discrimination, which is labor and cost intensive. Here, we describe a novel diagnostic tool based on droplet digital PCR for simultaneous identification and absolute quantification of the eggs of both of these ascarids in chickens' droppings using two different genus-specific primer-probe sets targeting the second internal transcribed spacer region (ITS-2) in the nuclear ribosomal (rRNA) gene array. No cross-reaction was observed when different combinations of DNA and species-specific primers and probes were tested. The lowest obtained frequency threshold for the detection of H. gallinarum in the presence of a constant A. galli DNA concentration was determined to be 0.8 %. After validation, we used the assay to analyze field samples collected from several Swedish laying hen farms. Out of 134 samples, 86 (64 %) were positive for A. galli while 11 (8.3 %) samples were positive for H. gallinarum. These samples were initially analyzed with flotation technique for detection of ascarid eggs. The results of the Cohen's kappa indicated substantial agreement (85.8 %) between the two tests. In conclusion, we have validated a novel molecular-based diagnostic tool for quantification and differentiation between intestinal parasites of major importance in chickens with high precision. Although this study focuses on identification of parasites of laying hens, the findings may well have a bearing on all types of chicken production systems. The present study lays the groundwork for future research into epidemiology of these two important chicken parasite species.
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Affiliation(s)
- B Tarbiat
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7036, SE-750 07, Uppsala, Sweden.
| | - N Enweji
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7036, SE-750 07, Uppsala, Sweden
| | - P Baltrusis
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7036, SE-750 07, Uppsala, Sweden
| | - P Halvarsson
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7036, SE-750 07, Uppsala, Sweden
| | - E Osterman-Lind
- Department of Microbiology, Section for Parasitological Diagnostics, National Veterinary Institute (SVA), SE-751 89, Uppsala, Sweden
| | - D S Jansson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Box 7054, SE-750 07, Uppsala, Sweden; Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), SE751 89, Uppsala, Sweden
| | - J Höglund
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences (SLU), P.O. Box 7036, SE-750 07, Uppsala, Sweden
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18
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Thörn F, Rödin-Mörch P, Cortazar-Chinarro M, Richter-Boix A, Laurila A, Höglund J. The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation. Heredity (Edinb) 2021; 126:656-667. [PMID: 33564181 PMCID: PMC8115047 DOI: 10.1038/s41437-020-00400-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 12/07/2020] [Accepted: 12/22/2020] [Indexed: 01/31/2023] Open
Abstract
Clinal variation is paramount for understanding the factors shaping genetic diversity in space and time. During the last glacial maximum, northern Europe was covered by glacial ice that rendered the region uninhabitable for most taxa. Different evolutionary processes during and after the recolonisation of this area from different glacial refugia have affected the genetic landscape of the present day European flora and fauna. In this study, we focus on the common toad (Bufo bufo) in Sweden and present evidence suggesting that these processes have resulted in two separate lineages of common toad, which colonised Sweden from two directions. Using ddRAD sequencing data for demographic modelling, structure analyses, and analysis of molecular variance (AMOVA), we provide evidence of a contact zone located between Uppland and Västerbotten in central Sweden. Genetic diversity was significantly higher in southern Sweden compared to the north, in accordance with a pattern of decreased genetic diversity with increasing distance from glacial refugia. Candidate genes under putative selection are identified through outlier detection and gene-environment association methods. We provide evidence of divergent selection related to stress response and developmental processes in these candidate genes. The colonisation of Sweden by two separate lineages may have implications for how future conservation efforts should be directed by identifying management units and putative local adaptations.
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Affiliation(s)
- Filip Thörn
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
- Department for Bioinformatics and Genetics, Swedish Natural History Museum, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Patrik Rödin-Mörch
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | | | - Alex Richter-Boix
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Anssi Laurila
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Charlier J, Rinaldi L, Musella V, Ploeger HW, Chartier C, Rose Vineer H, Hinney B, von Samson-Himmelstjerna G, Băcescu B, Mickiewicz M, Mateus TL, Martinez-Valladares M, Quealy S, Azaizeh H, Sekovska B, Akkari H, Petkevicius S, Hektoen L, Höglund J, Morgan ER, Bartley DJ, Claerebout E. Corrigendum to "Initial assessment of the economic burden of major parasitic helminth infections to the ruminant livestock industry in Europe" [Prev. Vet. Med. 182 (2020) 105103]. Prev Vet Med 2020; 188:105213. [PMID: 33261929 DOI: 10.1016/j.prevetmed.2020.105213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J Charlier
- Kreavet, H. Mertensstraat 17, 9150 Kruibeke, Belgium.
| | - L Rinaldi
- Department of Veterinary Medicine and Animal Production, CREMOPAR, University of Naples Federico II, 80137 Napoli, Italy
| | - V Musella
- Department of Health Sciences, University of Catanzaro "Magna Græcia", CISVetSUA, 88100 Catanzaro, Italy
| | - H W Ploeger
- Department of Infectious Diseases and Immunology, Clinical Infectiology Division, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - C Chartier
- INRAE, Oniris, BIOEPAR, 44307, Nantes, France
| | - H Rose Vineer
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Neston, Cheshire, CH64 7TE, UK
| | - B Hinney
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Wien, Austria
| | - G von Samson-Himmelstjerna
- Freie Universität Berlin, Institute for Parasitology and Tropical Veterinary Medicine, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | - B Băcescu
- Faculty of Veterinary Medicine, Spiru Haret University, Blv. Basarabia 256, Bucharest, Romania
| | - M Mickiewicz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-786 Warsaw, Poland
| | - T L Mateus
- CISAS - Center for Research and Development in Agrifood Systems and Sustainability, Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial Nun'Álvares, 4900-347 Viana do Castelo, Portugal; EpiUnit - Instituto de Saúde Pública da Universidade do Porto, Rua das Taipas, 135, 4050-091 Porto, Portugal
| | - M Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, 24236 Grulleros, León, Spain
| | - S Quealy
- VirtualVet, Grenan Upper, Kilmacthomas, Co., Waterford, Ireland
| | - H Azaizeh
- Institute of Applied Research, University of Haifa, The Galilee Society P.O. Box 437, Shefa-Amr 20200, Israel; Tel Hai College, Department of Environmental Sciences, Upper Galilee 12210, Israel
| | - B Sekovska
- Faculty of Veterinary Medicine, University St. Cyril and Methodius, Skopje, North Macedonia
| | - H Akkari
- Laboratory of Parasitology, University of Manouba, National School of Veterinary Medicine of Sidi Thabet, 2020 Sidi Thabet, Tunisia
| | - S Petkevicius
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine, Veterinary Academy, Lithuanian University of Health Sciences, Tilžės 18, LT-47181 Kaunas, Lithuania
| | - L Hektoen
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 369 Sentrum, 0102 Oslo, Norway
| | - J Höglund
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, SE-750 07 Uppsala, Sweden
| | - E R Morgan
