1
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Song Q, Quigley C, He R, Wang D, Nguyen H, Miranda C, Li Z. Development and implementation of nested single-nucleotide polymorphism (SNP) assays for breeding and genetic research applications. THE PLANT GENOME 2024:e20491. [PMID: 39034885 DOI: 10.1002/tpg2.20491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024]
Abstract
SoySNP50K and SoySNP6K are commonly used for soybean (Glycine max) genotyping. The SoySNP50K assay has been used to genetically analyze the entire USDA Soybean Germplasm Collection, while the SoySNP6K assay, containing a subset of 6000 single-nucleotide polymorphisms (SNPs) from SoySNP50K, has been used for quantitative trait loci mapping of different traits. To meet the needs for genomic selection, selection of parents for crosses, and characterization of breeding populations, especially early selection of ideal offspring from thousands of lines, we developed two assays, SoySNP3K and SoySNP1K, containing 3072 and 1252 SNPs, respectively, based on SoySNP50K and SoySNP6K mark sets. These two assays also contained the trait markers reported or contributed by soybean breeders. The SNPs in the SoySNP3K are a subset from SoySNP6K, while the SNPs in the SoySNP1K are a subset from SoySNP3K. These SNPs were chosen to reduce the SNP number in the large linkage blocks while capturing as much of the haplotype diversity as possible. They are highly polymorphic and of high quality. The mean minor allele frequencies of the SNPs in the southern and northern US elites were 0.25 and 0.27 for SoySNP3K, respectively, and 0.29 and 0.33 for SoySNP1K. The selected SNPs are a valuable source for developing targeted amplicon sequencing assay or beadchip assay in soybean. SoySNP3K and SoySNP1K assays are commercialized by Illumina Inc. and AgriPlex Genomics, respectively. Together with SoySNP50K and SoySNP6K, a series of nested assays with different marker densities will serve as additional low-cost genomic tools for genetic, genomic, and breeding research.
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Affiliation(s)
- Qijian Song
- USDA-ARS, Soybean Genomics & Improvement Laboratory, Beltsville, Maryland, USA
| | - Charles Quigley
- USDA-ARS, Soybean Genomics & Improvement Laboratory, Beltsville, Maryland, USA
| | - Ruifeng He
- USDA-ARS, Soybean Genomics & Improvement Laboratory, Beltsville, Maryland, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Henry Nguyen
- Molecular Genetics and Soybean Genomics Laboratory, Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | - Carrie Miranda
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Zenglu Li
- Institute of Plant Breeding, Genetics and Genomics/Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia, USA
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2
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Hu H, Scheben A, Wang J, Li F, Li C, Edwards D, Zhao J. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:544-554. [PMID: 37961986 PMCID: PMC10893937 DOI: 10.1111/pbi.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Fangping Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Centre for Crop & Food Innovation, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - David Edwards
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Australia & Centre for Applied BioinformaticsUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
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3
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Biedrzycka A, Konopiński MK, Popiołek M, Zawiślak M, Bartoszewicz M, Kloch A. Non-MHC immunity genes do not affect parasite load in European invasive populations of common raccoon. Sci Rep 2023; 13:15696. [PMID: 37735177 PMCID: PMC10514260 DOI: 10.1038/s41598-023-41721-1] [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: 02/08/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Understanding the evolutionary mechanisms behind invasion success enables predicting which alien species and populations are the most predisposed to become invasive. Parasites may mediate the success of biological invasions through their effect on host fitness. The evolution of increased competitive ability (EICA) hypothesis assumes that escape from parasites during the invasion process allows introduced species to decrease investment in immunity and allocate resources to dispersal and reproduction. Consequently, the selective pressure of parasites on host species in the invasive range should be relaxed. We used the case of the raccoon Procyon lotor invasion in Europe to investigate the effect of gastrointestinal pathogen pressure on non-MHC immune genetic diversity of newly established invasive populations. Despite distinct differences in parasite prevalence between analysed populations, we detected only marginal associations between two analysed SNPs and infection intensity. We argue that the differences in parasite prevalence are better explained by detected earlier associations with specific MHC-DRB alleles. While the escape from native parasites seems to allow decreased investment in overall immunity, which relaxes selective pressure imposed on immune genes, a wide range of MHC variants maintained in the invasive range may protect from newly encountered parasites.
