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Tims AR, Unmack PJ, Hammer MP, Brown C, Adams M, McGee MD. Museum genomics reveals the hybrid origin of an extinct crater lake endemic. Syst Biol 2024:syae017. [PMID: 38597146 DOI: 10.1093/sysbio/syae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Indexed: 04/11/2024] Open
Abstract
Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.
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Affiliation(s)
- Amy R Tims
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Peter J Unmack
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
- Institute for Applied Ecology, Centre for Applied Water Science, University of Canberra, Australian Capital Territory 2601, Australia
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory 0801, Australia
| | - Culum Brown
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Mark Adams
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew D McGee
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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2
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Nomura Y, Arima S, Kyogoku D, Yamauchi T, Tominaga T. Strong plastic responses in aerenchyma formation in F1 hybrids of Imperata cylindrica under different soil moisture conditions. Plant Biol (Stuttg) 2024; 26:446-456. [PMID: 38192087 DOI: 10.1111/plb.13618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/03/2023] [Indexed: 01/10/2024]
Abstract
Hybrids can express traits plastically, enabling them to occupy environments that differ from parental environments. However, there is insufficient evidence demonstrating how phenotypic plasticity in specific traits mediates hybrid performance. Two parental ecotypes of Imperata cylindrica produce F1 hybrids. The E-type in wet habitats has larger internal aerenchyma than the C-type in dry habitats. This study evaluated relationships between habitat utilisation, aerenchyma plasticity, and growth of I. cylindrica accessions. We hypothesize that plasticity in expressing parental traits explains hybrid establishment in habitats with various soil moisture conditions. Aerenchyma formation was examined in the leaf midribs, rhizomes and roots of two parental ecotypes and their F1 hybrids in their natural habitats. In common garden experiments, we examined plastic aerenchyma formation in leaf midribs, rhizomes and roots of natural and artificial F1 hybrids and parental ecotypes and quantified vegetative growth performance. In the natural habitats where soil moisture content varied widely, the F1 hybrids showed larger variation in aerenchyma formation in rhizomes than their parental ecotypes. In the common garden experiments, F1 hybrids showed high plasticity of aerenchyma formation in rhizomes, and their growth was similar to that of C-type and E-type under drained and flooded conditions, respectively. The results demonstrate that F1 hybrids of I. cylindrica exhibit plasticity in aerenchyma development in response to varying local soil moisture content. This characteristic allows the hybrids to thrive in diverse soil moisture conditions.
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Affiliation(s)
- Y Nomura
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - S Arima
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - D Kyogoku
- The Museum of Nature and Human Activities, Sanda, Hyogo, Japan
| | - T Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan
| | - T Tominaga
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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3
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Vašut RJ, Pospíšková M, Lukavský J, Weger J. Detection of Hybrids in Willows ( Salix, Salicaceae) Using Genome-Wide DArTseq Markers. Plants (Basel) 2024; 13:639. [PMID: 38475486 DOI: 10.3390/plants13050639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
The genus Salix, comprising some 400-500 species, is important in various alluvial or wet habitats of the northern hemisphere. It is a promising crop for applications such as biomass production, biofuels, or environmental projects. Clear species delimitation is crucial in ecology, biotechnology, and horticulture. DArTseq markers, a genome-wide technique, were tested for species and hybrid identification. A total of 179 willow samples were analysed, including six species of Salix subgen. Salix and four species of Salix subgen. Vetrix, including those used in biomass crop production, representing important European taxa. Identification of species-specific markers, clustering analyses (principal coordinate analysis, neighbor-joining) and Bayesian methods (Structure) unambiguously identified putative hybrids. In addition to demonstrating the high efficiency of DArT-seq markers in identifying willow hybrids, we also opened-up new questions about hybridisation processes and systematics. We detected unidirectional hybridisation between S. alba and S. fragilis, forming backcross hybrids, and we rejected the hypothesis that S. fragilis does not occur naturally in Europe. Further, the isolated position of Salix triandra within the genus was confirmed.
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Affiliation(s)
- Radim J Vašut
- Department of Biology, Faculty of Education, Palacky University Olomouc, 779 00 Olomouc, Czech Republic
- Department of Botany, Faculty of Science, Palacky University Olomouc, 783 71 Olomouc, Czech Republic
| | - Markéta Pospíšková
- Department of Phytoenergy, Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Public Research Institute, 252 43 Průhonice, Czech Republic
| | - Jan Lukavský
- Department of Botany, Faculty of Science, Palacky University Olomouc, 783 71 Olomouc, Czech Republic
- The Nature Conservation Agency of the Czech Republic, Moravian-Silesian Regional Branch, 756 61 Rožnov pod Radhoštěm, Czech Republic
| | - Jan Weger
- Department of Phytoenergy, Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Public Research Institute, 252 43 Průhonice, Czech Republic
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Croft L, Matheson P, Flemming C, Butterworth NJ, McGaughran A. Population structure and interspecific hybridisation of two invasive blowflies (Diptera: Calliphoridae) following replicated incursions into New Zealand. Ecol Evol 2024; 14:e10832. [PMID: 38192906 PMCID: PMC10772223 DOI: 10.1002/ece3.10832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Rates of biological invasion are increasing globally, with associated negative effects on native biodiversity and ecosystem services. Among other genetic processes, hybridisation can facilitate invasion by producing new combinations of genetic variation that increase adaptive potential and associated population fitness. Yet the role of hybridisation (and resulting gene flow) in biological invasion in invertebrate species is under-studied. Calliphora hilli and Calliphora stygia are blowflies proposed to have invaded New Zealand separately from Australia between 1779 and 1841, and are now widespread throughout the country. Here, we analysed genome-wide single nucleotide polymorphisms (SNPs), generating genotyping-by-sequencing data for 154 individuals collected from 24 populations across New Zealand and Australia to assess the extent of gene flow and hybridisation occurring within and between these blowflies and to better understand their overall population structure. We found that New Zealand populations of both species had weak genetic structure, suggesting high gene flow and an absence of dispersal limitations across the country. We also found evidence that interspecific hybridisation is occurring in the wild between C. hilli and C. stygia in both the native and invasive ranges, and that intraspecific admixture is occurring among populations at appreciable rates. Collectively, these findings provide new insights into the population structure of these two invasive invertebrates and highlight the potential importance of hybridisation and gene flow in biological invasion.
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Affiliation(s)
- Lilly Croft
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Paige Matheson
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Chloe Flemming
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | | | - Angela McGaughran
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
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5
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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6
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Cairns KM, Crowther MS, Parker HG, Ostrander EA, Letnic M. Genome-wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes. Mol Ecol 2023; 32:4133-4150. [PMID: 37246949 PMCID: PMC10524503 DOI: 10.1111/mec.16998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 05/30/2023]
Abstract
Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to interspecific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. But there exists a concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here, we apply genome-wide single-nucleotide polymorphism (SNP) genotyping to a set of 402 wild and captive dingoes collected from across Australia and then carry out comparisons to domestic dogs. We then perform ancestry modelling and biogeographic analyses to characterise population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes. Our work challenges previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in south-eastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policymakers to assess and inform dingo management policy and legislation moving forwards.
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Affiliation(s)
- Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mathew S. Crowther
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
| | - Heidi G. Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mike Letnic
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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7
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Wong ELY, Filatov DA. The role of recombination landscape in species hybridisation and speciation. Front Plant Sci 2023; 14:1223148. [PMID: 37484464 PMCID: PMC10361763 DOI: 10.3389/fpls.2023.1223148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023]
Abstract
It is now well recognised that closely related species can hybridize and exchange genetic material, which may promote or oppose adaptation and speciation. In some cases, interspecific hybridisation is very common, making it surprising that species identity is preserved despite active gene exchange. The genomes of most eukaryotic species are highly heterogeneous with regard to gene density, abundance of repetitive DNA, chromatin compactisation etc, which can make certain genomic regions more prone or more resistant to introgression of genetic material from other species. Heterogeneity in local recombination rate underpins many of the observed patterns across the genome (e.g. actively recombining regions are typically gene rich and depleted for repetitive DNA) and it can strongly affect the permeability of genomic regions to interspecific introgression. The larger the region lacking recombination, the higher the chance for the presence of species incompatibility gene(s) in that region, making the entire non- or rarely recombining block impermeable to interspecific introgression. Large plant genomes tend to have highly heterogeneous recombination landscape, with recombination frequently occurring at the ends of the chromosomes and central regions lacking recombination. In this paper we review the relationship between recombination and introgression in plants and argue that large rarely recombining regions likely play a major role in preserving species identity in actively hybridising plant species.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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8
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Satokangas I, Nouhaud P, Seifert B, Punttila P, Schultz R, Jones MM, Sirén J, Helanterä H, Kulmuni J. Semipermeable species boundaries create opportunities for gene flow and adaptive potential. Mol Ecol 2023. [PMID: 37222024 DOI: 10.1111/mec.16992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023]
Abstract
Hybridisation and gene flow can have both deleterious and adaptive consequences for natural populations and species. To better understand the extent of hybridisation in nature and the balance between its beneficial and deleterious outcomes in a changing environment, information on naturally hybridising nonmodel organisms is needed. This requires the characterisation of the structure and extent of natural hybrid zones. Here, we study natural populations of five keystone mound-building wood ant species in the Formica rufa group across Finland. No genomic studies across the species group exist, and the extent of hybridisation and genomic differentiation in sympatry is unknown. Combining genome-wide and morphological data, we demonstrate more extensive hybridisation than was previously detected between all five species in Finland. Specifically, we reveal a mosaic hybrid zone between Formica aquilonia, F. rufa and F. polyctena, comprising further generation hybrid populations. Despite this, we find that F. rufa, F. aquilonia, F. lugubris and F. pratensis form distinct gene pools in Finland. We also find that hybrids occupy warmer microhabitats than the nonadmixed populations of cold-adapted F. aquilonia, and suggest that warm winters and springs, in particular, may benefit hybrids over F. aquilonia, the most abundant F. rufa group species in Finland. In summary, our results indicate that extensive hybridisation may create adaptive potential that could promote wood ant persistence in a changing climate. Additionally, they highlight the potentially significant ecological and evolutionary consequences of extensive mosaic hybrid zones, within which independent hybrid populations face an array of ecological and intrinsic selection pressures.
