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Berling L, Collienne L, Gavryushkin A. Estimating the mean in the space of ranked phylogenetic trees. Bioinformatics 2024; 40:btae514. [PMID: 39177090 PMCID: PMC11364146 DOI: 10.1093/bioinformatics/btae514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/16/2024] [Accepted: 08/21/2024] [Indexed: 08/24/2024] Open
Abstract
MOTIVATION Reconstructing evolutionary histories of biological entities, such as genes, cells, organisms, populations, and species, from phenotypic and molecular sequencing data is central to many biological, palaeontological, and biomedical disciplines. Typically, due to uncertainties and incompleteness in data, the true evolutionary history (phylogeny) is challenging to estimate. Statistical modelling approaches address this problem by introducing and studying probability distributions over all possible evolutionary histories, but can also introduce uncertainties due to misspecification. In practice, computational methods are deployed to learn those distributions typically by sampling them. This approach, however, is fundamentally challenging as it requires designing and implementing various statistical methods over a space of phylogenetic trees (or treespace). Although the problem of developing statistics over a treespace has received substantial attention in the literature and numerous breakthroughs have been made, it remains largely unsolved. The challenge of solving this problem is 2-fold: a treespace has nontrivial often counter-intuitive geometry implying that much of classical Euclidean statistics does not immediately apply; many parametrizations of treespace with promising statistical properties are computationally hard, so they cannot be used in data analyses. As a result, there is no single conventional method for estimating even the most fundamental statistics over any treespace, such as mean and variance, and various heuristics are used in practice. Despite the existence of numerous tree summary methods to approximate means of probability distributions over a treespace based on its geometry, and the theoretical promise of this idea, none of the attempts resulted in a practical method for summarizing tree samples. RESULTS In this paper, we present a tree summary method along with useful properties of our chosen treespace while focusing on its impact on phylogenetic analyses of real datasets. We perform an extensive benchmark study and demonstrate that our method outperforms currently most popular methods with respect to a number of important 'quality' statistics. Further, we apply our method to three empirical datasets ranging from cancer evolution to linguistics and find novel insights into corresponding evolutionary problems in all of them. We hence conclude that this treespace is a promising candidate to serve as a foundation for developing statistics over phylogenetic trees analytically, as well as new computational tools for evolutionary data analyses. AVAILABILITY AND IMPLEMENTATION An implementation is available at https://github.com/bioDS/Centroid-Code.
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Affiliation(s)
- Lars Berling
- Biological Data Science Lab, School of Mathematics and Statistics, University of Canterbury, Christchurch 8041, New Zealand
| | - Lena Collienne
- Biological Data Science Lab, School of Mathematics and Statistics, University of Canterbury, Christchurch 8041, New Zealand
| | - Alex Gavryushkin
- Biological Data Science Lab, School of Mathematics and Statistics, University of Canterbury, Christchurch 8041, New Zealand
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Kotsakiozi P, Antoniou A, Psonis N, Sagonas Κ, Karameta E, Ilgaz Ç, Kumlutaş Y, Avcı A, Jablonski D, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N. Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region. Mol Phylogenet Evol 2024; 197:108091. [PMID: 38719080 DOI: 10.1016/j.ympev.2024.108091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024]
Abstract
Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.
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Affiliation(s)
- Panayiota Kotsakiozi
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece.
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion 71003, P.O. Box 2214, Crete, Greece
| | - Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Κostas Sagonas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Emmanouela Karameta
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Aziz Avcı
- Department of Biology, Faculty of Science, Aydın Adnan Menderes University, Aydın 09010, Türkiye
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Diego Darriba
- Computer Architecture Group, Centro de investigación CITIC, University of A Coruña, A Coruña, Spain
| | - Alexandros Stamatakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76128, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
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Khoshnamvand H, Vaissi S, Azimi M, Ahmadzadeh F. Phylogenetic climatic niche evolution and diversification of the Neurergus species (Salamandridae) in the Irano-Anatolian biodiversity hotspot. Ecol Evol 2024; 14:e70105. [PMID: 39100205 PMCID: PMC11294440 DOI: 10.1002/ece3.70105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 06/12/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024] Open
Abstract
This study explores how climate variables influenced the evolution and diversification of Neurergus newts within the Irano-Anatolian biodiversity hotspot. We use a dated phylogenetic tree and climatic niche models to analyze their evolutionary history and ecological preferences. Using genetic data from nuclear (KIAA) and mitochondrial (16s and 12s) genes, we estimate divergence times and identify four major Neurergus clades. The initial speciation event occurred approximately 11.3 million years ago, coinciding with the uplift of the Zagros and Anatolian mountains. This geological transformation isolated newt populations, likely triggering the first speciation event. By integrating potential geographic distribution with climate variables, we reconstruct ancestral niche occupancy profiles. This highlights the critical roles of temperature and precipitation in shaping Neurergus habitat preferences and distribution. We observe both phylogenetic niche conservatism and divergence, with niche divergence playing a dominant role in diversification. This research emphasizes the complex interplay of geography, climate, and ecology in speciation and the vulnerability of isolated mountain newt populations to environmental changes.