- Institute for Global Food Security, Queen's University Belfast, 19, Chlorine Gardens, Belfast, BT9 5DL, UK
| | - D J Bartley
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK
| | - E Claerebout
- Ghent University, Faculty of Veterinary Medicine, Laboratory of Parasitology, Salisburylaan 133, 9820 Merelbeke, Belgium
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Tarbiat B, Jansson DS, Wall H, Tydén E, Höglund J. Effect of a targeted treatment strategy against Ascaridia galli on egg production, egg quality and bird health in a laying hen farm. Vet Parasitol 2020; 286:109238. [PMID: 32949864 DOI: 10.1016/j.vetpar.2020.109238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
Worm control is an important aspect of the successful management of the egg production industry. Of particular concern is Ascaridia galli, which at high parasite loads affect health and production in layers. Application of a targeted treatment strategy (TT) to control A. galli has shown promise. The purpose of this study was to explore the effect of such a strategy on welfare indicators and production performance of layers. Six flocks (F1-6) on a commercial farm were allocated to three treatment groups. Flocks F1 and F4 were treated (TT) with fenbendazole at 22, 27 and 36 weeks post-placement (WPP). Flocks F2 and F5 were treated at 27 WPP (conventional treatment, CT) and hens in flocks F3 and F6 served as untreated (UT) control groups. At 19, 35 and 45 WPP twenty-five hens plus thirty eggs per flock were randomly selected. Hens were weighed and their plumage conditions (PC) were assessed. The eggs were subjected to various external and interior quality analyses. Production data such as number of eggs/hen/week, egg mass and feed conversion ratio (FCR) were calculated from raw data obtained from all flocks on a weekly basis. The number of eggs/hen/week, egg mass and FCR were higher (P < 0.05) in the TT flocks and hens had better PC both at 35 and 45 WPP compared with other flocks. No differences in body weight and physical egg quality were observed between groups except for egg shell strength which was higher (P < 0.05) in the CT flocks. These data suggest that better production performance and plumage, which suggests improved health, can be achieved through the application of a TT strategy. The insights gained from this research should help to justify the extra cost and labor associated with the TT strategy.
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Affiliation(s)
- B Tarbiat
- Swedish University of Agricultural Sciences (SLU), Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036 SE-750 07, Uppsala, Sweden.
| | - D S Jansson
- National Veterinary Institute (SVA), Department of Animal Health and Antimicrobial Strategies, SE-751 89 Uppsala, Sweden; Swedish University of Agricultural Sciences (SLU), Department of Clinical Sciences, Box 7054, SE-750 07, Uppsala, Sweden
| | - H Wall
- Swedish University of Agricultural Sciences (SLU), Department of Animal Nutrition and Management, P.O. Box 7024, SE -750 07, Uppsala, Sweden
| | - E Tydén
- Swedish University of Agricultural Sciences (SLU), Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036 SE-750 07, Uppsala, Sweden
| | - J Höglund
- Swedish University of Agricultural Sciences (SLU), Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036 SE-750 07, Uppsala, Sweden
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21
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Meurling S, Kärvemo S, Chondrelli N, Cortazar Chinarro M, Åhlen D, Brookes L, Nyström P, Stenberg M, Garner TWJ, Höglund J, Laurila A. Occurrence of Batrachochytrium dendrobatidis in Sweden: higher infection prevalence in southern species. Dis Aquat Organ 2020; 140:209-218. [PMID: 32880378 DOI: 10.3354/dao03502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The chytrid fungus Batrachochytrium dendrobatidis (Bd) has caused worldwide declines in amphibian populations. While Bd is widespread in southern and central Europe, its occurrence and distribution in northernmost Europe is mostly unknown. We surveyed for Bd in breeding anurans in Sweden by sampling 1917 amphibians from 101 localities and 3 regions in Sweden (southern, northern and central). We found that Bd was widespread in southern and central Sweden, occurring in all 9 investigated species and in 45.5% of the 101 localities with an overall prevalence of 13.8%. No infected individuals were found in the 4 northern sites sampled. The records from central Sweden represent the northernmost records of Bd in Europe. While the proportion of sites positive for Bd was similar between the southern and central regions, prevalence was much higher in the southern region. This was because southern species with a distribution mainly restricted to southernmost Sweden had a higher prevalence than widespread generalist species. The nationally red-listed green toad Bufotes variabilis and the fire-bellied toad Bombina bombina had the highest prevalence (61.4 and 48.9%, respectively). Across species, Bd prevalence was strongly positively, correlated with water temperature at the start of egg laying. However, no individuals showing visual signs of chytridiomycosis were found in the field. These results indicate that Bd is widespread and common in southern and central Sweden with southern species, breeding in higher temperatures and with longer breeding periods, having higher prevalence. However, the impact of Bd on amphibian populations in northernmost Europe remains unknown.
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Affiliation(s)
- Sara Meurling
- Animal Ecology/ Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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22
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Song K, Gao B, Halvarsson P, Fang Y, Jiang YX, Sun YH, Höglund J. Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi. BMC Genomics 2020; 21:581. [PMID: 32847513 PMCID: PMC7450560 DOI: 10.1186/s12864-020-06957-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 07/27/2020] [Indexed: 11/20/2022] Open
Abstract
Background The Quaternary had worldwide consequences in forming the contemporary diversity of many populations, species and communities, which is characterized by marked climatic oscillations between glacial and interglacial periods. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouse Tetrastes sewerzowi is a forest-dwelling species endemic to the mountains to the east of the Qinghai–Tibet Plateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. It is important to place current population status into a broader ecological and evolutionary context to understand their demographic history. Results Analyses of the Chinese Grouse genome revealed fluctuations throughout the Pleistocene in effective population size. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene which was then followed by a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that a suitable habitat shift between high altitude regions to low altitude regions was due to a changing climate. This result parallels patterns of population size change in Chinese Grouse estimated from PSMC modelling, which suggested an expansion in population size from the last interglacial period (LIG) and then a peak and a bottleneck occurring at the last glacial maximum (LGM). Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and fragmented. It will likely become even more fragmented in the future since coniferous forest cover is threatened in the region of their distribution and the availability of such habitat restricts their ecological niche. Conclusions The Chinese Grouse have experienced substantial population size changes from the beginning to the LIG and reached a peak before the LGM. A sharp decrease and bottleneck occurred during the LGM, when the coniferous forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support historical population fluctuations. The distribution of the Chinese Grouse is strongly dependent on the coniferous forest cover. To protect the fragmented coniferous forests is an essential action to protect the Chinese Grouse.
