1
|
Angst P, Haag CR, Ben-Ami F, Fields PD, Ebert D. Genome-Wide Allele Frequency Changes Reveal That Dynamic Metapopulations Evolve Differently. Mol Biol Evol 2024; 41:msae128. [PMID: 38935572 PMCID: PMC11229820 DOI: 10.1093/molbev/msae128] [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: 02/14/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024] Open
Abstract
Two important characteristics of metapopulations are extinction-(re)colonization dynamics and gene flow between subpopulations. These processes can cause strong shifts in genome-wide allele frequencies that are generally not observed in "classical" (large, stable, and panmictic) populations. Subpopulations founded by one or a few individuals, the so-called propagule model, are initially expected to show intermediate allele frequencies at polymorphic sites until natural selection and genetic drift drive allele frequencies toward a mutation-selection-drift equilibrium characterized by a negative exponential-like distribution of the site frequency spectrum. We followed changes in site frequency spectrum distribution in a natural metapopulation of the cyclically parthenogenetic pond-dwelling microcrustacean Daphnia magna using biannual pool-seq samples collected over a 5-yr period from 118 ponds occupied by subpopulations of known age. As expected under the propagule model, site frequency spectra in newly founded subpopulations trended toward intermediate allele frequencies and shifted toward right-skewed distributions as the populations aged. Immigration and subsequent hybrid vigor altered this dynamic. We show that the analysis of site frequency spectrum dynamics is a powerful approach to understand evolution in metapopulations. It allowed us to disentangle evolutionary processes occurring in a natural metapopulation, where many subpopulations evolve in parallel. Thereby, stochastic processes like founder and immigration events lead to a pattern of subpopulation divergence, while genetic drift leads to converging site frequency spectrum distributions in the persisting subpopulations. The observed processes are well explained by the propagule model and highlight that metapopulations evolve differently from classical populations.
Collapse
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Christoph R Haag
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier 34293, France
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
| | - Frida Ben-Ami
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
| |
Collapse
|
2
|
Cornetti L, Fields PD, Du Pasquier L, Ebert D. Long-term balancing selection for pathogen resistance maintains trans-species polymorphisms in a planktonic crustacean. Nat Commun 2024; 15:5333. [PMID: 38909039 PMCID: PMC11193740 DOI: 10.1038/s41467-024-49726-8] [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: 06/08/2023] [Accepted: 06/18/2024] [Indexed: 06/24/2024] Open
Abstract
Balancing selection is an evolutionary process that maintains genetic polymorphisms at selected loci and strongly reduces the likelihood of allele fixation. When allelic polymorphisms that predate speciation events are maintained independently in the resulting lineages, a pattern of trans-species polymorphisms may occur. Trans-species polymorphisms have been identified for loci related to mating systems and the MHC, but they are generally rare. Trans-species polymorphisms in disease loci are believed to be a consequence of long-term host-parasite coevolution by balancing selection, the so-called Red Queen dynamics. Here we scan the genomes of three crustaceans with a divergence of over 15 million years and identify 11 genes containing identical-by-descent trans-species polymorphisms with the same polymorphisms in all three species. Four of these genes display molecular footprints of balancing selection and have a function related to immunity. Three of them are located in or close to loci involved in resistance to a virulent bacterial pathogen, Pasteuria, with which the Daphnia host is known to coevolve. This provides rare evidence of trans-species polymorphisms for loci known to be functionally relevant in interactions with a widespread and highly specific parasite. These findings support the theory that specific antagonistic coevolution is able to maintain genetic diversity over millions of years.
Collapse
Affiliation(s)
- Luca Cornetti
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
- Syngenta Crop Protection AG, Stein, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Louis Du Pasquier
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.
| |
Collapse
|
3
|
Beam TC, Bright M, Pearson AC, Dua I, Smith M, Dutta AK, Bhadra SC, Salman S, Strickler CN, Anderson CE, Peshkin L, Yampolsky LY. Short lifespan is one's fate, long lifespan is one's achievement: lessons from Daphnia. GeroScience 2024:10.1007/s11357-024-01244-7. [PMID: 38900345 DOI: 10.1007/s11357-024-01244-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Studies of longevity rely on baseline life expectancy of reference genotypes measured in standardized conditions. Variation among labs, protocols, and genotypes makes longevity intervention studies difficult to compare. Furthermore, extending lifespan under suboptimal conditions or that of a short-lived genotype may be of a lesser theoretical and translational value than extending the maximal possible lifespan. Daphnia is becoming a model organism of choice for longevity research complementing data obtained on traditional models. In this study, we report longevity of several genotypes of a long-lived species D. magna under a variety of protocols, aiming to document the highest lifespan, factors reducing it, and parameters that change with age and correlate with longevity. Combining longevity data from 25 experiments across two labs, we report a strong intraspecific variation, moderate effects of group size and medium composition, and strong genotype-by-environment interactions with respect to food level. Specifically, short-lived genotypes show no caloric restriction (CR) effect, while long-lived ones expand their lifespan even further under CR. We find that the CR non-responsive clones show little correlation between longevity and two measures of lipid peroxidation. In contrast, the long-lived, CR-responsive clones show a positive correlation between longevity and lipid hydroperoxide abundance, and a negative correlation with MDA concentration. This indicates differences among genotypes in age-related accumulation and detoxification of LPO products and their effects on longevity. Our observations support the hypothesis that a long lifespan can be affected by CR and levels of oxidative damage, while genetically determined short lifespan remains short regardless.