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Affiliation(s)
- Aleksandra Biedrzycka
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland.
| | - Maciej K Konopiński
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Marcin Popiołek
- Department of Parasitology, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63/67, 51-148, Wrocław, Poland
| | - Marlena Zawiślak
- Department of Parasitology, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63/67, 51-148, Wrocław, Poland
| | | | - Agnieszka Kloch
- Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-089, Warszawa, Poland
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4
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Herczeg D, Palomar G, Zieliński P, van Riemsdijk I, Babik W, Dankovics R, Halpern B, Cvijanović M, Vörös J. Genomic analysis reveals complex population structure within the smooth newt, Lissotriton vulgaris, in Central Europe. Ecol Evol 2023; 13:e10478. [PMID: 37664508 PMCID: PMC10469019 DOI: 10.1002/ece3.10478] [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: 03/19/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Species with wide-range distributions usually display high genetic variation. This variation can be partly explained by historical lineages that were temporally isolated from each other and are back into secondary reproductive contact, and partly by local adaptations. The smooth newt (Lissotriton vulgaris) is one of the most widely distributed amphibians species across Eurasia and forms a species complex with a partially overlapping distribution and morphology. In the present study, we explored the population genomic structure of smooth newt lineages in the Carpathian Basin (CB) relying on single-nucleotide polymorphisms. Our dataset included new and previously published data to study the secondary contact zone between lineages in the CB and also tested for the barrier effect of rivers to gene flow between these lineages. We confirmed the presence of the South L. v. vulgaris Lineage distributed in Transdanubia and we provided new distribution records of L. v. ampelensis inhabiting the eastern territories of the CB. High genetic diversity of smooth newts was observed, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South with four distinct lineages of L. v. vulgaris and one lineage of L. v. ampelensis showing a low level of admixture with the spatially closest L. v. vulgaris lineage. Moreover, admixture detected at the interfluve of the main rivers (i.e. Danube and Tisza) suggested a secondary contact zone in the area. Finally, we found that the river Danube has a very weak effect on population divergence, while the river Tisza is a geographical barrier limiting gene flow between smooth newt lineages. As the range boundaries of L. v. vulgaris and L. v. ampelensis in the CB coincide with the river Tisza, our study underpins the influence of rivers in lineage diversification.
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Affiliation(s)
- Dávid Herczeg
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Wiesław Babik
- Institute of Environmental SciencesFaculty of Biology, Jagiellonian UniversityKrakówPoland
| | | | - Bálint Halpern
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
- MME Birdlife HungaryBudapestHungary
| | - Milena Cvijanović
- Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of SerbiaUniversity of BelgradeBelgradeSerbia
| | - Judit Vörös
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
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5
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Antunes B, Figueiredo-Vázquez C, Dudek K, Liana M, Pabijan M, Zieliński P, Babik W. Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris). Mol Ecol 2023; 32:4515-4530. [PMID: 35593303 DOI: 10.1111/mec.16543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
Ecologically distinct species may respond to landscape changes in different ways. In addition to basic ecological data, the extent of the geographic range has been successfully used as an indicator of species sensitivity to anthropogenic landscapes, with widespread species usually found to be less sensitive compared to range-restricted species. In this study, we investigate connectivity patterns of two closely related but ecologically distinct newt species - the range-restricted, Lissotriton montandoni and the widespread, L. vulgaris - using genomic data, a highly replicated setting (six geographic regions per species), and tools from landscape genetics. Our results show the importance of forest for connectivity in both species, but at the same time suggest differential use of forested habitat, with L. montandoni and L. vulgaris showing the highest connectivity at forest-core and forest-edges, respectively. Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased resistance in both species, but the effect was one to three orders of magnitude stronger in L. montandoni than in L. vulgaris. This result is consistent with a view of L. vulgaris as an ecological generalist. Even so, currently, the negative impact of anthropogenic landscapes is mainly seen in connectivity among L. vulgaris populations, which show significantly stronger isolation and lower effective sizes relative to L. montandoni. Overall, this study emphasizes how habitat destruction is compromising genetic connectivity not only in endemic, range-restricted species of conservation concern but also in widespread generalist species, despite their comparatively lower sensitivity to anthropogenic landscape changes.
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Affiliation(s)
- Bernardo Antunes
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Clara Figueiredo-Vázquez
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | - Maciej Pabijan
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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6
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Wang H, Campbell B, Happ M, McConaughy S, Lorenz A, Amundsen K, Song Q, Pantalone V, Hyten D. Development of molecular inversion probes for soybean progeny genomic selection genotyping. THE PLANT GENOME 2023; 16:e20270. [PMID: 36411593 DOI: 10.1002/tpg2.20270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 05/10/2023]
Abstract
Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome-wide single-nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) are a targeted genotyping-by-sequencing (GBS) method that could be used for soybean [Glycine max (L.) Merr.] that is both cost-effective, high-throughput, and provides high data quality to screen breeder's germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the northern-central and middle-southern regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line (RIL) population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. The MIP genotyping accuracy was 93% overall, whereas homozygous call accuracy was 98% with <10% missing data. The accuracy of MIPs combined with its low per-sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs.