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Affiliation(s)
- Hadi Khoshnamvand
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research InstituteShahid Beheshti University, G.C., EvinTehranIran
| | - Somaye Vaissi
- Department of Biology, Faculty of ScienceRazi UniversityKermanshahIran
| | - Maryam Azimi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research InstituteShahid Beheshti University, G.C., EvinTehranIran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research InstituteShahid Beheshti University, G.C., EvinTehranIran
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Hehe Z, Minna Z, Qin F, Tielin N, Yi F, Liping F, Fangfang C, Houlin T, Shi W, Maohe Y, Fan L. Application of molecular epidemiology in revealing HIV-1 transmission network and recombination patterns in Tianjin, China. J Med Virol 2024; 96:e29824. [PMID: 39072805 DOI: 10.1002/jmv.29824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
Using a comprehensive molecular epidemiological approach, we characterized the transmission dynamics of HIV-1 among the MSM population in Tianjin, China. Our findings revealed that 38.56% (386/1001) of individuals clustered across 109 molecular transmission clusters (TCs), with MSM aged 50 and below being the group most commonly transmitting HIV-1. Among the identified TCs, CRF01_AE predominated, followed by CRF07_BC. Notably, CRF07_BC demonstrated a higher propensity for forming large clusters compared to CRF01_AE. Birth-death skyline analyses of the two largest clusters indicated that the HIV/AIDS transmission may be at a critical point, nearly all had Re approximately 1 by now. A retrospective analysis revealed that the rapid expansion of these large clusters was primarily driven by the introduction of viruses in 2021, highlighting the crucial importance of continuous molecular surveillance in identifying newly emerging high-risk transmission chains and adapting measures to address evolving epidemic dynamics. Furthermore, we detected the transmission of drug-resistant mutations (DRMs) within the TCs, particularly in the CRF07_BC clusters (K103N, Y181C, and K101E) and CRF01_AE clusters (P225H and K219R), emphasizing the importance of monitoring to support the continued efficacy of first-line therapies and pre-exposure prophylaxis (PrEP). Recombination analyses indicated that complex recombinant patterns, associated with increased amino acid variability, could confer adaptive traits to the viruses, potentially providing a competitive advantage in certain host populations or regions. Our study highlights the potential of integrating molecular epidemiological and phylodynamic approaches to inform targeted interventions.
