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Furukawa M, Kitanobo S, Ohki S, Teramoto MM, Hanahara N, Morita M. Integrative taxonomic analyses reveal that rapid genetic divergence drives Acropora speciation. Mol Phylogenet Evol 2024; 195:108063. [PMID: 38493988 DOI: 10.1016/j.ympev.2024.108063] [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: 11/20/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
Reef-building corals provide the structural basis for one of Earth's most spectacular and diverse but increasingly threatened ecosystems. The reef-building coral genus Acropora may have undergone substantial speciation during the Pleistocene climate and sea-level changes. Here, we aimed to evaluate the speciation history of four morphologically similar tabular Acropora species (Acropora aff. hyacinthus, A. cf. bifurcata, A. cf. cytherea, and A. cf. subulata) using an integrative approach with morphology, genetic, and reproduction methodology. Extensive morphological analyses showed that these four species are distinct and exhibited high gamete incompatibility, preventing hybridization. Furthermore, population structure and principal component analyses with SNPs (>60,000) indicated that these species were genetically distinct, and the ABBA-BABA test did not support introgression among these species. Many of their coding and noncoding RNA sequences showed high genetic variance at loci with high Fst values along the genome. Comparison of these orthologs with those of other Acropora species suggested that many of these genes are under positive selection, which could be associated with spawning time, gamete, and morphological divergence. Our findings show that the speciation of tabular Acropora occurred without hybridization, and the divergence accompanying the rapid evolution of genes in species-rich Acropora could be associated with speciation.
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Affiliation(s)
- Mao Furukawa
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Seiya Kitanobo
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Shun Ohki
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Mariko M Teramoto
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Nozomi Hanahara
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Sesoko, Motobu, Okinawa 905-0227, Japan; Okinawa Churashima Foundation Research Center, 888 Ishikawa, Motobu, Okinawa 905-0206, Japan
| | - Masaya Morita
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Sesoko, Motobu, Okinawa 905-0227, Japan.
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2
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Schwartz LC, González VL, Strong EE, Truebano M, Hilbish TJ. Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone. Mol Ecol 2024; 33:e17333. [PMID: 38597343 DOI: 10.1111/mec.17333] [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: 06/21/2022] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.
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Affiliation(s)
- Lindsey C Schwartz
- Department of Biological Sciences, The University of South Carolina, Columbia, South Carolina, USA
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Vanessa L González
- Informatics and Data Science Center, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
| | - Ellen E Strong
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
| | - Manuela Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Thomas J Hilbish
- Department of Biological Sciences, The University of South Carolina, Columbia, South Carolina, USA
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Awan MJA, Farooq MA, Naqvi RZ, Karamat U, Bukhari SAR, Waqas MAB, Mahmood MA, Buzdar MI, Rasheed A, Amin I, Saeed NA, Mansoor S. Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages. Mol Biol Rep 2024; 51:537. [PMID: 38642174 DOI: 10.1007/s11033-024-09454-0] [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: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. METHODS In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages. RESULTS Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles. CONCLUSION These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Awais Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Umer Karamat
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sayyad Ali Raza Bukhari
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Abu Bakar Waqas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Ismail Buzdar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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Cantalapiedra-Hijar G, Nedelkov K, Crosson P, McGee M. Some plasma biomarkers of residual feed intake in beef cattle remain consistent regardless of intake level. Sci Rep 2024; 14:8540. [PMID: 38609462 PMCID: PMC11014993 DOI: 10.1038/s41598-024-59253-7] [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: 12/18/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
This study investigated whether plasma biomarkers of residual feed intake (RFI), identified under ad libitum feeding conditions in beef cattle, remained consistent during feed restriction. Sixty Charolais crossbred young bulls were divided into two groups for a crossover study. Group A was initially fed ad libitum (first test) and then restricted (second test) on the same diet, while Group B experienced the opposite sequence. Blood samples were collected from the 12 most divergent RFI animals in each group at the end of the first test and again after the second test. 12 plasma variables consistently increased, while three consistently decreased during feed restriction (FDR < 0.05). Only two metabolites, α-aminoadipic acid for Group A and 5-aminovaleric acid for Group B, were associated with RFI independent of feed intake level (FDR < 0.05), demonstrating moderate-to-high repeatability across feeding levels (intraclass correlation coefficient ≥ 0.59). Notably, both metabolites belong to the same metabolic pathway: lysine degradation. These metabolites consistently correlated with RFI, irrespective of fluctuations in feed intake, indicating a connection to individual metabolic processes influencing feed efficiency. These findings suggest that a portion of RFI phenotypic variance is inherent to an individual's metabolic efficiency beyond variations in feed intake.
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Affiliation(s)
- G Cantalapiedra-Hijar
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122, St-Genès-Champanelle, France.
| | - K Nedelkov
- Faculty of Veterinary Medicine, Trakia University, Stara Zagora, 6000, Bulgaria
| | - P Crosson
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - M McGee
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
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5
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Ying J, Qin Y, Zhang F, Duan L, Cheng P, Yin M, Wang Y, Tong X, Huang J, Li Z, Song X, Zhang J. A weak allele of TGW5 enables greater seed propagation and efficient size-based seed sorting for hybrid rice production. Plant Commun 2024; 5:100811. [PMID: 38213029 PMCID: PMC11009153 DOI: 10.1016/j.xplc.2024.100811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Affiliation(s)
- Jiezheng Ying
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yaobing Qin
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Fengyong Zhang
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Liu Duan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Peng Cheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Man Yin
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yifeng Wang
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Xiaohong Tong
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Jie Huang
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhiyong Li
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Xianjun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Jian Zhang
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China.
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6
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Yang R, Jin S, Fang S, Yan D, Zhang H, Nie J, Liu J, Lv M, Zhang B, Dong X. Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes. Genet Sel Evol 2024; 56:24. [PMID: 38566006 PMCID: PMC10985947 DOI: 10.1186/s12711-024-00893-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Gene flow is crucial for enhancing economic traits of livestock. In China, breeders have used hybridization strategies for decades to improve livestock performance. Here, we performed whole-genome sequencing of a native Chinese Lijiang pig (LJP) breed. By integrating previously published data, we explored the genetic structure and introgression of genetic components from commercial European pigs (EP) into the LJP, and examined the impact of this introgression on phenotypic traits. RESULTS Our analysis revealed significant introgression of EP breeds into the LJP and other domestic pig breeds in China. Using a haplotype-based approach, we quantified introgression levels and compared EP to LJP and other Chinese domestic pigs. The results show that EP introgression is widely prevalent in Chinese domestic pigs, although there are significant differences between breeds. We propose that LJP could potentially act as a mediator for the transmission of EP haplotypes. We also examined the correlation between EP introgression and the number of thoracic vertebrae in LJP and identified VRTN and STUM as candidate genes for this trait. CONCLUSIONS Our study provides evidence of introgressed European haplotypes in the LJP breed and describes the potential role of EP introgression on phenotypic changes of this indigenous breed.
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Affiliation(s)
- Ruifei Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Siqi Jin
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Suyun Fang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dawei Yan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hao Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingru Nie
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinqiao Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Minjuan Lv
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Bo Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Xinxing Dong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
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Dzungwe JT, Tozo K, Chrysostome CAAM, Tankouano RA, Oke OE, Tona K. Effect of crossbreeding on egg quality, incubation, and hatching activities of the pure and reciprocal cross between the Sasso and Wassache chickens. Poult Sci 2024; 103:103406. [PMID: 38335664 PMCID: PMC10869303 DOI: 10.1016/j.psj.2023.103406] [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: 07/26/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 02/12/2024] Open
Abstract
Understanding the effect of crossbreeding on egg quality and incubation is essential for the selection of superior genetic combinations in breeding programs. This study evaluated the effect of crossbreeding on egg quality and incubation activities of the Sasso and Wassache chickens in a pure (Sasso X Sasso [SS]; Wassache X Wassache [WW]) and reciprocal cross (Wassache X Sasso [WS]; Sasso X Wassache [SW]) design. A total of 1431 eggs were incubated while 400 eggs were selected for egg quality. Fertility, hatchability, and hatching activities were expressed in percentage, while egg quality traits were determined. The crosses with Sasso hens laid similar (P > 0.05) but heavier (P < 0.05) eggs with higher (P < 0.05) egg components compared to the crosses with Wassache hens. The SS, SW, and WW genotypes recorded similar (P > 0.05) early embryonic mortality (EEM) and were lower (P < 0.05) compared to the WS genotype. Late embryonic mortality (LEM) between the reciprocal crosses and SS was similar (P > 0.05) and lower (P < 0.05) compared to the WW. The hatchability and hatchability of fertile eggs between the purebreds and the SW cross were comparable (P > 0.05), while those of the WS genotype was lower compared to the SS cross. Hatch duration in the crossbreds was shorter (P < 0.05) compared to the pure Sasso. Mortality between the SW and WW was similar (P > 0.05) while the WS cross recorded a higher (P < 0.05) mortality compared to the purebreds. Crossbreeding improved egg quality, reduced LEM, and accelerated crossbred hatching events. The SW cross is recommended for better performance.