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Affiliation(s)
- Haichuan Wang
- Dep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA
| | - Benjamin Campbell
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA
| | - Mary Happ
- Dep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA
| | - Samantha McConaughy
- Dep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA
| | - Aaron Lorenz
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA
| | - Keenan Amundsen
- Dep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA
| | - Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, USA
| | | | - David Hyten
- Dep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA
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7
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Konopiński MK, Fijarczyk AM, Biedrzycka A. Complex patterns shape immune genes diversity during invasion of common raccoon in Europe - Selection in action despite genetic drift. Evol Appl 2023; 16:134-151. [PMID: 36699132 PMCID: PMC9850017 DOI: 10.1111/eva.13517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon Procyon lotor invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific single-nucleotide polymorphism markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, that is - less genetically diverse invasive population from the Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.
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Affiliation(s)
| | - Anna M. Fijarczyk
- Laval University Département de BiologieUniversité LavalQuébecQuébecCanada
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8
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Rajendran NR, Qureshi N, Pourkheirandish M. Genotyping by Sequencing Advancements in Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:931423. [PMID: 36003814 PMCID: PMC9394214 DOI: 10.3389/fpls.2022.931423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.
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Affiliation(s)
- Nirmal Raj Rajendran
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico, Mexico
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
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9
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Sequeira F, Arntzen JW, van Gulik D, Hajema S, Diaz RL, Wagt M, van Riemsdijk I. Genetic traces of hybrid zone movement across a fragmented habitat. J Evol Biol 2022; 35:400-412. [PMID: 35043504 DOI: 10.1111/jeb.13982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression across markers. We here investigate a hybrid zone formed by two subspecies of the Iberian golden-striped salamander, Chioglossa lusitanica, using a panel of 35 nuclear loci (31 SNPs and 4 allozymes) and one mitochondrial locus in a transect in central Portugal. We found concordant and coincident clines for most of the nuclear loci (n=22, 63%), defining a narrow hybrid zone of ca. 6 km wide, with the centre positioned ca. 15 km south of the Mondego river. Asymmetric introgression was observed at another 14 loci. Their clines are displaced towards the north, with positions located either close to the Mondego river (n=6), or further northwards (n=8). We interpret these profiles as genetic traces of the southward displacement of C. lusitanica lusitanica by C. l. longipes over the wider Mondego river valley. We noted the absence of significant linkage disequilibrium and we inferred low levels of effective selection per locus against hybrids, suggesting that introgression in the area of species replacement occurred under a neutral diffusion process. A species distribution model suggests that the C. lusitanica hybrid zone coincides with a narrow corridor of fragmented habitat. From the position of the displaced clines, we infer that patches of locally suitable habitat trapped some genetic variants that became disassociated from the southward moving hybrid zone. This study highlights the influence of habitat availability on hybrid zone movement.
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Affiliation(s)
- Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Jan W Arntzen
- Institute of Biology, Leiden University, Leiden, The Netherlands.,Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Davy van Gulik
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Steven Hajema
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Ruben Lopez Diaz
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Mattijn Wagt
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Isolde van Riemsdijk
- Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands.,Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
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10
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van Riemsdijk I, Arntzen JW, Babik W, Bogaerts S, Franzen M, Kalaentzis K, Litvinchuk SN, Olgun K, Wijnands JWPM, Wielstra B. Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure. Mol Phylogenet Evol 2021; 167:107361. [PMID: 34775056 DOI: 10.1016/j.ympev.2021.107361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.
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Affiliation(s)
- Isolde van Riemsdijk
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands; Institute for Evolution and Ecology, Auf der Morgenstelle 5, D-72076, Tübingen University, Tübingen, Germany
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | | | - Michael Franzen
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Konstantinos Kalaentzis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064 St. Petersburg, Russia
| | - Kurtuluş Olgun
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, 09010 Aydın, Turkey
| | - Jan Willem P M Wijnands
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands.