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Affiliation(s)
- I Satokangas
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - P Nouhaud
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - B Seifert
- Department of Entomology, Senckenberg Museum für Naturkunde, Görlitz, Germany
| | - P Punttila
- Biodiversity Centre, Finnish Environment Institute, Helsinki, Finland
| | - R Schultz
- Department of Entomology, Senckenberg Museum für Naturkunde, Görlitz, Germany
| | - M M Jones
- Institute of Biotechnology, HILIFE - Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - J Sirén
- Institute of Biotechnology, HILIFE - Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - H Helanterä
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - J Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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9
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Gaczorek TS, Chechetkin M, Dudek K, Caeiro-Dias G, Crochet PA, Geniez P, Pinho C, Babik W. Widespread introgression of MHC genes in Iberian Podarcis lizards. Mol Ecol 2023. [PMID: 37143304 DOI: 10.1111/mec.16974] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/24/2023] [Accepted: 04/12/2023] [Indexed: 05/06/2023]
Abstract
Major histocompatibility complex (MHC) genes are crucial for the adaptive immune response of jawed vertebrates. Their variation, reaching extreme levels, is driven mainly by an arms race between hosts and pathogens. One hypothesised mechanism contributing to MHC polymorphism is adaptive introgression, the exchange of genetic variants between hybridising species favoured by selection, yet its effect on MHC variation is poorly understood. Detection of adaptive MHC introgression, though challenging, may be facilitated by the analysis of species complexes forming multiple hybrid zones. Here, we investigated MHC introgression in six hybrid zones formed by seven species of Podarcis lizards inhabiting the Iberian Peninsula. To differentiate adaptive introgression from neutral introgression, we compared the patterns of gene exchange in MHC and genome-wide markers. We found elevated sharing of MHC alleles in the proximity of contact beyond the areas of detectable genome-wide admixture in most hybrid zones and, in half of them, asymmetric MHC exchange. In general, the elevated MHC allele sharing between species pairs with abutting ranges compared to geographically isolated species pairs also supports the prevalence of introgression. Collectively, our results demonstrate widespread MHC introgression in the Iberian Podarcis complex and suggest its adaptiveness. Contrary to previous results from Triturus newts, we did not observe differences in the rate of introgression between MHC classes. Our work adds support to the emerging view of adaptive introgression as a key mechanism shaping MHC diversity. It also raises questions about the effect of elevated MHC variation and factors leading to the asymmetry of adaptive introgression.
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Affiliation(s)
| | - Mateusz Chechetkin
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | | | - Philippe Geniez
- CEFE, EPHE-PSL University, Univ Montpellier, CNRS, IRD, Biogéographie et Ecologie des Vertébrés, Montpellier, France
| | - Catarina Pinho
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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10
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da Silva J. The kin selection theory of genomic imprinting and modes of reproduction in the eusocial Hymenoptera. Biol Rev Camb Philos Soc 2023; 98:677-695. [PMID: 36457233 DOI: 10.1111/brv.12925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
Genomic imprinting is known from flowering plants and mammals but has not been confirmed for the Hymenoptera even though the eusocial Hymenoptera are prime candidates for this peculiar form of gene expression. Here, the kin selection theory of genomic imprinting is reviewed and applied to the eusocial Hymenoptera. The evidence for imprinting in eusocial Hymenoptera with the typical mode of reproduction, involving the sexual production of diploid female offspring, which develop into workers or gynes, and the arrhenotokous parthenogenesis of haploid males, is also reviewed briefly. However, the focus of this review is how atypical modes of reproduction, involving thelytokous parthenogenesis, hybridisation and androgenesis, may also select for imprinting. In particular, naturally occurring hybridisation in several genera of ants may provide useful tests of the role of kin selection in the evolution of imprinting. Hybridisation is expected to disrupt the coadaptation of antagonistically imprinted loci, and thus affect the phenotypes of hybrids. Some of the limited data available on hybrid worker reproduction and on colony sex ratios support predictions about patterns of imprinting derived from kin selection theory.
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Affiliation(s)
- Jack da Silva
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
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11
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Benites P, Zaldívar-Riverón A, Meza-Lázaro RN, Samacá-Sáenz E, Gutiérrez-Rodríguez J, Hernández-López A. Multiple introgression events during the diversification history of the edible mexican grasshopper genus sphenarium (orthoptera: pyrgomorphidae). Mol Phylogenet Evol 2023; 183:107774. [PMID: 36972795 DOI: 10.1016/j.ympev.2023.107774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.
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Affiliation(s)
- Pilar Benites
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Rubi N Meza-Lázaro
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Ernesto Samacá-Sáenz
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México; Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Coyoacán, 04510 Ciudad de México, México
| | | | - Antonio Hernández-López
- Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Guanajuato, México
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12
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Baird SJE, Hiadlovská Z, Daniszová K, Piálek J, Macholán M. A gene copy number arms race in action: X,Y-chromosome transmission distortion across a species barrier. Evolution 2023:7085198. [PMID: 36959734 DOI: 10.1093/evolut/qpad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 03/25/2023]
Abstract
A remarkable gene copy number (CN) arms race system has recently been described in laboratory mice, where Slx;Slxl1 and Sly genes compete over transmission by altering fertilisation success of X and Y chromosome-bearing sperm, respectively. Here, we focus on this system in nature, where natural selection can counter CN/gene product escalation. Our model is house mouse subspecies hybridising in Europe. In some regions, Y chromosomes of the Eastern subspecies have introgressed onto Western genomic backgrounds, accompanied by sex ratio distortion in favour of males, consistent with the inbred-lines suggested mechanism: overabundance of SLY protein expressed by invading Y chromosomes. We take Slx as representative of the X side of this arms race and measure Slx|Sly CN and expression across an 'Invasion' transect where Ys introgress and a 'Control' transect with negligible introgression. Since we found similar Slx|Sly ratios in both transects, SLY overabundance is unlikely to explain the introgression. However, Slx CN is relatively low in the introgression area, suggesting Slx is less able to combat Sly effects here. Further, deterministic changes in Slx;Sly expression proportions versus CN proportions suggest standing variation for trans regulation of Slx|Sly is being co-opted in nature where their arms race reduces population fitness.
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Affiliation(s)
- Stuart J E Baird
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Research Facility in Studenec, Czech Republic
| | - Zuzana Hiadlovská
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Kristina Daniszová
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Research Facility in Studenec, Czech Republic
| | - Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
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13
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Kessler C, Wootton E, Shafer ABA. Speciation without gene-flow in hybridizing deer. Mol Ecol 2023; 32:1117-1132. [PMID: 36516402 DOI: 10.1111/mec.16824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Under the ecological speciation model, divergent selection acts on ecological differences between populations, gradually creating barriers to gene flow and ultimately leading to reproductive isolation. Hybridisation is part of this continuum and can both promote and inhibit the speciation process. Here, we used white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) to investigate patterns of speciation in hybridizing sister species. We quantified genome-wide historical introgression and performed genome scans to look for signatures of four different selection scenarios. Despite ample modern evidence of hybridisation, we found negligible patterns of ancestral introgression and no signatures of divergence with gene flow, rather localized patterns of allopatric and balancing selection were detected across the genome. Genes under balancing selection were related to immunity, MHC and sensory perception of smell, the latter of which is consistent with deer biology. The deficiency of historical gene-flow suggests that white-tailed and mule deer were spatially separated during the glaciation cycles of the Pleistocene and genome wide differentiation accrued via genetic drift. Dobzhansky-Muller incompatibilities and selection against hybrids are hypothesised to be acting, and diversity correlations to recombination rates suggests these sister species are far along the speciation continuum.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Eric Wootton
- Biochemistry & Molecular Biology, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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14
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Connolly JB, Romeis J, Devos Y, Glandorf DCM, Turner G, Coulibaly MB. Gene drive in species complexes: defining target organisms. Trends Biotechnol 2023; 41:154-64. [PMID: 35868886 DOI: 10.1016/j.tibtech.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 01/24/2023]
Abstract
Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.