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Affiliation(s)
- Joshua T Dzungwe
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo; Department of Animal Breeding and Physiology, Joseph Sarwuan Tarka University, Makurdi, Nigeria.
| | - Koffi Tozo
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo
| | | | - Rachida A Tankouano
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo
| | - Oyegunle E Oke
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo; Department of Animal Physiology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Kokou Tona
- Centre d'Excellence Régionale sur les Science Aviares (CERSA), Université de Lomé, Lomé, Togo
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Rosser N, Seixas F, Queste LM, Cama B, Mori-Pezo R, Kryvokhyzha D, Nelson M, Waite-Hudson R, Goringe M, Costa M, Elias M, Mendes Eleres de Figueiredo C, Freitas AVL, Joron M, Kozak K, Lamas G, Martins ARP, McMillan WO, Ready J, Rueda-Muñoz N, Salazar C, Salazar P, Schulz S, Shirai LT, Silva-Brandão KL, Mallet J, Dasmahapatra KK. Hybrid speciation driven by multilocus introgression of ecological traits. Nature 2024; 628:811-817. [PMID: 38632397 PMCID: PMC11041799 DOI: 10.1038/s41586-024-07263-w] [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: 09/26/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species1,2. However, convincing examples of homoploid hybrid speciation remain rare because it is challenging to demonstrate that hybridization was crucial in generating reproductive isolation3. Here we combine population genomic analysis with quantitative trait locus mapping of species-specific traits to examine a case of hybrid speciation in Heliconius butterflies. We show that Heliconius elevatus is a hybrid species that is sympatric with both parents and has persisted as an independently evolving lineage for at least 180,000 years. This is despite pervasive and ongoing gene flow with one parent, Heliconius pardalinus, which homogenizes 99% of their genomes. The remaining 1% introgressed from the other parent, Heliconius melpomene, and is scattered widely across the H. elevatus genome in islands of divergence from H. pardalinus. These islands contain multiple traits that are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones and mate choice. Collectively, these traits place H. elevatus on its own adaptive peak and permit coexistence with both parents. Our results show that speciation was driven by introgression of ecological traits, and that speciation with gene flow is possible with a multilocus genetic architecture.
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Affiliation(s)
- Neil Rosser
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Biology, University of York, York, UK.
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Bruna Cama
- Department of Biology, University of York, York, UK
| | - Ronald Mori-Pezo
- URKU Estudios Amazónicos, Tarapoto, Perú
- Universidad Nacional Autónoma de Alto Amazona, Yurimaguas, Perú
| | - Dmytro Kryvokhyzha
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | | | | | - Matt Goringe
- Department of Biology, University of York, York, UK
| | | | - Marianne Elias
- Institut Systématique, Evolution, Biodiversité, UMR 7205 MNHN-CNRS-EPHE-UPMC Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Clarisse Mendes Eleres de Figueiredo
- Institute for Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Centre for Advanced Studies of Biodiversity (CEABIO), Belém, Brazil
| | - André Victor Lucci Freitas
- Departamento de Biologia Animal and Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS, Université de Montpellier-Université Paul Valéry Montpellier-EPHE, Montpellier, France
| | - Krzysztof Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Centre for Advanced Studies of Biodiversity (CEABIO), Belém, Brazil
| | - Nicol Rueda-Muñoz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Patricio Salazar
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Stefan Schulz
- Institut für Organische Chemie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Leila T Shirai
- Departamento de Biologia Animal and Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Karina L Silva-Brandão
- Leibniz Institute for the Analysis of Biodiversity Change, Museum de Natur Hamburg Zoology, Hamburg, Germany
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Kanchon K Dasmahapatra
- Department of Biology, University of York, York, UK
- Leverhulme Centre for Anthropocene Biodiversity, Department of Biology, University of York, York, UK
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Maier PA, Vandergast AG, Bohonak AJ. Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression. Mol Ecol 2024; 33:e17317. [PMID: 38488670 DOI: 10.1111/mec.17317] [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: 05/11/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, San Diego, California, USA
- Family TreeDNA, Gene by Gene, Houston, Texas, USA
| | - Amy G Vandergast
- Western Ecological Research Center, San Diego Field Station, U.S. Geological Survey, San Diego, California, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, San Diego, California, USA
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10
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Ajakaye OG, Enabulele EE, Balogun JB, Oyeyemi OT, Grigg ME. Extant interspecific hybridization among trematodes within the Schistosoma haematobium species complex in Nigeria. PLoS Negl Trop Dis 2024; 18:e0011472. [PMID: 38620029 PMCID: PMC11045100 DOI: 10.1371/journal.pntd.0011472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 04/25/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Natural interspecific hybridization between the human parasite (Schistosoma haematobium [Sh]) and bovine parasites (Schistosoma bovis [Sb], Schistosoma curassoni [Sc]) is increasingly reported in Africa. We developed a multi-locus PCR DNA-Seq strategy that amplifies two unlinked nuclear (transITS, BF) and two linked organellar genome markers (CO1, ND5) to genotype S. haematobium eggs collected from infected people in Ile Oluji/Oke Igbo, Ondo State (an agrarian community) and Kachi, Jigawa State (a pastoral community) in Southwestern and Northern Nigeria, respectively. PRINCIPAL FINDINGS Out of a total of 219 urine samples collected, 57 were positive for schistosomes. All patients from Jigawa state possessed an Sh mitochondrial genome and were infected with a genetic profile consistent with an Sh x Sb hybrid based on sequences obtained at CO1, ND5, transITS and BF nuclear markers. Whereas samples collected from Ondo state were more varied. Mitonuclear discordance was observed in all 17 patients, worms possessed an Sb mitochondrial genome but one of four different genetic profiles at the nuclear markers, either admixed (heterozygous between Sh x Sc or Sh x Sb) at both markers (n = 10), Sh at BF and admixed at transITS (Sh x Sc) (n = 5), admixed (Sh x Sc) at BF and homozygous Sc at transITS (n = 1) or homozygous Sh at BF and homozygous Sc at transITS (n = 1). SIGNIFICANCE Previous work suggested that zoonotic transmission of S. bovis in pastoral communities, where humans and animals share a common water source, is a driving factor facilitating interspecific hybridization. However, our data showed that all samples were hybrids, with greater diversity identified in Southwestern Nigeria, a non-pastoral site. Further, one patient possessed an S. bovis mitochondrial genome but was homozygous for S. haematobium at BF and homozygous for S. curassoni at transITS supporting at least two separate backcrosses in its origin, suggesting that interspecific hybridization may be an ongoing process.
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Affiliation(s)
- Oluwaremilekun G. Ajakaye
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda Maryland, United States of America
- Department of Animal and Environmental Biology, Adekunle Ajasin University, Akungba Akoko, Nigeria
| | - Elisha E. Enabulele
- Disease Intervention and Prevention Program, Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Joshua B. Balogun
- Department of Biological Sciences Federal University, Dutse, Nigeria
| | - Oyetunde T. Oyeyemi
- Department of Biosciences and Biotechnology, University of Medical Sciences, Ondo, Nigeria
| | - Michael E. Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda Maryland, United States of America
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11
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Brown MR, Abbott RJ, Twyford AD. The emerging importance of cross-ploidy hybridisation and introgression. Mol Ecol 2024; 33:e17315. [PMID: 38501394 DOI: 10.1111/mec.17315] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024]
Abstract
Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross-mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross-ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross-ploidy hybridisation has been confirmed with genetic data. These results show cross-ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross-ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross-ploidy hybrid speciation shows the potential for important evolutionary outcomes.
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Affiliation(s)
- Max R Brown
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
- School of Life Sciences, Anglia Ruskin University, Cambridge, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, UK
| | - Alex D Twyford
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
- Royal Botanical Garden Edinburgh, Edinburgh, UK
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12
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Frayer ME, Coughlan JM. Surprise hybrid origins of a butterfly species. Nature 2024; 628:723-724. [PMID: 38632416 DOI: 10.1038/d41586-024-00858-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
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13
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Carvalho-Madrigal S, Sanín MJ. The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon). Mol Phylogenet Evol 2024; 193:108013. [PMID: 38195012 DOI: 10.1016/j.ympev.2024.108013] [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: 09/18/2023] [Revised: 12/22/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three 'pure' species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an 'evolutionary syngameon' where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.
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Affiliation(s)
| | - María José Sanín
- School of Mathematical and Natural Sciences, Arizona State University, West Valley Campus, Glendale, United States.
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14
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Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. Insect Sci 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [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: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
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Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
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15
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Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024; 24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [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: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
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Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eckart Stolle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Paris-Lodron-University, Salzburg, Austria
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lars Podsiadlowski
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
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16
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Tellini N, De Chiara M, Mozzachiodi S, Tattini L, Vischioni C, Naumova ES, Warringer J, Bergström A, Liti G. Ancient and recent origins of shared polymorphisms in yeast. Nat Ecol Evol 2024; 8:761-776. [PMID: 38472432 DOI: 10.1038/s41559-024-02352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.