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Affiliation(s)
- Zhao Hehe
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zheng Minna
- Department of HIV/AIDS and STDs Control and Prevention, Tianjin Provincial Center for Disease Control and Prevention, Tianjin, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin, China
| | - Fan Qin
- Department of HIV/AIDS and STDs Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ning Tielin
- Department of HIV/AIDS and STDs Control and Prevention, Tianjin Provincial Center for Disease Control and Prevention, Tianjin, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin, China
| | - Feng Yi
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Fei Liping
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chen Fangfang
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tang Houlin
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wang Shi
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Maohe
- Department of HIV/AIDS and STDs Control and Prevention, Tianjin Provincial Center for Disease Control and Prevention, Tianjin, China
- Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease, Tianjin, China
| | - Lyu Fan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
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Furness LH, Kersten O, Boilard A, Keith-Diagne L, Brito C, Barrett JH, Kitchener A, Sabin R, Lavery S, Plön S, Star B. Population structure of Dugong dugon across the Indo-Pacific revealed by historical mitogenomes. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240599. [PMID: 39113775 PMCID: PMC11304337 DOI: 10.1098/rsos.240599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 08/10/2024]
Abstract
Sirenia, an iconic marine taxon with a tropical and subtropical worldwide distribution, face an uncertain future. All species are designated 'Vulnerable' to extinction by the IUCN. Nonetheless, a comprehensive understanding of geographic structuring across the global range is lacking, impeding our ability to highlight particularly vulnerable populations for conservation priority. Here, we use ancient DNA to investigate dugong (Dugong dugon) population structure, analysing 56 mitogenomes from specimens comprising the known historical range. Our results reveal geographically structured and distinct monophyletic clades characterized by contrasting evolutionary histories. We observe deep-rooted and divergent lineages in the East (Indo-Pacific) and obtain new evidence for the relatively recent dispersal of dugongs into the western Indian Ocean. All populations are significantly differentiated from each other with western populations having approximately 10-fold lower levels of genetic variation than eastern Indo-Pacific populations. Additionally, we find a significant temporal loss of genetic diversity in western Indian Ocean dugongs since the mid-twentieth century, as well as a decline in population size beginning approximately 1000 years ago. Our results add to the growing body of evidence that dugong populations are becoming ever more susceptible to ongoing human action and global climate change.
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Affiliation(s)
- Lydia Hildebrand Furness
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo0313, Norway
| | - Oliver Kersten
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo0313, Norway
| | - Aurélie Boilard
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo0313, Norway
| | - Lucy Keith-Diagne
- African Aquatic Conservation Fund, BP 80 Joal23015, Senegal, West Africa
| | | | - James H. Barrett
- Norwegian University of Science and Technology, Trondheim7491, Norway
| | - Andrew Kitchener
- Department of Natural Sciences, National Museums Scotland, EdinburghEH1 1JF, UK
- School of Geosciences, University of Edinburgh, EdinburghEH10 5HF, UK
| | - Richard Sabin
- Vertebrates Division, Natural History Museum, LondonSW7 5BD, UK
| | - Shane Lavery
- School of Biological Sciences, University of Auckland, Auckland1010, New Zealand
| | - Stephanie Plön
- Department of Pathology, Stellenbosch University, Stellenbosch, South Africa
- Bayworld Centre for Research and Education, Port Elizabeth, 7602, South Africa
| | - Bastiaan Star
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo0313, Norway
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Iype A, Ajith Kumar KG, Joy A, Sebasteena PF, Varghese A, Deepa CK, Chandy G, Ravindran R. Molecular characterisation of Amblyomma integrum circulating in southern India. Parasitol Int 2024; 101:102877. [PMID: 38438076 DOI: 10.1016/j.parint.2024.102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
Amblyomma integrum is a large gooseberry sized longirostrate tick (when fully repleted) found in India and Sri Lanka. In Kerala (India), this tick is commonly found in the forest and its fringe areas frequently infesting deer and hence it is locally known as "maan chellu / maanunny" (deer tick). In the present study, molecular characterisation and phylogenetic analysis of A. integrum collected from the area grazed by the sambar deer (Rusa unicolor) of Kerala, south India was performed using three molecular markers viz., the mitochondrial cytochrome c oxidase subunit 1 (COI), mitochondrial 16S ribosomal RNA, and nuclear 18S ribosomal RNA genes. Cytochrome c oxidase subunit 1 (COI) gene showed better resolving ability for elucidating the evolutionary relationship of A. integrum and identified two distinct clades, viz., A and B. The Tamil Nadu isolates of south India and Marayoor isolate 1 (from Idukki district of Kerala bordering with Tamil Nadu) belonged to clade A. Majority of Wayanad isolates from Kerala, occupied clade B. The intraspecific genetic distance among the A. integrum species ranged from 0.00 to 13.34%. Between clades A and B, the genetic distance observed was 11.49%. The clade B isolates were genetically close to A. geoemydae (GD: 1.22%). Morphological variations between the clades included darker exoskeletal coloration in clade A and distinct differences in the shape of basis capitulum. Further analysis using Assemble Species by Automatic Partitioning (ASAP) and Generalized Mixed Yule Coalescent (GMYC) provided additional insights. Assemble Species by Automatic Partitioning (ASAP) identified 26 Molecular Operational Taxonomic Units (MOTUs) at a threshold distance of 5.38%, supporting the species partition of A. integrum clade B. Generalized Mixed Yule Coalescent (GMYC) analysis retained the same species complex (A. integrum-geoemydae Complex) inferred from the ASAP analyses. It could be inferred from the present study that the A. integrum clades A and B could be two different putative pseudocryptic species.
