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Lowe WH, Addis BR, Cochrane MM. Outbreeding reduces survival during metamorphosis in a headwater stream salamander. Mol Ecol 2024; 33:e17375. [PMID: 38699973 DOI: 10.1111/mec.17375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.
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Affiliation(s)
- Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brett R Addis
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Madaline M Cochrane
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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2
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Muharromah AF, Carvajal TM, Regilme MAF, Watanabe K. Fine-scale adaptive divergence and population genetic structure of Aedes aegypti in Metropolitan Manila, Philippines. Parasit Vectors 2024; 17:233. [PMID: 38769579 PMCID: PMC11107013 DOI: 10.1186/s13071-024-06300-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND The adaptive divergence of Aedes aegypti populations to heterogeneous environments can be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines. METHODS We used the Pool-Seq double digestion restriction-site association DNA sequencing (ddRAD-Seq) approach to generate a high number of single nucleotide polymorphisms (SNPs), with the aim to determine local adaptation and compare the population structure with 11 microsatellite markers. A total of 217 Ae. aegypti individuals from seven female and seven male populations collected from Metropolitan Manila were used in the assays. RESULTS We detected 65,473 SNPs across the populations, of which 76 were non-neutral SNPs. Of these non-neutral SNPs, the multivariate regression test associated 50 with eight landscape variables (e.g. open space, forest, etc.) and 29 with five climate variables (e.g. air temperature, humidity, etc.) (P-value range 0.005-0.045) in female and male populations separately. Male and female populations exhibited contrasting spatial divergence, with males exhibiting greater divergence than females, most likely reflecting the different dispersal abilities of male and female mosquitoes. In the comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of the neutral SNPs, indicating that the neutral SNPs generated via pool ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales. CONCLUSIONS Overall, our study demonstrates the utility of pool ddRAD-Seq for examining genetic differences in Ae. aegypti populations in areas at fine-spatial scales that could inform vector control programs such as Wolbachia-infected mosquito mass-release programs. This in turn would provide information on mosquito population dispersal patterns and the potential barriers to mosquito movement within and around the release area. In addition, the potential of environmental adaptability observed in Ae. aegypti could help population control efforts.
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Affiliation(s)
- Atikah Fitria Muharromah
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Graduate School of Science and Engineering, Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Thaddeus M Carvajal
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, 2401 Taft Avenue, 1004, Manila, Philippines
| | - Maria Angenica F Regilme
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan.
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3
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Nukazawa K, Chiu MC, Kazama S, Watanabe K. Contrasting adaptive genetic consequences of stream insects under changing climate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162258. [PMID: 36801338 DOI: 10.1016/j.scitotenv.2023.162258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Freshwater biodiversity undergoes degradation due to climate change. Researchers have inferred the effects of climate change on neutral genetic diversity, assuming the fixed spatial distributions of alleles. However, the adaptive genetic evolution of populations that may change the spatial distribution of allele frequencies along environmental gradients (i.e., evolutionary rescue) have largely been overlooked. We developed a modeling approach that projects the comparatively adaptive and neutral genetic diversities of four stream insects, using empirical neutral/ putative adaptive loci, ecological niche models (ENMs), and a distributed hydrological-thermal simulation at a temperate catchment under climate change. The hydrothermal model was used to generate hydraulic and thermal variables (e.g., annual current velocity and water temperature) at the present and the climatic change conditions, projected based on the eight general circulation models and the three representative concentration pathways scenarios for the two future periods (2031-2050, near future; 2081-2100, far future). The hydraulic and thermal variables were used for predictor variables of the ENMs and adaptive genetic modeling based on machine learning approaches. The increases in annual water temperature in the near- (+0.3-0.7 °C) and far-future (+0.4-3.2 °C) were projected. Of the studied species, with different ecologies and habitat ranges, Ephemera japonica (Ephemeroptera) was projected to lose rear-edge habitats (i.e., downstream) but retain the adaptive genetic diversity owing to evolutionary rescue. In contrast, the habitat range of the upstream-dwelling Hydropsyche albicephala (Trichoptera) was found to remarkably decline, resulting in decreases in the watershed genetic diversity. While the other two Trichoptera species expanded their habitat ranges, the genetic structures were homogenized over the watershed and experienced moderate decreases in gamma diversity. The findings emphasize the evolutionary rescue potential, depending on the extent of species-specific local adaptation.