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11
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Palomar G, Dudek K, Migalska M, Arntzen JW, Ficetola GF, Jelić D, Jockusch E, Martínez-Solano I, Matsunami M, Shaffer HB, Vörös J, Waldman B, Wielstra B, Babik W. Coevolution between MHC class I and Antigen Processing Genes in salamanders. Mol Biol Evol 2021; 38:5092-5106. [PMID: 34375431 PMCID: PMC8557411 DOI: 10.1093/molbev/msab237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins encoded by antigen-processing genes (APGs) provide major histocompatibility complex (MHC) class I (MHC-I) with antigenic peptides. In mammals, polymorphic multigenic MHC-I family is served by monomorphic APGs, whereas in certain nonmammalian species both MHC-I and APGs are polymorphic and coevolve within stable haplotypes. Coevolution was suggested as an ancestral gnathostome feature, presumably enabling only a single highly expressed classical MHC-I gene. In this view coevolution, while optimizing some aspects of adaptive immunity, would also limit its flexibility by preventing the expansion of classical MHC-I into a multigene family. However, some nonmammalian taxa, such as salamanders, have multiple highly expressed MHC-I genes, suggesting either that coevolution is relaxed or that it does not prevent the establishment of multigene MHC-I. To distinguish between these two alternatives, we use salamanders (30 species from 16 genera representing six families) to test, within a comparative framework, a major prediction of the coevolution hypothesis: the positive correlation between MHC-I and APG diversity. We found that MHC-I diversity explained both within-individual and species-wide diversity of two APGs, TAP1 and TAP2, supporting their coevolution with MHC-I, whereas no consistent effect was detected for the other three APGs (PSMB8, PSMB9, and TAPBP). Our results imply that although coevolution occurs in salamanders, it does not preclude the expansion of the MHC-I gene family. Contrary to the previous suggestions, nonmammalian vertebrates thus may be able to accommodate diverse selection pressures with flexibility granted by rapid expansion or contraction of the MHC-I family, while retaining the benefits of coevolution between MHC-I and TAPs.
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Affiliation(s)
- G Palomar
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - K Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - M Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - J W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA leiden, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, 2300 RA Leiden, The Netherlands
| | - G F Ficetola
- Department of Environmental Sciences and Policy, University of Milano, Italy.,Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes and Université Savoie Mont Blanc, Grenoble, France
| | - D Jelić
- Croatian Institute for Biodiversity, Zagreb, Croatia
| | - E Jockusch
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT USA
| | - I Martínez-Solano
- Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - M Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - H B Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - J Vörös
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - B Waldman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA.,School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - B Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA leiden, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, 2300 RA Leiden, The Netherlands
| | - W Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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12
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Palomar G, Dudek K, Wielstra B, Jockusch EL, Vinkler M, Arntzen JW, Ficetola GF, Matsunami M, Waldman B, Těšický M, Zieliński P, Babik W. Molecular Evolution of Antigen-Processing Genes in Salamanders: Do They Coevolve with MHC Class I Genes? Genome Biol Evol 2021; 13:6121093. [PMID: 33501944 PMCID: PMC7883663 DOI: 10.1093/gbe/evaa259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Proteins encoded by antigen-processing genes (APGs) prepare antigens for presentation by the major histocompatibility complex class I (MHC I) molecules. Coevolution between APGs and MHC I genes has been proposed as the ancestral gnathostome condition. The hypothesis predicts a single highly expressed MHC I gene and tight linkage between APGs and MHC I. In addition, APGs should evolve under positive selection, a consequence of the adaptive evolution in MHC I. The presence of multiple highly expressed MHC I genes in some teleosts, birds, and urodeles appears incompatible with the coevolution hypothesis. Here, we use urodele amphibians to test two key expectations derived from the coevolution hypothesis: 1) the linkage between APGs and MHC I was studied in Lissotriton newts and 2) the evidence for adaptive evolution in APGs was assessed using 42 urodele species comprising 21 genera from seven families. We demonstrated that five APGs (PSMB8, PSMB9, TAP1, TAP2, and TAPBP) are tightly linked (<0.5 cM) to MHC I. Although all APGs showed some codons under episodic positive selection, we did not find a pervasive signal of positive selection expected under the coevolution hypothesis. Gene duplications, putative gene losses, and divergent allelic lineages detected in some APGs demonstrate considerable evolutionary dynamics of APGs in salamanders. Overall, our results indicate that if coevolution between APGs and MHC I occurred in urodeles, it would be more complex than envisaged in the original formulation of the hypothesis.