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Affiliation(s)
- Nicolò Tellini
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France
| | | | | | | | | | - Elena S Naumova
- Kurchatov Complex for Genetic Research (GosNIIgenetika), National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.
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17
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Maruthachalam R. Haploids fast-track hybrid plant breeding. Nat Plants 2024; 10:530-532. [PMID: 38499775 DOI: 10.1038/s41477-024-01656-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Affiliation(s)
- Ravi Maruthachalam
- School of Biology, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, India.
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18
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Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation. Plant Physiol 2024; 194:2511-2532. [PMID: 38109503 PMCID: PMC10980416 DOI: 10.1093/plphys/kiad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (Mediator of paramutation1), with that of their parents, wild-type siblings, and backcrossed progeny in maize (Zea mays). Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of these DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that both TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in most TCM DMRs in F1 plants required Mop1, initiation of a new epigenetic state of these DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is independent of RNA-directed DNA methylation.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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19
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Sloan DB, Conover JL, Grover CE, Wendel JF, Sharbrough J. Polyploid plants take cytonuclear perturbations in stride. Plant Cell 2024; 36:829-839. [PMID: 38267606 PMCID: PMC10980399 DOI: 10.1093/plcell/koae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/26/2024]
Abstract
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Justin L Conover
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
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20
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Casiraghi L, Mambretti F, Tovo A, Paraboschi EM, Suweis S, Bellini T. Synthetic eco-evolutionary dynamics in simple molecular environment. eLife 2024; 12:RP90156. [PMID: 38530348 PMCID: PMC10965223 DOI: 10.7554/elife.90156] [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] [Indexed: 03/27/2024] Open
Abstract
The understanding of eco-evolutionary dynamics, and in particular the mechanism of coexistence of species, is still fragmentary and in need of test bench model systems. To this aim we developed a variant of SELEX in vitro selection to study the evolution of a population of ∼1015 single-strand DNA oligonucleotide 'individuals'. We begin with a seed of random sequences which we select via affinity capture from ∼1012 DNA oligomers of fixed sequence ('resources') over which they compete. At each cycle ('generation'), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences ('species') drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual resource binding dominates the selection in the first generations, while inter- and intra-individual interactions become important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.
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Affiliation(s)
- Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli CerviSegrateItaly
| | - Francesco Mambretti
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Anna Tovo
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi MontalciniPieve EmanueleItaly
- IRCCS, Humanitas Clinical and Research CenterRozzanoItaly
| | - Samir Suweis
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli CerviSegrateItaly
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21
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Rossi M, Hausmann AE, Alcami P, Moest M, Roussou R, Van Belleghem SM, Wright DS, Kuo CY, Lozano-Urrego D, Maulana A, Melo-Flórez L, Rueda-Muñoz G, McMahon S, Linares M, Osman C, McMillan WO, Pardo-Diaz C, Salazar C, Merrill RM. Adaptive introgression of a visual preference gene. Science 2024; 383:1368-1373. [PMID: 38513020 DOI: 10.1126/science.adj9201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/30/2024] [Indexed: 03/23/2024]
Abstract
Visual preferences are important drivers of mate choice and sexual selection, but little is known of how they evolve at the genetic level. In this study, we took advantage of the diversity of bright warning patterns displayed by Heliconius butterflies, which are also used during mate choice. Combining behavioral, population genomic, and expression analyses, we show that two Heliconius species have evolved the same preferences for red patterns by exchanging genetic material through hybridization. Neural expression of regucalcin1 correlates with visual preference across populations, and disruption of regucalcin1 with CRISPR-Cas9 impairs courtship toward conspecific females, providing a direct link between gene and behavior. Our results support a role for hybridization during behavioral evolution and show how visually guided behaviors contributing to adaptation and speciation are encoded within the genome.
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Affiliation(s)
- Matteo Rossi
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | | | - Markus Moest
- Department of Ecology and Research Department for Limnology, Mondsee, University of Innsbruck, Innsbruck, Austria
| | | | | | | | - Chi-Yun Kuo
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Daniela Lozano-Urrego
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Lina Melo-Flórez
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Geraldine Rueda-Muñoz
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Mauricio Linares
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | | | - Camilo Salazar
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Richard M Merrill
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
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22
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Cheng J, Zhang Z, Li Y, Zhang L, Hui M, Sha Z. Rolling with the punches: Organism-environment interactions shape spatial pattern of adaptive differentiation in the widespread mantis shrimp Oratosquilla oratoria. Sci Total Environ 2024; 917:170244. [PMID: 38278258 DOI: 10.1016/j.scitotenv.2024.170244] [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] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Investigating spatial pattern of adaptive variation and its underlying processes can inform the adaptive potential distributed within species ranges, which is increasingly important in the context of a changing climate. A correct interpretation of adaptive variation pattern requires that population history and the ensuing population genetic structure are taken into account. Here we carried out such a study by integrating population genomic analyses, demographic model testing and species distribution modeling to investigate patterns and causes of adaptive differentiation in a widespread mantis shrimp, Oratosquilla oratoria, along a replicated, broad-scale temperature gradient in the northwestern Pacific (NWP). Our results supported a strong hierarchical ecogeographic structure dominated by habitat-linked divergence among O. oratoria populations accompanied with introgressive hybridization. A combined FST outlier and environmental correlation analyses revealed remarkable temperature-associated clines in allele frequency across paired North-South populations on Chinese and Japanese coasts, and identified a suite of loci associated with temperature adaptation. Further demographic model testing revealed the observed clinal variation derived partly from Pleistocene divergence followed by recent secondary contact. More importantly, the likelihood of hybridization is predicted to increase as climate change progresses, which would break barriers to gene flow and enable the spread of adaptive genetic variation. These results support that not only is temperature-driven adaptive differentiation occurs in O. oratoria but that such pattern is likely attributed to ancient adaptive variation, sustained by contemporary ocean conditions and a semi-permeable barrier to gene flow maintained by selection. They moreover provide genomic insights into the distribution of adaptive potential across O. oratoria' s species range. This work can serve as a case study to characterize adaptive diversity of marine species in the NWP by integrating environmental and genetic data at temporal and spatial scales in a population genomic framework, which would improve management and conservation actions under climate change.
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Affiliation(s)
- Jiao Cheng
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510275, China
| | - Yulong Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Liwen Zhang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Hui
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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23
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Groh JS, Coop G. The temporal and genomic scale of selection following hybridization. Proc Natl Acad Sci U S A 2024; 121:e2309168121. [PMID: 38489387 PMCID: PMC10962946 DOI: 10.1073/pnas.2309168121] [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: 05/31/2023] [Accepted: 01/30/2024] [Indexed: 03/17/2024] Open
Abstract
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on the Discrete Wavelet Transform to study the genomic scale of local ancestry variation and its association with recombination rates and show that these methods capture temporal dynamics of drift and genome-wide selection after hybridization. We apply these methods to published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio) and to inferred Neanderthal introgression in modern humans. Across systems, upward of 20% of variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. Signatures of selection at fine genomic scales suggest selection over longer time scales; however, we suggest that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from contiguous segments of genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available and can help shed light on generalities of the genomic consequences of interspecific hybridization.
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Affiliation(s)
- Jeffrey S. Groh
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA95616
| | - Graham Coop
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA95616
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24
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Sianta SA, Moeller DA, Brandvain Y. The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system. Proc Natl Acad Sci U S A 2024; 121:e2316008121. [PMID: 38466849 PMCID: PMC10963018 DOI: 10.1073/pnas.2316008121] [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: 09/18/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introgression is pervasive across the tree of life but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well understood. Here, we used 200 genomes and a 15-y site-specific environmental dataset to investigate the effects of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser's admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.
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Affiliation(s)
- Shelley A. Sianta
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
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25
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Duan M, Huang C, Zhang G, Shi H, Zhang P, Li L, Xu T, Zhao Z, Fu Z, Han J, Xu Y, Ding X. Spin-state Conversion by Asymmetrical Orbital Hybridization in Ni-doped Co 3 O 4 to Boost Singlet Oxygen Generation for Microbial Disinfection. Angew Chem Int Ed Engl 2024; 63:e202318924. [PMID: 38270897 DOI: 10.1002/anie.202318924] [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: 12/08/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
Singlet oxygen (1 O2 ) plays a significant role in environmental and biomedical disinfection fields. Electrocatalytic processes hold great potential for 1 O2 generation, but remain challenging. Herein, a facile Ni doping converted spin-state transition approach is reported for boosting 1 O2 production. Magnetic analysis and theoretical calculations reveal that Ni occupied at the octahedral site of Co3 O4 can effectively induce a low-to-high spin-state transition. The high-spin Ni-Co3 O4 generate appropriate binding strength and enhance electron transfer between the Co centers with oxygen intermediates, thereby improving the catalytic activity of Ni-Co3 O4 for effective generating 1 O2 . In neutral conditions, 1×106 CFU mL-1 Gram-negative ESBL-producing Escherichia coli (E. coli) could be inactivated by Ni-Co3 O4 system within 5 min. Further antibacterial mechanisms indicate that 1 O2 can lead to cell membrane damage and DNA degradation so as to irreversible cell death. Additionally, the developed Ni-Co3 O4 system can effectively inactivate bacteria from wastewater and bioaerosols. This work provides an effective strategy for designing high-spin electrocatalysis to boost 1 O2 generation for disinfection process.