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Affiliation(s)
- Kei Nukazawa
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Gakuen Kibanadai-nishi 1-1, Miyazaki 889-2192, Japan.
| | - Ming-Chih Chiu
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama 790-8577, Japan; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430061, China
| | - So Kazama
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-06, Sendai 980-8579, Japan.
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama 790-8577, Japan.
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4
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Small-scale population divergence is driven by local larval environment in a temperate amphibian. Heredity (Edinb) 2020; 126:279-292. [PMID: 32958927 DOI: 10.1038/s41437-020-00371-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small-scale natural systems even when population sizes are small, and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16,707 ddRAD-seq SNPs, relating levels of differentiation with local environments, as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment, and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape, and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small-scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system, leading to observable population differentiation.
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Chiu M, Li B, Nukazawa K, Resh VH, Carvajal T, Watanabe K. Branching networks can have opposing influences on genetic variation in riverine metapopulations. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Ming‐Chih Chiu
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
- Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Bin Li
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
- Institute of Environment and Ecology Shandong Normal University Jinan China
| | - Kei Nukazawa
- Department of Civil and Environmental Engineering University of Miyazaki Miyazaki Japan
| | - Vincent H. Resh
- Department of Environmental Science, Policy & Management University of California Berkeley CA USA
| | - Thaddeus Carvajal
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES) Ehime University Matsuyama Ehime Japan
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6
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Li B, Yaegashi S, Carvajal TM, Gamboa M, Chiu M, Ren Z, Watanabe K. Machine-learning-based detection of adaptive divergence of the stream mayfly Ephemera strigata populations. Ecol Evol 2020; 10:6677-6687. [PMID: 32724541 PMCID: PMC7381564 DOI: 10.1002/ece3.6398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/21/2020] [Accepted: 04/30/2020] [Indexed: 11/07/2022] Open
Abstract
Adaptive divergence is a key mechanism shaping the genetic variation of natural populations. A central question linking ecology with evolutionary biology is how spatial environmental heterogeneity can lead to adaptive divergence among local populations within a species. In this study, using a genome scan approach to detect candidate loci under selection, we examined adaptive divergence of the stream mayfly Ephemera strigata in the Natori River Basin in northeastern Japan. We applied a new machine-learning method (i.e., random forest) besides traditional distance-based redundancy analysis (dbRDA) to examine relationships between environmental factors and adaptive divergence at non-neutral loci. Spatial autocorrelation analysis based on neutral loci was employed to examine the dispersal ability of this species. We conclude the following: (a) E. strigata show altitudinal adaptive divergence among the populations in the Natori River Basin; (b) random forest showed higher resolution for detecting adaptive divergence than traditional statistical analysis; and (c) separating all markers into neutral and non-neutral loci could provide full insight into parameters such as genetic diversity, local adaptation, and dispersal ability.
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Affiliation(s)
- Bin Li
- Insititute of Environmental and EcologyShandong Normal UniversityJinanChina
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
| | - Sakiko Yaegashi
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
- Department of Civil and Environmental EngineeringUniversity of YamanashiYamanashiJapan
| | | | - Maribet Gamboa
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
| | - Ming‐Chih Chiu
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
| | - Zongming Ren
- Insititute of Environmental and EcologyShandong Normal UniversityJinanChina
| | - Kozo Watanabe
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
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7
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Gamboa M, Watanabe K. Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan. BMC Genomics 2019; 20:84. [PMID: 30678640 PMCID: PMC6346529 DOI: 10.1186/s12864-019-5453-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022] Open
Abstract
Background Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geographic area in Japan and additionally identified putative environmental drivers and their effect on co-existing multiple stonefly species. Double-digest restriction-associated DNA (ddRAD) libraries were independently sequenced for 219 individuals from 23 sites across four geographical regions along a nationwide latitudinal gradient in Japan. Results A total of 4251 candidate single nucleotide polymorphisms (SNPs) strongly associated with local adaptation were discovered using Latent mixed models; of these, 294 SNPs showed strong correlation with environmental variables, specifically precipitation and altitude, using distance-based redundancy analysis. Genome–genome comparison among the seven species revealed a high sequence similarity of candidate SNPs within a geographical region, suggesting the occurrence of a parallel evolution process. Conclusions Our results revealed genomic signatures of local adaptation and their influence on multiple, co-occurring species. These results can be potentially applied for future studies on river management and climatic stressor impacts. Electronic supplementary material The online version of this article (10.1186/s12864-019-5453-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maribet Gamboa
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, 790-0871, Japan.