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Affiliation(s)
- Gemma Palomar
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, The Netherlands.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Elizabeth L Jockusch
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Gentile F Ficetola
- Department of Environmental Sciences and Policy, University of Milano, Italy.,Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes and Université Savoie Mont Blanc, Grenoble, France
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Bruce Waldman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA.,School of Biological Sciences, Seoul National University, South Korea
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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13
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López‐Delgado J, van Riemsdijk I, Arntzen JW. Tracing species replacement in Iberian marbled newts. Ecol Evol 2021; 11:402-414. [PMID: 33437438 PMCID: PMC7790658 DOI: 10.1002/ece3.7060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 11/25/2022] Open
Abstract
Secondary contact between closely related species can lead to the formation of hybrid zones, allowing for interspecific gene flow. Hybrid zone movement can take place if one of the species possesses a competitive advantage over the other, ultimately resulting in species replacement. Such hybrid zone displacement is predicted to leave a genomic footprint across the landscape in the form of asymmetric gene flow (or introgression) of selectively neutral alleles from the displaced to the advancing species. Hybrid zone movement has been suggested for marbled newts in the Iberian Peninsula, supported by asymmetric gene flow and a distribution relict (i.e., an enclave) of Triturus marmoratus in the range of T. pygmaeus. We developed a panel of nuclear and mitochondrial SNP markers to test for the presence of a T. marmoratus genomic footprint in the Lisbon peninsula, south of the enclave. We found no additional populations of T. marmoratus. Analysis with the software Structure showed no genetic traces of T. marmoratus in T. pygmaeus. A principal component analysis showed some variation within the local T. pygmaeus, but it is unclear if this represents introgression from T. marmoratus. The results may be explained by (a) species replacement without introgressive hybridization and (b) displacement with hybridization followed by the near-complete erosion of the footprint by purifying selection. We predict that testing for a genomic footprint north of the reported enclave would confirm that species replacement in these marbled newts occurred with hybridization.
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Affiliation(s)
- Julia López‐Delgado
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute for BiologyLeiden UniversityLeidenThe Netherlands
- Present address:
University of LeedsLeedsUnited Kingdom
| | - Isolde van Riemsdijk
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Present address:
Institute for Evolution and Ecology, Tübingen UniversityLeedsGermany
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14
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Song Q, Yan L, Quigley C, Fickus E, Wei H, Chen L, Dong F, Araya S, Liu J, Hyten D, Pantalone V, Nelson RL. Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:800-811. [PMID: 32772442 PMCID: PMC7702105 DOI: 10.1111/tpj.14960] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/30/2020] [Indexed: 05/10/2023]
Abstract
The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000-2000 genome-wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.
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Affiliation(s)
- Qijian Song
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Long Yan
- Shijiazhuang Branch Center of National Center for Soybean Improvement/the Key Laboratory of Crop Genetics and BreedingInstitute of Cereal and Oil CropsHebei Academy of Agricultural and Forestry SciencesShijiazhuangChina
| | - Charles Quigley
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Edward Fickus
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - He Wei
- Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouHenan ProvinceChina
| | - Linfeng Chen
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Faming Dong
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Susan Araya
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Jinlong Liu
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - David Hyten
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | | | - Randall L. Nelson
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop SciencesUSDA‐ARSUniversity of IllinoisUrbanaILUSA
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15
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Strianese O, Rizzo F, Ciccarelli M, Galasso G, D’Agostino Y, Salvati A, Del Giudice C, Tesorio P, Rusciano MR. Precision and Personalized Medicine: How Genomic Approach Improves the Management of Cardiovascular and Neurodegenerative Disease. Genes (Basel) 2020; 11:E747. [PMID: 32640513 PMCID: PMC7397223 DOI: 10.3390/genes11070747] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Life expectancy has gradually grown over the last century. This has deeply affected healthcare costs, since the growth of an aging population is correlated to the increasing burden of chronic diseases. This represents the interesting challenge of how to manage patients with chronic diseases in order to improve health care budgets. Effective primary prevention could represent a promising route. To this end, precision, together with personalized medicine, are useful instruments in order to investigate pathological processes before the appearance of clinical symptoms and to guide physicians to choose a targeted therapy to manage the patient. Cardiovascular and neurodegenerative diseases represent suitable models for taking full advantage of precision medicine technologies applied to all stages of disease development. The availability of high technology incorporating artificial intelligence and advancement progress made in the field of biomedical research have been substantial to understand how genes, epigenetic modifications, aging, nutrition, drugs, microbiome and other environmental factors can impact health and chronic disorders. The aim of the present review is to address how precision and personalized medicine can bring greater clarity to the clinical and biological complexity of these types of disorders associated with high mortality, involving tremendous health care costs, by describing in detail the methods that can be applied. This might offer precious tools for preventive strategies and possible clues on the evolution of the disease and could help in predicting morbidity, mortality and detecting chronic disease indicators much earlier in the disease course. This, of course, will have a major effect on both improving the quality of care and quality of life of the patients and reducing time efforts and healthcare costs.