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15
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Casu M, Azzena I, Scarpa F, Locci C, Niffoi A, Delmastro GB, Lo Conte P, Varcasia A, Bovero S, Candiotto A, Sanna D, Cossu P. Appraising the Genetic Makeup of an Allochthonous Southern Pike Population: An Opportunity to Predict the Evolution of Introgressive Hybridization in Isolated Populations? Animals (Basel) 2023; 13. [PMID: 36766269 DOI: 10.3390/ani13030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Biological invasions are a major threat to the conservation of biodiversity, as invasive species affect native biota through competition, predation, pathogen introduction, habitat alteration, and hybridisation. The present study focuses on a southern pike population, Esox cisalpinus (Teleostei: Esocidae), that has been introduced outside the species' native range. Using microsatellite markers, this study's objective was to gather baseline genetic information and assess the presence of hybrids between this species and E. lucius in the introduced population. The resulting estimates of genetic diversity and effective population size are comparable to those observed in the species' native range. Although different methods yield contrasting and uncertain evidence regarding introgressive hybridization, the presence of late-generation hybrids cannot be completely ruled out. Large numbers of breeders as well as multiple introductions of genetically divergent cohorts and introgressive hybridisation may explain the high genetic diversity of this recently introduced southern pike population. The present study issues a warning that the conservation of southern pike' introgressive hybridisation between northern and southern pike might be underestimated. The genetic information gathered herein may unravel the origin, number of introduction events, and evolutionary trajectory of the introduced population. This information may help us understand the evolution of introgressive hybridisation in the southern pike's native areas.
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16
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Kunerth HD, Tapisso JT, Valente R, Mathias MDL, Alves PC, Searle JB, Vega R, Paupério J. Characterising Mitochondrial Capture in an Iberian Shrew. Genes (Basel) 2022; 13. [PMID: 36553495 DOI: 10.3390/genes13122228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.
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Blanco Pastor JL. Alternative modes of introgression-mediated selection shaped crop adaptation to novel climates. Genome Biol Evol 2022; 14:6647590. [PMID: 35859297 PMCID: PMC9348624 DOI: 10.1093/gbe/evac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern genomic approaches and analytical methods now make it possible to better separate the introgression signal from the demographic signal thus providing a more comprehensive and complex picture of the role of introgression in local adaptation. Adaptive introgression has been fundamental for crop expansion and has involved complex patterns of gene flow. In addition to providing new and more favorable alleles of large effect, introgression during the early stages of domestication also increased allelic diversity at adaptive loci. Previous studies have largely underestimated the effect of such increased diversity following introgression. Recent genomic studies in wheat, potato, maize, grapevine, and ryegrass show that introgression of multiple genes, of as yet unknown effect, increased the effectiveness of purifying selection, and promoted disruptive or fluctuating selection in early cultivars and landraces. Historical selection processes associated with introgression from crop wild relatives provide an instructive analog for adaptation to current climate change and offer new avenues for crop breeding research that are expected to be instrumental for strengthening food security in the coming years.
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Nobis M, Krzempek M, Nowak A, Gudkova PD, Klichowska E. Resurrection of Stipatremula and taxonomy of the high-alpine species from the Stipapurpurea complex (Poaceae, Pooideae). PhytoKeys 2022; 196:21-47. [PMID: 36762029 PMCID: PMC9849017 DOI: 10.3897/phytokeys.196.82598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/11/2022] [Indexed: 06/18/2023]
Abstract
Stipapurpurea is a high-alpine species that occurs in cryophilous steppes, semi-deserts and stony slopes, from the Tian Shan and Pamirian Plateau through Qinghai-Xizang Plateau to the Himalayas and is characterised by a great morphological variability. During the revision of specimens of the taxon, we observed that the pattern of this variability is linked to the geographical distribution of the specimens. Numerical analyses (PCA and UPGMA) revealed three groups of OTUs corresponding to three morphotypes within the S.purpurea complex. A set of macro- and micromorphological characters, supported by a map of general distributional ranges, are presented to distinguish each of the three taxa within the complex and we reassess the status of Lasiagrostistremula described by Ruprecht in 1869. As a result, Stipatremula, S.purpurea and S.arenosa were distinguished within the complex. The intermediate characters of S.arenosa may suggest its putative hybrid origin (S.tremula × S.purpurea), whereas the presence of extremely long florets may be an expression of the gigas effect. We propose two new combinations (S.tremula and S.arenosa), describe a new nothospecies (S.×ladakhensis) that originated from hybridisation between S.klimesii and S.purpurea s.l. and designate the lectotype for Ptilagrostissemenovii. An identification key and detailed morphological description of species from the S.purpurea complex are also presented.
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Affiliation(s)
- Marcin Nobis
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakowPoland
| | - Marta Krzempek
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakowPoland
| | - Arkadiusz Nowak
- Institute of Biology, University of Opole, 45–052 Opole, PolandUniversity of OpoleOpolePoland
- Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, 02–976 Warszawa, PolandCenter for Biological Diversity Conservation, Polish Academy of SciencesWarsawaPoland
| | - Polina D. Gudkova
- Research Laboratory ‘Herbarium’, National Research Tomsk State University, Lenin 36 Ave., 634050 Tomsk, RussiaTomsk State UniversityTomskRussia
- Institute of Biology, Altai State University, Lenin 61 Ave., 656049, Barnaul, RussiaAltai State UniversityBarnaulRussia
| | - Ewelina Klichowska
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakowPoland
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19
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Särkinen T, Gagnon E, Knapp S. Out of the wild: the wild (and often weedy) roots of our crops. New Phytol 2022; 234:1107-1108. [PMID: 35383934 DOI: 10.1111/nph.18107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Affiliation(s)
| | - Edeline Gagnon
- Chair of Phytopathology, TUM School of Life Sciences, Technische Universität München, Freising 85354, Germany
| | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
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20
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Abstract
The wild rice gene pool, i.e., AA-genome, in Australia is geographically and genetically distinct from that in Asia. Two distinct taxa are found growing together in northern Australia, Oryza meridionalis (including annual and perennial forms) and an Oryza rufipogon like taxa that have been shown to have a chloroplast genome sequence that is closer to that of O. meridionalis than to O. rufipogon from Asia. Rare plants of intermediate morphology have been observed in the wild despite a reported reproductive barrier between these two species. We now report the resequencing of plants from 26 populations including both taxa and putative hybrids. A comparison of chloroplast and nuclear genome sequences indicated re-combinations that demonstrated hybridisation in both directions. Individuals with intermediate morphology had high nuclear genome heterozygosity consistent with a hybrid origin. An examination of specific genes (e.g., starch biosynthesis genes) revealed the presence of heterozygotes with alleles from both parents suggesting that some wild plants were early generation hybrids. These plants may have low cross-fertility preserving the continuation of the two distinct species. Repeated backcrossing of these rare hybrids to one parent would explain the plants exhibiting chloroplast capture. These observations suggest that reticulate evolution is continuing in wild Oryza populations and may have been a key process in rice evolution and domestication.
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Affiliation(s)
- Sharmin Hasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- Department of Botany, Jagannath University, Dhaka, Bangladesh
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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21
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Hagberg L, Celemín E, Irisarri I, Hawlitschek O, Bella JL, Mott T, Pereira RJ. Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones. Mol Ecol 2022; 31:2384-2399. [PMID: 35191134 DOI: 10.1111/mec.16406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
The process of species formation is characterised by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane's rule, typically characterises later stages of species formation, when reproductive isolation is strongest. Yet, understanding how quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species remains a challenging task because it requires studying taxa that hybridise in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus, where populations that show multiple reproductive barriers, including hybrid male sterility, hybridise in two natural hybrid zones. Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, at the beginning of the last glacial cycle in Europe. Nuclear data shows that contractions at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find extensive introgression throughout the sampled species range, irrespective of current strength of reproductive isolation. Populations exhibiting hybrid male sterility in two hybrid zones show repeatable patterns of genomic differentiation, consistent with shared genomic constraints affecting ancestral divergence or with the role of those regions in reproductive isolation. Together, our results suggest that reproductive barriers that characterise late stages of species formation can evolve relatively quickly, particularly when associated with strong demographic changes. Moreover, we show that such barriers persist in the face of extensive gene flow, allowing future studies to identify associated genomic regions.
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Affiliation(s)
- Linda Hagberg
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Enrique Celemín
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany.,Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077, Göttingen, Germany.,Campus Institute Data Science (CIDAS), Göttingen, Germany
| | - Oliver Hawlitschek
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Zoologische Staatssammlung (SNSB-ZSM), Münchhausenstr. 21, 81247, Munich, Germany
| | - José L Bella
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Tamí Mott
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, 57072-900, Maceió, Alagoas, Brazil
| | - Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
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22
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Chew BC, Liew FF, Tan HW, Chung I. Chemical Advances in Therapeutic Application of Exosomes and Liposomes. Curr Med Chem 2022; 29:4445-4473. [PMID: 35189798 DOI: 10.2174/0929867329666220221094044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022]
Abstract
Exosomes and liposomes are vesicular nanoparticles that can encapsulate functional cargo. The chemical similarities between naturally occurring exosomes and synthetic liposomes have accelerated the development of exosome mimetics as a therapeutic drug delivery platform under physiological and pathological environments. To maximise the applications of exosomes and liposomes in the clinical setting, it is essential to look into their basic chemical properties and utilise these characteristics to optimise the preparation, loading, modification and hybridisation. This review summarises the chemical and biological properties of both exosomal and liposomal systems as well as some of the challenges related to their production and application. This article concludes with a discussion on potential perspectives for the integration of exosomal and liposomal technologies in mapping better approaches for their biomedical use, especially in therapeutics.