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Affiliation(s)
- Kai Song
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden. .,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Peter Halvarsson
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.,Unit of Parasitology, Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 75007, Uppsala, Sweden
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Ying-Xin Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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23
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Charlier J, Rinaldi L, Musella V, Ploeger HW, Chartier C, Vineer HR, Hinney B, von Samson-Himmelstjerna G, Băcescu B, Mickiewicz M, Mateus TL, Martinez-Valladares M, Quealy S, Azaizeh H, Sekovska B, Akkari H, Petkevicius S, Hektoen L, Höglund J, Morgan ER, Bartley DJ, Claerebout E. Initial assessment of the economic burden of major parasitic helminth infections to the ruminant livestock industry in Europe. Prev Vet Med 2020; 182:105103. [PMID: 32750638 DOI: 10.1016/j.prevetmed.2020.105103] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/29/2020] [Accepted: 07/23/2020] [Indexed: 01/16/2023]
Abstract
We report a European wide assessment of the economic burden of gastrointestinal nematodes, Fasciola hepatica (common liver fluke) and Dictyocaulus viviparus (bovine lungworm) infections to the ruminant livestock industry. The economic impact of these parasitic helminth infections was estimated by a deterministic spreadsheet model as a function of the proportion of the ruminant population exposed to grazing, the infection frequency and intensity, the effect of the infection on animal productivity and mortality and anthelmintic treatment costs. In addition, we estimated the costs of anthelmintic resistant nematode infections and collected information on public research budgets addressing helminth infections in ruminant livestock. The epidemiologic and economic input data were collected from international databases and via expert opinion of the Working Group members of the European Co-operation in Science and Technology (COST) action COMbatting Anthelmintic Resistance in ruminants (COMBAR). In order to reflect the effects of uncertainty in the input data, low and high cost estimates were obtained by varying uncertain input data arbitrarily in both directions by 20 %. The combined annual cost [low estimate-high estimate] of the three helminth infections in 18 participating countries was estimated at € 1.8 billion [€ 1.0-2.7 billion]. Eighty-one percent of this cost was due to lost production and 19 % was attributed to treatment costs. The cost of gastrointestinal nematode infections with resistance against macrocyclic lactones was estimated to be € 38 million [€ 11-87 million] annually. The annual estimated costs of helminth infections per sector were € 941 million [€ 488 - 1442 million] in dairy cattle, € 423 million [€ 205-663 million] in beef cattle, € 151million [€ 90-213 million] in dairy sheep, € 206 million [€ 132-248 million] in meat sheep and € 86 million [€ 67-107 million] in dairy goats. Important data gaps were present in all phases of the calculations which lead to large uncertainties around the estimates. Accessibility of more granular animal population datasets at EU level, deeper knowledge of the effects of infection on production, levels of infection and livestock grazing exposure across Europe would make the largest contribution to improved burden assessments. The known current public investment in research on helminth control was 0.15 % of the estimated annual costs for the considered parasitic diseases. Our data suggest that the costs of enzootic helminth infections which usually occur at high prevalence annually in ruminants, are similar or higher than reported costs of epizootic diseases. Our data can support decision making in research and policy to mitigate the negative impacts of helminth infections and anthelmintic resistance in Europe, and provide a baseline against which to measure future changes.
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Affiliation(s)
- J Charlier
- Kreavet, H. Mertensstraat 17, 9150, Kruibeke, Belgium.
| | - L Rinaldi
- Department of Veterinary Medicine and Animal Production, CREMOPAR, University of Naples Federico II, 80137, Napoli, Italy
| | - V Musella
- Department of Health Sciences, University of Catanzaro "Magna Græcia", CISVetSUA, 88100, Catanzaro, Italy
| | - H W Ploeger
- Department of Infectious Diseases and Immunology, Clinical Infectiology Division, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, the Netherlands
| | - C Chartier
- INRAE, Oniris, BIOEPAR, 44307, Nantes, France
| | - H Rose Vineer
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Neston, Cheshire, CH64 7TE, UK
| | - B Hinney
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Wien, Austria
| | - G von Samson-Himmelstjerna
- Freie Universität Berlin, Institute for Parasitology and Tropical Veterinary Medicine, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - B Băcescu
- Faculty of Veterinary Medicine, Spiru Haret University, Blv. Basarabia 256, Bucharest, Romania
| | - M Mickiewicz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-786, Warsaw, Poland
| | - T L Mateus
- CISAS - Center for Research and Development in Agrifood Systems and Sustainability, Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial Nun'Álvares, 4900-347, Viana do Castelo, Portugal; EpiUnit - Instituto de Saúde Pública da Universidade do Porto, Rua das Taipas, 135, 4050-091, Porto, Portugal
| | - M Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal. 24236, Grulleros, León, Spain
| | - S Quealy
- VirtualVet, Grenan Upper, Kilmacthomas, Co. Waterford, Ireland
| | - H Azaizeh
- Institute of Applied Research, University of Haifa, The Galilee Society, Israel & Tel Hai College, Department of Environmental Sciences, Upper Galilee 12210, P.O. Box 437, Shefa-Amr, 20200, Israel
| | - B Sekovska
- Faculty of Veterinary Medicine, University St. Cyril and Methodius, Skopje, Macedonia
| | - H Akkari
- Laboratory of Parasitology, University of Manouba, National School of Veterinary Medicine of Sidi Thabet, 2020, Sidi Thabet, Tunisia
| | - S Petkevicius
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine, Veterinary Academy, Lithuanian University of Health Sciences, Tilžės 18, LT-47181, Kaunas, Lithuania
| | - L Hektoen
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O.Box 369 Sentrum, 0102, Oslo, Norway
| | - J Höglund
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, SE-750 07, Uppsala, Sweden
| | - E R Morgan
- Institute for Global Food Security, Queen's University Belfast, 19, Chlorine Gardens, Belfast, BT9 5DL, UK
| | - D J Bartley
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK
| | - E Claerebout
- Ghent University, Faculty of Veterinary Medicine, Laboratory of Parasitology, Salisburylaan 133, 9820, Merelbeke, Belgium
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Johansson F, Berger D, Höglund J, Meyer-Lucht Y, Rödin-Mörch P, Sniegula S, Watts PC. High variation in last male sperm precedence and genital morphology in the emerald damselfly, Lestes sponsa. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
In organisms in which individuals mate multiply, knowledge of the proportion of offspring sired by the last male to mate (P2) under field conditions is important for a thorough understanding of how sexual selection works in nature. In many insect groups, pronounced intraspecific variation in P2 is commonplace. Interestingly, however, in stark contrast to these observations, compilation of P2 data in dragonflies and damselflies (Odonata) indicates that a high P2, seldom below 0.95, is a feature of this taxon. Here we used double digest restriction-site associated DNA sequencing to generate a panel of single nucleotide polymorphisms (SNPs) with which we could determine paternity and estimate values of P2 in the offspring of 19 field-collected pairs of the emerald damselfly Lestes sponsa. We also estimated the relationship between P2 and male genital shape of 16 males using geometric morphometric analysis. P2 was variable (range = 0.0–1.0; mean = 0.5), and there was a marginally non-significant (P = 0.069) relationship between genital shape and P2, suggesting that males with a high P2 had an aedeagus with a broader tip. We suggest that the high P2-values reported in past studies in Odonata are partly due to the methods used to infer paternity. Use of SNPs to determine patterns of paternity and P2 in odonates is needed for a better appraisal of fitness in odonates, and would open many future avenues for use of odonates as models of sexual selection.
