1
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Claypool DJ, Zhang YG, Xia Y, Sun J. Conditional Vitamin D Receptor Deletion Induces Fungal and Archaeal Dysbiosis and Altered Metabolites. Metabolites 2024; 14:32. [PMID: 38248835 PMCID: PMC10819266 DOI: 10.3390/metabo14010032] [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: 12/03/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
A vitamin D receptor (VDR) deficiency leads to the dysbiosis of intestinal bacteria and is associated with various diseases, including cancer, infections, and inflammatory bowel disease. However, the impact of a VDR deficiency on fungi and archaea is unknown. We conditionally deleted the VDR in Paneth cells (VDRΔPC), intestinal epithelial cells (VDRΔIEC), or myeloid cells (VDRΔLyz) in mice and collected feces for shotgun metagenomic sequencing and untargeted metabolomics. We found that fungi were significantly altered in each knockout (KO) group compared to the VDRLoxp control. The VDRΔLyz mice had the most altered fungi species (three depleted and seven enriched), followed by the VDRΔPC mice (six depleted and two enriched), and the VDRΔIEC mice (one depleted and one enriched). The methanogen Methanofollis liminatans was enriched in the VDRΔPC and VDRΔLyz mice and two further archaeal species (Thermococcus piezophilus and Sulfolobus acidocaldarius) were enriched in the VDRΔLyz mice compared to the Loxp group. Significant correlations existed among altered fungi, archaea, bacteria, and viruses in the KO mice. Functional metagenomics showed changes in several biologic functions, including decreased sulfate reduction and increased biosynthesis of cobalamin (vitamin B12) in VDRΔLyz mice relative to VDRLoxp mice. Fecal metabolites were analyzed to examine the involvement of sulfate reduction and other pathways. In conclusion, a VDR deficiency caused the formation of altered fungi and archaea in a tissue- and sex-dependent manner. These results provide a foundation about the impact of a host factor (e.g., VDR deficiency) on fungi and archaea. It opens the door for further studies to determine how mycobiome and cross-kingdom interactions in the microbiome community and metabolites contribute to the risk of certain diseases.
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Affiliation(s)
- Duncan J. Claypool
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Department of Bioengineering, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Yong-Guo Zhang
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
| | - Yinglin Xia
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.C.); (Y.-G.Z.)
- Department of Bioengineering, University of Illinois Chicago, Chicago, IL 60607, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois Chicago, Chicago, IL 60612, USA
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2
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Morrison ML, Rosenberg NA. Mathematical bounds on Shannon entropy given the abundance of the ith most abundant taxon. J Math Biol 2023; 87:76. [PMID: 37884812 PMCID: PMC10603011 DOI: 10.1007/s00285-023-01997-3] [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: 03/23/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 10/28/2023]
Abstract
The measurement of diversity is a central component of studies in ecology and evolution, with broad uses spanning multiple biological scales. Studies of diversity conducted in population genetics and ecology make use of analogous concepts and even employ equivalent mathematical formulas. For the Shannon entropy statistic, recent developments in the mathematics of diversity in population genetics have produced mathematical constraints on the statistic in relation to the frequency of the most frequent allele. These results have characterized the ways in which standard measures depend on the highest-frequency class in a discrete probability distribution. Here, we extend mathematical constraints on the Shannon entropy in relation to entries in specific positions in a vector of species abundances, listed in decreasing order. We illustrate the new mathematical results using abundance data from examples involving coral reefs and sponge microbiomes. The new results update the understanding of the relationship of a standard measure to the abundance vectors from which it is calculated, potentially contributing to improved interpretation of numerical measurements of biodiversity.
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Affiliation(s)
- Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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3
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Cole R, Holroyd N, Tracey A, Berriman M, Viney M. The parasitic nematode Strongyloides ratti exists predominantly as populations of long-lived asexual lineages. Nat Commun 2023; 14:6427. [PMID: 37833369 PMCID: PMC10575991 DOI: 10.1038/s41467-023-42250-1] [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: 02/21/2022] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Nematodes are important parasites of people and animals, and in natural ecosystems they are a major ecological force. Strongyloides ratti is a common parasitic nematode of wild rats and we have investigated its population genetics using single-worm, whole-genome sequencing. We find that S. ratti populations in the UK consist of mixtures of mainly asexual lineages that are widely dispersed across a host population. These parasite lineages are likely very old and may have originated in Asia from where rats originated. Genes that underly the parasitic phase of the parasite's life cycle are hyperdiverse compared with the rest of the genome, and this may allow the parasites to maximise their fitness in a diverse host population. These patterns of parasitic nematode population genetics have not been found before and may also apply to Strongyloides spp. that infect people, which will affect how we should approach their control.
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Affiliation(s)
- Rebecca Cole
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Matt Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- School of Infection & Immunity, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK.
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4
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Karlin EF. A Comparison of Entropic Diversity and Variance in the Study of Population Structure. ENTROPY (BASEL, SWITZERLAND) 2023; 25:492. [PMID: 36981380 PMCID: PMC10048111 DOI: 10.3390/e25030492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/10/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
AMOVA is a widely used approach that focuses on variance within and among strata to study the hierarchical genetic structure of populations. The recently developed Shannon Informational Diversity Translation Analysis (SIDTA) instead tackles exploration of hierarchical genetic structure using entropic allelic diversity. A mix of artificial and natural population data sets (including allopolyploids) is used to compare the performance of SIDTA (a 'q = 1' diversity measure) vs. AMOVA (a 'q = 2' measure) under different conditions. An additive allelic differentiation index based on entropic allelic diversity measuring the mean difference among populations (ΩAP) was developed to facilitate the comparison of SIDTA with AMOVA. These analyses show that the genetic population structure seen by AMOVA is notably different in many ways from that provided by SIDTA, and the extent of this difference is greatly affected by the stability of the markers employed. Negative among group values are lacking with SIDTA but occur with AMOVA, especially with allopolyploids. To provide more focus on measuring allelic differentiation among populations, additional measures were also tested including Bray-Curtis Genetic Differentiation (BCGD) and several expected heterozygosity-based indices (e.g., GST, G″ST, Jost's D, and DEST). Corrections, such as almost unbiased estimators, that were designed to work with heterozygosity-based fixation indices (e.g., FST, GST) are problematic when applied to differentiation indices (eg., DEST, G″ST, G'STH).
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Affiliation(s)
- Eric F Karlin
- School of Theoretical & Applied Science, Ramapo College, Mahwah, NJ 07430, USA
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5
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Frère CH, O'Reilly GD, Strickland K, Schultz A, Hohwieler K, Hanger J, de Villiers D, Cristescu R, Powell D, Sherwin W. Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas. Mol Ecol 2023; 32:2174-2185. [PMID: 36756702 DOI: 10.1111/mec.16877] [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: 03/13/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023]
Abstract
The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.