Collapse
Affiliation(s)
- Thomas C Beam
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Mchale Bright
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Amelia C Pearson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Ishaan Dua
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Meridith Smith
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Ashit K Dutta
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Shymal C Bhadra
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, IN, 46805, USA
| | - Saad Salman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Caleb N Strickler
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Cora E Anderson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Lev Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA.
| |
Collapse
|
4
|
Hiki K, Oka K, Nakajima N, Watanabe H, Yamamoto H, Yamagishi T. The complete mitochondrial genome of water flea Ceriodaphnia dubia (Crustacea: Cladocera) NIES strain. Mitochondrial DNA B Resour 2023; 8:831-835. [PMID: 37560176 PMCID: PMC10408566 DOI: 10.1080/23802359.2023.2241663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Water flea Ceriodaphnia dubia has been widely used for risk assessments of chemicals and environmental contamination. In this study, the complete mitochondrial genome (mitogenome) of this species NIES strain was determined using short-read high throughput and long-read sequencing technologies. The mitogenome of C. dubia was 15,170 bp in length and consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs). The gene order was identical to the pattern conserved across crustaceans. The complete mitogenome of the NIES strain will serve as genetical reference in ecological risk assessments in Japan, as well as resources for future phylogenetical studies using cladocerans.
Collapse
Affiliation(s)
- Kyoshiro Hiki
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kenta Oka
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Haruna Watanabe
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Hiroshi Yamamoto
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Takahiro Yamagishi
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| |
Collapse
|
5
|
Angst P, Ebert D, Fields PD. Population genetic analysis of the microsporidium Ordospora colligata reveals the role of natural selection and phylogeography on its extremely compact and reduced genome. G3 (BETHESDA, MD.) 2023; 13:jkad017. [PMID: 36655395 PMCID: PMC9997559 DOI: 10.1093/g3journal/jkad017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
The determinants of variation in a species' genome-wide nucleotide diversity include historical, environmental, and stochastic aspects. This diversity can inform us about the species' past and present evolutionary dynamics. In parasites, the mode of transmission and the interactions with the host might supersede the effects of these aspects in shaping parasite genomic diversity. We used genomic samples from 10 populations of the microsporidian parasite Ordospora colligata to investigate present genomic diversity and how it was shaped by evolutionary processes, specifically, the role of phylogeography, co-phylogeography (with the host), natural selection, and transmission mode. Although very closely related microsporidia cause diseases in humans, O. colligata is specific to the freshwater crustacean Daphnia magna and has one of the smallest known eukaryotic genomes. We found an overlapping phylogeography between O. colligata and its host highlighting the long-term, intimate relationship between them. The observed geographic distribution reflects previous findings that O. colligata exhibits adaptations to colder habitats, which differentiates it from other microsporidian gut parasites of D. magna predominantly found in warmer areas. The co-phylogeography allowed us to calibrate the O. colligata phylogeny and thus estimate its mutation rate. We identified several genetic regions under potential selection. Our whole-genome study provides insights into the evolution of one of the most reduced eukaryotic genomes and shows how different processes shape genomic diversity of an obligate parasite.
Collapse
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| |
Collapse
|
6
|
Ye Z, Yuan J, Damgaard J, Berchi GM, Cianferoni F, Pintar MR, Olosutean H, Zhu X, Jiang K, Yang X, Fu S, Bu W. Climate Warming Since the Holocene Accelerates West-East Communication for the Eurasian Temperate Water Strider Species Aquarius paludum. Mol Biol Evol 2022; 39:6575397. [PMID: 35482393 PMCID: PMC9087890 DOI: 10.1093/molbev/msac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.