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Affiliation(s)
- Oriana Strianese
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
| | - Gennaro Galasso
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
| | - Ylenia D’Agostino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Carmine Del Giudice
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
| | - Paola Tesorio
- Unit of Cardiology, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy;
| | - Maria Rosaria Rusciano
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
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16
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Pogoda M, Hilke FJ, Lohmann E, Sturm M, Lenz F, Matthes J, Muyas F, Ossowski S, Hoischen A, Faust U, Sepahi I, Casadei N, Poths S, Riess O, Schroeder C, Grundmann K. Single Molecule Molecular Inversion Probes for High Throughput Germline Screenings in Dystonia. Front Neurol 2020; 10:1332. [PMID: 31920950 PMCID: PMC6930228 DOI: 10.3389/fneur.2019.01332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022] Open
Abstract
Background: This study's aim was to investigate a large cohort of dystonia patients for pathogenic and rare variants in the ATM gene, making use of a new, cost-efficient enrichment technology for NGS-based screening. Methods: Single molecule Molecular Inversion Probes (smMIPs) were used for targeted enrichment and sequencing of all protein coding exons and exon-intron boundaries of the ATM gene in 373 dystonia patients and six positive controls with known ATM variants. Additionally, a rare-variant association study was performed. Results: One patient (0.3%) was compound heterozygous and 21 others were carriers of variants of unknown significance (VUS) in the ATM gene. Although mutations in sporadic dystonia patients are not common, exclusion of pathogenic variants is crucial to recognize a potential tumor predisposition syndrome. SmMIPs produced similar results as routinely used NGS-based approaches. Conclusion: Our results underline the importance of implementing ATM in the routine genetic testing of dystonia patients and confirm the reliability of smMIPs and their usability for germline screenings in rare neurodegenerative conditions.
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Affiliation(s)
- Michaela Pogoda
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Franz-Joachim Hilke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ebba Lohmann
- Behavioral Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey.,Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Florian Lenz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Jakob Matthes
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Francesc Muyas
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Bioinformatics and Genomics Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Bioinformatics and Genomics Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands.,Radboud Institute of Molecular Life Sciences, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ilnaz Sepahi
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,DFG NGS Competence Center Tübingen, Tübingen, Germany
| | - Sven Poths
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,DFG NGS Competence Center Tübingen, Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Kathrin Grundmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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17
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van Riemsdijk I, Butlin RK, Wielstra B, Arntzen JW. Testing an hypothesis of hybrid zone movement for toads in France. Mol Ecol 2019; 28:1070-1083. [PMID: 30609055 DOI: 10.1111/mec.15005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/08/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.
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Affiliation(s)
- Isolde van Riemsdijk
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ben Wielstra
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California
| | - Jan W Arntzen
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands
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18
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Zieliński P, Dudek K, Arntzen JW, Palomar G, Niedzicka M, Fijarczyk A, Liana M, Cogǎlniceanu D, Babik W. Differential introgression across newt hybrid zones: Evidence from replicated transects. Mol Ecol 2019; 28:4811-4824. [DOI: 10.1111/mec.15251] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Piotr Zieliński
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | | | - Gemma Palomar
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Anna Fijarczyk
- Département de Biologie Faculté des Sciences et de génie Université Laval Québec QC Canada
| | | | - Dan Cogǎlniceanu
- Faculty of Natural Sciences and Agricultural Sciences University Ovidius Constanţa Constanţa Romania
| | - Wiesław Babik
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
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19
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Shukor S, Tamayo A, Tosi L, Larman HB, Parekkadan B. Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning. BMC Biotechnol 2019; 19:50. [PMID: 31340783 PMCID: PMC6657055 DOI: 10.1186/s12896-019-0547-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/11/2019] [Indexed: 12/02/2022] Open
Abstract
Background Long Adapter Single-Stranded Oligonucleotide (LASSO) probes were developed as a novel tool for massively parallel cloning of kilobase-long genomic DNA sequences. LASSO dramatically improves the capture length limit of current DNA padlock probe technology from approximately 150 bps to several kbps. High-throughput LASSO capture involves the parallel assembly of thousands of probes. However, malformed probes are indiscernible from properly formed probes using gel electrophoretic techniques. Therefore, we used next-generation sequencing (NGS) to assess the efficiency of LASSO probe assembly and how it relates to the nature of DNA capture and amplification. Additionally, we introduce a simplified single target LASSO protocol using classic molecular biology techniques for qualitative and quantitative assessment of probe specificity. Results A LASSO probe library targeting 3164 unique E. coli ORFs was assembled using two different probe assembly reaction conditions with a 40-fold difference in DNA concentration. Unique probe sequences are located within the first 50 bps of the 5′ and 3′ ends, therefore we used paired-end NGS to assess probe library quality. Properly mapped read pairs, representing correctly formed