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Affiliation(s)
- C H Frère
- School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - G D O'Reilly
- The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - K Strickland
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - A Schultz
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands), Reykjavik, Iceland
| | - K Hohwieler
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - J Hanger
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Queensland, Australia
| | - D de Villiers
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, Queensland, Australia
| | - R Cristescu
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - D Powell
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - W Sherwin
- The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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6
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A suite of ecological indicators for evaluating the integrity of structural eco-complexity in Mexican forests. ECOLOGICAL COMPLEXITY 2022. [DOI: 10.1016/j.ecocom.2022.101001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Dai Y, Sakornwimon W, Chantra R, Zhao L, Wu F, Aierken R, Kittiwattanawong K, Wang X. High genetic differentiation of Indo‐Pacific humpback dolphins (
Sousa chinensis
) along the Asian Coast of the Pacific Ocean. Ecol Evol 2022; 12:e8901. [PMID: 35571759 PMCID: PMC9077734 DOI: 10.1002/ece3.8901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yufei Dai
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Watchara Sakornwimon
- Marine and Coastal Resources Research Center The Central Gulf of Thailand Chumphon Thailand
| | - Rachawadee Chantra
- Marine and Coastal Resources Research Center The Upper Gulf of Thailand Samut Sakhon Thailand
| | - Liyuan Zhao
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Fuxing Wu
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Reyilamu Aierken
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
| | | | - Xianyan Wang
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
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8
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Sentinella AT, Moles AT, Bragg JG, Rossetto M, Sherwin WB. Detecting steps in spatial genetic data: Which diversity measures are best? PLoS One 2022; 17:e0265110. [PMID: 35287164 PMCID: PMC8920294 DOI: 10.1371/journal.pone.0265110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/23/2022] [Indexed: 12/05/2022] Open
Abstract
Accurately detecting sudden changes, or steps, in genetic diversity across landscapes is important for locating barriers to gene flow, identifying selectively important loci, and defining management units. However, there are many metrics that researchers could use to detect steps and little information on which might be the most robust. Our study aimed to determine the best measure/s for genetic step detection along linear gradients using biallelic single nucleotide polymorphism (SNP) data. We tested the ability to differentiate between linear and step-like gradients in genetic diversity, using a range of diversity measures derived from the q-profile, including allelic richness, Shannon Information, GST, and Jost-D, as well as Bray-Curtis dissimilarity. To determine the properties of each measure, we repeated simulations of different intensities of step and allele proportion ranges, with varying genome sample size, number of loci, and number of localities. We found that alpha diversity (within-locality) based measures were ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g., Jaccard and Sørensen dissimilarity) were not reliable for detecting steps, but instead detected departures from fixation. The beta diversity measures best able to detect steps were: Shannon Information based measures, GST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best overall, with a trade-off between those measures with high step detection sensitivity (GST and Bray-Curtis) and those that minimised false positives (a variant of Shannon Information). Therefore, when detecting steps, we recommend understanding the differences between measures and using a combination of approaches.
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Affiliation(s)
- Alexander T. Sentinella
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- * E-mail:
| | - Angela T. Moles
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jason G. Bragg
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW, Australia
| | - William B. Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
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9
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Schultz AJ, Strickland K, Cristescu RH, Hanger J, de Villiers D, Frère CH. Testing the effectiveness of genetic monitoring using genetic non-invasive sampling. Ecol Evol 2022; 12:e8459. [PMID: 35127011 PMCID: PMC8794716 DOI: 10.1002/ece3.8459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.
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Affiliation(s)
- Anthony James Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Kasha Strickland
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Department of Aquaculture and Fish BiologyHólar UniversityHólarIceland
| | - Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
| | | | | | - Céline H. Frère
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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10
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Cagnano G, Roulund N, Jensen CS, Forte FP, Asp T, Leuchtmann A. Large Scale Screening of Epichloë Endophytes Infecting Schedonorus pratensis and Other Forage Grasses Reveals a Relation Between Microsatellite-Based Haplotypes and Loline Alkaloid Levels. FRONTIERS IN PLANT SCIENCE 2019; 10:765. [PMID: 31249582 PMCID: PMC6582706 DOI: 10.3389/fpls.2019.00765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/24/2019] [Indexed: 06/09/2023]
Abstract
Species belonging to the Festuca-Lolium complex are often naturally infected with endophytic fungi of genus Epichloë. Recent studies on endophytes have shown the beneficial roles of host-endophyte associations as protection against insect herbivores in agriculturally important grasses. However, large-scale screenings are crucial to identify animal friendly strains suitable for agricultural use. In this study we analyzed collected populations of meadow fescue (Schedonorus pratensis) from 135 different locations across Europe, 255 accessions from the United States Department of Agriculture and 96 accessions from The Nordic Genetic Resource Centre. The analysis also included representatives of S. arundinaceus, S. giganteus, and Lolium perenne. All plants were screened for the presence of Epichloë endophytes, resulting in a nursery of about 2500 infected plants from 176 different locations. Genetic diversity was investigated on 250 isolates using a microsatellite-based PCR fingerprinting assay at 7 loci, 5 of which were uncharacterized for these species. Phylogenetic and principal components analysis showed a strong interspecific genetic differentiation among isolates, and, with E. uncinata isolates, a small but significant correlation between genetic diversity and geographical effect (r = 0.227) was detected. Concentrations of loline alkaloids were measured in 218 infected meadow fescue plants. Average amount of total loline and the proportions of the single loline alkaloids differed significantly among endophyte haplotypes (P < 0.005). This study provides insight into endophyte genetic diversity and geographic variation in Europe and a reference database of allele sizes for fast discrimination of isolates. We also discuss the possibility of multiple hybridization events as a source of genetic and alkaloid variation observed in E. uncinata.
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Affiliation(s)
- Giovanni Cagnano
- DLF Trifolium A/S, Roskilde, Denmark
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | | | | | - Flavia Pilar Forte
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
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11
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Affiliation(s)
- C. Ricotta
- Department of Environmental Biology, University of Rome ‘LaSapienza’, Piazzale Aldo Moro 5, 00185 Rome, Italy
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12
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Baroudy F, Putman AI, Habib W, Puri KD, Subbarao KV, Nigro F. Genetic Diversity of Verticillium dahliae Populations From Olive and Potato in Lebanon. PLANT DISEASE 2019; 103:656-667. [PMID: 30823856 DOI: 10.1094/pdis-03-18-0420-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Verticillium dahliae is widely distributed in potato and olive fields in Lebanon, causing serious economic losses. However, little is known about the inoculum source, population structure, and genetic diversity of the pathogen or the mechanisms of dissemination within Lebanon. To understand the population structure, a total of 203 isolates sampled from olive (n = 78) and potato (n = 125) were characterized for species, mating type, and race, and the genetic relationships were delineated using 13 microsatellite markers. All isolates except one from potato were V. dahliae, with 55.1 and 12.1% race 1, and 43.6 and 83.1% race 2 in olive and potato, respectively. The genetic structure of the studied population was best described by two large and two small clusters. Membership in the two large clusters was determined by the presence or absence of the effector gene Ave1. Furthermore, genetic structure was moderately associated with the host of origin but was weakly associated with the geographic origin. All but four isolates represented by three multilocus haploid genotypes were MAT1-2. This study identified a clear lack of gene flow between virulence genotypes of V. dahliae despite the proximity of these cropping systems and the wide distribution of genetic diversity among hosts and geographic regions in Lebanon.
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Affiliation(s)
- Farah Baroudy
- 1 Dipartimento di Scienze del Suolo, Università degli Studi di Bari - Aldo Moro, Bari, 70126 Bari, Italy
- 2 Lebanese Agricultural Research Institute, Laboratory of Mycology, Department of Plant Protection, Fanar, Jdeidet El Metn, Lebanon
| | - Alexander I Putman
- 3 Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A.; and
| | - Wassim Habib
- 2 Lebanese Agricultural Research Institute, Laboratory of Mycology, Department of Plant Protection, Fanar, Jdeidet El Metn, Lebanon
| | - Krishna D Puri
- 4 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905, U.S.A
| | - Krishna V Subbarao
- 4 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905, U.S.A
| | - Franco Nigro
- 1 Dipartimento di Scienze del Suolo, Università degli Studi di Bari - Aldo Moro, Bari, 70126 Bari, Italy
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13
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Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye. PLoS One 2019; 14:e0214519. [PMID: 30921415 PMCID: PMC6438500 DOI: 10.1371/journal.pone.0214519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Rye (Secale cereale L.) is known for its wide adaptation due to its ability to tolerate harsh environments in semiarid areas. To assess the diversity in rye we genotyped a panel of 178 geographically diverse accessions of four Secale sp. from U.S. National Small Grains Collection using 4,037 high-quality SNPs (single nucleotide polymorphisms) developed by genotyping-by-sequencing (GBS). PCA and STRUCTURE analysis revealed three major clusters that separate S. cereale L. from S. strictum and S. sylvestre, however, genetic clusters did not correlate with geographic origins and growth habit (spring/winter). The panel was evaluated for response to Pyrenophora tritici-repentis race 5 (PTR race 5) and nearly 59% accessions showed resistance or moderate resistance. Genome-wide association study (GWAS) was performed on S. cereale subsp. cereale using the 4,037 high-quality SNPs. Two QTLs (QTs.sdsu-5R and QTs.sdsu-2R) on chromosomes 5R and 2R were identified conferring resistance to PTR race 5 (p < 0.001) that explained 13.1% and 11.6% of the phenotypic variation, respectively. Comparative analysis showed a high degree of synteny between rye and wheat with known rearrangements as expected. QTs.sdsu-2R was mapped in the genomic region corresponding to wheat chromosome group 2 and QTs.sdsu-5R was mapped to a small terminal region on chromosome 4BL. Based on the genetic diversity, a set of 32 accessions was identified to represents more than 99% of the allelic diversity with polymorphic information content (PIC) of 0.25. This set can be utilized for genetic characterization of useful traits and genetic improvement of rye, triticale, and wheat.