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Affiliation(s)
- Frank Johansson
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - David Berger
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Yvonne Meyer-Lucht
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Patrik Rödin-Mörch
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Szymon Sniegula
- Department of Ecosystem Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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25
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Song K, Halvarsson P, Fang Y, Barnaby J, Germogenov N, Sun Y, Höglund J. Genetic differentiation in Sichuan jay (Perisoreus internigrans) and its sibling species Siberian jay (P. infaustus). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01252-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractThe Pleistocene ice age and recent forest fragmentation have both played a significant role in shaping the population genetic variation of boreal coniferous species in the Qinghai-Tibet Plateau (QTP) and Eurasian coniferous forests. The Sichuan jay is one of the least know endemic bird species in QTP coniferous forests in western China while its sibling species, the Siberian Jay, is widespread within the coniferous forests in northern Eurasia. Here we used 11 microsatellite markers to assay genetic diversity across 58 Sichuan jay samples from China and 205 Siberian jay samples from Sweden and Russia. Results showed three distinct genetic clusters from the Sichuan jay sampling. Furthermore, the pair-wise FST values indicated high genetic differentiation not only among the two species but also between Swedish and Russian Siberian jay populations. What is more, a pattern of isolation by distance was found among the analyzed populations. Our study suggests that targeted habitat restoration in fragmented forests and more genetic work is urgently needed for conservation of the Sichuan jay.
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Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, Richter-Boix A, Laurila A, Höglund J. Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans. BMC Genet 2020; 21:38. [PMID: 32228443 PMCID: PMC7106915 DOI: 10.1186/s12863-020-00839-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. RESULTS We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. CONCLUSION Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.,Centre for Paleogenetics Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Tom Van der Valk
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Alex Richter-Boix
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
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Kärvemo S, Wikström G, Widenfalk L, Höglund J, Laurila A. Chytrid fungus dynamics and infections associated with movement distances in a red‐listed amphibian. J Zool (1987) 2020. [DOI: 10.1111/jzo.12773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- S. Kärvemo
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
- Department of Ecology and Genetics/Animal Ecology Uppsala University Uppsala Sweden
| | - G. Wikström
- Department of Ecology and Genetics/Animal Ecology Uppsala University Uppsala Sweden
| | - L.A. Widenfalk
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
- Greensway AB Uppsala Sweden
| | - J. Höglund
- Department of Ecology and Genetics/Animal Ecology Uppsala University Uppsala Sweden
| | - A. Laurila
- Department of Ecology and Genetics/Animal Ecology Uppsala University Uppsala Sweden
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Liu Y, Liu S, Zhang N, Chen D, Que P, Liu N, Höglund J, Zhang Z, Wang B. Genome Assembly of the Common Pheasant Phasianus colchicus: A Model for Speciation and Ecological Genomics. Genome Biol Evol 2019; 11:3326-3331. [PMID: 31713630 PMCID: PMC7145668 DOI: 10.1093/gbe/evz249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2019] [Indexed: 12/04/2022] Open
Abstract
The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Biocontrol, College of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, College of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nan Zhang
- State Key Laboratory of Biocontrol, College of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - De Chen
- MOE Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
| | - Pinjia Que
- MOE Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
| | - Naijia Liu
- College of Life Sciences and Oceanography, Shenzhen University, China
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
| | - Biao Wang
- School of Biosciences, University of Melbourne, Parkville, Victoria, Australia
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29
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Lindsay WR, Andersson S, Bererhi B, Höglund J, Johnsen A, Kvarnemo C, Leder EH, Lifjeld JT, Ninnes CE, Olsson M, Parker GA, Pizzari T, Qvarnström A, Safran RJ, Svensson O, Edwards SV. Endless forms of sexual selection. PeerJ 2019; 7:e7988. [PMID: 31720113 PMCID: PMC6839514 DOI: 10.7717/peerj.7988] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/04/2019] [Indexed: 12/11/2022] Open
Abstract
In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a “stock-taking” workshop on sexual selection and sexual conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the ‘aesthetic sense’ proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate ‘null model’ of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.
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Affiliation(s)
- Willow R Lindsay
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Badreddine Bererhi
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Arild Johnsen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Charlotta Kvarnemo
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Erica H Leder
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Jan T Lifjeld
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Calum E Ninnes
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Mats Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Geoff A Parker
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Tommaso Pizzari
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States of America
| | - Ola Svensson
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology, Göteborg, Sweden
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30
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Rödin‐Mörch P, Luquet E, Meyer‐Lucht Y, Richter‐Boix A, Höglund J, Laurila A. Latitudinal divergence in a widespread amphibian: Contrasting patterns of neutral and adaptive genomic variation. Mol Ecol 2019; 28:2996-3011. [DOI: 10.1111/mec.15132] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/17/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Patrik Rödin‐Mörch
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Emilien Luquet
- CNRS, ENTPE, UMR5023 LEHNA Univ Lyon, Université Claude Bernard Lyon 1 Villeurbanne France
| | - Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Alex Richter‐Boix
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
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31
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Liu A, Su G, Höglund J, Zhang Z, Thomasen J, Christiansen I, Wang Y, Kargo M. Genotype by environment interaction for female fertility traits under conventional and organic production systems in Danish Holsteins. J Dairy Sci 2019; 102:8134-8147. [PMID: 31229284 DOI: 10.3168/jds.2018-15482] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/26/2019] [Indexed: 01/07/2023]
Abstract
Conventional and organic production systems mainly differ in feeding strategies, outdoor and pasture access, and the use of antibiotic treatments. These environmental differences could lead to a genotype by environment interaction (G × E) and a requirement for including G × E in breeding decisions. The objectives of this study were to estimate variance components and heritabilities for conventional and organic production systems and investigate G × E under these 2 production systems for female fertility traits in Danish Holsteins. The analyzed traits included the interval from calving to first insemination (ICF), the interval from first to last insemination, number of inseminations per conception (NINS), and non-return rate within 56 d after the first insemination. Records of female fertility in heifers and the first 3 lactations in cows as well as grass ratio of feed at herd level were collected during the period from 2011 to 2016. The performances of a trait in heifers and cows (lactation 1 to 3) were considered as different traits. The (co)variance components and the resulting heritabilities and genetic correlations were estimated using 2 models. One was a bivariate model treating performances of a trait under organic and conventional production systems as 2 different traits using a reduced data set, and the other was a reaction norm model with random regression on the production system and the grass ratio of feed using a full data set. The full data set comprised records of 37,836 females from 112 organic herds and 513,599 females from 1,224 conventional herds, whereas the reduced data set comprised records from all these 112 organic herds and 92,696 females from 185 convention herds extracted from the full data set with grass ratio of feed lower than 0.20. All female fertility performances of the organic production system were superior to those of the conventional production system. Besides, heterogeneities in additive genetic variances and heritabilities were observed between conventional and organic production systems for all traits. Furthermore, genetic correlations between these 2 production systems ranged from 0.607 to 1.000 estimated from bivariate models and from 0.848 to 0.999 estimated from reaction norm models. Statistically significant G × E were observed for NINS in heifers, non-return rate within 56 d after the first insemination in heifers, and ICF from the bivariate model, and for ICF and NINS in cows from the reaction norm model.