Collapse
Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Juanjuan Yuan
- College of Life Sciences, Zaozhuang University, 1 Beian Road, Shandong 277000, China
| | - Jakob Damgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Gavril Marius Berchi
- Department of Taxonomy & Ecology, Faculty of Biology & Geology, Babeş-Bolyai University, 5-7 Clinicilor Street, 400015 Cluj-Napoca, Romania.,Institute for Advanced Environmental Research, West University of Timișoara, 4 Oituz Street, 300086 Timișoara, Romania
| | - Fabio Cianferoni
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy.,Zoology, "La Specola", Natural History Museum, University of Florence, Via Romana 17, I-50125 Florence, Italy
| | - Matthew R Pintar
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Horea Olosutean
- Applied Ecology Research Center, Lucian Blaga University of Sibiu, 5-7 Ion Ratiu Street, 550012 Sibiu, Romania
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xin Yang
- School of Sports, Taiyuan University of Science and Technology, 66 Waliu Road, Shanxi 030024, China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| |
Collapse
|
7
|
Gu YL, Sun CH, Liu P, Zhang X, Sinev AY, Dumont HJ, Han BP. Complete mitochondrial genome of Ovalona pulchella (Branchiopoda, Cladocera) as the first representative in the family Chydoridae: Gene rearrangements and phylogenetic analysis of Cladocera. Gene X 2022; 818:146230. [PMID: 35093448 DOI: 10.1016/j.gene.2022.146230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/10/2021] [Accepted: 01/13/2022] [Indexed: 11/18/2022] Open
Abstract
Chydoridae are phytophilic-benthic microcrustaceans that make up a significant proportion of species diversity and play an important role in the littoral zone of freshwater ecosystems worldwide. Here, we provide the complete mitochondrial genome of Ovalona pulchella (King, 1853), determined by next-generation sequencing. The entire mitochondrial genome is 15,362 bp in length; this is the first sequenced mitochondrial genome in the family Chydoridae. The base composition and codon usage were typical of Cladocera species. The mitochondrial gene arrangement (37 genes) was not consistent with that of other Branchiopoda. Both maximum likelihood and Bayesian analyses supported each suborder and family of Branchiopoda as monophyletic groups. The relationships among the families were as follows: [(Leptestheriidae + Limnadiidae) + (Sididae + (Bosminidae + (Chydoridae + Daphniidae)))] + Triopsidae. The newly sequenced O. pulchella was most closely related to the family Daphniidae. The complete mitochondrial genome of O. pulchella also provides valuable molecular information for further analysis of the phylogeny of the Chydoridae and the taxonomic status of the Branchiopoda.
Collapse
Affiliation(s)
- Yang-Liang Gu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China; South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou 510530, China
| | - Cheng-He Sun
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China.
| | - Ping Liu
- College of Environmental Science and Engineering, Yangzhou University, Jiangsu 225127, China.
| | - Xiaoli Zhang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Artem Y Sinev
- Department of Invertebrate Zoology, Biological Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Henri J Dumont
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| |
Collapse
|
8
|
Angst P, Ebert D, Fields PD. Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution. Mol Ecol 2022; 31:2528-2544. [DOI: 10.1111/mec.16419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Peter D. Fields
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| |
Collapse
|
9
|
Fields PD, McTaggart S, Reisser CMO, Haag C, Palmer WH, Little TJ, Ebert D, Obbard DJ. Population-genomic analysis identifies a low rate of global adaptive fixation in the proteins of the cyclical parthenogen Daphnia magna. Mol Biol Evol 2022; 39:6542319. [PMID: 35244177 PMCID: PMC8963301 DOI: 10.1093/molbev/msac048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative ‘arms race’ genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.
Collapse
Affiliation(s)
- Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Seanna McTaggart
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Céline M O Reisser
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, campus CNRS, 1919, route de Mende, 34293 Montpellier Cedex 5, France.,MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Christoph Haag
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, campus CNRS, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - William H Palmer
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Tom J Little
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Darren J Obbard
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| |
Collapse
|
10
|
Kitano T, Sato H, Takahashi N, Igarashi S, Hatanaka Y, Igarashi K, Umetsu K. Complete mitochondrial genomes of three fairy shrimps from snowmelt pools in Japan. BMC ZOOL 2022; 7:11. [PMID: 37170326 PMCID: PMC10127424 DOI: 10.1186/s40850-022-00111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/27/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Fairy shrimps belong to order Anostraca, class Branchiopoda, subphylum Crustacea, and phylum Arthropoda. Three fairy shrimp species (Eubranchipus uchidai, E. asanumai, and E. hatanakai) that inhabit snowmelt pools are currently known in Japan. Whole mitochondrial genomes are useful genetic information for conducting phylogenetic analyses. Mitochondrial genome sequences for Branchiopoda members are gradually being collated.