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14
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Karlin EF, Smouse PE. Holantarctic diversity varies widely among genetic loci within the gametophytically allotriploid peat moss Sphagnum × falcatulum. AMERICAN JOURNAL OF BOTANY 2019; 106:137-144. [PMID: 30644542 DOI: 10.1002/ajb2.1220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY The traditional approach used in analyses of population genetic data for historical inference is to average across multiple marker loci, but averaging conflates the different evolutionary signals provided by stable vs. labile markers. METHODS We used a battery of microsatellites with a wide range of mutation/substitution rates, grouping them into two sets (stable and hypervariable) to provide a more nuanced reconstruction of the population genetics and evolutionary history of the allotriploid peat moss Sphagnum × falcatulum across three disjunct regions. KEY RESULTS Shannon diversity translation analyses show that the relative apportionment of total within-species allelic diversity (∆WS ) within and among strata ranges widely, both between the two sets and within and among regions. The majority of diversity in the stable set was inherited directly from the ancestors of this genetically complex allopolyploid, but most of the diversity in the hypervariable set has developed post-hybrid-origin. CONCLUSIONS It is useful to group markers into sets having similar evolutionary lability, with each set being analyzed separately, particularly for allopolyploids. A methodology for determining how to group markers into such sets is presented, which can be applied to the requirements of other studies. Within-individual allelic diversity (ΔWI ) should be addressed in genetic studies on allopolyploids. Allotriploid haplotypes based on a set of nine highly stable microsatellites appear to serve as a clonal-detection set for S. × falcatulum. An additive "allele-metric" diversity approach is introduced, which facilitates a direct comparison of within- and among-stratum diversity components at all levels of diversity.
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Affiliation(s)
- Eric F Karlin
- Department of Environmental Science, School of Theoretical and Applied Science, Ramapo College, Mahwah, New Jersey, 07430-1680, USA
| | - Peter E Smouse
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, 08901-8551, USA
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O’Reilly GD, Jabot F, Gunn MR, Sherwin WB. Predicting Shannon’s information for genes in finite populations: new uses for old equations. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1079-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Brzyski JR, Stieha CR, Nicholas McLetchie D. The impact of asexual and sexual reproduction in spatial genetic structure within and between populations of the dioecious plant Marchantia inflexa (Marchantiaceae). ANNALS OF BOTANY 2018; 122:993-1003. [PMID: 29924293 PMCID: PMC6266107 DOI: 10.1093/aob/mcy106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Background and Aims In dioecious plants, sexual reproduction requires close proximity to potential mates, but clonal growth can increase this distance and, therefore, reduce the probability of mating. Reduction in sexual propagules can lead to decreased dispersal and gene flow between populations. Gene flow and clonal growth may be further influenced by the size of the habitat patch. The effects of habitat size and reproductive mode (sexual or asexual reproduction) on spatial genetic structure and segregation of the sexes were tested by quantifying the distributions of genotypes and the sexes using the dioecious liverwort Marchantia inflexa. Methods Plants were sampled from five pairs of small-large habitat patches to identify within- and among-population spatial genetic structure using 12 microsatellite markers. Spatial distributions were calculated as the likelihood that pairs of individuals were the same sex or genotype, and it was determined how that likelihood was affected by habitat patch size (small/large). Key Results Asexual reproduction dominates within populations, and asexual dispersal also occurred across populations. Spatial segregation of the sexes was observed within populations; males were more likely to be near individuals of the same sex than were females. Although the likelihood of both sexes being near members of the same sex was similarly greater on small habitat patches, on large habitat patches male genotypes were almost 15 % more likely to be near clonemates than were female genotypes. Conclusions The results show a sex difference in clonal clumping that was dependent upon habitat size, suggesting differential colonization and/or survival between males and females. The sexes and genotypes being structured differently within and among populations have implications for the persistence of populations and the interactions between them. This study demonstrates that studying only the sexes and not their genotypes (or vice versa) can limit our understanding of the extent to which reproductive modes (sexual or asexual) influence genetic structure both within and between populations.
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Entropy, or Information, Unifies Ecology and Evolution and Beyond. ENTROPY 2018; 20:e20100727. [PMID: 33265816 PMCID: PMC7512290 DOI: 10.3390/e20100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/18/2018] [Accepted: 09/11/2018] [Indexed: 02/07/2023]
Abstract
This article discusses how entropy/information methods are well-suited to analyzing and forecasting the four processes of innovation, transmission, movement, and adaptation, which are the common basis to ecology and evolution. Macroecologists study assemblages of differing species, whereas micro-evolutionary biologists study variants of heritable information within species, such as DNA and epigenetic modifications. These two different modes of variation are both driven by the same four basic processes, but approaches to these processes sometimes differ considerably. For example, macroecology often documents patterns without modeling underlying processes, with some notable exceptions. On the other hand, evolutionary biologists have a long history of deriving and testing mathematical genetic forecasts, previously focusing on entropies such as heterozygosity. Macroecology calls this Gini-Simpson, and has borrowed the genetic predictions, but sometimes this measure has shortcomings. Therefore it is important to note that predictive equations have now been derived for molecular diversity based on Shannon entropy and mutual information. As a result, we can now forecast all major types of entropy/information, creating a general predictive approach for the four basic processes in ecology and evolution. Additionally, the use of these methods will allow seamless integration with other studies such as the physical environment, and may even extend to assisting with evolutionary algorithms.
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Peretolchina T, Pavan MG, Corrêa-Antônio J, Gurgel-Gonçalves R, Lima MM, Monteiro FA. Phylogeography and demographic history of the Chagas disease vector Rhodnius nasutus (Hemiptera: Reduviidae) in the Brazilian Caatinga biome. PLoS Negl Trop Dis 2018; 12:e0006731. [PMID: 30248092 PMCID: PMC6195287 DOI: 10.1371/journal.pntd.0006731] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 10/19/2018] [Accepted: 08/03/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Rhodnius nasutus, a vector of the etiological agent Trypanosoma cruzi, is one of the epidemiologically most relevant triatomine species of the Brazilian Caatinga, where it often colonizes rural peridomestic structures such as chicken coops and occasionally invades houses. Historical colonization and determination of its genetic diversity and population structure may provide new information towards the improvement of vector control in the region. In this paper we present thoughtful analyses considering the phylogeography and demographic history of R. nasutus in the Caatinga. METHODOLOGY/PRINCIPAL FINDINGS A total of 157 R. nasutus specimens were collected from Copernicia prunifera palm trees in eight geographic localities within the Brazilian Caatinga biome, sequenced for 595-bp fragment of the mitochondrial cytochrome b gene (cyt b) and genotyped for eight microsatellite loci. Sixteen haplotypes were detected in the cyt b sequences, two of which were shared among different localities. Molecular diversity indices exhibited low diversity levels and a haplotype network revealed low divergence among R. nasutus sequences, with two central haplotypes shared by five of the eight populations analyzed. The demographic model that better represented R. nasutus population dynamics was the exponential growth model. Results of the microsatellite data analyses indicated that the entire population is comprised of four highly differentiated groups, with no obvious contemporary geographic barriers that could explain the population substructure detected. A complex pattern of migration was observed, in which a western Caatinga population seems to be the source of emigrants to the eastern populations. CONCLUSIONS/SIGNIFICANCE R. nasutus that inhabit C. prunifera palms do not comprise a species complex. The species went through a population expansion at 12-10 ka, during the Holocene, which coincides with end of the largest dry season in South America. It colonized the Caatinga in a process that occurred from west to east in the region. R. nasutus is presently facing an important ecological impact caused by the continuous deforestation of C. prunifera palms in northeast Brazil. We hypothesize that this ecological disturbance might contribute to an increase in the events of invasion and colonization of human habitations.