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, 790-0871, Japan
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8
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Prentice MB, Bowman J, Lalor JL, McKay MM, Thomson LA, Watt CM, McAdam AG, Murray DL, Wilson PJ. Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high-pace adaptation. Ecol Evol 2017; 7:7254-7276. [PMID: 28944015 PMCID: PMC5606889 DOI: 10.1002/ece3.3223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/31/2017] [Accepted: 06/06/2017] [Indexed: 12/14/2022] Open
Abstract
Climate change is predicted to affect the reproductive ecology of wildlife; however, we have yet to understand if and how species can adapt to the rapid pace of change. Clock genes are functional genes likely critical for adaptation to shifting seasonal conditions through shifts in timing cues. Many of these genes contain coding trinucleotide repeats, which offer the potential for higher rates of change than single nucleotide polymorphisms (SNPs) at coding sites, and, thus, may translate to faster rates of adaptation in changing environments. We characterized repeats in 22 clock genes across all annotated mammal species and evaluated the potential for selection on repeat motifs in three clock genes (NR1D1,CLOCK, and PER1) in three congeneric species pairs with different latitudinal range limits: Canada lynx and bobcat (Lynx canadensis and L. rufus), northern and southern flying squirrels (Glaucomys sabrinus and G. volans), and white‐footed and deer mouse (Peromyscus leucopus and P. maniculatus). Signatures of positive selection were found in both the interspecific comparison of Canada lynx and bobcat, and intraspecific analyses in Canada lynx. Northern and southern flying squirrels showed differing frequencies at common CLOCK alleles and a signature of balancing selection. Regional excess homozygosity was found in the deer mouse at PER1 suggesting disruptive selection, and further analyses suggested balancing selection in the white‐footed mouse. These preliminary signatures of selection and the presence of trinucleotide repeats within many clock genes warrant further consideration of the importance of candidate gene motifs for adaptation to climate change.
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Affiliation(s)
- Melanie B Prentice
- Department of Environmental and Life Sciences Trent University Peterborough ON Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Peterborough ON Canada
| | | | - Michelle M McKay
- Department of Environmental and Life Sciences Trent University Peterborough ON Canada
| | | | - Cristen M Watt
- Department of Environmental and Life Sciences Trent University Peterborough ON Canada
| | - Andrew G McAdam
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | | | - Paul J Wilson
- Biology Department Trent University Peterborough ON Canada
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9
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Watanabe K, Monaghan MT. Comparative tests of the species-genetic diversity correlation at neutral and nonneutral loci in four species of stream insect. Evolution 2017; 71:1755-1764. [PMID: 28485820 DOI: 10.1111/evo.13261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 03/29/2017] [Accepted: 04/16/2017] [Indexed: 11/30/2022]
Abstract
A fundamental question linking population genetics and community ecology is how adaptive processes (e.g., natural selection) and neutral processes (e.g., drift-migration equilibrium) underpin the species-genetic diversity correlation (SGDC). Here, we combine genome scans and outlier loci detection with community analysis to separately test for neutral and nonneutral SGDCs in four species of stream insect. We sampled 60 localities in Japan and examined the relationships among population AFLP band richness (Br), taxon richness of the total community (S) and of the trophic guild (Str ), and 15 habitat parameters that could potentially drive adaptation and influence richness. Neutral Br was positively correlated with S only in the dominant species of these communities, suggesting Br may be constrained when intraspecific competition is pronounced. Nonneutral Br was correlated with Str in a species restricted to high elevations where habitat heterogeneity was highest. Community distance and genetic distance (β-SGDC) was correlated in two of the four species at both neutral and nonneutral loci. Distance-based redundancy analysis found geographic isolation and elevation to drive divergence of both communities and populations. This suggests that both neutral and adaptive divergence occurred through the shared influences of geographic isolation and local adaptation at the two levels of diversity.