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Affiliation(s)
- Boon Cheng Chew
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Jalan Universiti, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Fong Fong Liew
- Department of Oral Biology and Biomedical Science, Faculty of Dentistry, MAHSA University, Jalan SP2, Bandar Saujana Putra, 42610 Jenjarom, Selangor, Malaysia
| | - Hsiao Wei Tan
- Institute of Research Management and Services, Research and Innovation Management Complex, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ivy Chung
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Jalan Universiti, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
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23
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Panzeri D, Guidi Nissim W, Labra M, Grassi F. Revisiting the Domestication Process of African Vigna Species (Fabaceae): Background, Perspectives and Challenges. Plants (Basel) 2022; 11:plants11040532. [PMID: 35214865 PMCID: PMC8879845 DOI: 10.3390/plants11040532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 05/14/2023]
Abstract
Legumes are one of the most economically important and biodiverse families in plants recognised as the basis to develop functional foods. Among these, the Vigna genus stands out as a good representative because of its relatively recent African origin as well as its outstanding potential. Africa is a great biodiversity centre in which a great number of species are spread, but only three of them, Vigna unguiculata, Vigna subterranea and Vigna vexillata, were successfully domesticated. This review aims at analysing and valorising these species by considering the perspective of human activity and what effects it exerts. For each species, we revised the origin history and gave a focus on where, when and how many times domestication occurred. We provided a brief summary of bioactive compounds naturally occurring in these species that are fundamental for human wellbeing. The great number of wild lineages is a key point to improve landraces since the domestication process caused a loss of gene diversity. Their genomes hide a precious gene pool yet mostly unexplored, and genes lost during human activity can be recovered from the wild lineages and reintroduced in cultivated forms through modern technologies. Finally, we describe how all this information is game-changing to the design of future crops by domesticating de novo.
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Affiliation(s)
- Davide Panzeri
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Correspondence: (D.P.); (F.G.)
| | - Werther Guidi Nissim
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Viale delle Idee 30, 50019 Sesto Fiorentino, Italy
| | - Massimo Labra
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
| | - Fabrizio Grassi
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Correspondence: (D.P.); (F.G.)
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24
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Durán-Castillo M, Hudson A, Wilson Y, Field DL, Twyford AD. A phylogeny of Antirrhinum reveals parallel evolution of alpine morphology. New Phytol 2022; 233:1426-1439. [PMID: 34170548 DOI: 10.1111/nph.17581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Parallel evolution of similar morphologies in closely related lineages provides insight into the repeatability and predictability of evolution. In the genus Antirrhinum (snapdragons), as in other plants, a suite of morphological characters are associated with adaptation to alpine environments. We tested for parallel trait evolution in Antirrhinum by investigating phylogenetic relationships using restriction-site associated DNA (RAD) sequencing. We then associated phenotypic information to our phylogeny to reconstruct the patterns of morphological evolution and related this to evidence for hybridisation between emergent lineages. Phylogenetic analyses showed that the alpine character syndrome is present in multiple groups, suggesting that Antirrhinum has repeatedly colonised alpine habitats. Dispersal to novel environments happened in the presence of intraspecific and interspecific gene flow. We found support for a model of parallel evolution in Antirrhinum. Hybridisation in natural populations, and a complex genetic architecture underlying the alpine morphology syndrome, support an important role of natural selection in maintaining species divergence in the face of gene flow.
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Affiliation(s)
- Mario Durán-Castillo
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yvette Wilson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David L Field
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, 6027, Australia
| | - Alex D Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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25
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Wong ELY, Hiscock SJ, Filatov DA. The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio. Front Plant Sci 2022; 13:907363. [PMID: 35812981 PMCID: PMC9260247 DOI: 10.3389/fpls.2022.907363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/03/2022] [Indexed: 05/08/2023]
Abstract
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Edgar L. Y. Wong,
| | - Simon J. Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Botanic Garden and Arboretum, Oxford, United Kingdom
| | - Dmitry A. Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Murthy VS, Tamboli Y, Krishna VS, Sriram D, Akber Ansari S, Alarfaj AA, Hirad AH, Vijayakumar V. Design and characterisation of piperazine-benzofuran integrated dinitrobenzenesulfonamide as Mycobacterium tuberculosis H37Rv strain inhibitors. J Enzyme Inhib Med Chem 2021; 36:1751-1759. [PMID: 34325595 PMCID: PMC8330757 DOI: 10.1080/14756366.2021.1956914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular hybridisation of four bioactive fragments piperazine, substituted-benzofuran, amino acids, and 2,4-dinitrobenzenesulfonamide as single molecular architecture was designed. A series of new hybrids were synthesised and subjected to evaluation for their inhibitory activity against Mycobacterium tuberculosis (Mtb) H37Rv. 4d-f and 4o found to exhibit MIC as 1.56 µg/mL, equally active as ethambutol whereas 4a, 4c, 4j displayed MIC 0.78 µg/mL were superior to ethambutol. Tested compounds demonstrated an excellent safety profile with very low toxicity, good selectivity index, and antioxidant properties. All the newly synthesised compounds were thoroughly characterised by analytical methods. The result was further supported by molecular modelling studies on the crystal structure of Mycobacterium tuberculosis enoyl reductase.
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Affiliation(s)
- Vallabhaneni S. Murthy
- Centre for Organic and Medicinal Chemistry, Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, India
| | - Yasinalli Tamboli
- Centre for Organic and Medicinal Chemistry, Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, India
| | - Vagolu Siva Krishna
- Medicinal Chemistry and Antimycobacterial Research Laboratory, Pharmacy Group, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad, India
| | - Dharmarajan Sriram
- Medicinal Chemistry and Antimycobacterial Research Laboratory, Pharmacy Group, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad, India
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah A. Alarfaj
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdurahman H. Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Vijayaparthasarathi Vijayakumar
- Centre for Organic and Medicinal Chemistry, Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, India
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Dool SE, Picker MD, Eberhard MJB. Limited dispersal and local adaptation promote allopatric speciation in a biodiversity hotspot. Mol Ecol 2021; 31:279-295. [PMID: 34643310 DOI: 10.1111/mec.16219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 01/20/2023]
Abstract
Recently diverged or diverging populations can offer unobstructed insights into early barriers to gene flow during the initial stages of speciation. The current study utilised a novel insect system (order Mantophasmatodea) to shed light on the early drivers of speciation. The members of this group have limited dispersal abilities, small allopatric distributions and strong habitat associations in the Cape Floristic Region biodiversity hotspot in South Africa. Sister taxa from the diverse family Austrophasmatidae were chosen as focal species (Karoophasma biedouwense, K. botterkloofense). Population genetics and Generalized Dissimilarity Modelling (GDM) were used to characterise spatial patterns of genetic variation and evaluate the contribution of environmental factors to population divergence and speciation. Extensive sampling confirmed the suspected allopatry of these taxa. However, hybrids were identified in a narrow region occurring between the species' distributions. Strong population structure was found over short geographic distances; particularly in K. biedouwense in which geographic distance accounted for 32% of genetic variation over a scale of 50 km (r = .56, p < .001). GDM explained 42%-78% of the deviance in observed genetic dissimilarities. Geographic distance was consistently indicated to be important for between species and within population differentiation, suggesting that limited dispersal ability may be an important neutral driver of divergence. Temperature, altitude, precipitation and vegetation were also indicated as important factors, suggesting the possible role of adaptation to local environmental conditions for species divergence. The discovery of the hybrid-zone, and the multiple allopatric species pairs in Austrophasmatidae support the idea that this could be a promising group to further our understanding of speciation modes.
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Affiliation(s)
- Serena E Dool
- General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany.,CBGP, INRAE, CIRAD, IRD, Institut Agro, University of Montpellier, Montpellier, France
| | - Mike D Picker
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Monika J B Eberhard
- General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
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Knipler ML, Dowton M, Mikac KM. Genome-Wide SNPs Detect Hybridisation of Marsupial Gliders ( Petaurus breviceps breviceps × Petaurus norfolcensis) in the Wild. Genes (Basel) 2021; 12:1327. [PMID: 34573311 DOI: 10.3390/genes12091327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
Petaurus breviceps and Petaurus norfolcensis have produced hybrids in captivity, however there are no reported cases of Petaurus hybridisation in the wild. This study uses morphological data, mitochondrial DNA, and nuclear genome-wide SNP markers to confirm P. breviceps breviceps × P. norfolcensis hybridisation within their natural range on the central coast of New South Wales, Australia. Morphological data identified a potential hybrid that was confirmed with next-generation sequencing technology and 10,111 genome-wide SNPs. Both STRUCTURE and NewHybrid analyses identified the hybrid as a P. norfolcensis backcross, which suggests an initial F1 hybrid was fertile. The mitochondrial DNA matched that of a P. b. breviceps, indicating that a P. b. breviceps female initially mated with a P. norfolcensis male to produce a fertile female offspring. Our study is an important example of how genome-wide SNPs can be used to identify hybrids where the distribution of congeners overlaps. Hybridisation between congeners is likely to become more frequent as climate changes and habitats fragment, resulting in increased interactions and competition for resources and mates.