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Affiliation(s)
- Meilin Duan
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Chao Huang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
| | - Gong Zhang
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hao Shi
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Pengfei Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, 266071, P.R. China
| | - Limin Li
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Tong Xu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, P.R. China
| | - Zhen Zhao
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Zhujun Fu
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Jingrui Han
- School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, P.R. China
| | - Yuanhong Xu
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
| | - Xiaoteng Ding
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, P.R. China
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26
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Lorenzi A, Bauland C, Pin S, Madur D, Combes V, Palaffre C, Guillaume C, Touzy G, Mary-Huard T, Charcosset A, Moreau L. Portability of genomic predictions trained on sparse factorial designs across two maize silage breeding cycles. Theor Appl Genet 2024; 137:75. [PMID: 38453705 DOI: 10.1007/s00122-024-04566-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
KEY MESSAGE We validated the efficiency of genomic predictions calibrated on sparse factorial training sets to predict the next generation of hybrids and tested different strategies for updating predictions along generations. Genomic selection offers new prospects for revisiting hybrid breeding schemes by replacing extensive phenotyping of individuals with genomic predictions. Finding the ideal design for training genomic prediction models is still an open question. Previous studies have shown promising predictive abilities using sparse factorial instead of tester-based training sets to predict single-cross hybrids from the same generation. This study aims to further investigate the use of factorials and their optimization to predict line general combining abilities (GCAs) and hybrid values across breeding cycles. It relies on two breeding cycles of a maize reciprocal genomic selection scheme involving multiparental connected reciprocal populations from flint and dent complementary heterotic groups selected for silage performances. Selection based on genomic predictions trained on a factorial design resulted in a significant genetic gain for dry matter yield in the new generation. Results confirmed the efficiency of sparse factorial training sets to predict candidate line GCAs and hybrid values across breeding cycles. Compared to a previous study based on the first generation, the advantage of factorial over tester training sets appeared lower across generations. Updating factorial training sets by adding single-cross hybrids between selected lines from the previous generation or a random subset of hybrids from the new generation both improved predictive abilities. The CDmean criterion helped determine the set of single-crosses to phenotype to update the training set efficiently. Our results validated the efficiency of sparse factorial designs for calibrating hybrid genomic prediction experimentally and showed the benefit of updating it along generations.
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Affiliation(s)
- Alizarine Lorenzi
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
- RAGT2n, Genetics and Analytics Unit, 12510, Druelle, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Sophie Pin
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | | | - Gaëtan Touzy
- RAGT2n, Genetics and Analytics Unit, 12510, Druelle, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France.
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27
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Bladen J, Cooper JC, Ridges JT, Guo P, Phadnis N. A new hybrid incompatibility locus between Drosophila melanogaster and Drosophila sechellia. Genetics 2024; 226:iyae001. [PMID: 38184848 PMCID: PMC10917521 DOI: 10.1093/genetics/iyae001] [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: 11/11/2023] [Revised: 11/11/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
Despite the fundamental importance of hybrid incompatibilities to the process of speciation, there are few cases where the evolution and genetic architecture of hybrid incompatibilities are understood. One of the longest studied hybrid incompatibilities causes F1 hybrid male inviability in crosses between Drosophila melanogaster females and males from the Drosophila simulans clade of species-Drosophila simulans, Drosophila mauritiana, and Drosophila sechellia. Here, we discover dramatic differences in the manifestation of this lethal hybrid incompatibility among the D. simulans clade of species. In particular, F1 hybrid males between D. melanogaster and D. sechellia are resistant to hybrid rescue through RNAi knockdown of an essential hybrid incompatibility gene. To understand the genetic basis of this inter-species difference in hybrid rescue, we developed a triple-hybrid mapping method. Our results show that 2 discrete large effect loci and many dispersed small effect changes across the genome underlie D. sechellia aversion to hybrid rescue. The large effect loci encompass a known incompatibility gene Lethal hybrid rescue (Lhr) and previously unknown factor, Sechellia aversion to hybrid rescue (Satyr). These results show that the genetic architecture of F1 hybrid male inviability is overlapping but not identical in the 3 inter-species crosses. Our results raise questions about whether new hybrid incompatibility genes can integrate into an existing hybrid incompatibility thus increasing in complexity over time, or if the continued evolution of genes can gradually strengthen an existing hybrid incompatibility.
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Affiliation(s)
- Jackson Bladen
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jacob C Cooper
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jackson T Ridges
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ping Guo
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nitin Phadnis
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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28
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Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (Bethesda) 2024; 14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [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: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.
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Affiliation(s)
- William Vilas Boas Nunes
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Daniel Siqueira Oliveira
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Guilherme de Rezende Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Antonio Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Ícaro Putinhon Caruso
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Joice Matos Biselli
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Nathalie Guegen
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Abdou Akkouche
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claudia M A Carareto
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
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29
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Morimoto T, Narazaki R, Okabe H, Zhang L, Nishimura K, Itai A. Introduction of a diverse genetic background of Pyrus into Malus through intergeneric hybridization. Mol Genet Genomics 2024; 299:21. [PMID: 38429502 DOI: 10.1007/s00438-024-02131-8] [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: 01/10/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Wide hybridizations across species and genera have been employed to enhance agriculturally important traits in crops. Within the tribe Maleae of the Rosaceae family, different genera and species exhibit several traits useful for increasing diversity and gene pool through hybridization. This study aimed to develop and characterize intergeneric hybrid individuals between Malus and Pyrus. Through seed germination, shoot multiplication, and rooting in vitro, acclimatized seedlings showing vegetative growth on their own roots were obtained from crosses of Malus × domestica pollinated by Pyrus communis, P. bretschneideri, and the Pyrus interspecific hybrid (P. communis × P. pyrifolia). Comparative analysis of leaf morphology, flow cytometry, and molecular genotyping confirmed the hybrid status of the individuals. Genome-wide genotyping revealed that all the hybrid individuals inherited genomic fragments symmetrically from the Malus and Pyrus parents. To the best of our knowledge, this is the first report on the development of intergeneric hybrid seedlings between Malus × domestica and P. bretschneideri. Furthermore, the Pyrus interspecific hybrid individual served as a bridge plant for introducing the genetic background of P. pyrifolia into Malus × domestica. The results of this study provided a crucial foundation for breeding through intergeneric hybridization between Malus and Pyrus, facilitating the incorporation of valuable traits from diverse gene pools.
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Affiliation(s)
- Takuya Morimoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan.
| | - Ryuya Narazaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Hiroaki Okabe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Lumin Zhang
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
- Institute of Tropical Eco-agriculture, Yunnan Academy of Agricultural Sciences, Yunnan, China
| | - Kazusa Nishimura
- Graduate School of Environmental, Natural Science and Technology, Okayama University, Life, Okayama, Japan
| | - Akihiro Itai
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
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30
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Campestre MP, Antonelli CJ, Castagno NL, Maguire VG, Ruiz OA. Interspecific hybridization and inoculation with Pantoea eucalypti improve forage performance of Lotus crop species under alkaline stress. Plant Biol (Stuttg) 2024; 26:245-256. [PMID: 38196283 DOI: 10.1111/plb.13614] [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] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024]
Abstract
This study was designed to elucidate the physiological responses of three Lotus forage accessions to alkaline stress, and the influence of inoculating with Pantoea eucalypti endophyte strain on alkaline stress mitigation. A diploid L. corniculatus (Lc) accession, L. tenuis (Lt), and the interspecific hybrid Lt × Lc obtained from these two parental lines were exposed to alkaline stress (pH 8.2). Both Lt and the Lt × Lc hybrid are alkaline-tolerant compared to Lc, based on observations that dry mass was not reduced under stress, and there were no chlorosis symptoms on leaf blades. In all three Lotus accessions, Fe2+ concentration under stress decreased in aerial parts and simultaneously increased in roots. Inoculation with P. eucalypti considerably increased Fe2+ content in shoots of all three Lotus forage species under alkaline treatment. Photochemical efficiency of PSII was affected in Lc accession only when exposed to alkaline treatment. However, when cultivated under alkalinity with inoculation, plants recovered and had photosynthetic parameters equivalent to those in the control treatment. Together, the results highlight the importance of inoculation with P. eucalypti, which contributes significantly to mitigating alkaline stress. All results provide useful information for improving alkaline tolerance traits of Lotus forage species and their interspecific hybrids.