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Affiliation(s)
- Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
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10
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Prentice MB, Bowman J, Khidas K, Koen EL, Row JR, Murray DL, Wilson PJ. Selection and drift influence genetic differentiation of insular Canada lynx ( Lynx canadensis) on Newfoundland and Cape Breton Island. Ecol Evol 2017; 7:3281-3294. [PMID: 28480025 PMCID: PMC5415520 DOI: 10.1002/ece3.2945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/27/2017] [Accepted: 03/05/2017] [Indexed: 01/16/2023] Open
Abstract
Island populations have long been important for understanding the dynamics and mechanisms of evolution in natural systems. While genetic drift is often strong on islands due to founder events and population bottlenecks, the strength of selection can also be strong enough to counteract the effects of drift. Here, we used several analyses to identify the roles of genetic drift and selection on genetic differentiation and diversity of Canada lynx (Lynx canadensis) across eastern Canada, including the islands of Cape Breton and Newfoundland. Specifically, we assessed whether we could identify a genetic component to the observed morphological differentiation that has been reported across insular and mainland lynx. We used a dinucleotide repeat within the promoter region of a functional gene that has been linked to mammalian body size, insulin-like growth factor-1 (IGF-1). We found high genetic differentiation at neutral molecular markers but convergence of allele frequencies at the IGF-1 locus. Thus, we showed that while genetic drift has influenced the observed genetic structure of lynx at neutral molecular markers, natural selection has also played a role in the observed patterns of genetic diversity at the IGF-1 locus of insular lynx.
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Affiliation(s)
- Melanie B Prentice
- Department of Environmental and Life Sciences Trent University Peterborough ON Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Peterborough ON Canada
| | - Kamal Khidas
- Vertebrate Zoology Canadian Museum of Nature Ottawa ON Canada
| | - Erin L Koen
- Biology Department Trent University Peterborough ON Canada
| | - Jeffrey R Row
- Department of Environment and Resource Studies University of Waterloo Waterloo ON Canada
| | | | - Paul J Wilson
- Biology Department Trent University Peterborough ON Canada
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11
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Boumans L, Hogner S, Brittain J, Johnsen A. Ecological speciation by temporal isolation in a population of the stonefly Leuctra hippopus (Plecoptera, Leuctridae). Ecol Evol 2017; 7:1635-1649. [PMID: 28261472 PMCID: PMC5330929 DOI: 10.1002/ece3.2638] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/19/2016] [Accepted: 11/05/2016] [Indexed: 11/08/2022] Open
Abstract
Stream dwelling invertebrates are ideal candidates for the study of ecological speciation as they are often adapted to particular environmental conditions within a stream and inhabit only certain reaches of a drainage basin, separated by unsuitable habitat. We studied an atypical population of the stonefly Leuctra hippopus at a site in central Norway, the Isterfoss rapids, in relation to three nearby and two remote conspecific populations. Adults of this population emerge about a month earlier than those of nearby populations, live on large boulders emerging from the rapids, and are short-lived. This population also has distinct morphological features and was studied earlier during the period 1975-1990. We reassessed morphological distinctness with new measurements and added several analyses of genetic distinctness based on mitochondrial and nuclear sequence markers, as well as AFLP fingerprinting and SNPs mined from RAD sequences. The Isterfoss population is shown to be most closely related to its geographical neighbors, yet clearly morphologically and genetically distinct and homogeneous. We conclude that this population is in the process of sympatric speciation, with temporal isolation being the most important direct barrier to gene flow. The shift in reproductive season results from the particular temperature and water level regime in the Isterfoss rapids. The distinct adult body shape and loss of flight are hypothesized to be an adaptation to the unusual habitat. Ecological diversification on small spatial and temporal scales is one of the likely causes of the high diversity of aquatic insects.