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Alagumalai V, Shanmugam V, Balasubramanian NK, Krishnamoorthy Y, Ganesan V, Försth M, Sas G, Berto F, Chanda A, Das O. Impact Response and Damage Tolerance of Hybrid Glass/Kevlar-Fibre Epoxy Structural Composites. Polymers (Basel) 2021; 13:2591. [PMID: 34451131 DOI: 10.3390/polym13162591] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
The present study is aimed at investigating the effect of hybridisation on Kevlar/E-Glass based epoxy composite laminate structures. Composites with 3 mm thickness and 16 layers of fibre (14 layers of E-glass centred and 2 outer layers of Kevlar) were fabricated using compression moulding technique. The fibre orientation of the Kevlar layers had 3 variations (0, 45 and 60°), whereas the E-glass fibre layers were maintained at 0° orientation. Tensile, flexural, impact (Charpy and Izod), interlaminar shear strength and ballistic impact tests were conducted. The ballistic test was performed using a gas gun with spherical hard body projectiles at the projectile velocity of 170 m/s. The pre- and post-impact velocities of the projectiles were measured using a high-speed camera. The energy absorbed by the composite laminates was further reported during the ballistic test, and a computerised tomographic scan was used to analyse the impact damage. The composites with 45° fibre orientation of Kevlar fibres showed better tensile strength, flexural strength, Charpy impact strength, and energy absorption. The energy absorbed by the composites with 45° fibre orientation was 58.68 J, which was 14% and 22% higher than the 0° and 60° oriented composites.
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Pellicer J, López-Pujol J, Aixarch M, Garnatje T, Vallès J, Hidalgo O. Detecting Introgressed Populations in the Iberian Endemic Centaurea podospermifolia through Genome Size. Plants (Basel) 2021; 10:plants10081492. [PMID: 34451537 PMCID: PMC8401423 DOI: 10.3390/plants10081492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 05/25/2023]
Abstract
Based on results from previous studies, populations of the Iberian endemic Centaurea podospermifolia north of the Ebro River are considered genetically pure, while those southward are introgressed, with genetic input from C. cephalariifolia. This phenomenon is particularly relevant, especially given both the endangered and protected status for the species, which can have consequences in how to best apply conservation strategies to maintain genetic resources in the species. The main goal of this study was to evaluate whether genome size assessments using flow cytometry can help distinguishing between pure, hybrid and introgressed populations, and hence become a powerful and cost-effective tool to complement comprehensive population genetic surveys. The results indicate that there are significant genome size differences between populations of C. podospermifolia, which are coincident with previous considerations of pure and introgressed populations. Given the simplicity and reproducibility of this technique, flow cytometry could become an effective tool for monitoring pure populations of this species and, indeed, become an integral part of the management plans that are mandatory for listed taxa.
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Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, Catalonia, 08038 Barcelona, Spain; (J.L.-P.); (T.G.)
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
| | - Jordi López-Pujol
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, Catalonia, 08038 Barcelona, Spain; (J.L.-P.); (T.G.)
| | - Marc Aixarch
- c/Mossèn Manyà 15, Catalonia, 43500 Tortosa, Spain;
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, Catalonia, 08038 Barcelona, Spain; (J.L.-P.); (T.G.)
| | - Joan Vallès
- Laboratori de Botànica, Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Institut de la Biodiversitat IRBio, Universitat de Barcelona, Av. Joan XXIII 27-31, Catalonia, 08028 Barcelona, Spain;
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, Catalonia, 08038 Barcelona, Spain; (J.L.-P.); (T.G.)
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
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Howard-McCombe J, Ward D, Kitchener AC, Lawson D, Senn HV, Beaumont M. On the use of genome-wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat. Mol Ecol 2021; 30:3688-3702. [PMID: 34042240 DOI: 10.1111/mec.16000] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022]
Abstract
While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of Scottish wildcats and domestic cats is a good example in this regard. Here, we developed a modelling framework to determine the timescale of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland. These individuals were found almost exclusively within the captive breeding programme. Most wild-living cats sampled were introgressed to some extent. The demographic model predicts high levels of gene-flow between domestic cats and Scottish wildcats (13% migrants per generation) over a short timeframe, the posterior mean for the onset of hybridisation (T1 ) was 3.3 generations (~10 years) before present. Although the model had limited power to detect signals of ancient admixture, we found evidence that significant recent hybridisation may have occurred subsequent to the founding of the captive breeding population (T2 ). The model consistently predicts T1 after T2 , estimated here to be 19.3 generations (~60 years) ago, highlighting the importance of this population as a resource for conservation management. Additionally, we evaluate the effectiveness of current methods to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.
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Affiliation(s)
| | - Daniel Ward
- School of Mathematics, University of Bristol, Bristol, UK
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, Bristol, UK
| | - Helen V Senn
- RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
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Gabriele-Rivet V, Brookes VJ, Stephens D, Arsenault J, Ward MP. Hybridisation between dingoes and domestic dogs in proximity to Indigenous communities in northern Australia. Aust Vet J 2021; 99:388-391. [PMID: 34109613 DOI: 10.1111/avj.13095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/02/2021] [Accepted: 05/22/2021] [Indexed: 11/29/2022]
Abstract
In northern Australia, wild dog populations potentially interact with domestic dogs from remote communities, which would create opportunities for disease transmission at the wild-domestic interface. An example is rabies, in the event of an incursion into northern Australia. However, the likelihood of such wild-domestic interactions is ambiguous. Hybridisation analyses based on 23 microsatellite DNA markers were performed on canine-origin scats collected in bushland areas around remote Indigenous communities in the Northern Peninsula Area, Queensland. Sufficient DNA was extracted from 6 of 41 scats to assess the percentage of dingo purity. These scats most likely originated from two 'pure' domestic dogs (0% dingo purity), one hybrid (20% dingo purity) and three 'pure' dingoes (92%-98% dingo purity). The two domestic dog samples were collected in the vicinity of communities. The location of two of the dingo-origin samples provides genetic evidence that dingoes are present in areas close to the communities. The availability of anthropogenic food resources likely creates opportunities for interactions with domestic dogs in the region. The hybrid sample demonstrates the occurrence of antecedent contacts between both populations by means of mating and supports the likelihood of a spatio-temporal overlap at the wild-domestic interface. This represents the first genetic survey involving a wild dog population of equatorial northern Queensland, with evidence of dingo purity. Our results have implications for potential disease transmission within a priority area for biosecurity in northern Australia.
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Affiliation(s)
- V Gabriele-Rivet
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Werombi Road, Camden, New South Wales, 2570, Australia
| | - V J Brookes
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Werombi Road, Camden, New South Wales, 2570, Australia.,School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales, 2678, Australia.,Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Pugsley Place, Wagga Wagga, New South Wales, 2650, Australia
| | - D Stephens
- Zoological Genetics, Blackhill Rd, Inglewood, South Australia, 5133, Australia
| | - J Arsenault
- Faculty of Veterinary Medicine, Université de Montréal, rue Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
| | - M P Ward
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Werombi Road, Camden, New South Wales, 2570, Australia
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Brasier C, Franceschini S, Forster J, Kirk S. Enhanced Outcrossing, Directional Selection and Transgressive Segregation Drive Evolution of Novel Phenotypes in Hybrid Swarms of the Dutch Elm Disease Pathogen Ophiostoma novo-ulmi. J Fungi (Basel) 2021; 7:jof7060452. [PMID: 34204036 PMCID: PMC8228177 DOI: 10.3390/jof7060452] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
In the 1970s, clones of the two subspecies of Ophiostoma novo-ulmi, subsp. americana (SSAM) and subsp. novo-ulmi (SSNU) began to overlap in Europe, resulting in hybrid swarms. By 1983-1986, hybrids with high, SSAM-like growth and pathogenic fitness comprised ~75% of popula-tions at Limburg, Netherlands and Orvieto, Italy. We resampled these populations in 2008 to examine trends in hybrid fitness traits. Since preliminary sampling in 1979-1980, MAT-1 locus frequency had increased from ~0% to ~32% at Orvieto and 5% to ~43% at Limburg, and vegeta-tive incompatibility type frequency had changed from near clonal to extremely diverse at both sites. This represents an enormous increase in outcrossing and recombination potential, due in part to selective acquisition (under virus pressure) of MAT-1 and vic loci from the resident O. ulmi and in part to SSAM × SSNU hybridisation. Overt virus infection in the 2008 samples was low (~4%), diagnostic SSAM and SSNU cu and col1 loci were recombinant, and no isolates exhib-ited a parental SSAM or SSNU colony pattern. At both sites, mean growth rate and mean patho-genicity to 3-5 m clonal elm were high SSAM-like, indicating sustained directional selection for these characters, though at Orvieto growth rate was slower. The once frequent SSNU-specific up-mut colony dimorphism was largely eliminated at both sites. Perithecia formed by Limburg isolates were mainly an extreme, long-necked SSNU-like form, consistent with transgressive segregation resulting from mismatch of SSAM and SSNU developmental loci. Orvieto isolates produced more parental-like perithecia, suggesting the extreme phenotypes may have been se-lected against. The novel phenotypes in the swarms are remodelling O. novo-ulmi in Europe. Locally adapted genotypes may emerge.