probes, accounted for 10.81 and 0.65% of total reads, corresponding to ~ 80% and ~ 20% coverage of the total probe library for the lower and higher DNA concentration conditions, respectively. Subsequently, we used single-end NGS to correlate probe assembly efficiency and capture quality. Significant enrichment of LASSO targets over non-targets was only observed for captures done using probes assembled with a lower DNA concentration. Additionally, semi-quantitative polyacrylamide gel electrophoresis revealed a ~ 10-fold signal-to-noise ratio of LASSO capture in a simplified system. Conclusions These results suggest that LASSO probe coverage for target sequences is more predictive of successful capture than probe assembly depth-enrichment. Concomitantly, these results demonstrate that DNA concentration at a critical step in the probe assembly reaction significantly impacts probe formation. Additionally, we show that a simplified LASSO capture protocol coupled to PAGE (polyacrylamide gel electrophoresis) is highly specific and more amenable to small-scale LASSO approaches, such as screening novel probes and templates. Electronic supplementary material The online version of this article (10.1186/s12896-019-0547-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Syukri Shukor
- Center for Surgery, Innovation, and Bioengineering, Department of Surgery, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom Street, Boston, MA, 02114, USA
| | - Alfred Tamayo
- Center for Surgery, Innovation, and Bioengineering, Department of Surgery, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom Street, Boston, MA, 02114, USA
| | - Lorenzo Tosi
- Center for Surgery, Innovation, and Bioengineering, Department of Surgery, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom Street, Boston, MA, 02114, USA
| | - H Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Biju Parekkadan
- Center for Surgery, Innovation, and Bioengineering, Department of Surgery, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom Street, Boston, MA, 02114, USA. .,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA. .,Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, 08854, USA.
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20
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Lv J, Jiao W, Guo H, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S. HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay. Genome Res 2018; 28:1919-1930. [PMID: 30409770 PMCID: PMC6280760 DOI: 10.1101/gr.235820.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 10/25/2018] [Indexed: 01/03/2023]
Abstract
Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called HD-Marker), which addresses the array-related issues of original GoldenGate methodology and allows for highly multiplexed and flexible targeted genotyping of more than 12,000 loci in a single-tube assay (in contrast to fewer than 3100 in the original GoldenGate assay). We perform extensive analyses to demonstrate the power and performance of HD-Marker on various multiplex levels (296, 795, 1293, and 12,472 genic SNPs) across two sequencing platforms in two nonmodel species (the scallops Chlamys farreri and Patinopecten yessoensis), with extremely high capture rate (98%-99%) and genotyping accuracy (97%-99%). We also demonstrate the potential of HD-Marker for high-throughput targeted genotyping of alternative marker types (e.g., microsatellites and indels). With its remarkable cost-effectiveness (as low as $0.002 per genotype) and high flexibility in choice of multiplex levels and marker types, HD-Marker provides a highly attractive tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.
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Affiliation(s)
- Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haobing Guo
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ruijia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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21
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Fijarczyk A, Dudek K, Niedzicka M, Babik W. Balancing selection and introgression of newt immune-response genes. Proc Biol Sci 2018; 285:20180819. [PMID: 30111606 PMCID: PMC6111169 DOI: 10.1098/rspb.2018.0819] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022] Open
Abstract
The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favour novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common non-synonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, Université Laval, 1030, Avenue de la Médecine, Québec, Canada G1V 0A6
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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22
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Guppy JL, Jones DB, Jerry DR, Wade NM, Raadsma HW, Huerlimann R, Zenger KR. The State of " Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization. Front Genet 2018; 9:282. [PMID: 30123237 PMCID: PMC6085479 DOI: 10.3389/fgene.2018.00282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.
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Affiliation(s)
- Jarrod L. Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - David B. Jones
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Dean R. Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Nicholas M. Wade
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Aquaculture Program, CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Herman W. Raadsma
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Roger Huerlimann
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Kyall R. Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
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23
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Wielstra B, Canestrelli D, Cvijanović M, Denoël M, Fijarczyk A, Jablonski D, Liana M, Naumov B, Olgun K, Pabijan M, Pezzarossa A, Popgeorgiev G, Salvi D, Si Y, Sillero N, Sotiropoulos K, Zieliński P, Babik W. The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe. AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
The ‘smooth newt’, the taxon traditionally referred to as Lissotriton vulgaris, consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, L. vulgaris sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, L. graecus, L. kosswigi, L. lantzi, L. schmidtleri and a more restricted L. vulgaris. The Carpathian newt L. montandoni was confirmed to be a closely related sister species. We propose to refer to this collective of six Lissotriton species as the smooth newt or Lissotriton vulgaris species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones.