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Affiliation(s)
- Tatiana Peretolchina
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Laboratory of Molecular Systematics, Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Márcio G. Pavan
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Jessica Corrêa-Antônio
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Rodrigo Gurgel-Gonçalves
- Laboratório de Parasitologia Médica e Biologia de Vetores, Faculdade de Medicina, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Marli M. Lima
- Laboratório de Ecoepidemiologia da doença de Chagas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Fernando A. Monteiro
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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Gaggiotti OE, Chao A, Peres‐Neto P, Chiu C, Edwards C, Fortin M, Jost L, Richards CM, Selkoe KA. Diversity from genes to ecosystems: A unifying framework to study variation across biological metrics and scales. Evol Appl 2018; 11:1176-1193. [PMID: 30026805 PMCID: PMC6050189 DOI: 10.1111/eva.12593] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/21/2017] [Indexed: 02/03/2023] Open
Abstract
Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organization (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap, we present a unifying framework for the measurement of biodiversity across hierarchical levels of organization. Our weighted, information-based decomposition framework is based on a Hill number of order q = 1, which weights all elements in proportion to their frequency and leads to diversity measures based on Shannon's entropy. We investigated the numerical behaviour of our approach with simulations and showed that it can accurately describe complex spatial hierarchical structures. To demonstrate the intuitive and straightforward interpretation of our diversity measures in terms of effective number of components (alleles, species, etc.), we applied the framework to a real data set on coral reef biodiversity. We expect our framework will have multiple applications covering the fields of conservation biology, community genetics and eco-evolutionary dynamics.
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Affiliation(s)
- Oscar E. Gaggiotti
- School of BiologyScottish Oceans InstituteUniversity of St AndrewsSt AndrewsUK
| | - Anne Chao
- Institute of StatisticsNational Tsing Hua UniversityHsin‐ChuTaiwan
| | | | - Chun‐Huo Chiu
- Department of AgronomyNational Taiwan UniversityTaipeiTaiwan
| | - Christine Edwards
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSaint LouisMOUSA
| | - Marie‐Josée Fortin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Lou Jost
- Ecominga FundationBanosTungurahuaEcuador
| | | | - Kimberly A. Selkoe
- National Center for Ecological Analysis and SynthesisUniversity of California Santa BarbaraSanta BarbaraCAUSA
- Hawai'i Institute of Marine BiologyUniversity of Hawai'i at MānoaKaneoheHIUSA
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Makumbi D, Assanga S, Diallo A, Magorokosho C, Asea G, Worku M, Bänziger M. Genetic Analysis of Tropical Midaltitude- Adapted Maize Populations under Stress and Nonstress Conditions. CROP SCIENCE 2018; 58:1492-1507. [PMID: 33343010 PMCID: PMC7680935 DOI: 10.2135/cropsci2017.09.0531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 04/21/2018] [Indexed: 05/20/2023]
Abstract
Maize (Zea mays L.) yield in sub-Saharan Africa (SSA) is low because of both abiotic and biotic constraints, and limited availability or use of improved seed in some areas. This study was conducted (i) to estimate combining ability and heterosis among seven stress-tolerant populations, and (ii) to assess diversity among the populations and the relationship between diversity and heterosis. Twenty-one hybrids developed from diallel crosses of seven populations, parents, and two checks were evaluated in 10 optimal and 11 stressed environments (drought, low N, and random stress) in Kenya, Ethiopia, Uganda, and Zimbabwe for 2 yr. Analysis II of Gardner and Eberhart showed that variety and heterosis were significant for grain yield (GY) under optimal and managed stress, and across environments. Heterosis accounted for most of the variation for GY among populations under optimal conditions (67%) and drought stress (53%), which suggested the importance of dominance in inheritance of GY under these conditions. Genetic distance (GD) among populations ranged from 0.328 to 0.477 (mean = 0.404). The correlation between GD and heterosis was low (r = 0.14-0.40) in all environments. The simple sequence repeat (SSR) marker-based and GY-based clustering of parental populations showed similar patterns, with three populations distinct from the rest, suggesting significant differentiation of allelic variation in these three populations. The SSR-based diversity and phenotypic analysis results should be useful in defining breeding strategies and maintaining heterotic patterns among these populations.
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Affiliation(s)
- Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041-00621, Nairobi, Kenya
- Corresponding author ()
| | - Silvano Assanga
- International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041-00621, Nairobi, Kenya
| | - Alpha Diallo
- Monsanto Company, 1506 Hwy 69 Suite 100, Waco, NE 68460, USA
| | - Cosmos Magorokosho
- Guinee-Semences, Immeuble Guinomar, Camayenne, Corniche Nord, BP 5603, Conakry, Guinea
| | - Godfrey Asea
- International Maize and Wheat Improvement Center (CIMMYT), PO Box MP 163, Harare, Zimbabwe
| | - Mosisa Worku
- International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041-00621, Nairobi, Kenya
| | - Marianne Bänziger
- National Agricultural Research Organization, National Crops Resources Research Institute, Namulonge, PO Box 7084, Kampala, Uganda
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Dong Z, Li Y, Zhang Z. Genetic diversity of melon aphids Aphis gossypii associated with landscape features. Ecol Evol 2018; 8:6308-6316. [PMID: 29988436 PMCID: PMC6024126 DOI: 10.1002/ece3.4181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 04/06/2018] [Accepted: 04/22/2018] [Indexed: 11/10/2022] Open
Abstract
Despite increasing evidence that landscape features strongly influence the abundance and dispersal of insect populations, landscape composition has seldom been explicitly linked to genetic structure. We conducted a genetic study of the melon aphid, Aphis gossypii, in two counties of Beijing, China during spring migration using samples from watermelon. We performed aphid genetic analysis using restriction site associated DNA sequencing (2b-RAD) and investigated the relationship between land cover and the genetic diversity. The percentage area of land cover (cropland, vegetable, orchard, grassland, woodland) was quantified in each particular scale (ranging from 0.5 km to 3 km) and was used as a predictor variable in our generalized linear models. We found a moderate level of genetic differentiation among nine sampled populations. Geographic distance and genetic distance were not significantly associated, indicating that geographic location was not a barrier to migration. These nine populations could be clustered depending on their level of genetic diversity (high and low). The genetic diversity (Shannon's information index) was positively correlated with grassland at the spatial scales of 1 and 2 km and negatively with orchard and vegetable at 0.5 and 1 km. Genetic diversity was best predicted by the grassland + orchard + vegetable model at a spatial scale of 1 km. Based on the method of relative weights, orchard land had the greatest relative importance, followed by grassland and vegetable land, in that order. This study contributes to our understanding of the genetic variation of aphids in agricultural landscapes.