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Abstract
Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
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Affiliation(s)
- Jesper Svedberg
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Vladimir Shchur
- National Research University Higher School of Economics, Moscow, Russian Federation
| | - Solomon Reinman
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Rasmus Nielsen
- National Research University Higher School of Economics, Moscow, Russian Federation
- Department of Integrative Biology and Department of Statistics, UC Berkeley, Berkeley, CA, USA
- Center for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
- National Research University Higher School of Economics, Moscow, Russian Federation
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Oleksa A, Kusza S, Tofilski A. Mitochondrial DNA Suggests the Introduction of Honeybees of African Ancestry to East-Central Europe. Insects 2021; 12:410. [PMID: 34063321 DOI: 10.3390/insects12050410] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary In Europe, a well-known threat to the conservation of honeybee diversity is the loss of genetic uniqueness of local populations due to beekeepers’ preference for a few genetic lineages. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees of African origin could represent another threat. This issue has not yet been recognised in detail, although bees bearing African mitochondrial DNA occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mitochondrial DNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35%) had African mitochondrial DNA. It is unlikely that their presence in the area resulted from natural migration but instead human-driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases. Abstract In Europe, protecting the genetic diversity of Apis mellifera is usually perceived in the context of limiting the spread of the evolutionary C-lineage within the original range of the M-lineage. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees from the African A-lineage could represent another threat. This issue has not yet been investigated in detail, although A-mitotypes occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mtDNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35 %) had A-mitotypes. It is unlikely that their presence in the area resulted from natural migration but instead human driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.
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Bird KA, Niederhuth CE, Ou S, Gehan M, Pires JC, Xiong Z, VanBuren R, Edger PP. Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. New Phytol 2021; 230:354-371. [PMID: 33280122 PMCID: PMC7986222 DOI: 10.1111/nph.17137] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/30/2020] [Indexed: 05/03/2023]
Abstract
Allopolyploidisation merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is 'dominant' over the other subgenome, often being more highly expressed. Here, we 'replayed the evolutionary tape' with six isogenic resynthesised Brassica napus allopolyploid lines and investigated subgenome dominance patterns over the first 10 generations postpolyploidisation. We found that the same subgenome was consistently more dominantly expressed in all lines and generations and that >70% of biased gene pairs showed the same dominance patterns across all lines and an in silico hybrid of the parents. Gene network analyses indicated an enrichment for network interactions and several biological functions for the Brassica oleracea subgenome biased pairs, but no enrichment was identified for Brassica rapa subgenome biased pairs. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the dominant subgenome in all lines and generations. Many of these differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting that subgenome dominance is partly related to parental genome differences rather than just a byproduct of allopolyploidisation. These findings demonstrate that 'replaying the evolutionary tape' in an allopolyploid results in largely repeatable and predictable subgenome expression dominance patterns.
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Affiliation(s)
- Kevin A. Bird
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
- Ecology, Evolutionary Biology and BehaviorMichigan State UniversityEast LansingMI48824USA
| | - Chad E. Niederhuth
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
| | - Shujun Ou
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Malia Gehan
- Donald Danforth Plant Science CenterSt LouisMO63123USA
| | - J. Chris Pires
- Division of Biological SciencesUniversity of MissouriColumbiaMO65211USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop BiotechnologyInner Mongolia UniversityHohhot010070China
| | - Robert VanBuren
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
- Plant Resilience InstituteMichigan State UniversityEast LansingMI48824USA
| | - Patrick P. Edger
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
- Ecology, Evolutionary Biology and BehaviorMichigan State UniversityEast LansingMI48824USA
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Al-Warhi T, Abo-Ashour MF, Almahli H, Alotaibi OJ, Al-Sanea MM, Al-Ansary GH, Ahmed HY, Elaasser MM, Eldehna WM, Abdel-Aziz HA. Novel [( N-alkyl-3-indolylmethylene)hydrazono]oxindoles arrest cell cycle and induce cell apoptosis by inhibiting CDK2 and Bcl-2: synthesis, biological evaluation and in silico studies. J Enzyme Inhib Med Chem 2020; 35:1300-1309. [PMID: 32522063 PMCID: PMC7717600 DOI: 10.1080/14756366.2020.1773814] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/03/2020] [Accepted: 05/17/2020] [Indexed: 12/21/2022] Open
Abstract
As a continuation for our previous work, a novel set of N-alkylindole-isatin conjugates (7, 8a-c, 9 and 10a-e) is here designed and synthesised with the prime aim to develop more efficient isatin-based antitumor candidates. Utilising the SAR outputs from the previous study, our design here is based on appending four alkyl groups with different length (ethyl and n-propyl), bulkiness (iso-propyl) and unsaturation (allyl) on N-1 of indole motif, with subsequent conjugation with different N-unsubstituted isatin moieties to furnish the target conjugates. As planned, the adopted strategy achieved a substantial improvement in the growth inhibitory profile for the target conjugates in comparison to the reported lead VI. The best results were obtained with N-propylindole -5-methylisatin hybrid 8a which displayed broad spectrum anti-proliferative action with efficient sub-panel GI50 (MG-MID) range from 1.33 to 4.23 µM, and promising full-panel GI50 (MG-MID) equals 3.10 µM, at the NCI five-dose assay. Also, hybrid 8a was able to provoke cell cycle disturbance and apoptosis in breast T-47D cells as evidenced by the DNA flow cytometry and Annexin V-FITC/PI assays. Furthermore, hybrid 8a exhibited good inhibitory action against cell cycle regulator CDK2 protein kinase and the anti-apoptotic Bcl-2 protein (IC50= 0.85 ± 0.03 and 0.46 ± 0.02 µM, respectively). Interestingly, molecular docking for hybrid 8a in CDK2 and Bcl-2 active sites unveiled that N-propyl group is involved in significant hydrophobic interactions. Taken together, the results suggested conjugate 8a as a promising lead for further development and optimisation as an efficient antitumor drug.
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Affiliation(s)
- Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mahmoud F. Abo-Ashour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt
| | - Hadia Almahli
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Ohoud J. Alotaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Ghada H. Al-Ansary
- Department of Pharmaceutical Chemistry, Pharmacy Program, Batterejee Medical College, Jeddah, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Hanaa Y. Ahmed
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Mahmoud M. Elaasser
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Hatem A. Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Giza, Egypt
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White OW, Reyes-Betancort JA, Chapman MA, Carine MA. Geographical isolation, habitat shifts and hybridisation in the diversification of the Macaronesian endemic genus Argyranthemum (Asteraceae). New Phytol 2020; 228:1953-1971. [PMID: 33006142 DOI: 10.1111/nph.16980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Inferring the processes responsible for the rich endemic diversity of oceanic island floras is important for our understanding of plant evolution and setting practical conservation priorities. This requires an accurate knowledge of phylogenetic relationships, which have often been difficult to resolve due to a lack of genetic variation. We employed genotyping-by-sequencing (GBS) to investigate how geographical isolation, habitat shifts, and hybridisation have contributed to the evolution of diversity observed in Argyranthemum Webb (Asteraceae), the largest genus of flowering plants endemic to the Macaronesian archipelagos. Species relationships were resolved, and biogeographical stochastic mapping identified intra-island speciation as the most frequent biogeographic process underlying diversification, contrary to the prevailing view in Argyranthemum and the Canary Islands. D-statistics revealed significant evidence of hybridisation between lineages co-occurring on the same island, however there was little support for the hypothesis that hybridisation may be responsible for the occurrence of nonmonophyletic multi-island endemic (MIE) species. Geographic isolation, habitat shifts and hybridisation have all contributed to the diversification of Argyranthemum, with intra-island speciation found to be more frequent than previously thought. Morphological convergence is also proposed to explain the occurrence of nonmonophyletic MIE species. This study reveals greater complexity in the evolutionary processes generating Macaronesian endemic diversity.