Results
Six whole mitochondrial genomes from the three Eubranchipus species are presented here. Eubranchipus species share the anostracan pattern of gene arrangement in their mitochondrial genomes. The mitochondrial genomes of the Eubranchipus species have a higher GC content than those of other anostracans. Accelerated substitution rates in the lineage of Eubranchipus species were observed.
Conclusion
This study is the first to obtain whole mitochondrial genomes for Far Eastern Eubranchipus species. We show that the nucleotide sequences of cytochrome oxidase subunit I and the 16S ribosomal RNA of E. asanumai presented in a previous study were nuclear mitochondrial DNA segments. Higher GC contents and accelerated substitution rates are specific characteristics of the mitochondrial genomes of Far Eastern Eubranchipus. The results will be useful for further investigations of the evolution of Anostraca as well as Branchiopoda.
Collapse
|
11
|
Karabanov DP, Bekker EI, Kotov AA. Underestimation of the Effect of Biologiocal Invasions in Phylogeographic Reconstructions as Seen in Daphnia magna (Crustacea, Cladocera). BIOL BULL+ 2021. [DOI: 10.1134/s1062359021080136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Xu SL, Han BP, Martínez A, Schwentner M, Fontaneto D, Dumont HJ, Kotov AA. Mitogenomics of Cladocera (Branchiopoda): Marked gene order rearrangements and independent predation roots. Mol Phylogenet Evol 2021; 164:107275. [PMID: 34339827 DOI: 10.1016/j.ympev.2021.107275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022]
Abstract
Cladocera (Crustacea: Branchiopoda) is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high-throughput sequencing (HTS) and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister-group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister-group relationship between Ctenopoda and Haplopoda. We provide a fossil-calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non-Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata.
Collapse
Affiliation(s)
- Shao-Lin Xu
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Bo-Ping Han
- Jinan University, Department of Ecology, Guangzhou 510632, China.
| | - Alejandro Martínez
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | | | - Diego Fontaneto
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | - Henri J Dumont
- Jinan University, Department of Ecology, Guangzhou 510632, China; Ghent University, Department of Biology, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Alexey A Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
13
|
Bourgeois Y, Fields P, Bento G, Ebert D. Balancing selection for pathogen resistance reveals an intercontinental signature of Red Queen coevolution. Mol Biol Evol 2021; 38:4918-4933. [PMID: 34289047 PMCID: PMC8557431 DOI: 10.1093/molbev/msab217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The link between long-term host–parasite coevolution and genetic diversity is key to understanding genetic epidemiology and the evolution of resistance. The model of Red Queen host–parasite coevolution posits that high genetic diversity is maintained when rare host resistance variants have a selective advantage, which is believed to be the mechanistic basis for the extraordinarily high levels of diversity at disease-related genes such as the major histocompatibility complex in jawed vertebrates and R-genes in plants. The parasites that drive long-term coevolution are, however, often elusive. Here we present evidence for long-term balancing selection at the phenotypic (variation in resistance) and genomic (resistance locus) level in a particular host–parasite system: the planktonic crustacean Daphnia magna and the bacterium Pasteuria ramosa. The host shows widespread polymorphisms for pathogen resistance regardless of geographic distance, even though there is a clear genome-wide pattern of isolation by distance at other sites. In the genomic region of a previously identified resistance supergene, we observed consistent molecular signals of balancing selection, including higher genetic diversity, older coalescence times, and lower differentiation between populations, which set this region apart from the rest of the genome. We propose that specific long-term coevolution by negative-frequency-dependent selection drives this elevated diversity at the host's resistance loci on an intercontinental scale and provide an example of a direct link between the host’s resistance to a virulent pathogen and the large-scale diversity of its underlying genes.
