101
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Liu S, Hansen MM, Jacobsen MW. Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences. Mol Ecol 2016; 25:5187-5202. [PMID: 27569902 DOI: 10.1111/mec.13827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 02/04/2023]
Abstract
We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe, demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions, marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe, this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations.
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Affiliation(s)
- Shenglin Liu
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark.
| | - Magnus W Jacobsen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
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102
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Rahn AK, Krassmann J, Tsobanidis K, MacColl ADC, Bakker TCM. Strong neutral genetic differentiation in a host, but not in its parasite. INFECTION GENETICS AND EVOLUTION 2016; 44:261-271. [PMID: 27421211 DOI: 10.1016/j.meegid.2016.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 11/28/2022]
Abstract
The genetic diversity and population structure of a parasite with a complex life cycle generally depends on the dispersal by its most motile host. Given that high gene flow is assumed to hinder local adaptation, this can impose significant constraints on a parasite's potential to adapt to local environmental conditions, intermediate host populations, and ultimately to host-parasite coevolution. Here, we aimed to examine the population genetic basis for local host-parasite interactions between the eye fluke Diplostomum lineage 6, a digenean trematode with a multi-host life cycle (including a snail, a fish, and a bird) and its second intermediate host, the three-spined stickleback Gasterosteus aculeatus L. We developed the first microsatellite primers for D. lineage 6 and used them together with published stickleback markers to analyse host and parasite population structures in 19 freshwater lakes, which differ in their local environmental characteristics regarding water chemistry and Diplostomum abundance. Our analyses suggest that one parasite population successfully infects a range of genetically differentiated stickleback populations. The lack of neutral genetic differentiation in D. lineage 6, which could be attributed to the motility of the parasite's definitive host as well as its life cycle characteristics, makes local host-parasite co-adaptations seem more likely on a larger geographical scale than among the lakes of our study site. Our study provides a suitable background for future studies in this system and the first microsatellite primers for a widespread fish parasite.
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Affiliation(s)
- Anna K Rahn
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany.
| | - Johannes Krassmann
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
| | - Kostas Tsobanidis
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
| | - Andrew D C MacColl
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Theo C M Bakker
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
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103
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Crisci JL, Dean MD, Ralph P. Adaptation in isolated populations: when does it happen and when can we tell? Mol Ecol 2016; 25:3901-11. [DOI: 10.1111/mec.13729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 05/06/2016] [Accepted: 05/11/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica L. Crisci
- Molecular and Computational Biology Department of Biological Sciences University of Southern California 1050 Childs Way Los Angeles CA 90089 USA
| | - Matthew D. Dean
- Molecular and Computational Biology Department of Biological Sciences University of Southern California 1050 Childs Way Los Angeles CA 90089 USA
| | - Peter Ralph
- Molecular and Computational Biology Department of Biological Sciences University of Southern California 1050 Childs Way Los Angeles CA 90089 USA
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106
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Kautt AF, Machado-Schiaffino G, Torres-Dowdall J, Meyer A. Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats? Ecol Evol 2016; 6:5342-57. [PMID: 27551387 PMCID: PMC4984508 DOI: 10.1002/ece3.2287] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022] Open
Abstract
Understanding how speciation can occur without geographic isolation remains a central objective in evolutionary biology. Generally, some form of disruptive selection and assortative mating are necessary for sympatric speciation to occur. Disruptive selection can arise from intraspecific competition for resources. If this competition leads to the differential use of habitats and variation in relevant traits is genetically determined, then assortative mating can be an automatic consequence (i.e., habitat isolation). In this study, we caught Midas cichlid fish from the limnetic (middle of the lake) and benthic (shore) habitats of Crater Lake Asososca Managua to test whether some of the necessary conditions for sympatric speciation due to intraspecific competition and habitat isolation are given. Lake As. Managua is very small (<900 m in diameter), extremely young (maximally 1245 years of age), and completely isolated. It is inhabited by, probably, only a single endemic species of Midas cichlids, Amphilophus tolteca. We found that fish from the limnetic habitat were more elongated than fish collected from the benthic habitat, as would be predicted from ecomorphological considerations. Stable isotope analyses confirmed that the former also exhibit a more limnetic lifestyle than the latter. Furthermore, split‐brood design experiments in the laboratory suggest that phenotypic plasticity is unlikely to explain much of the observed differences in body elongation that we observed in the field. Yet, neutral markers (microsatellites) did not reveal any genetic clustering in the population. Interestingly, demographic inferences based on RAD‐seq data suggest that the apparent lack of genetic differentiation at neutral markers could simply be due to a lack of time, as intraspecific competition may only have begun a few hundred generations ago.
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Affiliation(s)
- Andreas F Kautt
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | | | - Julian Torres-Dowdall
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
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107
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Swift H, Gómez Daglio L, Dawson M. Three routes to crypsis: Stasis, convergence, and parallelism in the Mastigias species complex (Scyphozoa, Rhizostomeae). Mol Phylogenet Evol 2016; 99:103-115. [DOI: 10.1016/j.ympev.2016.02.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 01/17/2016] [Accepted: 02/17/2016] [Indexed: 01/16/2023]
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108
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Hansson TH, Fischer B, Mazzarella AB, Voje KL, Vøllestad LA. Lateral plate number in low-plated threespine stickleback: a study of plasticity and heritability. Ecol Evol 2016; 6:3154-60. [PMID: 27096076 PMCID: PMC4829041 DOI: 10.1002/ece3.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 11/06/2022] Open
Abstract
In the threespine stickleback Gasterosteus aculeatus model system, phenotypes are often classified into three morphs according to lateral plate number. Morph identity has been shown to be largely genetically determined, but substantial within-morph variation in plate number exists. In this study, we test whether plate number has a plastic component in response to salinity in the low-plated morph using a split-clutch experiment where families were split in two, one half raised in water at 0 and the other at 30 ppt salt. We find a small salinity-induced plastic effect on plate number in an unexpected direction, opposite to what we predicted: Fish raised in freshwater on average have slightly more plates than fish raised in saltwater. Our results confirm that heritability of plate number is high. Additionally, we find that variance in plate number at the family level can be predicted from other family level traits, which might indicate that epistatic interactions play a role in creating the observed pattern of lateral plate number variation.
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Affiliation(s)
- Truls H Hansson
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern N-0316 Oslo Norway
| | - Barbara Fischer
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern N-0316 Oslo Norway; Department of Theoretical Biology University of Vienna Althanstrasse 141090 Vienna Austria; Konrad Lorenz Institute for Evolution and Cognition Research Martinstrasse 12A-3400 Klosterneuburg Austria
| | - Anna B Mazzarella
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern N-0316 Oslo Norway
| | - Kjetil L Voje
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern N-0316 Oslo Norway
| | - Leif Asbjørn Vøllestad
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern N-0316 Oslo Norway
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109
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Marques DA, Lucek K, Meier JI, Mwaiko S, Wagner CE, Excoffier L, Seehausen O. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback. PLoS Genet 2016; 12:e1005887. [PMID: 26925837 PMCID: PMC4771382 DOI: 10.1371/journal.pgen.1005887] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/29/2016] [Indexed: 01/18/2023] Open
Abstract
Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this.
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Affiliation(s)
- David A. Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- * E-mail:
| | - Kay Lucek
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Department of Animal and Plant Science, University of Sheffield, Sheffield, United Kingdom
| | - Joana I. Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Salome Mwaiko
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Catherine E. Wagner
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Biodiversity Institute, University of Wyoming, Wyoming, United States of America
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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