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Affiliation(s)
- Oliver W White
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - J Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Oratava, Instituto Canario de Investigaciones Agrarias - ICIA), C/ Retama 2, Puerto de la Cruz, Tenerife, 38400, Spain
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark A Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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Brookes VJ, Degeling C, van Eeden LM, Ward MP. What Is a Dingo? The Phenotypic Classification of Dingoes by Aboriginal and Torres Strait Islander Residents in Northern Australia. Animals (Basel) 2020; 10:ani10071230. [PMID: 32698324 PMCID: PMC7401616 DOI: 10.3390/ani10071230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/07/2020] [Accepted: 07/15/2020] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Dingoes are an Australian icon with cultural, as well as ecological, value, yet defining a dingo is complicated by hybridisation with domestic dogs. Northern Australia is a high-risk zone for the arrival of rabies, a disease which affects dogs (including dingoes) and people. In a rabies outbreak, Aboriginal and Torres Strait Islander peoples who live in this region would want dingoes protected. We visited the Northern Peninsula Area (NPA), Queensland, in 2018–2019 and surveyed Aboriginal and Torres Strait Islander residents about how they define dingoes, using pictures from camera traps previously placed and operated in the area. We found that dingo definition was based on characteristics traditionally associated with the iconic dingo (medium to large-framed dogs, with a long nose, pointed ears, narrow abdomen, bushy tail, smooth tan coats, and white feet and tail tip) but hybrid features, such as curled tail or a lack of white points, were also acceptable features. Local definitions are important when designing and implementing management plans so that actions are supported by local communities, and our findings are a useful guide for identifying dingoes in the NPA so that, in the event of a rabies outbreak, locally valued dingoes could be identified and protected. Abstract Dingo classification and management is complicated by hybridisation with domestic dogs. Northern Australia is a relatively high-risk zone for a rabies incursion, and in the event of an incursion, Aboriginal and Torres Strait Islander peoples who reside in this region would prioritise the protection of dingoes. Therefore, the classification of dingoes in this context is important. Twelve pictures of canids with features associated with both dingoes and domestic dogs from camera traps in the Northern Peninsula Area (NPA), northern Queensland, were shown to Aboriginal and Torres Strait Islander rangers (n = 3), biosecurity officers (n = 2), environmental health workers (n = 2), and residents (n = 39) in the NPA. Nearly all pictures (10/12) were classified as dingo or domestic dog (none as hybrid) and two were inconclusive (no overall agreement). Dingoes were consistently identified as medium to large-framed dogs, with a long nose, pointed ears, narrow abdomen, a bushy or feathered tail, and smooth coats of a single base colour. Some hybrid features were acceptable, including sable coats, lack of white tail tip or feet, and curled tail. These findings are a preliminary guide for identifying canids in the NPA region for whom management might be controversial. Building on this approach via further consultation with residents is needed to inform rabies response policy. Our approach using locally acquired camera trap pictures could also be extended to other regions in which dingoes have value but their management is controversial.
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Affiliation(s)
- Victoria J. Brookes
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden 2570, Australia;
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga 2650, Australia
- Correspondence:
| | - Chris Degeling
- Australian Centre for Health Engagement, Evidence & Values, School of Health and Society, Faculty of the Arts, Social Sciences, and Humanities, University of Wollongong, Wollongong 2252, Australia;
| | - Lily M. van Eeden
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown 2006, Australia;
| | - Michael P. Ward
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden 2570, Australia;
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Crowl AA, Manos PS, McVay JD, Lemmon AR, Lemmon EM, Hipp AL. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). New Phytol 2020; 226:1158-1170. [PMID: 30963585 DOI: 10.1111/nph.15842] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/29/2019] [Indexed: 05/10/2023]
Abstract
Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci. Concatenation, species-tree and network analyses were carried out in an attempt to uncover the genomic signal of ancient introgression and infer the divergent phylogenetic topology for the white oak clade. Locus and site-level likelihood comparisons were then conducted to further explore the introgressed signal within our dataset. Historical, intersectional gene flow is suggested to have occurred between an ancestor of the Eurasian Roburoid lineage and Quercus pontica and North American Dumosae and Prinoideae lineages. Despite extensive time past, our approach proved successful in detecting the genomic signature of ancient introgression. Our results, however, highlight the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history.
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Affiliation(s)
- Andrew A Crowl
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Paul S Manos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - John D McVay
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32317, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 89 Chieftan Way, Tallahassee, FL, 32317, USA
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
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Borzée A, Fong JJ, Nguyen HQ, Jang Y. Large-Scale Hybridisation as an Extinction Threat to the Suweon Treefrog (Hylidae: Dryophytes suweonensis). Animals (Basel) 2020; 10:ani10050764. [PMID: 32349428 PMCID: PMC7278489 DOI: 10.3390/ani10050764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/05/2020] [Accepted: 04/13/2020] [Indexed: 01/09/2023] Open
Abstract
Simple Summary A large number of amphibian species are now endangered, mostly because of human activities. An example is land modification, which may bring species that were previously isolated in contact, and allows them to hybridise. Here, we assessed the presence of hybrid individuals between the endangered Suweon treefrog (Dryophytes suweonensis) and the widespread Japanese treefrog (Dryophytes japonicus). We found hybrids to be relatively widespread and present at all populations where the Suweon treefrog occurred. This is important, as it results in an additional threat to the Suweon treefrog. Abstract Amphibians are in the midst of a sixth mass extinction, and human activities play a major role in pushing species towards extinction. Landscape anthropisation has impacts that indirectly threaten species, in addition to the obvious destruction of natural habitats. For instance, land modification may bring human-commensal species in contact with sister-clades from which they were previously isolated. The species in these new contact zones are then able to hybridise to the point of reaching lineage fusion, through which the gene pool of the two species merges and one of the parental lineages becomes extirpated. Here, we documented the patterns of hybridisation between the spatially restricted D. suweonensis and the widespread D. japonicus. On the basis of the analysis of Cytochrome c oxidase subunit I mitochondrial DNA sequences (404 individuals from 35 sites) and six polymorphic microsatellites (381 individuals from 34 sites), we revealed a generalised, bi-directional, and geographically widespread hybridisation between the two species. Evidence of fertile back-crosses is provided by relatively high numbers of individuals in cyto-nuclear disequilibrium, as well as the presence of hybrid individuals further south than the species distribution limit, determined on the basis of call properties. Hybridisation is an additional threat to the endangered D. suweonensis.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
| | | | - Hoa Quynh Nguyen
- Department of Life Sciences and Division of EcoScience, Ewha Woman’s University, Seoul 03760, Korea
- Centre for Research and Development of Membrane Technology, Institute of Environmental Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Woman’s University, Seoul 03760, Korea
- Correspondence:
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Somenzi E, Ajmone-Marsan P, Barbato M. Identification of Ancestry Informative Marker (AIM) Panels to Assess Hybridisation between Feral and Domestic Sheep. Animals (Basel) 2020; 10:E582. [PMID: 32235592 DOI: 10.3390/ani10040582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Once present in the entirety of Europe, mouflon (wild sheep) became extinct due to intense hunting, but remnant populations survived and became feral on the Mediterranean islands of Corsica and Sardinia. Although now protected by regional laws, Sardinian mouflon is threatened by crossbreeding with domestic sheep causing genetic hybridisation. The spread of domestic genes can be detrimental for wild populations as it dilutes the genetic features that characterise them. This work aimed to identify diagnostic tools that could be applied to monitor the level of hybridisation between mouflon and domestic sheep. Tens of thousands of genetic markers known as single nucleotide polymorphisms (SNPs) were screened and we identified the smallest number of SNPs necessary to discriminate between pure mouflon and sheep. We produced four SNP panels of different sizes which were able to assess the hybridisation level of a mouflon and we verified that the SNP panels efficacy is independent of the domestic sheep breed involved in the hybrid. The implementation of these results into actual diagnostic tools will help the conservation of this unique and irreplaceable mouflon population, and the methodology applied can easily be transferred to other case studies of interest. Abstract Hybridisation of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features. The Mediterranean island of Sardinia hosts one of the last extant autochthonous European mouflon (Ovis aries musimon) populations. Although conservation policies, including reintroduction plans, have been enforced to preserve Sardinian mouflon, crossbreeding with domestic sheep has been documented. We identified panels of single nucleotide polymorphisms (SNPs) that could act as ancestry informative markers able to assess admixture in feral x domestic sheep hybrids. The medium-density SNP array genotyping data of Sardinian mouflon and domestic sheep (O. aries aries) showing pure ancestry were used as references. We applied a two-step selection algorithm to this data consisting of preselection via Principal Component Analysis followed by a supervised machine learning classification method based on random forest to develop SNP panels of various sizes. We generated ancestry informative marker (AIM) panels and tested their ability to assess admixture in mouflon x domestic sheep hybrids both in simulated and real populations of known ancestry proportions. All the AIM panels recorded high correlations with the ancestry proportion computed using the full medium-density SNP array. The AIM panels proposed here may be used by conservation practitioners as diagnostic tools to exclude hybrids from reintroduction plans and improve conservation strategies for mouflon populations.
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Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, Dujardin JC, Sanders MJ, Mauricio I, Miles MA, Schnur LF, Jaffe CL, Nasereddin A, Schallig H, Yeo M, Bhattacharyya T, Alam MZ, Berriman M, Wirth T, Schönian G, Cotton JA. Global genome diversity of the Leishmania donovani complex. eLife 2020; 9:e51243. [PMID: 32209228 PMCID: PMC7105377 DOI: 10.7554/elife.51243] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/27/2020] [Indexed: 12/30/2022] Open
Abstract
Protozoan parasites of the Leishmania donovani complex - L. donovani and L. infantum - cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.