Collapse
Affiliation(s)
- Yann Bourgeois
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Gilberto Bento
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| |
Collapse
|
14
|
Lv SS, Zhang YJ, Gong N, Chen XS. Characterization and Phylogenetic Analysis of the Mitochondrial Genome Sequence of Nisia fuliginosa (Hemiptera: Fulgoroidea: Meenoplidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:8. [PMID: 34327530 PMCID: PMC8322432 DOI: 10.1093/jisesa/ieab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 06/13/2023]
Abstract
We explored characterization of the mitochondrial genome (mitogenome or mtGenome) and phylogenetic analysis between 32 Fulgoroid species by sequencing and analyzing the mitogenome of Nisia fuliginosa Yang and Hu, 1985 (Hemiptera: Fulgoroidea: Meenoplidae), thereby making it the first determined mitogenome from the family Meenoplidae. The mitogenome was found to be 15,754 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, two ribosomal RNA genes (rRNAs), and a control region. All PCGs started with typical ATN codons, except for nad1, which used GTG as the start codon. Canonical TAA termination codons were found in 10 PCGs and the remaining three genes (cox2, nad6, and nad1) had incomplete stop codons T. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnC, trnV, and trnS1. Additionally, we compared the AT and GC skews of 13 PCGs of 32 Fulgoroidea mitogenomes, on the L-strand, the AT and GC skews were negative and positive, respectively. However, on the H-strand, the AT skew could be positive or negative and the GC skew was always negative. Phylogenetic results showed that the eight families of Fulgoroidea were divided into two large groups. Delphacidae formed a monophyletic group sister to a clade comprising Meenoplidae and other six families (Fulgoridae, Ricaniidae, Flatidae, Issidae, Caliscelidae, and Achilidae). Meenoplidae was located near the clade of Delphacidae, and Fulgoridae was located near the clade of Meenoplidae. Furthermore, Caliscelidae, Issidae, Ricaniidae, and Flatidae are closely related and they collectively formed a sister group to Achilidae.
Collapse
Affiliation(s)
| | - Yu-Jie Zhang
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| | - Nian Gong
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| | - Xiang-Sheng Chen
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| |
Collapse
|
15
|
Coggins BL, Pearson AC, Yampolsky LY. Does geographic variation in thermal tolerance in Daphnia represent trade-offs or conditional neutrality? J Therm Biol 2021; 98:102934. [PMID: 34016356 DOI: 10.1016/j.jtherbio.2021.102934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/20/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
Geographic variation in thermal tolerance in Daphnia seems to represent genetic load at the loci specifically responsible for heat tolerance resulting from conditional neutrality. We see no evidence of trade-offs between fitness-related traits at 25 °C vs. 10 °C or between two algal diets across Daphnia magna clones from a variety of locations representing the opposite ends of the distribution of long-term heat tolerance. Likewise, we found no evidence of within-environment trade-offs between heat tolerance and fitness-related traits in any of the environments. Neither short-term and long-term heat tolerance shows any consistent relationship with lipid fluorescence polarization and lipid peroxidation across clones or environments. Pervasive positive correlations between fitness-related traits indicate differences in genetic load rather than trade-off based local adaptation or thermal specialization. For heat tolerance such differences may be caused by either relaxation of stabilizing selection due to lower exposure to high temperature extremes, i.e., conditional neutrality, or by small effective population size followed by the recent range expansion.
Collapse
Affiliation(s)
- B L Coggins
- Department of Biological Sciences, East Tennessee State University, Johnson City TN, 37601, USA; Department of Biological Sciences, University of Notre Dame, IN, 46556, USA
| | - A C Pearson
- Department of Biological Sciences, East Tennessee State University, Johnson City TN, 37601, USA
| | - L Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City TN, 37601, USA; University of Basel, Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| |
Collapse
|
16
|
Du Z, Wu Y, Chen Z, Cao L, Ishikawa T, Kamitani S, Sota T, Song F, Tian L, Cai W, Li H. Global phylogeography and invasion history of the spotted lanternfly revealed by mitochondrial phylogenomics. Evol Appl 2021; 14:915-930. [PMID: 33897812 PMCID: PMC8061274 DOI: 10.1111/eva.13170] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasion has been a serious global threat due to increasing international trade and population movements. Tracking the source and route of invasive species and evaluating the genetic differences in their native regions have great significance for the effective monitoring and management, and further resolving the invasive mechanism. The spotted lanternfly Lycorma delicatula is native to China and invaded South Korea, Japan, and the United States during the last decade, causing severe damages to the fruits and timber industries. However, its global phylogeographic pattern and invasion history are not clearly understood. We applied high-throughput sequencing to obtain 392 whole mitochondrial genome sequences from four countries to ascertain the origin, dispersal, and invasion history of the spotted lanternfly. Phylogenomic analyses revealed that the spotted lanternfly originated from southwestern China, diverged into six phylogeographic lineages, and experienced northward expansion across the Yangtze River in the late Pleistocene. South Korea populations were derived from multiple invasions from eastern China and Japan with two different genetic sources of northwestern (Loess Plateau) and eastern (East Plain) lineages in China, whereas the each of Japan and the United States had only one. The United States populations originated through single invasive event from South Korea, which served as a bridgehead of invasion. The environmental conditions, especially the distribution of host Ailanthus trees, and adaptability possibly account for the rapid spread of the spotted lanternfly in the native and introduced regions.