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Affiliation(s)
- M P Campestre
- Laboratorio de Estrés Biótico y Abiótico en Plantas, Chascomús, Argentina
| | - C J Antonelli
- Laboratorio de Estrés Biótico y Abiótico en Plantas, Chascomús, Argentina
| | - N L Castagno
- Laboratorio de Interacciones Planta-Microorganismo, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Chascomús, Argentina
| | - V G Maguire
- Laboratorio de Estrés Biótico y Abiótico en Plantas, Chascomús, Argentina
| | - O A Ruiz
- Laboratorio de Estrés Biótico y Abiótico en Plantas, Chascomús, Argentina
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31
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Wang S. Divergent island hybrids mixed waves of ancient gene flow. Mol Ecol 2024; 33:e17279. [PMID: 38308460 DOI: 10.1111/mec.17279] [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: 09/25/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024]
Abstract
In this issue of Molecular Ecology, Salter et al. (2023) discovered that the Cuban Northern Bobwhite subspecies, Colinus virginianus cubanensis (Gould, 1850), is an ancient hybrid population formed due to historical hybridization potentially brought by waves of historical human migration. This study revealed a complex mixture of gene flow from distinct spatiotemporal origins underlying a seemingly semi-independent evolutionary trajectory. Hybridization can be more common and complex than we thought.
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Affiliation(s)
- Silu Wang
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, USA
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32
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Belcik JT, Ashley MV. Riverscape genetics of the orangethroat darter complex. J Fish Biol 2024; 104:837-850. [PMID: 37971888 DOI: 10.1111/jfb.15619] [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: 05/22/2023] [Revised: 09/16/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
Freshwater darters belonging to the orangethroat darter species complex, or Ceasia, are widely distributed in the Central and Southern United States, with ranges that span both glaciated and unglaciated regions. Up to 15 species have been recognized in the complex, with one, Etheostoma spectabile, having a widespread northern distribution and another, Etheostoma pulchellum, having a sizeable southern distribution. The other species in the complex have much more restricted distributions in unglaciated regions of the Central Highlands. We sampled 384 darters from 52 sites covering much of the range of Ceasia and evaluated patterns of genetic diversity, genetic structure, and pre- and post-glacial patterns of range contraction and expansion. We anticipated finding much stronger signals of genetic differentiation and diversification in unglaciated regions, given the higher species diversity and levels of endemism reported there. Surprisingly, microsatellite genotyping revealed two well-differentiated genetic clusters of E. spectabile in samples from glaciated regions, one confined to the Illinois River basin and another found in the Wabash drainage and Great Lakes tributaries. This suggests that there was expansion from two isolated glacial refugia, with little subsequent post-glacial gene flow. Fish collected from throughout the unglaciated region were less genetically differentiated. Fish assigned to Etheostoma burri and Etheostoma uniporum based on collection sites and morphological characters were not genetically differentiated from E. spectabile samples from the region. Hybridization and introgression occurring in the Central Highlands may confound genetic delineation of species in this region of high endemism and diversity.
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Affiliation(s)
- John T Belcik
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
- U.S. Army Corps of Engineers Chicago District, Chicago, Illinois, USA
| | - Mary V Ashley
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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33
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Salter JF, Brumfield RT, Faircloth BC. An island 'endemic' born out of hybridization between introduced lineages. Mol Ecol 2024; 33:e16990. [PMID: 37208829 DOI: 10.1111/mec.16990] [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: 11/16/2022] [Revised: 04/06/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023]
Abstract
Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human-mediated movement of individuals, either through translocation of individuals within their range or through the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human-mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographical patterns. Studies combining genetic data with archaeological, linguistic and historical evidence have confirmed prehistoric examples of human-mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical museum specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human-mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages.
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Affiliation(s)
- Jessie F Salter
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Louisiana, Baton Rouge, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Louisiana, Baton Rouge, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Louisiana, Baton Rouge, USA
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34
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Wu H, Zhang Y, Yu L. Opportunities and challenges in studies of mammalian hybrid speciation. Sci China Life Sci 2024; 67:614-617. [PMID: 37955779 DOI: 10.1007/s11427-023-2469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023]
Affiliation(s)
- Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yuxing Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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35
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Srihi H, López-Carbonell D, Ibáñez-Escriche N, Casellas J, Hernández P, Negro S, Varona L. A multivariate gametic model for the analysis of purebred and crossbred data. An example between two populations of Iberian pigs. J Anim Breed Genet 2024; 141:153-162. [PMID: 37888514 DOI: 10.1111/jbg.12832] [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: 06/28/2023] [Revised: 09/06/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023]
Abstract
Crossbreeding plays a pivotal role within pig breeding programmes, aiming to maximize heterosis and improve reproductive traits in crossbred maternal lines. Nevertheless, there is evidence indicating that the performance of reciprocal crosses between two genetic lines might exhibit variability. These variations in performance can be attributed to differences in the correlations between gametic effects, acting as either sire or dam, within purebred and crossbred populations. To address this issue, we propose a multivariate gametic model that incorporates up to four correlated gametic effects for each parental population. The model is employed on a data set comprising litter size data (total number of piglets born-TNB- and number of piglets born alive-NBA-) derived from a reciprocal cross involving two Iberian pig populations: Entrepelado and Retinto. The data set comprises 6933 records from 1564 purebred Entrepelado (EE) sows, 4995 records from 1015 Entrepelado × Retinto (ER) crosses, 2977 records from 756 Retinto × Entrepelado (RE) crosses and 7497 records from 1577 purebred Retinto (RR) sows. The data set is further supplemented by a pedigree encompassing 6007 individual-sire-dam entries. The statistical model also included the order of parity (with six levels), the breed of the service sire (five levels) and the herd-year-season effects (141 levels). Additionally, the model integrates random dominant and permanent environmental sow effects. The analysis employed a Bayesian approach, and the results revealed all the posterior estimates of the gametic correlations to be positive. The range of the posterior mean estimates of the correlations varied across different gametic effects and traits, with a range between 0.04 (gametic correlation between the paternal effects for purebred and the maternal for crossbred in Retinto) and 0.53 (gametic correlation between the paternal effects for purebred and the paternal for crossbred in Entrepelado). Furthermore, the posterior mean variance estimates of the maternal gametic effects were consistently surpassed those for paternal effects within all four populations. The results suggest the possible influence of imprinting effects on the genetic control of litter size, and underscore the importance of incorporating crossbred data into the breeding value predictions for purebred individuals.
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Affiliation(s)
- Houssemeddine Srihi
- Facultad de Veterinaria, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, Zaragoza, Spain
| | - David López-Carbonell
- Facultad de Veterinaria, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, Zaragoza, Spain
| | | | | | | | - Sara Negro
- INGA FOOD S.A. (Nutreco), Almendralejo, Spain
| | - Luis Varona
- Facultad de Veterinaria, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, Zaragoza, Spain
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36
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Lafond J, Angers B. Maternal ploidy shapes reproductive pathways in the triploid hybrid Chrosomus eos × eos-neogaeus. Mol Ecol 2024; 33:e17264. [PMID: 38205506 DOI: 10.1111/mec.17264] [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: 09/29/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Elements transferred from a mother to her eggs may strongly influence the phenotype of her offspring. Such maternal effects depend on the genotype of the mother, and while multiple ploidy levels occur naturally in some vertebrate species, studies evaluating the impact of maternal ploidy on offspring are scarce. This paper aimed to test whether maternal ploidy is responsible for the two reproductive phenotypes observed in the triploid fish Chrosomus eos × eos-neogaeus. Indeed, these hybrids have two different maternal origins (diploid or triploid) and display two reproductive phenotypes, ameiotic and meiotic hybridogenesis, resulting in diploid and haploid eggs, respectively. To this end, we first conducted a genomic survey to identify epigenetic variations in triploid larvae reared under common garden conditions, concordantly with their maternal origin. The results revealed that the polymorphic epigenetic loci of the larvae clustered into two highly distinct groups consistently with the ploidy of their mother. Diagnostic epigenetic loci were then tested in triploid adult females whose reproductive pathways were already known, to infer their own maternal origin. Altogether, the results suggest that triploid larvae from diploid and triploid mothers will develop the ameiotic and meiotic hybridogenesis pathway, respectively. This confirms that the development of a given reproductive pathway in triploid females results from the ploidy of their mother. Overall, this study supports a strong maternal effect, introducing maternal ploidy and reproductive pathways as additional cause and effect of maternal effects, respectively.