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Affiliation(s)
- Zhaoke Dong
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
| | - Yifan Li
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
- College of Plant ProtectionNorthwest A &F UniversityYanglingChina
| | - Zhiyong Zhang
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
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Cardilini APA, Sherman CDH, Sherwin WB, Rollins LA. Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers. PeerJ 2018; 6:e4573. [PMID: 29610709 PMCID: PMC5878929 DOI: 10.7717/peerj.4573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/14/2018] [Indexed: 12/23/2022] Open
Abstract
Empirical genetic datasets used for estimating contemporary dispersal in wild populations and to correctly identify dispersers are rarely tested to determine if they are capable of providing accurate results. Here we test whether a genetic dataset provides sufficient information to accurately identify first-generation dispersers. Using microsatellite data from three wild populations of common starlings (Sturnus vulgaris), we artificially simulated dispersal of a subset of individuals; we term this ‘Simulated Disperser Analysis’. We then ran analyses for diminishing numbers of loci, to assess at which point simulated dispersers could no longer be correctly identified. Not surprisingly, the correct identification of dispersers varied significantly depending on the individual chosen to ‘disperse’, the number of loci used, whether loci had high or low Polymorphic Information Content and the location to which the dispersers were moved. A review of the literature revealed that studies that have implemented first-generation migrant detection to date have used on average 10 microsatellite loci. Our results suggest at least 27 loci are required to accurately identify dispersers in the study system evaluated here. We suggest that future studies use the approach we describe to determine the appropriate number of markers needed to accurately identify dispersers in their study system; the unique nature of natural systems means that the number of markers required for each study system will vary. Future studies can use Simulated Disperser Analysis on pilot data to test marker panels for robustness to contemporary dispersal identification, providing a powerful tool in the efficient and accurate design of studies using genetic data to estimate dispersal.
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Affiliation(s)
- Adam P A Cardilini
- Faculty of Science, Engineering and Built Envrionment, Deakin University, Waurn Ponds, Vic, Australia
| | - Craig D H Sherman
- Centre for Integrative Ecology, Deakin University, Waurn Ponds, Vic, Australia
| | - William B Sherwin
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Lee A Rollins
- Centre for Integrative Ecology, Deakin University, Waurn Ponds, Vic, Australia.,Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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Sherwin WB, Chao A, Jost L, Smouse PE. Information Theory Broadens the Spectrum of Molecular Ecology and Evolution. Trends Ecol Evol 2017; 32:948-963. [PMID: 29126564 DOI: 10.1016/j.tree.2017.09.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 01/18/2023]
Abstract
Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance.
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Affiliation(s)
- W B Sherwin
- Evolution and Ecology Research Centre, School of Biological Earth and Environmental Science, University of New South Wales, Sydney, NSW 2052, Australia; Murdoch University Cetacean Research Unit, Murdoch University, South Road, Murdoch, WA 6150, Australia.
| | - A Chao
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - L Jost
- EcoMinga Foundation, Via a Runtun, Baños, Tungurahua, Ecuador
| | - P E Smouse
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8551, USA
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Smouse PE, Banks SC, Peakall R. Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others. PLoS One 2017; 12:e0185499. [PMID: 29088229 PMCID: PMC5663342 DOI: 10.1371/journal.pone.0185499] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/13/2017] [Indexed: 12/14/2022] Open
Abstract
The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.
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Affiliation(s)
- Peter E. Smouse
- Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Sam C. Banks
- The Fenner School of Environment and Society, The Australian National University, Acton, ACT, Australia
- * E-mail:
| | - Rod Peakall
- Research School of Biology, The Australian National University, Acton, ACT, Australia
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Ricotta C, Podani J. On some properties of the Bray-Curtis dissimilarity and their ecological meaning. ECOLOGICAL COMPLEXITY 2017. [DOI: 10.1016/j.ecocom.2017.07.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Karlin EF, Smouse PE. Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers. ANNALS OF BOTANY 2017; 120:221-231. [PMID: 28088765 PMCID: PMC5737827 DOI: 10.1093/aob/mcw269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/28/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations. METHODS Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures. KEY RESULTS The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information. CONCLUSIONS Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation, rather than by subsequent evolutionary radiation. However, some post-hybridization genetic diversification has become fixed in at least one regional population. Methodology allowing statistical analysis of any ploidy level is presented.
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Affiliation(s)
- Eric F. Karlin
- Environmental Science, School of Theoretical & Applied Science, Ramapo College, Mahwah, NJ 07430-1680, USA
| | - Peter E. Smouse
- Department of Ecology, Evolution, and Natural Resources, School of Environmental & Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8551, USA
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Littleford-Colquhoun BL, Clemente C, Whiting MJ, Ortiz-Barrientos D, Frère CH. Archipelagos of the Anthropocene: rapid and extensive differentiation of native terrestrial vertebrates in a single metropolis. Mol Ecol 2017; 26:2466-2481. [DOI: 10.1111/mec.14042] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/12/2016] [Accepted: 01/04/2017] [Indexed: 12/24/2022]
Affiliation(s)
| | - Christofer Clemente
- School of Science and Engineering; University of the Sunshine Coast; Maroochydore DC Qld 4556 Australia
| | - Martin J. Whiting
- Department of Biological Sciences; Macquarie University; Sydney NSW 2109 Australia
| | | | - Celine H. Frère
- School of Science and Engineering; University of the Sunshine Coast; Maroochydore DC Qld 4556 Australia
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Evidence of Subdivisions on Evolutionary Timescales in a Large, Declining Marsupial Distributed across a Phylogeographic Barrier. PLoS One 2016; 11:e0162789. [PMID: 27732594 PMCID: PMC5061365 DOI: 10.1371/journal.pone.0162789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 08/29/2016] [Indexed: 01/25/2023] Open
Abstract
Major prehistoric forces, such as the climatic shifts of the Pleistocene, can remain visible in a species’ population genetics. Inference of refuges via genetic tools is useful for conservation management as it can identify populations whose preservation may help retain a species’ adaptive potential. Such investigation is needed for Australia’s southern hairy-nosed wombat (Lasiorhinus latifrons), whose conservation status has recently deteriorated, and whose phylogeographic history during the Pleistocene may be atypical compared to other species. Its contemporary range spans approximately 2000 km of diverse habitat on either side of the Spencer Gulf, which was a land bridge during periods of Pleistocene aridity that may have allowed for migration circumventing the arid Eyrean barrier. We sampled from animals in nearly all known sites within the species’ current distribution, mainly using non-invasive methods, and employed nuclear and mitochondrial DNA analyses to assess alternative scenarios for Pleistocene impacts on population structure. We found evidence for mildly differentiated populations at the range extremes on either side of Spencer Gulf, with secondary contact between locations neighbouring each side of the barrier. These extreme western and eastern regions, and four other regions in between, were genetically distinct in genotypic clustering analyses. Estimates indicate modest, but complex gene flow patterns among some of these regions, in some cases possibly restricted for several thousand years. Prior to this study there was little information to aid risk assessment and prioritization of conservation interventions facilitating gene flow among populations of this species. The contributions of this study to that issue are outlined.
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Mandel JR, Ramsey AJ, Iorizzo M, Simon PW. Patterns of Gene Flow between Crop and Wild Carrot, Daucus carota (Apiaceae) in the United States. PLoS One 2016; 11:e0161971. [PMID: 27603516 PMCID: PMC5014312 DOI: 10.1371/journal.pone.0161971] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/18/2022] Open
Abstract
Studies of gene flow between crops and their wild relatives have implications for both management practices for cultivation and understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene flow for wild relatives of crop species. Moreover, the comparison of genetic markers with different modes of inheritance, or transmission, such as those of the nuclear and chloroplast genomes, can inform the relative risk of transgene escape via pollen versus seed. Here we investigate patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in two regions of the United States. We employed 15 nuclear simple sequence repeat (SSR) markers and one polymorphic chloroplast marker. Further, we utilized both conventional population genetic metrics along with Shannon diversity indices as the latter have been proposed to be more sensitive to allele frequency changes and differentiation. We found that populations in both regions that were proximal to crop fields showed lower levels of differentiation to the crops than populations that were located farther away. We also found that Shannon measures were more sensitive to differences in both genetic diversity and differentiation in our study. Finally, we found indirect evidence of paternal transmission of chloroplast DNA and accompanying lower than expected levels of chloroplast genetic structure amongst populations as might be expected if chloroplast DNA genes flow through both seed and pollen. Our findings of substantial gene flow for both nuclear and chloroplast markers demonstrate the efficiency of both pollen and seed to transfer genetic information amongst populations of carrot.