Collapse
Affiliation(s)
- Zhenyong Du
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Yunfei Wu
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Zhuo Chen
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Liangming Cao
- The Key Laboratory of Forest ProtectionNational Forestry and Grassland AdministrationResearch Institute of Forest Ecology, Environment and ProtectionChinese Academy of ForestryBeijingChina
| | - Tadashi Ishikawa
- Laboratory of EntomologyFaculty of AgricultureTokyo University of AgricultureAtsugiJapan
| | - Satoshi Kamitani
- Entomological LaboratoryGraduate School of Bioresource and Bioenvironmental SciencesKyushu UniversityFukuokaJapan
| | - Teiji Sota
- Department of ZoologyGraduate School of ScienceKyoto UniversitySakyoJapan
| | - Fan Song
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Li Tian
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Wanzhi Cai
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hu Li
- Department of EntomologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| |
Collapse
|
17
|
Cornetti L, Fields PD, Ebert D. Genomic characterization of selfing in the cyclic parthenogen Daphnia magna. J Evol Biol 2021; 34:792-802. [PMID: 33704857 DOI: 10.1111/jeb.13780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 11/29/2022]
Abstract
Inbreeding refers to the fusion of related individuals' gametes, with self-fertilization (selfing) being an extreme form of inbreeding-involving gametes produced by the same individual. Selfing is expected to reduce heterozygosity by an average of 50% in one generation; however, little is known about the empirical variation on a genome level surrounding this figure and the factors that affect variation. We selfed genotypes of the cyclic parthenogen Daphnia magna and analysed whole genomes of mothers and selfed offspring, observing the predicted 50% heterozygosity reduction on average. We also saw substantial variation around this value and significant differences among mother-offspring pairs. Crossover analysis confirmed the known trend of recombination occurring more often towards the telomeres. This effect was shown, through simulations, to increase the variance of heterozygosity reduction compared to when a uniform distribution of crossovers was used. Similarly, we simulated inbred line production after several generations of selfing and we observed higher variance in achieved homozygosity when we consider a higher recombination rate towards the telomeres. Our empirical and simulation study highlights that the expected mean values of heterozygosity reduction show remarkable variation, which can help understand, for example, differences among inbred individuals.
Collapse
Affiliation(s)
- Luca Cornetti
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| |
Collapse
|
18
|
Haag KL, Pombert JF, Sun Y, de Albuquerque NRM, Batliner B, Fields P, Lopes TF, Ebert D. Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes. Genome Biol Evol 2020; 12:3599-3614. [PMID: 31825473 PMCID: PMC6944219 DOI: 10.1093/gbe/evz270] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
Microsporidia have the leanest genomes among eukaryotes, and their physiological and genomic simplicity has been attributed to their intracellular, obligate parasitic life-style. However, not all microsporidia genomes are small or lean, with the largest dwarfing the smallest ones by at least an order of magnitude. To better understand the evolutionary mechanisms behind this genomic diversification, we explore here two clades of microsporidia with distinct life histories, Ordospora and Hamiltosporidium, parasitizing the same host species, Daphnia magna. Based on seven newly assembled genomes, we show that mixed-mode transmission (the combination of horizontal and vertical transmission), which occurs in Hamiltosporidium, is found to be associated with larger and AT-biased genomes, more genes, and longer intergenic regions, as compared with the exclusively horizontally transmitted Ordospora. Furthermore, the Hamiltosporidium genome assemblies contain a variety of repetitive elements and long segmental duplications. We show that there is an excess of nonsynonymous substitutions in the microsporidia with mixed-mode transmission, which cannot be solely attributed to the lack of recombination, suggesting that bursts of genome size in these microsporidia result primarily from genetic drift. Overall, these findings suggest that the switch from a horizontal-only to a mixed mode of transmission likely produces population bottlenecks in Hamiltosporidium species, therefore reducing the effectiveness of natural selection, and allowing their genomic features to be largely shaped by nonadaptive processes.