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Affiliation(s)
- Joëlle Lafond
- Department of Biological Sciences, Université de Montréal, Montreal, Quebec, Canada
| | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montreal, Quebec, Canada
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Martínez-Marín G, Toledo-Alvarado H, Amalfitano N, Gallo L, Bittante G. Lactation modeling and the effects of rotational crossbreeding on milk production traits and milk-spectra-predicted enteric methane emissions. J Dairy Sci 2024; 107:1485-1499. [PMID: 37944799 DOI: 10.3168/jds.2023-23551] [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: 03/30/2023] [Accepted: 09/19/2023] [Indexed: 11/12/2023]
Abstract
Rotational crossbreeding has not been widely studied in relation to the enteric methane emissions of dairy cows, nor has the variation in emissions during lactation been modeled. Milk infrared spectra could be used to predict proxies of methane emissions in dairy cows. Therefore, the objective of this work was to study the effects of crossbreeding on the predicted infrared proxies of methane emissions and the variation in the latter during lactation. Milk samples were taken once from 1,059 cows reared in 2 herds, and infrared spectra of the milk were used to predict milk fat (mean ± SD; 3.79 ± 0.81%) and protein (3.68 ± 0.36%) concentrations, yield (21.4 ± 1.5 g/kg dry matter intake), methane intensity (14.2 ± 2.0 g/kg corrected milk), and daily methane production (358 ± 108 g/d). Of these cows, 620 were obtained from a 3-breed (Holstein, Montbéliarde, and Viking Red) rotational mating system, and the rest were purebred Holsteins. Milk production data and methane traits were analyzed using a nonlinear model that included the fixed effects of herd, genetic group, and parity, and the 4 parameters (a, b, c, and k) of a lactation curve modeled using the Wilmink function. Milk infrared spectra were found to be useful for direct prediction of qualitative proxies, such as methane yield and intensity, but not quantitative traits, such as daily methane production, which appears to be better estimated (450 ± 125 g/d) by multiplying a measured daily milk yield by infrared-predicted methane intensity. Lactation modeling of methane traits showed daily methane production to have a zenith curve, similar to that of milk yield but with a delayed peak (53 vs. 37 d in milk), whereas methane intensity is characterized by an upward curve that increases rapidly during the first third of lactation and then slowly till the end of lactation (10.5 g/kg at 1 d in milk to 15.2 g/kg at 300 d in milk). However, lactation modeling was not useful in explaining methane yield, which is almost constant during lactation. Lastly, the methane yield and intensity of cows from 3-breed rotational crossbreeding are not greater, and their methane production is lower than that of purebred Holsteins (452 vs. 477 g/d). Given the greater longevity of crossbred cows, and their lower replacement rate, rotational crossbreeding could be a way of mitigating the environmental impact of milk production.
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Affiliation(s)
- Gustavo Martínez-Marín
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova (Padua), 35020 Legnaro (PD), Italy
| | - Hugo Toledo-Alvarado
- Department of Genetics and Biostatistics, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Nicolò Amalfitano
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova (Padua), 35020 Legnaro (PD), Italy.
| | - Luigi Gallo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova (Padua), 35020 Legnaro (PD), Italy
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova (Padua), 35020 Legnaro (PD), Italy
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38
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Dean LL, Whiting JR, Jones FC, MacColl ADC. Reproductive isolation in a three-way contact zone. Mol Ecol 2024; 33:e17275. [PMID: 38235507 DOI: 10.1111/mec.17275] [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: 09/19/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - James R Whiting
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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39
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Chai MW, Lu HP, Tseng YT, Liao PC. Maintenance of species boundaries amid hybridization in two island gingers with similar ecological niches. Evolution 2024; 78:526-538. [PMID: 38150395 DOI: 10.1093/evolut/qpad233] [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: 06/07/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Understanding species boundaries maintenance in the face of hybridization/introgression is an intriguing yet complex topic in evolutionary biology. The underlying mechanisms, however, remain elusive. To address this, we propose to investigate the role of climatic shifts in shaping genetic structure and influencing species boundaries. We combine multilocus genetic data and species distribution modeling to explore how past and current climatic shifts affect the genetic structure and demographic history of two Taiwan endemic gingers, Zingiber pleiostachyum and Z. shuanglongense. We identified a well-delimited genetic structure with evidence of admixture, indicating incomplete reproductive isolation between the two gingers. This is likely due to secondary contact and range overlap during the last glacial maximum, leading to sporadic instances of hybridization. Niche overlap tests based on climate and soil data indicate that these two gingers occupy similar but nonidentical ecological niches. Furthermore, we found that the considerable differences in their current geographic distribution and altitude preferences might have resulted from different seed dispersal capabilities and competitive exclusion due to their similar niche preferences. Our results reveal a model where altitudinal differentiation and dispersal strategy synergistically reinforce the species divergence, thereby illuminating the importance of these factors in shaping and maintaining the island's biodiversity.
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Affiliation(s)
- Min-Wei Chai
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Hsin-Pei Lu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Yi-Ting Tseng
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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40
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Sinaga P, Klichowska E, Nowak A, Nobis M. Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia. PLoS One 2024; 19:e0298760. [PMID: 38412151 PMCID: PMC10898772 DOI: 10.1371/journal.pone.0298760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.
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Affiliation(s)
- Patar Sinaga
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden – Center for Biological Diversity Conservation in Powsin, Warszawa, Poland
- Botanical Garden of the Wrocław University, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
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41
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Ombayev A, Parzhanov Z, Azhimetov N, Zhylkibayev A, Abishov M, Issabayeva A. Increasing the meat productivity of young sheep based on the use of the gene pool of the Dorper and Hissar breeds. BRAZ J BIOL 2024; 83:e278807. [PMID: 38422273 DOI: 10.1590/1519-6984.278807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/01/2023] [Indexed: 03/02/2024] Open
Abstract
In the pursuit of enhanced mutton production, improving the genetic reservoir of sheep with early maturation and high meat productivity is imperative. This study aims to assess the efficacy of integrating Dorper and Hissar rams into the breeding program of Kazakh fat-tailed coarse-haired ewes for generating young mutton. The research involved forming three groups, each comprising 40 ewes of the Kazakh fat-tailed coarse-haired breed, based on analog pairs. Ewes in Group I were inseminated with Dorper ram semen, those in Group II were inseminated with Hissar ram semen, and Group III served as a control with purebred Kazakh fat-tailed coarse-haired sheep breeding. Results revealed that crossbred rams in Group II achieved a significantly higher live weight of 45.2 kg at 120 days of age, surpassing the other groups by 9.7 kg and 10.6 kg. Crossbred gimmers in Group II reached a live weight of 42.0 kg by 4 months, outpacing the other groups by 12.2 kg. The crossbred lambs exhibited an expansive, deep, and sturdy physique, indicative of elevated meat productivity. Physique index analysis displayed that crossbred rams exhibited elongated limbs, bulkiness, and massiveness compared to purebred Kazakh fat-tailed coarse-haired lambs. In the 4.0-4.5-month age range, crossbred rams demonstrated a higher carcass muscle yield than their purebred counterparts, albeit the latter exhibited a 0.18% greater bone yield. Moreover, the meat of groups I and II sheep contained 19.6% and 20.1% protein content, respectively, surpassing the local Kazakh fat-tailed sheep population by 0.7% and 1.2% in absolute terms.
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Affiliation(s)
- A Ombayev
- Kazakh National Agrarian Research University, Almaty, the Republic of Kazakhstan
| | - Zh Parzhanov
- Shymkent University, Faculty of "Natural Sciences and Humanities", Karatau district, Shymkent city, the Republic of Kazakhstan
| | - N Azhimetov
- Shymkent University, Department of Science, Karatau district, Shymkent city, the Republic of Kazakhstan
| | - A Zhylkibayev
- NJSC "M. Auezov South Kazakhstan University", Faculty of Agriculture, Shymkent, the Republic of Kazakhstan
| | - M Abishov
- Central Asian Innovation University, Faculty of Natural Sciences, Shymkent, the Republic of Kazakhstan
| | - A Issabayeva
- Central Asian Innovation University, Faculty of Natural Sciences, Shymkent, the Republic of Kazakhstan
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42
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Vidal AKF, Daher RF, Freitas RS, Santana JGS, Stida WF, Ambrósio M, Silva VB, Souza AG, Nascimento MR, Santos RM, Leite CL, Farias JEC. Genetic diversity based on multivariate techniques in elephant grass genotypes for bioenergy. BRAZ J BIOL 2024; 84:e278601. [PMID: 38422291 DOI: 10.1590/1519-6984.278601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/02/2024] [Indexed: 03/02/2024] Open
Abstract
The use of biomass for energy production constitutes a promising strategy that warrants the search for new sources of biomass. Elephant grass has been gaining notoriety due to its high dry matter yield and rapid growth. The present study was carried out to quantify the genetic divergence of nine elephant grass half-sib families in order to identify genotypes with greater genetic divergence and productive potential for hybridization, using the hierarchical clustering methodology based on principal components. Half-sib families were generated using genotypes from the Active Germplasm Bank of Elephant Grass. The experiment was laid out in a randomized-block design with nine half-sib families, three replicates, and eight plants per plot. A total of 216 genotypes of elephant grass were evaluated. Principal component (PC), biplot, and hierarchical clustering analyses for diversity estimation were conducted using R software. The first two PCs of biplot analysis accounted for 64% of the cumulative variation. Dry matter yield was the most important trait for genotype discrimination (0.89), followed by plant height (0.67) and stem diameter (0.61) in PC1. In this analysis, the distances between accessions were considered and there were no family links, which indicates the existence of wide variability within the evaluated families, since genotypes belonging to the same family were not grouped together, but rather distributed into different groups. Crosses between genotypes of group three and genotypes of groups one and two are recommended for the development of high-yielding genotypes when aiming at energy production.