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Affiliation(s)
- Jennifer R. Mandel
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, United States of America
- W. Harry Feinstone Center for Genomic Research, The University of Memphis, Memphis, Tennessee, United States of America
- * E-mail:
| | - Adam J. Ramsey
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, United States of America
| | - Massimo Iorizzo
- Plants for Human Health Institute, Department of Horticultural Science, North Carolina State University, Kannapolis, North Carolina, United States of America
| | - Philipp W. Simon
- USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, Wisconsin, United States of America
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Gugala NA, Ishida Y, Georgiadis NJ, Roca AL. Development and characterization of microsatellite markers in the African forest elephant (Loxodonta cyclotis). BMC Res Notes 2016; 9:364. [PMID: 27456228 PMCID: PMC4960834 DOI: 10.1186/s13104-016-2167-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/16/2016] [Indexed: 11/26/2022] Open
Abstract
Background African elephants comprise two species, the savanna elephant (Loxodonta africana) and the forest elephant (L. cyclotis), which are distinct morphologically and genetically. Forest elephants are seriously threatened by poaching for meat and ivory, and by habitat destruction. However, microsatellite markers have thus far been developed only in African savanna elephants and Asian elephants, Elephas maximus. The application of microsatellite markers across deeply divergent lineages may produce irregular patterns such as large indels or null alleles. Thus we developed novel microsatellite markers using DNA from two African forest elephants. Findings One hundred microsatellite loci were identified in next generation shotgun sequences from two African forest elephants, of which 53 were considered suitable for testing. Twenty-three microsatellite markers successfully amplified elephant DNA without amplifying human DNA; these were further characterized in 15 individuals from Lope National Park, Gabon. Three of the markers were monomorphic and four of them carried only two alleles. The remaining sixteen polymorphic loci carried from 3 to 8 alleles, with observed heterozygosity ranging from 0.27 to 0.87, expected heterozygosity from 0.40 to 0.86, and the Shannon diversity index from 0.73 to 1.86. Linkage disequilibrium was not detected between loci, and no locus deviated from Hardy–Weinberg equilibrium. Conclusions The markers developed in this study will be useful for genetic analyses of the African forest elephant and contribute to their conservation and management. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2167-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalie A Gugala
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | | | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,The Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Sherwin WB. Genes are information, so information theory is coming to the aid of evolutionary biology. Mol Ecol Resour 2016; 15:1259-61. [PMID: 26452559 DOI: 10.1111/1755-0998.12458] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
Abstract
Speciation is central to evolutionary biology, and to elucidate it, we need to catch the early genetic changes that set nascent taxa on their path to species status (Via 2009). That challenge is difficult, of course, for two chief reasons: (i) serendipity is required to catch speciation in the act; and (ii) after a short time span with lingering gene flow, differentiation may be low and/or embodied only in rare alleles that are difficult to sample. In this issue of Molecular Ecology Resources, Smouse et al. (2015) have noted that optimal assessment of differentiation within and between nascent species should be robust to these challenges, and they identified a measure based on Shannon's information theory that has many advantages for this and numerous other tasks. The Shannon measure exhibits complete additivity of information at different levels of subdivision. Of all the family of diversity measures ('0' or allele counts, '1' or Shannon, '2' or heterozygosity, F(ST) and related metrics) Shannon's measure comes closest to weighting alleles by their frequencies. For the Shannon measure, rare alleles that represent early signals of nascent speciation are neither down-weighted to the point of irrelevance, as for level 2 measures, nor up-weighted to overpowering importance, as for level 0 measures (Chao et al. 2010, )2015. Shannon measures have a long history in population genetics, dating back to Shannon's PhD thesis in 1940 (Crow 2001), but have received only sporadic attention, until a resurgence of interest in the last ten years, as reviewed briefly by Smouse et al. (2015).
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Affiliation(s)
- William B Sherwin
- Evolution and Ecology Research Centre, University of NSW, Sydney, NSW, 2052, Australia.,Murdoch University Cetacean Research Unit, Murdoch University, South Road, Murdoch, WA, 6150, Australia
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Cooke GM, Schlub TE, Sherwin WB, Ord TJ. Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis. PLoS One 2016; 11:e0150991. [PMID: 27195493 PMCID: PMC4873183 DOI: 10.1371/journal.pone.0150991] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/21/2016] [Indexed: 11/19/2022] Open
Abstract
Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.
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Affiliation(s)
- Georgina M. Cooke
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
- The Australian Museum, Australian Museum Research Institute, Ichthyology, 6 College Street, Sydney NSW 2010, Australia
| | - Timothy E. Schlub
- Sydney School of Public Health, Sydney Medical School, University of Sydney, 2006 NSW, Australia
| | - William B. Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
| | - Terry J. Ord
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
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Keyel AC, Wiegand K. Validating the use of unique trait combinations for measuring multivariate functional richness. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Alexander C. Keyel
- Department of Ecosystem Modelling, Büsgenweg 4 University of Göttingen 37077 Göttingen Germany
| | - Kerstin Wiegand
- Department of Ecosystem Modelling, Büsgenweg 4 University of Göttingen 37077 Göttingen Germany
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Zinck JWR, Rajora OP. Post-glacial phylogeography and evolution of a wide-ranging highly-exploited keystone forest tree, eastern white pine (Pinus strobus) in North America: single refugium, multiple routes. BMC Evol Biol 2016; 16:56. [PMID: 26936598 PMCID: PMC4774161 DOI: 10.1186/s12862-016-0624-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/16/2016] [Indexed: 01/28/2023] Open
Abstract
Background Knowledge of the historical distribution and postglacial phylogeography and evolution of a species is important to better understand its current distribution and population structure and potential fate in the future, especially under climate change conditions, and conservation of its genetic resources. We have addressed this issue in a wide-ranging and heavily exploited keystone forest tree species of eastern North America, eastern white pine (Pinus strobus). We examined the range-wide population genetic structure, tested various hypothetical population history and evolutionary scenarios and inferred the location of glacial refugium and post-glacial recolonization routes. Our hypothesis was that eastern white pine survived in a single glacial refugium and expanded through multiple post-glacial recolonization routes. Results We studied the range-wide genetic diversity and population structure of 33 eastern white pine populations using 12 nuclear and 3 chloroplast microsatellite DNA markers. We used Approximate Bayesian Computation approach to test various evolutionary scenarios. We observed high levels of genetic diversity, and significant genetic differentiation (FST = 0.104) and population structure among eastern white pine populations across its range. A south to north trend of declining genetic diversity existed, consistent with repeated founder effects during post-glaciation migration northwards. We observed broad consensus from nuclear and chloroplast genetic markers supporting the presence of two main post-glacial recolonization routes that originated from a single southern refugium in the mid-Atlantic plain. One route gave rise to populations at the western margin of the species’ range in Minnesota and western Ontario. The second route gave rise to central-eastern populations, which branched into two subgroups: central and eastern. We observed minimal sharing of chloroplast haplotypes between recolonization routes but there was evidence of admixture between the western and west-central populations. Conclusions Our study reveals a single southern refugium, two recolonization routes and three genetically distinguishable lineages in eastern white pine that we suggest to be treated as separate Evolutionarily Significant Units. Like many wide-ranging North American species, eastern white pine retains the genetic signatures of post-glacial recolonization and evolution, and its contemporary population genetic structure reflects not just the modern distribution and effects of heavy exploitation but also routes northward from its glacial refugium. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0624-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John W R Zinck
- Faculty of Forestry and Environmental Management, University of New Brunswick, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada. .,Present address: Athletigen Technologies Inc., 535 Legget Drive, Kanata, ON, K2K 3B8, Canada.
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada.