Collapse
Affiliation(s)
- Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Yukun Sun
- Department of Biology, Illinois Institute of Technology
| | - Nathalia Rammé M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Peter Fields
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
| | - Tiago Falcon Lopes
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
| |
Collapse
|
19
|
Beninde J, Möst M, Meyer A. Optimized and affordable high-throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens. Mol Ecol Resour 2020; 20:1632-1646. [PMID: 32677266 DOI: 10.1111/1755-0998.13228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022]
Abstract
Genomic analysis of hundreds of individuals is increasingly becoming standard in evolutionary and ecological research. Individual-based sequencing generates large amounts of valuable data from experimental and field studies, while using preserved samples is an invaluable resource for studying biodiversity in remote areas or across time. Yet, small-bodied individuals or specimens from collections are often of limited use for genomic analyses due to a lack of suitable extraction and library preparation protocols for preserved or small amounts of tissues. Currently, high-throughput sequencing in zooplankton is mostly restricted to clonal species, that can be maintained in live cultures to obtain sufficient amounts of tissue, or relies on a whole-genome amplification step that comes with several biases and high costs. Here, we present a workflow for high-throughput sequencing of single small individuals omitting the need for prior whole-genome amplification or live cultures. We establish and demonstrate this method using 27 species of the genus Daphnia, aquatic keystone organisms, and validate it with small-bodied ostracods. Our workflow is applicable to both live and preserved samples at low costs per sample. We first show that a silica-column based DNA extraction method resulted in the highest DNA yields for nonpreserved samples while a precipitation-based technique gave the highest yield for ethanol-preserved samples and provided the longest DNA fragments. We then successfully performed short-read whole genome sequencing from single Daphnia specimens and ostracods. Moreover, we assembled a draft reference genome from a single Daphnia individual (>50× coverage) highlighting the value of the workflow for non-model organisms.
Collapse
Affiliation(s)
- Jannik Beninde
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Markus Möst
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
20
|
Du H, Liu M, Zhang S, Liu F, Zhang Z, Kong X. Lineage Divergence of Dendrolimus punctatus in Southern China Based on Mitochondrial Genome. Front Genet 2020; 11:65. [PMID: 32153637 PMCID: PMC7045034 DOI: 10.3389/fgene.2020.00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
In southern China, the masson pine caterpillar, Dendrolimus punctatus, has caused serious damage to the Pinus massoniana (Lamb.) pine forests. Here, the whole mitochondrial DNA (mtDNA) was employed to analyze the population evolution of D. punctatus and to understand the process underlying its current phylogenetic pattern. D. punctatus populations within its distribution range in China were categorized into five subgroups: central and eastern China (CEC), southwestern China (SWC), Yibin in Sichuan (SC), Baise in Guangxi (GX), and Luoding in Guangdong (GD), with a high level of haplotype diversity and nucleotide diversity among them. The genetic distances between subgroups are relatively large; however, the genetic distances between populations within the CEC subgroup were relatively small, suggesting that many populations were closely related in this subgroup. The mantel test showed that geographic distance had an important impact on the genetic distance of different geographic populations (r = 0.3633, P < 0.001). The neutrality tests, Bayesian skyline plot, and haplotype network showed that D. punctatus experienced a population expansion around 100,000 years ago. The divergence times of GX/SC, SWC, GD, and CEC were 0.347, 0.236, 0.200, and 0.110 million years ago, respectively. The SWC, CEC, and GD subgroups might have evolved from GX or SC subgroups. The population genetic structure of D. punctatus was closely related to its host tree species, geographic distance among populations, the weak flight capacity, and many eco-environment conditions.
Collapse
Affiliation(s)
- Huicong Du
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Man Liu
- Guizhou Institute of Biology, Guizhou Academy of Sciences, Guiyang, China
| | - Sufang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Fu Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhen Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiangbo Kong
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
21
|
Unexpected endemism in the Daphnia longispina complex (Crustacea: Cladocera) in Southern Siberia. PLoS One 2019; 14:e0221527. [PMID: 31479467 PMCID: PMC6719860 DOI: 10.1371/journal.pone.0221527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/09/2019] [Indexed: 02/01/2023] Open
Abstract
The biological significance of regional cladoceran morphotypes in the montane regions of the central Palearctic remains poorly understood. In the Holarctic Daphnia longispina complex (Cladocera: Daphniidae), several variants, lineages and species have been proposed as endemic for Southern Siberia. Daphnia turbinata Sars, for example, named after its unusual head shape, is known only from Southern Siberia. Here we sequence DNA of Daphnia from three mitochondrial genes (12S rRNA, 16S rRNA, and NADH dehydrogenase subunit 2, ND2) from 57 localities in Russia and Mongolia (the majority being from Southern Siberia) and place them in evolutionary context with existing data. Our aim was to examine regional endemism of the Daphnia longispina complex in Southern Siberian; to improve the phylogenetic understanding with improved taxonomic and regional sampling, and to better understand the influence of Pleistocene glaciation on the biogeography of these lineages. At least three lineages showed genetic evidence for endemism in Southern Siberia. There was strong support for D. turbinata as a sister lineage to to D. longispina/D. dentifera. Another endemic, Siberian D. cf. longispina, is a sister group to the longispina group in general. Within D. longispina s. str. there was an endemic Siberian clade with a western range boundary near the Yenisei River Basin. Gene flow estimates among populations (based on FST values) were very low for clades of D. longispina on a regional (the original 12S dataset), and on a pan-Eurasian (the extended 12S dataset) scale. Negative values of Fu’s FS and Tajima’s D tests prevailed for the species examined with significant values found for two D. longispina clades, D. dentifera, D. galeata and D. cristata. Our results support the notion that Southern Siberia is an important biogeographic region for cladocerans as it contained unexpected diversity of endemics (such as D. turbinata, D. cf. longispina and lineages of D. umbra and D. longsipina s.str.) and from being the geographic meeting place of expanding postglacial lineages from eastern and western refugia.