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Affiliation(s)
- Louis Boumans
- Natural History Museum University of Oslo Oslo Norway
| | - Silje Hogner
- Natural History Museum University of Oslo Oslo Norway
| | - John Brittain
- Natural History Museum University of Oslo Oslo Norway
| | - Arild Johnsen
- Natural History Museum University of Oslo Oslo Norway
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12
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Wei X, Yan G, Zhou G, Zhong D, Fang Q, Yang X, Hu D, Chang X. A neural network prediction of environmental determinants of Anopheles sinensis knockdown resistance mutation to pyrethroids in China. JOURNAL OF VECTOR ECOLOGY : JOURNAL OF THE SOCIETY FOR VECTOR ECOLOGY 2016; 41:295-302. [PMID: 27860007 DOI: 10.1111/jvec.12226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
Selection pressure caused by long-term intensive use of insecticides is the key driving force in resistance development. Additional parameters such as environmental conditions may affect both the mosquito response to insecticides and the selection of resistance mechanisms. In this context, we analyzed the environmental determinants of kdr prevalence in Anopheles sinensis across China. We collected kdr frequency from 48 sites across central and southern China, together with key environmental factors including long-term climatic data, topographic features, main crops, and land cover types. Trend surface analysis found that the distribution of kdr frequency can be partitioned into three regions, namely central China (kdr frequency >80%), western China (kdr frequency varies from 0% to 60%), and southern China (kdr frequency <10%). Seven predictor variables were selected based on a radial basis function neural network model. A multilayer perceptron (MLP) network model revealed that the number of crops in a year was the most important predictor for the kdr mutation rate. Topography, long-term mean climate and land cover all contributed to the kdr mutation rate. The observed mean kdr frequency was 53.0% and the MLP network model-predicted mean was 52.6%, a 0.1% relative error. Predicted kdr frequencies closely matched the observed values. The model explained 92% of the total variance in kdr frequency. The results indicated that kdr was associated with the intensity of pesticide usage. Crop cultivation information, together with environmental factors, may well predict the spatial heterogeneity of kdr mutations in An. sinensis in China.
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Affiliation(s)
- Xing Wei
- Institute of Information Security and Big Data, Central South University, Changsha 410083, Hunan, China
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, California 92697, U.S.A
| | - Guofa Zhou
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, California 92697, U.S.A
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, California 92697, U.S.A
| | - Qiang Fang
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Xiaodi Yang
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Dehua Hu
- Institute of Information Security and Big Data, Central South University, Changsha 410083, Hunan, China
| | - Xuelian Chang
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu 233000, Anhui, China
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13
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Population Genetic Structure of the Endangered Kaiser's Mountain Newt, Neurergus kaiseri (Amphibia: Salamandridae). PLoS One 2016; 11:e0149596. [PMID: 26918642 PMCID: PMC4769016 DOI: 10.1371/journal.pone.0149596] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
Species often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in an endemic and critically endangered stream breeding mountain newt, Neurergus kaiseri, within its entire range in southwestern Iran. We identified two geographic regions based on phylogenetic relationships using Bayesian inference and maximum likelihood of 779 bp mtDNA (D-loop) in 111 individuals from ten of twelve known breeding populations. This analysis revealed a clear divergence between northern populations, located in more humid habitats at higher elevation, and southern populations, from drier habitats at lower elevations regions. From seven haplotypes found in these populations none was shared between the two regions. Analysis of molecular variance (AMOVA) of N. kaiseri indicates that 94.03% of sequence variation is distributed among newt populations and 5.97% within them. Moreover, a high degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.94, P = 0.002). The positive and significant correlation between geographic and genetic distances (r = 0.61, P = 0.002) following controlling for environmental distance suggests an important influence of geographic divergence of the sites in shaping the genetic variation and may provide tools for a possible conservation based prioritization policy for the endangered species.
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