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Affiliation(s)
- Ben Wielstra
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- 2Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, UK
- 3Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Daniele Canestrelli
- 4Department of Ecological and Biological Science, Tuscia University, 01100 Viterbo, Italy
| | - Milena Cvijanović
- 5Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bul. Despota Stefana 142, 11060 Belgrade, Serbia
| | - Mathieu Denoël
- 6Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
| | - Anna Fijarczyk
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
- 8Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, Canada
| | - Daniel Jablonski
- 9Department of Zoology, Comenius University in Bratislava Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | | | - Borislav Naumov
- 11Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Kurtuluş Olgun
- 12Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, 09010 Aydın, Turkey
| | - Maciej Pabijan
- 13Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Alice Pezzarossa
- 4Department of Ecological and Biological Science, Tuscia University, 01100 Viterbo, Italy
| | - Georgi Popgeorgiev
- 14National Museum of Natural History, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd, 1000 Sofia, Bulgaria
| | - Daniele Salvi
- 15Department of Health, Life and Environmental Sciences, University of L’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, Italy
- 16CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Yali Si
- 17Ministry of Education Key Laboratory for Earth System Modeling, and Department of Earth System Science, Tsinghua University, Beijing, China
- 18Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Yong Drive South, Los Angeles, CA 90095, USA
| | - Neftalí Sillero
- 19CICGE – Centro de Investigação em Ciências Geo-Espaciais, Observatório Astronómico Prof. Manuel de Barros, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - Konstantinos Sotiropoulos
- 20Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Piotr Zieliński
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Wiesław Babik
- 7Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
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24
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Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation. G3-GENES GENOMES GENETICS 2017; 7:2115-2124. [PMID: 28500054 PMCID: PMC5499121 DOI: 10.1534/g3.117.041178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.
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25
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Abstract
Human genetic studies have been the driving force in bringing to light the underlying biology of psychiatric conditions. As these studies fill in the gaps in our knowledge of the mechanisms at play, we will be better equipped to design therapies in rational and targeted ways, or repurpose existing therapies in previously unanticipated ways. This review is intended for those unfamiliar with psychiatric genetics as a field and provides a primer on different modes of genetic variation, the technologies currently used to probe them, and concepts that provide context for interpreting the gene-phenotype relationship. Like other subfields in human genetics, psychiatric genetics is moving from microarray technology to sequencing-based approaches as barriers of cost and expertise are removed, and the ramifications of this transition are discussed here. A summary is then given of recent genetic discoveries in a number of neuropsychiatric conditions, with particular emphasis on neurodevelopmental conditions. The general impact of genetics on drug development has been to underscore the extensive etiological heterogeneity in seemingly cohesive diagnostic categories. Consequently, the path forward is not in therapies hoping to reach large swaths of patients sharing a clinically defined diagnosis, but rather in targeting patients belonging to specific "biotypes" defined through a combination of objective, quantifiable data, including genotype.
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Affiliation(s)
- Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
- Department of Biomedical Engineering, University of Iowa College of Engineering, Iowa City, IA, USA.
- Department of Communication Sciences and Disorders, University of Iowa College of Liberal Arts and Sciences, Iowa City, IA, USA.
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA.
- Genetics Cluster Initiative, University of Iowa, Iowa City, IA, USA.
- The DeLTA Center, University of Iowa, Iowa City, IA, USA.
- University of Iowa Informatics Initiative, University of Iowa, Iowa City, IA, USA.
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26
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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27
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Fijarczyk A, Dudek K, Babik W. Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation. Genome Biol Evol 2016; 8:3417-3432. [PMID: 27702815 PMCID: PMC5203778 DOI: 10.1093/gbe/evw236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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28
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Yeates DK, Zwick A, Mikheyev AS. Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections. CURRENT OPINION IN INSECT SCIENCE 2016; 18:83-88. [PMID: 27939715 DOI: 10.1016/j.cois.2016.09.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/23/2016] [Indexed: 05/25/2023]
Abstract
Museums and herbaria represent vast repositories of biological material. Until recently, working with these collections has been difficult, due to the poor condition of historical DNA. However, recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option. Here we describe the unique technical challenges of working with collection specimens, and innovative molecular methods developed to tackle them. We also highlight possible applications of collection specimens, for taxonomy, ecology and evolution. The application of next-generation sequencing methods to museum and herbaria collections is still in its infancy. However, by giving researchers access to billions of specimens across time and space, it holds considerable promise for generating future discoveries across many fields.
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Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia.
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun 904-0412, Japan
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29
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Harvey MG, Smith BT, Glenn TC, Faircloth BC, Brumfield RT. Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics. Syst Biol 2016; 65:910-24. [PMID: 27288477 DOI: 10.1093/sysbio/syw036] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of historical processes across biotas. We argue that sequence capture should be given greater attention as a method of obtaining data for studies in shallow systematics and comparative phylogeography.
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Affiliation(s)
- Michael G Harvey
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA,
| | - Brian Tilston Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA, and
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Brant C Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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