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Affiliation(s)
- A Liu
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
| | - G Su
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - J Höglund
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Z Zhang
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark; School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - J Thomasen
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark; VikingGenetics, Ebeltoftvej 16, 8960, Assentoft, Denmark
| | - I Christiansen
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark; Organic Denmark, Silkeborgvej 260, 8230, Aarhus, Denmark
| | - Y Wang
- College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - M Kargo
- Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark; SEGES, Agro Food Park 15, 8200, Aarhus, Denmark
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32
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Meyer‐Lucht Y, Luquet E, Jóhannesdóttir F, Rödin‐Mörch P, Quintela M, Richter‐Boix A, Höglund J, Laurila A. Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor
C/EBP‐1. Mol Ecol 2019; 28:2786-2801. [DOI: 10.1111/mec.15123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Emilien Luquet
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 Villeurbanne France
| | - Fríða Jóhannesdóttir
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Patrik Rödin‐Mörch
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - María Quintela
- Department of Population Genetics Institute of Marine Research Bergen Norway
| | - Alex Richter‐Boix
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
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Kärvemo S, Laurila A, Höglund J. Urban environment and reservoir host species are associated with Batrachochytrium dendrobatidis infection prevalence in the common toad. Dis Aquat Organ 2019; 134:33-42. [PMID: 32132271 DOI: 10.3354/dao03359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Human-induced changes of the environment, including landscape alteration and habitat loss, may affect wildlife disease dynamics and have important ramifications for wildlife conservation. Amphibians are among the vertebrate taxa most threatened by anthropogenic habitat change. The emerging fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused extinctions and population declines in hundreds of anuran species globally. We studied how the urban landscape is associated with the prevalence of Bd infections by sampling 655 anurans of 3 species (mainly the common toad Bufo bufo) in 42 ponds surrounded by different amounts of urban habitat (defined as towns, cities or villages). We also examined the association between Bd infections and a potential reservoir host species (the moor frog Rana arvalis). We found that 38% of the sites were positive for Bd with an infection prevalence of 4.4%. The extent of urban landscape was negatively correlated with Bd infection prevalence. However, the positive association of Bd with the presence of the possible reservoir species was substantially stronger than the urban effects. The body condition index of B. bufo was negatively associated with Bd infection. This Bd effect was stronger than the negative effect of urban landscape on body condition. Our results suggest that urban environments in Sweden have a negative impact on Bd infections, while the presence of the reservoir species has a positive impact on Bd prevalence. Our study also highlights the potential importance of Bd infection on host fitness, especially in rural landscapes.
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Affiliation(s)
- Simon Kärvemo
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, 75236 Uppsala, Sweden
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Luquet E, Rödin Mörch P, Cortázar‐Chinarro M, Meyer‐Lucht Y, Höglund J, Laurila A. Post‐glacial colonization routes coincide with a life‐history breakpoint along a latitudinal gradient. J Evol Biol 2019; 32:356-368. [DOI: 10.1111/jeb.13419] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Emilien Luquet
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA Villeurbanne France
| | - Patrik Rödin Mörch
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Maria Cortázar‐Chinarro
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
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Abstract
Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region.
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Affiliation(s)
- Radoslav Kozma
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Patrik Rödin-Mörch
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden.
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36
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Kärvemo S, Meurling S, Berger D, Höglund J, Laurila A. Effects of host species and environmental factors on the prevalence of Batrachochytrium dendrobatidis in northern Europe. PLoS One 2018; 13:e0199852. [PMID: 30359384 PMCID: PMC6201871 DOI: 10.1371/journal.pone.0199852] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/09/2018] [Indexed: 11/18/2022] Open
Abstract
The fungal pathogen Batrachochytrium dendrobatidis (Bd) poses a major threat to amphibian populations. To assist efforts to address such threats, we examined differences in Bd host infection prevalence among amphibian species and its relations to both local environmental factors in breeding habitats and landscape variables measured at three scales (500, 2000 and 5000 m radii) around breeding sites in southernmost Sweden. We sampled 947 anurans of six species in 31 ponds and assessed their infection status. We then examined correlations of infection prevalence with canopy cover, pond perimeter and pH (treated as local-scale pond characteristics), and the number of ponds, area of arable land, area of mature forest, number of resident people and presence of sea within the three radii (treated as landscape variables). The Bd infection prevalence was very low, 0.5–1.0%, in two of the six anuran species (Bufo bufo and Rana temporaria), and substantially higher (13–64%) in the other four (Bombina bombina, Bufotes variabilis, Epidalea calamita, Rana arvalis). In the latter four species Bd infection prevalence was positively associated with ponds’ pH (site range: 5.3–8.1), and negatively associated with areas of mature forest and/or wetlands in the surroundings. Our results show that the infection dynamics of Bd are complex and associated with host species, local pond characteristics and several landscape variables at larger spatial scales. Knowledge of environmental factors associated with Bd infections and differences in species’ susceptibility may help to counter further spread of the disease and guide conservation action plans, especially for the most threatened species.