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Affiliation(s)
- A K F Vidal
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - R F Daher
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - R S Freitas
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - J G S Santana
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - W F Stida
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - M Ambrósio
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - V B Silva
- Universidade Federal do Piauí - UFPI, Centro de Ciências Agrárias - CCA, Programa de Pós-graduação em Agronomia - PPGA, Campus Universitário Ministro Petrônio Portella, Teresina, PI, Brasil
| | - A G Souza
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - M R Nascimento
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - R M Santos
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - C L Leite
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
| | - J E C Farias
- Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Centro de Ciências e Tecnologias Agropecuárias - CCTA, Campos dos Goytacazes, RJ, Brasil
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Baiseitova G, Berkimbay K, Mynbayeva D, Nussupova A, Amirova AK, Usenbekov B, Kulakhmetova Z, Yernazarova G, Yussayeva D, Kazkeyev D, Mukhambetzhanov S. Heritability and amylose content in hybrid lines of late-generation rice with colored pericarp. BRAZ J BIOL 2024; 83:e280919. [PMID: 38422279 DOI: 10.1590/1519-6984.280919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/20/2023] [Indexed: 03/02/2024] Open
Abstract
Improving grain quality in rice breeding is one of the main tasks. This concerns the creation of rice varieties with colored pericarp uncommon in the Republic of Kazakhstan, and the assessment of its quality is an important stage of breeding. Rice with colored pericarp is an important dietary crop, more useful for the human body than white rice. Regardless of the type of rice, the amount of amylose in rice grain is a crucial indicator that determines the quality of rice. The paper presents the results of electrophoretic separation of spare grain proteins of rice hybrids and dihaploids with colored pericarp and their parent forms obtained as a result of the hybridization of varieties with colored pericarp (Black Rice (China), Mavr (Russia), and Yir 5815 (Ukraine)) with white rice varieties zoned in Kazakhstan. The hybridization of the rice varieties with colored pericarp with white rice varieties was carried out to obtain rice varieties with colored pericarp oriented to the soil and climate of Kazakhstan. Analyzing the results of electrophoresis and the amount of amylose, it was found that hybrid lines differed in amylose content. One of the studied hybrids was high in amylose, four had a medium amylose content, ten had a low amylose content, three had a very low amylose content, and six were glutinous. According to the results of electrophoretic separation of spare rice grain proteins, the spectrum of the enzyme determining amylose was detected in five hybrids, which corresponds to the results of spectrophotometric determination of amylose: high amylose in one hybrid and medium amylose content in four. The results show that the hybrids obtained as a result of hybridization are true hybrids and as a result of long-term selection, the amylose content in the F7-F8 hybrids stabilized. The hybrids can be used in further breeding of rice with colored pericarp.
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Affiliation(s)
- G Baiseitova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Kazakh National Agrarian Research University, Almaty, Kazakhstan
| | - Kh Berkimbay
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Kazakh National Agrarian Research University, Almaty, Kazakhstan
| | - D Mynbayeva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - A Nussupova
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - A K Amirova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - B Usenbekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Z Kulakhmetova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - G Yernazarova
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - D Yussayeva
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - D Kazkeyev
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - S Mukhambetzhanov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Pogodaev V, Parzhanov Z, Azhimetov N, Sergeeva N, Akhynova U, Tenlibayeva A, Mustiyar T. The Dorper breed as a stage in the sustainable development of the agroindustry. BRAZ J BIOL 2024; 83:e278882. [PMID: 38422274 DOI: 10.1590/1519-6984.278882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/19/2023] [Indexed: 03/02/2024] Open
Abstract
The economic condition, national economic significance and prospects for the development of sheep breeding in our country directly depend on the meat productivity of sheep. The purpose of our research was to study the qualitative indicators of sheepskins and the histological structure of the skin of Kalmyk fat-tailed rams and crossbreeds obtained on the basis of crossing of Kalmyk fat-tailed ewes with Dorper rams. The work was carried out in LLC "Agrofirma Aduchi", Republic of Kalmykia. It was found that the coarser wool of the rams of group I was 4.7 microns or 12.9%, in contrast to the peers of group II. The control animals have 40 quality wool, and the experimental ones - 36, that is, the wool of hybrid young animals is thinner by two whole qualities, which is a very good indicator for the textile industry. The fineness of the awn was thicker in purebred rams by 8.5%, the fineness of transitional hair and fluff by 17.8%, in contrast to hybrid young. In the study of the histological parameters of the skin, it was revealed that the rams of group I had 352.57 µm thicker skin (14.52%) in comparison with their peers in group II. In this case, the thickness of the layers of the total thickness of the skin in animals of group I is: epidermis - 0.8%, pilar - 69.8%, reticular - 29.4%; Group II - epidermis - 1.2%, pilar - 60.5%, reticular - 38.3%. The densest epidermis was found in crossbred young animals of group II. Their superiority in this indicator over their peers in the control group was 6.12 microns or 27.7%. This is due to the fact that in animals of the meat direction, the epidermal part (flesh) is thicker. Crossbred rams have a larger area of sheepskins, the skin is more elastic, durable and less thick, such sheepskins are first-class raw materials for the industrial production of fur products. The density of the coat (the ratio of WF / PF) in crossbred rams is greater than that of purebred peers.
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Affiliation(s)
- V Pogodaev
- Federal State Budgetary Scientific Institution "North Caucasian Federal Scientific Agrarian Center", Laboratory of Breeding and Selection of Farm Animals, Mikhailovsk, The Russian Federation
| | - Zh Parzhanov
- Shymkent University, Faculty of "Natural Sciences and Humanities", Shymkent, Karatau District, The Republic of Kazakhstan
| | - N Azhimetov
- Shymkent University, Department of Science, Shymkent, Karatau District, The Republic of Kazakhstan
| | - N Sergeeva
- Federal State Budgetary Scientific Institution "North Caucasian Federal Scientific Agrarian Center", Laboratory of Industrial Technology of Livestock Production, Mikhailovsk, The Russian Federation
| | - U Akhynova
- Shymkent University, Department of Science, Shymkent, Karatau District, The Republic of Kazakhstan
| | - A Tenlibayeva
- Jumabek Tashenov University, Natural and Pedagogical Faculty, Department of Chemistry and Biology, Shymkent, The Republic of Kazakhstan
| | - T Mustiyar
- Peoples' Friendship University Named After Academician A. Kuatbekov, Faculty of "Natural Sciences", Shymkent, The Republic of Kazakhstan
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Duan M, Zhao Y, Liu Y, He Y, Dai R, Chen J, Li X, Jia F. A low-background and wash-free signal amplification F-CRISPR biosensor for sensitive quantitative and visible qualitative detection of Salmonella Typhimurium. Sci Total Environ 2024; 912:168905. [PMID: 38016549 DOI: 10.1016/j.scitotenv.2023.168905] [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] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023]
Abstract
In traditional CRISPR-based biosensors, the cleavage-induced signal generation is insufficient because only a signals is generated at a CRISPR-induced cleavage. Herein, we developed an improved CRISPR/Cas12a-based biosensor with an enlarged signal generation which integrated the hybridization chain reaction (HCR) and low-background Förster Resonance Energy Transfer (FRET) signal output mode. The HCR with nucleic acid self-assembly capability was used as a signal carrier to load more signaling molecules. To get the best signal amplification, three different fluorescence signal output modes (fluorescence recovery, FRET and low-background FRET) generated by two fluoresceins, FAM and Cy5, were fully investigated and compared. The results indicated that the low-background FRET signal output mode with the strictest signal generation conditions yielded the highest signal-to-noise ratio (S/N) (19.17) and the most obvious fluorescence color change (from red to yellow). In optimal conditions, the proposed biosensor was successfully applied for Salmonella Typhimurium (S. Typhimurium) detection with 6 h (including 4 h for sample pre-treatment) from the initial target processing to the final detection result. The qualitative sensitivity, reliant on color changes, was 103 CFU/mL. The quantitative sensitivity, calculated by the fluorescence value, were 1.62 × 101 CFU/mL, 3.72 × 102 CFU/mL, and 8.71 × 102 CFU/mL in buffer solution, S. Typhimurium-spiked milk samples, and S.Typhimurium-spiked chicken samples, respectively. The excellent detection performance of the proposed biosensor endowed its great application potential in food and environment safety monitoring.