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Dennison S, Frankham GJ, Neaves LE, Flanagan C, FitzGibbon S, Eldridge MDB, Johnson RN. Population genetics of the koala (Phascolarctos cinereus) in north-eastern New South Wales and south-eastern Queensland. AUST J ZOOL 2016. [DOI: 10.1071/zo16081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Habitat loss and fragmentation are key threats to local koala (Phascolarctos cinereus) populations. Broad-scale management is suboptimal for koalas because distribution models are not easily generalised across regions. Therefore, it is imperative that data relevant to local management bodies are available. Genetic data provides important information on gene flow and potential habitat barriers, including anthropogenic disturbances. Little genetic data are available for nationally significant koala populations in north-eastern New South Wales, despite reported declines due to urbanisation and habitat loss. In this study, we develop 14 novel microsatellite loci to investigate koala populations in north-eastern New South Wales (Port Macquarie, Coffs Harbour, Tyagarah, Ballina) and south-eastern Queensland (Coomera). All locations were significantly differentiated (FST = 0.096–0.213; FʹST = 0.282–0.582), and this pattern was not consistent with isolation by distance (R2 = 0.228, P = 0.058). Population assignment clustered the more northern populations (Ballina, Tyagarah and Coomera), suggesting contemporary gene flow among these sites. For all locations, low molecular variation among (16%) rather than within (84%) sites suggests historical connectivity. These results suggest that koala populations in north-eastern New South Wales and south-eastern Queensland are experiencing contemporary impediments to gene flow, and highlight the importance of maintaining habitat connectivity across this region.
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Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Island Model. PLoS One 2015; 10:e0125471. [PMID: 26067448 PMCID: PMC4465833 DOI: 10.1371/journal.pone.0125471] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 03/24/2015] [Indexed: 01/21/2023] Open
Abstract
Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.
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Smouse PE, Whitehead MR, Peakall R. An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation. Mol Ecol Resour 2015; 15:1375-84. [PMID: 25916981 DOI: 10.1111/1755-0998.12422] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/20/2015] [Accepted: 04/23/2015] [Indexed: 11/30/2022]
Abstract
Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require 'common currency' translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi-parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum-spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (N(ep) < (N(en)), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation.
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Affiliation(s)
- Peter E Smouse
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901-8551, USA
| | - Michael R Whitehead
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Rod Peakall
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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Dempewolf H, Tesfaye M, Teshome A, Bjorkman AD, Andrew RL, Scascitelli M, Black S, Bekele E, Engels JMM, Cronk QCB, Rieseberg LH. Patterns of domestication in the Ethiopian oil-seed crop noug (Guizotia abyssinica). Evol Appl 2015; 8:464-75. [PMID: 26029260 PMCID: PMC4430770 DOI: 10.1111/eva.12256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/13/2015] [Indexed: 11/27/2022] Open
Abstract
Noug (Guizotia abyssinica) is a semidomesticated oil-seed crop, which is primarily cultivated in Ethiopia. Unlike its closest crop relative, sunflower, noug has small seeds, small flowering heads, many branches, many flowering heads, and indeterminate flowering, and it shatters in the field. Here, we conducted common garden studies and microsatellite analyses of genetic variation to test whether high levels of crop-wild gene flow and/or unfavorable phenotypic correlations have hindered noug domestication. With the exception of one population, analyses of microsatellite variation failed to detect substantial recent admixture between noug and its wild progenitor. Likewise, only very weak correlations were found between seed mass and the number or size of flowering heads. Thus, noug's 'atypical' domestication syndrome does not seem to be a consequence of recent introgression or unfavorable phenotypic correlations. Nonetheless, our data do reveal evidence of local adaptation of noug cultivars to different precipitation regimes, as well as high levels of phenotypic plasticity, which may permit reasonable yields under diverse environmental conditions. Why noug has not been fully domesticated remains a mystery, but perhaps early farmers selected for resilience to episodic drought or untended environments rather than larger seeds. Domestication may also have been slowed by noug's outcrossing mating system.
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Affiliation(s)
- Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Misteru Tesfaye
- Ethiopian Institute of Agricultural Research, Holetta Agricultural Research Centre Addis Ababa, Ethiopia
| | - Abel Teshome
- Department of Plant Breeding, Swedish University of Agricultural Sciences Alnarp, Sweden
| | - Anne D Bjorkman
- Department of Geography and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Rose L Andrew
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Scott Black
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Endashaw Bekele
- College of Natural Sciences, Addis Ababa University Addis Ababa, Ethiopia
| | | | - Quentin C B Cronk
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada ; Department of Biology, Indiana University Bloomington, IN, USA
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Nagel MM, Sewell MA, Lavery SD. Differences in population connectivity of a benthic marine invertebrate Evechinus chloroticus (Echinodermata: Echinoidea) across large and small spatial scales. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0716-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Day T. Information entropy as a measure of genetic diversity and evolvability in colonization. Mol Ecol 2015; 24:2073-83. [DOI: 10.1111/mec.13082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Troy Day
- Department of Mathematics and Statistics; Jeffery Hall, Queen's University; Kingston ON K7L 3N6 Canada
- Department of Biology; Queen's University; Kingston ON K7L 3N6 Canada
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Zielke DE, Ibáñez-Justicia A, Kalan K, Merdić E, Kampen H, Werner D. Recently discovered Aedes japonicus japonicus (Diptera: Culicidae) populations in The Netherlands and northern Germany resulted from a new introduction event and from a split from an existing population. Parasit Vectors 2015; 8:40. [PMID: 25608763 PMCID: PMC4311435 DOI: 10.1186/s13071-015-0648-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/08/2015] [Indexed: 11/21/2022] Open
Abstract
Background Originally native to East Asia, Aedes japonicus japonicus, a potential vector of several arboviruses, has become one of the most invasive mosquito species in the world. After having established in the USA, it is now spreading in Europe, with new populations emerging. In contrast to the USA, the introduction pathways and modes of dispersal in Europe are largely obscure. Methods To find out if two recently detected populations of Ae. j. japonicus in The Netherlands and northern Germany go back to new importations or to movements within Europe, the genetic makeup of mosquito specimens from all known European populations was compared. For this purpose, seven microsatellite loci from a representative number of mosquito specimens were genotyped and part of their mitochondrial nad4 gene sequenced. Results A novel nad4 haplotype found in the newly discovered Dutch population of Ae. j. japonicus suggests that this population is not closely related to the other European populations but has emanated from a further introduction event. With five nad4 haplotypes, the Dutch population also shows a very high genetic diversity indicating that either the founder population was very large or multiple introductions took place. By contrast, the recently detected North German population could be clearly assigned to one of the two previously determined European Ae. j. japonicus microsatellite genotypes and shows nad4 haplotypes that are known from West Germany. Conclusion As the European populations of Ae. j. japonicus are geographically separated but genetically mixed, their establishment must be attributed to passive transportation. In addition to intercontinental shipment, it can be assumed that human activities are also responsible for medium- and short-distance overland spread. A better understanding of the processes underlying the introduction and spread of this invasive species will help to increase public awareness of the human-mediated displacement of mosquitoes and to find strategies to avoid it.
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Affiliation(s)
- Dorothee E Zielke
- Institute for Land Use Systems, Leibniz-Centre for Agricultural Landscape Research, Eberswalder Straße 84, 15374, Muencheberg, Germany.
| | - Adolfo Ibáñez-Justicia
- National Centre for Monitoring of Vectors, Netherlands Food and Consumer Product Safety Authority, Ministry of Economic Affairs Wageningen, Wageningen, The Netherlands.
| | | | | | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Greifswald, Germany.
| | - Doreen Werner
- Institute for Land Use Systems, Leibniz-Centre for Agricultural Landscape Research, Eberswalder Straße 84, 15374, Muencheberg, Germany.
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Demers JE, Gugino BK, Jiménez-Gasco MDM. Highly diverse endophytic and soil Fusarium oxysporum populations associated with field-grown tomato plants. Appl Environ Microbiol 2015; 81:81-90. [PMID: 25304514 PMCID: PMC4272710 DOI: 10.1128/aem.02590-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/07/2014] [Indexed: 12/23/2022] Open
Abstract
The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates.
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Affiliation(s)
- Jill E Demers
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Beth K Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - María Del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
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Greenbaum G, Templeton AR, Zarmi Y, Bar-David S. Allelic richness following population founding events--a stochastic modeling framework incorporating gene flow and genetic drift. PLoS One 2014; 9:e115203. [PMID: 25526062 PMCID: PMC4272294 DOI: 10.1371/journal.pone.0115203] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/19/2014] [Indexed: 11/19/2022] Open
Abstract
Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.