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Affiliation(s)
- Simon Kärvemo
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Sara Meurling
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden
| | - David Berger
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Anssi Laurila
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden
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Kozma R, Lillie M, Benito BM, Svenning J, Höglund J. Past and potential future population dynamics of three grouse species using ecological and whole genome coalescent modeling. Ecol Evol 2018; 8:6671-6681. [PMID: 30038766 PMCID: PMC6053575 DOI: 10.1002/ece3.4163] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/05/2018] [Accepted: 04/12/2018] [Indexed: 12/30/2022] Open
Abstract
Studying demographic history of species provides insight into how the past has shaped the current levels of overall biodiversity and genetic composition of species, but also how these species may react to future perturbations. Here we investigated the demographic history of the willow grouse (Lagopus lagopus), rock ptarmigan (Lagopus muta), and black grouse (Tetrao tetrix) through the Late Pleistocene using two complementary methods and whole genome data. Species distribution modeling (SDM) allowed us to estimate the total range size during the Last Interglacial (LIG) and Last Glacial Maximum (LGM) as well as to indicate potential population subdivisions. Pairwise Sequentially Markovian Coalescent (PSMC) allowed us to assess fluctuations in effective population size across the same period. Additionally, we used SDM to forecast the effect of future climate change on the three species over the next 50 years. We found that SDM predicts the largest range size for the cold-adapted willow grouse and rock ptarmigan during the LGM. PSMC captured intraspecific population dynamics within the last glacial period, such that the willow grouse and rock ptarmigan showed multiple bottlenecks signifying recolonization events following the termination of the LGM. We also see signals of population subdivision during the last glacial period in the black grouse, but more data are needed to strengthen this hypothesis. All three species are likely to experience range contractions under future warming, with the strongest effect on willow grouse and rock ptarmigan due to their limited potential for northward expansion. Overall, by combining these two modeling approaches, we have provided a multifaceted examination of the biogeography of these species and how they have responded to climate change in the past. These results help us understand how cold-adapted species may respond to future climate changes.
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Affiliation(s)
- Radoslav Kozma
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Mette Lillie
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden
| | - Blas M. Benito
- Department of BioscienceSection for Ecoinformatics and BiodiversityUniversity of AarhusAarhus CDenmark
| | - Jens‐Christian Svenning
- Department of BioscienceSection for Ecoinformatics and BiodiversityUniversity of AarhusAarhus CDenmark
| | - Jacob Höglund
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
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38
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Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, Bataille A, Berger L, Böll S, Bosch J, Clare FC, A Courtois E, Crottini A, Cunningham AA, Doherty-Bone TM, Gebresenbet F, Gower DJ, Höglund J, James TY, Jenkinson TS, Kosch TA, Lambertini C, Laurila A, Lin CF, Loyau A, Martel A, Meurling S, Miaud C, Minting P, Ndriantsoa S, O'Hanlon SJ, Pasmans F, Rakotonanahary T, Rabemananjara FCE, Ribeiro LP, Schmeller DS, Schmidt BR, Skerratt L, Smith F, Soto-Azat C, Tessa G, Toledo LF, Valenzuela-Sánchez A, Verster R, Vörös J, Waldman B, Webb RJ, Weldon C, Wombwell E, Zamudio KR, Longcore JE, Garner TWJ. Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi. Sci Rep 2018; 8:7772. [PMID: 29773857 PMCID: PMC5958081 DOI: 10.1038/s41598-018-24472-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/23/2018] [Indexed: 11/09/2022] Open
Abstract
Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.
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Affiliation(s)
- Matthew C Fisher
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.
| | - Pria Ghosh
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.,Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
| | - Jennifer M G Shelton
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Kieran Bates
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Lola Brookes
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK
| | - Claudia Wierzbicki
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Gonçalo M Rosa
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK.,Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Rhys A Farrer
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - David M Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.,Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridgeshire, UK
| | - Mario Alvarado-Rybak
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | - Arnaud Bataille
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.,CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Lee Berger
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Susanne Böll
- Agency for Population Ecology and Nature Conservancy, Gerbrunn, Germany
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC c/Jose Gutierrez Abascal 2, 28006, Madrid, Spain
| | - Frances C Clare
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Elodie A Courtois
- Laboratoire Ecologie, évolution, interactions des systèmes amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, 97300, Cayenne, French Guiana
| | - Angelica Crottini
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, 4485-661, Vairão, Portugal
| | | | | | - Fikirte Gebresenbet
- Department of Integrative Biology, Oklahoma State University, 113 Life Sciences West, Stillwater, OK, 74078, USA
| | - David J Gower
- Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Jacob Höglund
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Thomas S Jenkinson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tiffany A Kosch
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.,One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Carolina Lambertini
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Anssi Laurila
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Chun-Fu Lin
- Zoology Division, Endemic Species Research Institute, 1 Ming-shen East Road, Jiji, Nantou, 552, Taiwan
| | - Adeline Loyau
- Helmholtz Centre for Environmental Research - UFZ, Department of Conservation Biology, Permoserstrasse 15, 04318, Leipzig, Germany.,ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Sara Meurling
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Claude Miaud
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Biogéographie et Ecologie des vertébrés, Montpellier, France
| | - Pete Minting
- Amphibian and Reptile Conservation (ARC) Trust, 655A Christchurch Road, Boscombe, Bournemouth, Dorset, BH1 4AP, UK
| | - Serge Ndriantsoa
- Durrell Wildlife Conservation Trust, Madagascar Programme, Antananarivo, Madagascar
| | - Simon J O'Hanlon
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.,Institute of Zoology, Regent's Park, London, NW1 4RY, UK
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | | | - Falitiana C E Rabemananjara
- Durrell Wildlife Conservation Trust, Madagascar Programme, Antananarivo, Madagascar.,IUCN SSC Amphibian Specialist Group-Madagascar, 101, Antananarivo, Madagascar
| | - Luisa P Ribeiro
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Dirk S Schmeller
- Helmholtz Centre for Environmental Research - UFZ, Department of Conservation Biology, Permoserstrasse 15, 04318, Leipzig, Germany.,ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Info Fauna Karch, Université de Neuchâtel, Bellevaux 51, UniMail Bâtiment 6, 2000, Neuchâtel, Switzerland
| | - Lee Skerratt
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Freya Smith
- National Wildlife Management Centre, APHA, Woodchester Park, Gloucestershire, GL10 3UJ, UK
| | - Claudio Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | - Giulia Tessa
- Non-profit Association Zirichiltaggi - Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100, Sassari, Italy
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Andrés Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile.,ONG Ranita de Darwin, Nataniel Cox 152, Santiago, Chile
| | - Ruhan Verster
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
| | - Judit Vörös
- Collection of Amphibians and Reptiles, Department of Zoology, Hungarian Natural History Museum, Budapest, Baross u, 13., 1088, Hungary
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Rebecca J Webb
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Che Weldon
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
| | - Emma Wombwell
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Joyce E Longcore
- School of Biology and Ecology, University of Maine, Orono, Maine, 04469, USA
| | - Trenton W J Garner
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK.,Non-profit Association Zirichiltaggi - Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100, Sassari, Italy.,Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
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39
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O'Hanlon SJ, Rieux A, Farrer RA, Rosa GM, Waldman B, Bataille A, Kosch TA, Murray KA, Brankovics B, Fumagalli M, Martin MD, Wales N, Alvarado-Rybak M, Bates KA, Berger L, Böll S, Brookes L, Clare F, Courtois EA, Cunningham AA, Doherty-Bone TM, Ghosh P, Gower DJ, Hintz WE, Höglund J, Jenkinson TS, Lin CF, Laurila A, Loyau A, Martel A, Meurling S, Miaud C, Minting P, Pasmans F, Schmeller DS, Schmidt BR, Shelton JMG, Skerratt LF, Smith F, Soto-Azat C, Spagnoletti M, Tessa G, Toledo LF, Valenzuela-Sánchez A, Verster R, Vörös J, Webb RJ, Wierzbicki C, Wombwell E, Zamudio KR, Aanensen DM, James TY, Gilbert MTP, Weldon C, Bosch J, Balloux F, Garner TWJ, Fisher MC. Recent Asian origin of chytrid fungi causing global amphibian declines. Science 2018; 360:621-627. [PMID: 29748278 PMCID: PMC6311102 DOI: 10.1126/science.aar1965] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.