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Affiliation(s)
- Miaolin Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yijie Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yana Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Ruitong Dai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xingmin Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Fei Jia
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
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46
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Urairi C, Fujito S. Interbiotype hybridization between biotypes A and B of Liriomyza chinensis (Diptera: Agromyzidae). J Econ Entomol 2024; 117:240-250. [PMID: 38071646 DOI: 10.1093/jee/toad223] [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] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 02/13/2024]
Abstract
Liriomyza chinensis (Kato) is a formidable pest of Allium species, especially the Japanese bunching onion Allium fistulosum L. Recently, a novel biotype of L. chinensis (biotype B) has emerged, which causes more severe damage than the native biotype A. It has been reported that biotype B has frequently displaced biotype A in the Japanese bunching onion fields in Japan. As interbiotype hybridization is a possible factor that influences such displacement, interbiotype hybridization was conducted between L. chinensis biotypes A and B. Eggs were not laid under one-by-one crossing conditions; however, adult hybrid progeny of both sexes emerged from no-choice mating combinations-when multiple males and females were present. The fertility of F1 hybrid adults was also investigated, and backcrossed adults emerged from F1 females in both mating combinations. F1 males might have exhibited reproductive abnormalities because only a small number of backcross progeny emerged from the mating combinations using F1 males. Additionally, 3 representative endosymbionts (Wolbachia, Spiroplasma, and Cardinium) were investigated, and both biotypes were found to be infected by the same strain of Wolbachia. In addition, the courtship signals (tapping) of male adults differed between biotypes A and B as well as between F1 hybrids; the F1 males exhibited tapping behavior that was intermediate between biotypes A and B. Therefore, mating sounds serve as a form of premating reproductive isolation between biotypes A and B.
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Affiliation(s)
- Chihiro Urairi
- Institute of Vegetable and Floriculture Science, NARO, Tsu, Mie, Japan
| | - Satoshi Fujito
- Institute of Vegetable and Floriculture Science, NARO, Tsu, Mie, Japan
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47
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Alfieri JM, Hingoranee R, Athrey GN, Blackmon H. Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes). J Hered 2024; 115:1-10. [PMID: 37769441 PMCID: PMC10838130 DOI: 10.1093/jhered/esad059] [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: 05/16/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 09/30/2023] Open
Abstract
Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among hybridizing species on reproductive isolation in the bird order Galliformes. We compiled and analyzed hybridization occurrences from literature and recorded measures of postzygotic reproductive isolation. We used a text-mining approach leveraging a historical aviculture magazine to quantify the degree of domestication across species. We obtained divergence time, morphology, habitat, and clutch size data from open sources. We found 123 species pairs (involving 77 species) with known offspring fertility (sterile, only males fertile, or both sexes fertile). We found that divergence time and clutch size were significant predictors of reproductive isolation (McFadden's Pseudo-R2 = 0.59), but not habitat or morphological mismatch. Perhaps most interesting, we found a significant relationship between domestication and reproductive compatibility after correcting for phylogeny, removing extreme values, and addressing potential biases (F1,74 = 5.43, R2 = 0.06, P-value = 0.02). We speculate that the genetic architecture and disruption in selective reproductive regimes associated with domestication may impact reproductive isolation, causing domesticated species to be more reproductively labile.
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Affiliation(s)
- James M Alfieri
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Reina Hingoranee
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, TX, USA
| | - Giridhar N Athrey
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - Heath Blackmon
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Biology, Texas A&M University, College Station, TX, USA
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Liao B, Xiang YH, Li Y, Yang KY, Shan JX, Ye WW, Dong NQ, Kan Y, Yang YB, Zhao HY, Yu HX, Lu ZQ, Zhao Y, Zhao Q, Guo D, Guo SQ, Lei JJ, Mu XR, Cao YJ, Han B, Lin HX. Dysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier. Nat Commun 2024; 15:996. [PMID: 38307858 PMCID: PMC10837208 DOI: 10.1038/s41467-024-45377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
Postzygotic reproductive isolation, which results in the irreversible divergence of species, is commonly accompanied by hybrid sterility, necrosis/weakness, or lethality in the F1 or other offspring generations. Here we show that the loss of function of HWS1 and HWS2, a couple of duplicated paralogs, together confer complete interspecific incompatibility between Asian and African rice. Both of these non-Mendelian determinants encode the putative Esa1-associated factor 6 (EAF6) protein, which functions as a characteristic subunit of the histone H4 acetyltransferase complex regulating transcriptional activation via genome-wide histone modification. The proliferating tapetum and inappropriate polar nuclei arrangement cause defective pollen and seeds in F2 hybrid offspring due to the recombinant HWS1/2-mediated misregulation of vitamin (biotin and thiamine) metabolism and lipid synthesis. Evolutionary analysis of HWS1/2 suggests that this gene pair has undergone incomplete lineage sorting (ILS) and multiple gene duplication events during speciation. Our findings have not only uncovered a pair of speciation genes that control hybrid breakdown but also illustrate a passive mechanism that could be scaled up and used in the guidance and optimization of hybrid breeding applications for distant hybridization.
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Affiliation(s)
- Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yan Li
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Kai-Yang Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yan Zhao
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qiang Zhao
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dongling Guo
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Shuang-Qin Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie-Jie Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Rui Mu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Jie Cao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Han
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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49
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Hernández F, Janzen T, Lavretsky P. simRestore: A decision-making tool for adaptive management of the native genetic status of wild populations. Mol Ecol Resour 2024; 24:e13892. [PMID: 37966172 DOI: 10.1111/1755-0998.13892] [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: 11/21/2022] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023]
Abstract
Anthropogenic hybridization, or higher and non-natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non-native genes. To alleviate or reverse trends for such scenarios requires the direct integration of genomic data within a model framework for effective management. Towards this end, we developed the simRestore R program as a decision-making tool that integrates ecological and genomic information to simulate ancestry outcomes from optimized conservation strategies. In short, the program optimizes supplementation and removal strategies across generations until a set native genetic threshold is reached within the studied population. Importantly, in addition to helping with initial decision-making, simulations can be updated with the outcomes of ongoing efforts, allowing for the adaptive management of populations. After demonstrating functionality, we apply and optimize among actionable management strategies for the endangered Hawaiian duck for which the current primary threat is genetic extinction through ongoing anthropogenic hybridization with feral mallards. Simulations demonstrate that supplemental and removal efforts can be strategically tailored to move the genetic ancestry of Hawaii's hybrid populations towards Hawaiian duck without the need to completely start over. Further, we discuss ecological parameter sensitivity, including which factors are most important to ensure genetic outcomes (i.e. number of offspring). Finally, to facilitate use, the program is also available online as a Shiny Web application.
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Affiliation(s)
- Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Thijs Janzen
- Department of Ecological Genomics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
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50
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Fabbri MC, Lozada-Soto E, Tiezzi F, Čandek-Potokar M, Bovo S, Schiavo G, Fontanesi L, Muñoz M, Ovilo C, Bozzi R. Persistence of autozygosity in crossbreds between autochthonous and cosmopolitan breeds of swine: a simulation study. Animal 2024; 18:101070. [PMID: 38401921 DOI: 10.1016/j.animal.2023.101070] [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: 09/15/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/26/2024] Open
Abstract
Crossbreeding might be a valid strategy to valorize local pig breeds. Crossbreeding should reduce homozygosity and, as a consequence, yield hybrid vigor for fitness and production traits. This study aimed to quantify the persistence of autozygosity in terminal crossbred pigs compared with purebreds and, in turn, identify genomic regions where autozygosity's persistence would not be found. The study was based on genotyping data from 20 European local pig breeds and three cosmopolitan pig breeds used to simulate crossbred offspring. This study consisted of two steps. First, one hundred matings were simulated for each pairwise combination of the 23 considered breeds (for a total of 276 combinations), ignoring the sex of the parent individuals in order to generate purebred and crossbred matings leveraging all the germplasm available. Second, a few preselected terminal-maternal breed pairs were used to mimic a realistic terminal crossbreeding system: (i) Mora Romagnola (boars) or Cinta Senese (boars) crossed with Large White (sows) or Landrace (sows); (ii) Duroc (boars) crossed with Mora Romagnola (sows) or Cinta Senese (sows). Runs of homozygosity was used to estimate genome-wide autozygosity (FROH). Observed FROH was higher in purebreds than in crossbreds, although some crossbred combinations showed higher FROH than other purebred combinations. Among the purebreds, the highest FROH values were observed in Mora Romagnola and Turopolje (0.50 and 0.46, respectively). FROH ranged from 0.04 to 0.16 in the crossbreds Alentejana × Large White and Alentejana × Iberian, respectively. Persistence of autozygosity was found in several genomic segments harboring regions where quantitative trait loci (QTLs) were found in the literature. The regions were enriched in QTLs involved in fatty acid metabolism and associated with performance traits. This simulation shows that autozygosity persists in most breed combinations of terminal crosses. Results suggest that a strategy for crossbreeding is implemented when leveraging autochthonous and cosmopolitan breeds to obtain most of the hybrid vigor.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy.
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, United States
| | - Francesco Tiezzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
| | | | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
| | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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