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Affiliation(s)
| | - Caroline Durrant
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | | | - Tim Downing
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Dublin City UniversityDublinIreland
| | | | - Jean-Claude Dujardin
- Institute of Tropical MedicineAntwerpBelgium
- Department of Biomedical Sciences, University of AntwerpAntwerpBelgium
| | - Mandy J Sanders
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Isabel Mauricio
- Universidade Nova de Lisboa Instituto de Higiene e MedicinaLisboaPortugal
| | - Michael A Miles
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Lionel F Schnur
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Charles L Jaffe
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Abdelmajeed Nasereddin
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Henk Schallig
- Amsterdam University Medical Centres – Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology – Experimental ParasitologyAmsterdamNetherlands
| | - Matthew Yeo
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | | | - Mohammad Z Alam
- Department of Parasitology, Bangladesh Agricultural UniversityMymensinghBangladesh
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des AntillesParisFrance
- École Pratique des Hautes Études (EPHE)Paris Sciences & Lettres (PSL)ParisFrance
| | | | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
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Samarasinghe H, Vogan A, Pum N, Xu J. Patterns of allele distribution in a hybrid population of the Cryptococcus neoformans species complex. Mycoses 2019; 63:275-283. [PMID: 31774582 DOI: 10.1111/myc.13040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND The sister yeast species Cryptococcus neoformans (serotype A) and Cryptococcus deneoformans (serotype D) are causative agents of deadly cryptococcosis and fungal meningoencephalitis. These haploid yeasts can hybridise in nature, giving rise to AD hybrids that are predominantly diploid or aneuploid. Despite their increasing prevalence in clinical settings, much remains unknown about the allelic distribution patterns in AD hybrid strains. OBJECTIVES This study aims to characterise allele distributions in AD hybrids derived from the same basidium as well as from multiple basidia in a laboratory-derived C neoformans × C deneoformans hybrid cross. METHODS We dissected a total of 1625 basidiospores from 31 basidia. The 297 basidiospores that successfully germinated were genotyped by molecular characterisation of 33 markers using PCR-RFLP, with at least two markers on each of the 14 chromosomes in the genome. RESULTS Of the 297 strains, 294 contained at least one heterozygous locus, with a mean heterozygosity of ~30% per strain. Most hybrid genomes and chromosomes displayed significantly distorted allele distributions, with offspring originating from the same basidium tended to have alleles at different loci from the same parent. More basidia were skewed in favour of C deneoformans alleles, the mitochondria-donor parent, than the C neoformans alleles. CONCLUSIONS The divergence between C neoformans and C deneoformans genomes has likely created co-adapted allelic combinations, with their co-segregation in hybrid offspring imparting a significant fitness benefit. However, the diversity of genotypes recovered here in a single hybridisation event indicates the enormous capacity of AD hybrids for adaptation and diversification.
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Affiliation(s)
| | - Aaron Vogan
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Nicole Pum
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Abstract
Fagaceae can be found in tropical and temperate regions and contain species of major ecological and economic importance. In times of global climate change, tree populations need to adapt to rapidly changing environmental conditions. The predicted warmer and drier conditions will potentially result in locally maladapted populations. There is evidence that major genera of the Fagaceae are already negatively affected by climate change-related factors such as drought and associated biotic stressors. Therefore, knowledge of the mechanisms underlying adaptation is of great interest. In this review, we summarise current literature related to genetic adaptation to abiotic environmental conditions. We begin with an overview of genetic diversity in Fagaceae species and then summarise current knowledge related to drought stress tolerance, bud burst timing and frost tolerance in the Fagaceae. Finally, we discuss the role of hybridisation, epigenetics and phenotypic plasticity in adaptation.
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Affiliation(s)
- M Müller
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
| | - O Gailing
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
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Gilchrist C, Stelkens R. Aneuploidy in yeast: Segregation error or adaptation mechanism? Yeast 2019; 36:525-539. [PMID: 31199875 PMCID: PMC6772139 DOI: 10.1002/yea.3427] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 01/24/2023] Open
Abstract
Aneuploidy is the loss or gain of chromosomes within a genome. It is often detrimental and has been associated with cell death and genetic disorders. However, aneuploidy can also be beneficial and provide a quick solution through changes in gene dosage when cells face environmental stress. Here, we review the prevalence of aneuploidy in Saccharomyces, Candida, and Cryptococcus yeasts (and their hybrid offspring) and analyse associations with chromosome size and specific stressors. We discuss how aneuploidy, a segregation error, may in fact provide a natural route for the diversification of microbes and enable important evolutionary innovations given the right ecological circumstances, such as the colonisation of new environments or the transition from commensal to pathogenic lifestyle. We also draw attention to a largely unstudied cross link between hybridisation and aneuploidy. Hybrid meiosis, involving two divergent genomes, can lead to drastically increased rates of aneuploidy in the offspring due to antirecombination and chromosomal missegregation. Because hybridisation and aneuploidy have both been shown to increase with environmental stress, we believe it important and timely to start exploring the evolutionary significance of their co-occurrence.
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Affiliation(s)
- Ciaran Gilchrist
- Division of Population Genetics, Department of ZoologyStockholm UniversityStockholmSweden
| | - Rike Stelkens
- Division of Population Genetics, Department of ZoologyStockholm UniversityStockholmSweden
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Abstract
In sigma complexes, intermediates in nucleophilic and electrophilic aromatic substitution and other reactions, delocalization in the aromatic ring is formally disrupted. Unexpectedly, computational evidence is presented that favorable processes contain aromatic sigma complexes. Tetracoordinated carbon therein surprisingly employs orbitals that are more similar to sp2 than to sp3 hybrids in sigma bonds with adjacent ring atoms. Both leaving groups and nucleo- or electrophiles may donate electrons to the π-system depending on the availability of p-type orbitals to fulfill Hückel (4N+2) or Möbius (4N) rules of aromaticity in analogy to conjugated transition-metal metallacycles.
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Affiliation(s)
- Michael Mauksch
- Department of Chemistry and Pharmacy, Institute of Theoretical Chemistry, Computer Chemistry Center, Nägelsbachstrasse 25a, 91052, Erlangen, Germany
| | - Svetlana B Tsogoeva
- Department of Chemistry and Pharmacy, Organic Chemistry Chair I and Interdisciplinary, Center for Molecular Materials (ICMM), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger Str. 10, 91058, Erlangen, Germany
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Gubili C, Schabetsberger R, Poellabauer C, Bates B, Wagstaff RM, Woodward LM, Sichrowsky U, Scheck A, Boseto DT, Feunteun E, Acou A, Jehle R. High genetic diversity and lack of pronounced population structure in five species of sympatric Pacific eels. Fish Manag Ecol 2019; 26:31-41. [PMID: 33244193 PMCID: PMC7116419 DOI: 10.1111/fme.12287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Understanding the population structure of tropical anguillids residing in the Pacific is vital for their conservation management. Here, the population genetic structure of five sympatric freshwater eels (Anguilla marmorata Quoy & Gaimard, A. megastoma Kaup, A. obscura Steindachner, A. reinhardtii Günther and A. australis Richardson) across 11 western South Pacific (WSP) islands was investigated based on partial nucleotide sequences of the mtDNA control region and the nuclear GTH2b genes of 288 newly collected samples jointly with existing sequences. WSP anguillids are characterised by overall high levels of genetic diversity. Both mtDNA and nuclear sequences provided no evidence for distinct geographic clines or barriers in any of the species across the WSP. The occurrence of admixed individuals between A. marmorata and A. megastoma was confirmed, and a new possible occurrence of a further species was revealed (A. interioris Whitley on Bougainville Island). All species showed evidence for demographic population growth in the Pleistocene, and a subsequent population reduction for A. megastoma. Common spawning grounds and mixing of larvae by ocean currents could promote the lack of pronounced isolation by distance, a finding that has significant implications for the future management of anguillids in the area.
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Affiliation(s)
- Chrysoula Gubili
- Fisheries Research Institute, Hellenic Agricultural Organisation, Nea Peramos, Kavala, Macedonia, Greece
| | | | | | - Becky Bates
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Rosa M. Wagstaff
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Lewis M. Woodward
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | | | - Alexander Scheck
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - David T. Boseto
- Ecological Solution, Western Province, Gizo, Solomon Islands
| | - Erik Feunteun
- UMR BOREA (MNHN, CNRS, Sorbonne Université, IRD, UCN, UAG), MNHN Station Marine de Dinard, Dinard, France
| | - Antony Acou
- AFB UMS PatriNat, MNHN Station Marine de Dinard, Dinard, France
| | - Robert Jehle
- School of Environment and Life Sciences, University of Salford, Salford, UK
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Decker P. Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). Zookeys 2019:1-14. [PMID: 30598611 PMCID: PMC6306475 DOI: 10.3897/zookeys.809.30087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/26/2018] [Indexed: 11/12/2022] Open
Abstract
Discord between molecular and morphological datasets was observed in two pairs of species of Australian millipedes in the family Paradoxosomatidae using morphological and molecular phylogenetic analysis (mitochondrial COI rDNA and 16 rRNA, and nuclear 28S rRNA). Close to the presumed distributional boundary between Pogonosternumnigrovirgatum (Carl, 1912) and Pogonosternumjeekeli Decker, 2017, near Dargo in Central Gippsland, Victoria, Pogonosternum specimens were collected which are phylogenetically closer to P.jeekeli in COI and 16S sequences, but are morphologically closer to P.nigrovirgatum. At Mount Osmond, Adelaide, South Australia, eight morphologically typical Somethuscastaneus (Attems, 1944) specimens were collected are phylogenetically closer to S.castaneus in 28S genealogy, but three of the eight are closer to S.lancearius Jeekel, 2002 in COI genealogy. These two cases are discussed in terms of hybridisation, past introgressive hybridisation events and aberrant morphology.
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Affiliation(s)
- Peter Decker
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, Germany Senckenberg Museum of Natural History Görlitz Görlitz Germany
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