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Affiliation(s)
- Simon J O'Hanlon
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK.
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Adrien Rieux
- CIRAD, UMR PVBMT, 97410 St. Pierre, Reunion, France
| | - Rhys A Farrer
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Gonçalo M Rosa
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Arnaud Bataille
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Tiffany A Kosch
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Kris A Murray
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT Utrecht, Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 49, NO-7012 Trondheim, Norway
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mario Alvarado-Rybak
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | - Kieran A Bates
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Lee Berger
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Susanne Böll
- Agency for Population Ecology and Nature Conservancy, Gerbrunn, Germany
| | - Lola Brookes
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Frances Clare
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Elodie A Courtois
- Laboratoire Ecologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, 97300 Cayenne, French Guiana
| | | | | | - Pria Ghosh
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - David J Gower
- Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - William E Hintz
- Biology Department, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Jacob Höglund
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Thomas S Jenkinson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chun-Fu Lin
- Zoology Division, Endemic Species Research Institute, 1 Ming-shen East Road, Jiji, Nantou 552, Taiwan
| | - Anssi Laurila
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Adeline Loyau
- Department of Conservation Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Sara Meurling
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Claude Miaud
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Pete Minting
- Amphibian and Reptile Conservation (ARC) Trust, Boscombe, Bournemouth, Dorset BH1 4AP, UK
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Dirk S Schmeller
- Department of Conservation Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland, and Info Fauna Karch, UniMail-Bâtiment G, Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Jennifer M G Shelton
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Lee F Skerratt
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Freya Smith
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- National Wildlife Management Centre, APHA, Woodchester Park, Gloucestershire GL10 3UJ, UK
| | - Claudio Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | | | - Giulia Tessa
- Non-profit Association Zirichiltaggi-Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100 Sassari, Italy
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Unicamp, Campinas, Brazil
| | - Andrés Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
- ONG Ranita de Darwin, Nataniel Cox 152, Santiago, Chile
| | - Ruhan Verster
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - Judit Vörös
- Collection of Amphibians and Reptiles, Department of Zoology, Hungarian Natural History Museum, Budapest, Baross u. 13., 1088, Hungary
| | - Rebecca J Webb
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Claudia Wierzbicki
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Emma Wombwell
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - David M Aanensen
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridgeshire, UK
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 49, NO-7012 Trondheim, Norway
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ché Weldon
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC c/ Jose Gutierrez Abascal 2, 28006 Madrid, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Trenton W J Garner
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
- Non-profit Association Zirichiltaggi-Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100 Sassari, Italy
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK.
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40
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Tarbiat B, Rahimian S, Jansson D, Halvarsson P, Höglund J. Developmental capacity of Ascaridia galli eggs is preserved after anaerobic storage in faeces. Vet Parasitol 2018; 255:38-42. [DOI: 10.1016/j.vetpar.2018.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 11/27/2022]
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41
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Cortázar-Chinarro M, Meyer-Lucht Y, Laurila A, Höglund J. Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis). Immunogenetics 2018; 70:477-484. [PMID: 29387920 PMCID: PMC6006221 DOI: 10.1007/s00251-017-1051-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022]
Abstract
MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient. Sequences were obtained from 207 individuals and consecutively assigned into two different clusters (northern and southern clusters, respectively) in concordance with a previously described dual post-glacial colonization route. Selection analyses comparing the relative rates of non-synonymous to synonymous substitutions (dN/dS) suggested evidence of different selection patterns in the northern and the southern clusters, with divergent selection prevailing in the south but uniform positive selection predominating in the north. Also, models of codon evolution revealed considerable differences in the strength of selection: The southern cluster appeared to be under strong selection while the northern cluster showed moderate signs of selection. Our results indicate that the MHC alleles in the north diverged from southern MHC alleles as a result of differential selection patterns.
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Affiliation(s)
- M Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
| | - Y Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - A Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - J Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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Charlier J, Thamsborg SM, Bartley DJ, Skuce PJ, Kenyon F, Geurden T, Hoste H, Williams AR, Sotiraki S, Höglund J, Chartier C, Geldhof P, van Dijk J, Rinaldi L, Morgan ER, von Samson-Himmelstjerna G, Vercruysse J, Claerebout E. Mind the gaps in research on the control of gastrointestinal nematodes of farmed ruminants and pigs. Transbound Emerg Dis 2017; 65 Suppl 1:217-234. [PMID: 29124904 DOI: 10.1111/tbed.12707] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Indexed: 12/31/2022]
Abstract
Gastrointestinal (GI) nematode control has an important role to play in increasing livestock production from a limited natural resource base and to improve animal health and welfare. In this synthetic review, we identify key research priorities for GI nematode control in farmed ruminants and pigs, to support the development of roadmaps and strategic research agendas by governments, industry and policymakers. These priorities were derived from the DISCONTOOLS gap analysis for nematodes and follow-up discussions within the recently formed Livestock Helminth Research Alliance (LiHRA). In the face of ongoing spread of anthelmintic resistance (AR), we are increasingly faced with a failure of existing control methods against GI nematodes. Effective vaccines against GI nematodes are generally not available, and anthelmintic treatment will therefore remain a cornerstone for their effective control. At the same time, consumers and producers are increasingly concerned with environmental issues associated with chemical parasite control. To address current challenges in GI nematode control, it is crucial to deepen our insights into diverse aspects of epidemiology, AR, host immune mechanisms and the socio-psychological aspects of nematode control. This will enhance the development, and subsequent uptake, of the new diagnostics, vaccines, pharma-/nutraceuticals, control methods and decision support tools required to respond to the spread of AR and the shifting epidemiology of GI nematodes in response to climatic, land-use and farm husbandry changes. More emphasis needs to be placed on the upfront evaluation of the economic value of these innovations as well as the socio-psychological aspects to prioritize research and facilitate uptake of innovations in practice. Finally, targeted regulatory guidance is needed to create an innovation-supportive environment for industries and to accelerate the access to market of new control tools.