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Affiliation(s)
- Gili Greenbaum
- Department of Solar Energy and Environmental Physics, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- * E-mail:
| | - Alan R. Templeton
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
- Institute of Evolution, and Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Yair Zarmi
- Department of Solar Energy and Environmental Physics, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Shirli Bar-David
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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Putman AI, Carbone I. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol 2014; 4:4399-428. [PMID: 25540699 PMCID: PMC4267876 DOI: 10.1002/ece3.1305] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 12/14/2022] Open
Abstract
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (F ST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.
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Affiliation(s)
- Alexander I Putman
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
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Ernest HB, Vickers TW, Morrison SA, Buchalski MR, Boyce WM. Fractured genetic connectivity threatens a southern california puma (Puma concolor) population. PLoS One 2014; 9:e107985. [PMID: 25295530 PMCID: PMC4189954 DOI: 10.1371/journal.pone.0107985] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/30/2014] [Indexed: 11/18/2022] Open
Abstract
Pumas (Puma concolor; also known as mountain lions and cougars) in southern California live among a burgeoning human population of roughly 20 million people. Yet little is known of the consequences of attendant habitat loss and fragmentation, and human-caused puma mortality to puma population viability and genetic diversity. We examined genetic status of pumas in coastal mountains within the Peninsular Ranges south of Los Angeles, in San Diego, Riverside, and Orange counties. The Santa Ana Mountains are bounded by urbanization to the west, north, and east, and are separated from the eastern Peninsular Ranges to the southeast by a ten lane interstate highway (I-15). We analyzed DNA samples from 97 pumas sampled between 2001 and 2012. Genotypic data for forty-six microsatellite loci revealed that pumas sampled in the Santa Ana Mountains (n = 42) displayed lower genetic diversity than pumas from nearly every other region in California tested (n = 257), including those living in the Peninsular Ranges immediately to the east across I-15 (n = 55). Santa Ana Mountains pumas had high average pairwise relatedness, high individual internal relatedness, a low estimated effective population size, and strong evidence of a bottleneck and isolation from other populations in California. These and ecological findings provide clear evidence that Santa Ana Mountains pumas have been experiencing genetic impacts related to barriers to gene flow, and are a warning signal to wildlife managers and land use planners that mitigation efforts will be needed to stem further genetic and demographic decay in the Santa Ana Mountains puma population.
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Affiliation(s)
- Holly B. Ernest
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Wildlife and Ecology Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - T. Winston Vickers
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Scott A. Morrison
- The Nature Conservancy, San Francisco, California, United States of America
| | - Michael R. Buchalski
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Wildlife and Ecology Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Walter M. Boyce
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
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Zielke DE, Werner D, Schaffner F, Kampen H, Fonseca DM. Unexpected patterns of admixture in German populations of Aedes japonicus japonicus (Diptera: Culicidae) underscore the importance of human intervention. PLoS One 2014; 9:e99093. [PMID: 24992470 PMCID: PMC4081119 DOI: 10.1371/journal.pone.0099093] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 05/11/2014] [Indexed: 11/19/2022] Open
Abstract
The mosquito Aedes japonicus japonicus, originally restricted to temperate East Asia, is now widespread in North America and more recently has become established in Europe. To ascertain the putative number of separate introductions to Europe and examine patterns of expansion we analyzed the genetic makeup of Ae. j. japonicus populations from five cemeteries in North Rhine-Westphalia and Rhineland-Palatinate, two western German federal states, as well as of specimens from populations in Belgium, Switzerland, and Austria/Slovenia. To do so, we genotyped individual specimens at seven pre-existing polymorphic microsatellite loci and sequenced part of the nad4 mitochondrial locus. We found evidence of two different genotypic signatures associated with different nad4 mitochondrial haplotypes, indicating at least two genetically differentiated populations of Ae. j. japonicus in Europe (i.e. two distinct genotypes). Belgian, Swiss, and Austrian/Slovenian populations all share the same genotypic signature although they have become differentiated since isolation. Contrary to expectations, the German Ae. j. japonicus are not closely related to those in Belgium which are geographically nearest but are also highly inbred. German populations have a unique genotype but also evidence of mixing between the two genotypes. Also unexpectedly, the populations closest to the center of the German infestation had the highest levels of admixture indicating that separate introductions did not expand and merge but instead their expansion was driven by punctuated human-mediated transport. Critically, the resulting admixed populations have higher genetic diversity and appear invasive as indicated by their increased abundance and recent spread across western Germany.
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Affiliation(s)
- Dorothee E. Zielke
- Leibniz-Centre for Agricultural Landscape Research, Müncheberg, Germany
- * E-mail:
| | - Doreen Werner
- Leibniz-Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Francis Schaffner
- National Centre for Vector Entomology, Institute of Parasitology, University of Zurich, Zurich, Switzerland
- Avia-GIS, Zoersel, Belgium
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems, Germany
| | - Dina M. Fonseca
- Center for Vector Biology and Department of Entomology, Rutgers University, New Brunswick, New Jersey, United States of America
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Egizi A, Fonseca DM. Ecological limits can obscure expansion history: patterns of genetic diversity in a temperate mosquito in Hawaii. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0710-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Graça RN, Ross-Davis AL, Klopfenstein NB, Kim MS, Peever TL, Cannon PG, Aun CP, Mizubuti ESG, Alfenas AC. Rust disease of eucalypts, caused by Puccinia psidii, did not originate via host jump from guava in Brazil. Mol Ecol 2013; 22:6033-47. [PMID: 24112757 DOI: 10.1111/mec.12545] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 11/27/2022]
Abstract
The rust fungus, Puccinia psidii, is a devastating pathogen of introduced eucalypts (Eucalyptus spp.) in Brazil where it was first observed in 1912. This pathogen is hypothesized to be endemic to South and Central America and to have first infected eucalypts via a host jump from native guava (Psidium guajava). Ten microsatellite markers were used to genotype 148 P. psidii samples from eucalypts and guava plus five additional myrtaceous hosts across a wide geographic range of south-eastern Brazil and Uruguay. Principal coordinates analysis, a Bayesian clustering analysis and a minimum-spanning network revealed two major genetic clusters among the sampled isolates, one associated with guava and another associated with eucalypts and three additional hosts. Multilocus genotypes infecting guava differed by multiple mutational steps at eight loci compared with those infecting eucalypts. Approximate Bayesian computation revealed that evolutionary scenarios involving a coalescence event between guava- and eucalypt-associated pathogen populations within the past 1000 years are highly unlikely. None of the analyses supported the hypothesis that eucalypt-infecting P. psidii in Brazil originated via host jump from guava following the introduction of eucalypts to Brazil approximately 185 years ago. The existence of host-associated biotypes of P. psidii in Brazil indicates that this diversity must be considered when assessing the invasive threat posed by this pathogen to myrtaceous hosts worldwide.
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Affiliation(s)
- Rodrigo N Graça
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
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Chao A, Wang YT, Jost L. Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12108] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anne Chao
- Institute of Statistics; National Tsing Hua University; Hsin-Chu Taiwan 30043
| | - Y. T. Wang
- Institute of Statistics; National Tsing Hua University; Hsin-Chu Taiwan 30043
| | - Lou Jost
- EcoMinga Foundation; Via a Runtun Baños Tungurahua Ecuador
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50
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Rollins LA, Moles AT, Lam S, Buitenwerf R, Buswell JM, Brandenburger CR, Flores-Moreno H, Nielsen KB, Couchman E, Brown GS, Thomson FJ, Hemmings F, Frankham R, Sherwin WB. High genetic diversity is not essential for successful introduction. Ecol Evol 2013; 3:4501-17. [PMID: 24340190 PMCID: PMC3856749 DOI: 10.1002/ece3.824] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 08/16/2013] [Accepted: 08/28/2013] [Indexed: 01/08/2023] Open
Abstract
Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.
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Affiliation(s)
- Lee A Rollins
- School of Life & Environmental Sciences, Centre for Integrative Ecology, Deakin University Geelong, Vic., 3216, Australia ; School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, University of New South Wales Sydney, NSW, 2052, Australia
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