Collapse
|
22
|
Cornetti L, Fields PD, Van Damme K, Ebert D. A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae. Mol Phylogenet Evol 2019; 137:250-262. [DOI: 10.1016/j.ympev.2019.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
|
23
|
Seefeldt L, Ebert D. Temperature- versus precipitation-limitation shape local temperature tolerance in a Holarctic freshwater crustacean. Proc Biol Sci 2019; 286:20190929. [PMID: 31337313 PMCID: PMC6661336 DOI: 10.1098/rspb.2019.0929] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Species with wide geographical distributions are often adapted locally to the prevailing temperatures. To understand how they respond to ongoing climatic change, we must appreciate the interplay between temperature, seasonality and the organism's life cycle. The temperature experienced by many organisms results from an often-overlooked combination of climate and phenology. Summer-active (high latitude) populations are expected to adapt to local summer temperatures, but this is not expected for populations that outlive the summer in their dormant stage (low latitude, precipitation-limited). We recorded reproduction and survival in genotypes from 123 Holarctic populations of Daphnia magna during a multi-generation thermal ramp experiment. Genotypes from summer-active populations showed a positive relationship between heat tolerance and local summer temperature, whereas winter-active populations did not. These findings are consistent with the hypothesis that D. magna adapts to the local temperatures the animals experience during their planktonic phase. We conclude that predicting local temperature adaptation, in particular in the light of climate change, needs to consider the phenology of geographically wide-ranging species.
Collapse
Affiliation(s)
- Leonie Seefeldt
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| |
Collapse
|
24
|
Du Z, Hasegawa H, Cooley JR, Simon C, Yoshimura J, Cai W, Sota T, Li H. Mitochondrial Genomics Reveals Shared Phylogeographic Patterns and Demographic History among Three Periodical Cicada Species Groups. Mol Biol Evol 2019; 36:1187-1200. [PMID: 30850829 PMCID: PMC6526903 DOI: 10.1093/molbev/msz051] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mass application of whole mitogenome (MG) sequencing has great potential for resolving complex phylogeographic patterns that cannot be resolved by partial mitogenomic sequences or nuclear markers. North American periodical cicadas (Magicicada) are well known for their periodical mass emergence at 17- and 13-year intervals in the north and south, respectively. Magicicada comprises three species groups, each containing one 17-year species and one or two 13-year species. Within each life cycle, single-aged cohorts, called broods, of periodical cicadas emerge in different years, and most broods contain members of all three species groups. There are 12 and three extant broods of 17- and 13-year cicadas, respectively. The phylogeographic relationships among the populations and broods within the species groups have not been clearly resolved. We analyzed 125 whole MG sequences from all broods and seven species within three species groups to ascertain the divergence history of the geographic and allochronic populations and their life cycles. Our mitogenomic phylogeny analysis clearly revealed that each of the three species groups had largely similar phylogeographic subdivisions (east, middle, and west) and demographic histories (rapid population expansion after the last glacial period). The mitogenomic phylogeny also partly resolved the brood diversification process, which could be explained by hypothetical temporary life cycle shifts, and showed that none of the 13- and 17-year species within the species groups was monophyletic, possibly due to gene flow between them. Our findings clearly reveal phylogeographic structures in the three Magicicada species groups, demonstrating the advantage of whole MG sequence data in phylogeographic studies.
Collapse
Affiliation(s)
- Zhenyong Du
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hiroki Hasegawa
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - John R Cooley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Jin Yoshimura
- Graduate School of Science and Technology and Department of Mathematical and Systems Engineering, Shizuoka University, Hamamatsu, Japan.,Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY.,Marine Biosystems Research Center, Chiba University, Kamogawa, Chiba, Japan
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| |
Collapse
|
25
|
Vieira GA, Prosdocimi F. Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data. PeerJ 2019; 7:e6271. [PMID: 30697483 PMCID: PMC6348091 DOI: 10.7717/peerj.6271] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/10/2018] [Indexed: 11/20/2022] Open
Abstract
The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the "no budget mitogenomics" approach ideal for comprehensive molecular studies, especially for subsampled taxa.
Collapse
Affiliation(s)
- Gabriel A. Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francisco Prosdocimi
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|