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Affiliation(s)
- J Charlier
- Kreavet, Kruibeke, Belgium.,Avia-GIS, Zoersel, Belgium
| | - S M Thamsborg
- Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg C, Denmark
| | | | - P J Skuce
- Moredun Research Institute, Edinburgh, UK
| | - F Kenyon
- Moredun Research Institute, Edinburgh, UK
| | | | - H Hoste
- UMR IHAP 1225, INRA, ENVT, Université de Toulouse, Toulouse, France
| | - A R Williams
- Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg C, Denmark
| | - S Sotiraki
- VetResInst, HAO-DEMETER, Thessaloniki, Greece
| | - J Höglund
- BVF, Section for Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - P Geldhof
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - J van Dijk
- Institute of Infection and Global Health, University of Liverpool, Neston, Cheshire, UK
| | - L Rinaldi
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Napoli, Italy
| | - E R Morgan
- Institute for Global Food Security, Queen's University Belfast, Belfast, UK.,School of Veterinary Science, University of Bristol, North Somerset, UK
| | | | - J Vercruysse
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - E Claerebout
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Johansson F, Halvarsson P, Mikolajewski DJ, Höglund J. Phylogeography and larval spine length of the dragonfly Leucorhinia dubia in Europe. PLoS One 2017; 12:e0184596. [PMID: 28902918 PMCID: PMC5597221 DOI: 10.1371/journal.pone.0184596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/26/2017] [Indexed: 11/19/2022] Open
Abstract
Presence or absence of predators selects for different kind of morphologies. Hence, we expect variation in traits that protect against predators to vary over geographical areas where predators vary in past and present abundance. Abdominal larval spines in dragonfly larvae provide protection against fish predators. We studied geographical variation in larval spine length of the dragonfly Leucorrhinia dubia across Western Europe using a phylogenetic approach. Larvae were raised in a common garden laboratory experiment in the absence of fish predators. Results show that larvae from northern Europe (Sweden and Finland) had significantly longer larval spines compared to larvae from western and central Europe. A phylogeny based on SNP data suggests that short larval spines is the ancestral stage in the localities sampled in this study, and that long spines have evolved in the Fenno-Scandian clade. The role of predators in shaping the morphological differences among the sampled localities is discussed.
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Affiliation(s)
- Frank Johansson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Peter Halvarsson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | | | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Cortázar-Chinarro M, Lattenkamp EZ, Meyer-Lucht Y, Luquet E, Laurila A, Höglund J. Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian. BMC Evol Biol 2017; 17:189. [PMID: 28806900 PMCID: PMC5557520 DOI: 10.1186/s12862-017-1022-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/26/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. RESULTS Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. CONCLUSION Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
| | - Ella Z Lattenkamp
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Department of Neurogenetics of Vocal Communication, Max Planck Institute of Psycholinguistics, Box 310, 6500, Nijmegen, Netherlands
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Emilien Luquet
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Present address: Université Claude Bernard - Lyon I, CNRS, UMR 5023 - LEHNA, 3-6, rue Raphaël Dubois - Bâtiments Darwin C and Forel, 69622 Villeurbanne Cedex 43, Boulevard du 11 novembre, 1918, Lyon, France
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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Höglund J, Wang B, Saether SA, Blom MPK, Fiske P, Halvarsson P, Horsburgh GJ, Burke T, Kålås JA, Ekblom R. Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media). Mol Ecol 2017; 26:3458-3471. [PMID: 28345264 DOI: 10.1111/mec.14118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/07/2017] [Indexed: 11/30/2022]
Abstract
We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin α-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.
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Affiliation(s)
- Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Biao Wang
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Mozes Pil Kyu Blom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Peder Fiske
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Peter Halvarsson
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - John Atle Kålås
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Robert Ekblom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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Lagerholm VK, Sandoval-Castellanos E, Vaniscotte A, Potapova OR, Tomek T, Bochenski ZM, Shepherd P, Barton N, Van Dyck MC, Miller R, Höglund J, Yoccoz NG, Dalén L, Stewart JR. Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds. Glob Chang Biol 2017; 23:1425-1435. [PMID: 27762483 DOI: 10.1111/gcb.13522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/13/2016] [Indexed: 06/06/2023]
Abstract
Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum.
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Affiliation(s)
- Vendela K Lagerholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Edson Sandoval-Castellanos
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Amélie Vaniscotte
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Teresa Tomek
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Zbigniew M Bochenski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | | | - Nick Barton
- Institute of Archaeology, University of Oxford, Oxford, UK
| | - Marie-Claire Van Dyck
- Institute for the Analysis of Change in Contemporary and Historical Societies, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rebecca Miller
- Service of Prehistory, University of Liège, Liège, Belgium
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Nigel G Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - John R Stewart
- School of Applied Sciences, Bournemouth University, Dorset House, Talbot Campus, Poole, UK
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Johansson F, Halvarsson P, Mikolajewski D, Höglund J. Genetic differentiation in the boreal dragonfly Leucorrhinia dubia in the Palearctic region. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Tarbiat B, Jansson D, Tydén E, Höglund J. Comparison between anthelmintic treatment strategies against Ascaridia galli in commercial laying hens. Vet Parasitol 2016; 226:109-15. [DOI: 10.1016/j.vetpar.2016.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 10/21/2022]
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Kozma R, Melsted P, Magnússon KP, Höglund J. Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences. Mol Ecol 2016; 25:570-80. [PMID: 26607571 DOI: 10.1111/mec.13496] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 01/08/2023]
Abstract
Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (psmc) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne ) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430 kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) - black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying psmc signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne . Our results highlight the usefulness of the psmc approach in investigating species' reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.
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Affiliation(s)
- Radoslav Kozma
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Páll Melsted
- Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, 107, Iceland.,deCODE Genetics/Amgen, Reykjavik, Iceland
| | - Kristinn P Magnússon
- The Icelandic Institute of Natural History, Borgir v. Nordurslod, Akureyri, 600, Iceland.,Department of Natural Resource Sciences, University of Akureyri, Borgir vid Nordurslod, Akureyri, 600, Iceland.,Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, Reykjavik, 101, Iceland
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
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Pavlovska M, Höglund J. Ukrainian Black GrouseTetrao tetrix: Genetic Diversity and Population Structure. Wildlife Biology 2015. [DOI: 10.2981/wlb.00093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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