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Affiliation(s)
- Aleena Iype
- Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala 673576, India; Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, Kerala 673576, India
| | - Karapparambu Gopalan Ajith Kumar
- Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala 673576, India.
| | - Anisha Joy
- Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala 673576, India; Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, Kerala 673576, India
| | - Peekkunnel Francis Sebasteena
- Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala 673576, India; Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, Kerala 673576, India
| | - Anju Varghese
- Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala 673576, India
| | - Chundayil Kalarikkal Deepa
- Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala 673576, India
| | - George Chandy
- Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, Kerala 673576, India
| | - Reghu Ravindran
- Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala 673576, India.
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Hofmann S, Rödder D, Andermann T, Matschiner M, Riedel J, Baniya CB, Flecks M, Yang J, Jiang K, Jianping J, Litvinchuk SN, Martin S, Masroor R, Nothnagel M, Vershinin V, Zheng Y, Jablonski D, Schmidt J, Podsiadlowski L. Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae). Mol Ecol 2024; 33:e17446. [PMID: 38946613 DOI: 10.1111/mec.17446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/25/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO.
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Affiliation(s)
- Sylvia Hofmann
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Dennis Rödder
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Tobias Andermann
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Jendrian Riedel
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Chitra B Baniya
- Central Department of Botany, Tribhuvan University, Kathmandu, Nepal
| | - Morris Flecks
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Jianhuan Yang
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Hong Kong, China
| | - Ke Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jiang Jianping
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Sebastian Martin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | | | - Michael Nothnagel
- Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Vladimir Vershinin
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Institute of Natural Sciences and Mathematics, Eltsyn Ural Federal University, Yekaterinburg, Russia
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Joachim Schmidt
- General and Systematic Zoology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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Xavier A, Yadav R, Gowda V. Evolutionary patterns of variations in chromosome counts and genome sizes show positive correlations with taxonomic diversity in tropical gingers. AMERICAN JOURNAL OF BOTANY 2024; 111:e16334. [PMID: 38825815 DOI: 10.1002/ajb2.16334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/04/2024]
Abstract
PREMISE Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical as they are instrumental in defining angiosperm diversity. Variations in these traits can be traced to evolutionary processes such as polyploidization, although geographic variations across cytogenetic traits remain underexplored. In the pantropical monocot family Zingiberaceae (~1500 species), cytogenetic traits have been well documented; however, the role of these traits in shaping taxonomic diversity and biogeographic patterns of gingers is not known. METHODS A time-calibrated Bayesian phylogenetic tree was constructed for 290 taxa covering three of the four subfamilies in Zingiberaceae. We tested models of chromosome number and genome size evolution within the family and whether lineage age, taxonomic diversity, and distributional range explain the variations in the cytogenetic traits. Tests were carried out at two taxonomic ranks: within Zingiberaceae and within genus Hedychium using correlations, generalized linear models and phylogenetic least square models. RESULTS The most frequent changes in chromosome number within Zingiberaceae were noted to be demi-polyploidization and polyploidization (~57% of the time), followed by ascending dysploidy (~27%). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent; higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution. CONCLUSIONS Within Zingiberaceae, multiple incidences of polyploidization were discovered, and cytogenetic events appear to have reduced the genome sizes and increased taxonomic diversity, distributional ranges and invasiveness.
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Affiliation(s)
- Aleena Xavier
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
| | - Ritu Yadav
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
| | - Vinita Gowda
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
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Davis HR, Sanford HT, Das I, Nashriq I, Leaché AD. Establishing species boundaries in Bornean geckos. Biol Lett 2024; 20:20240157. [PMID: 39140204 PMCID: PMC11322891 DOI: 10.1098/rsbl.2024.0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/29/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024] Open
Abstract
Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering and delimiting species. However, delimiting species with a single locus (e.g. DNA barcoding) is biased towards overestimating species diversity. The highly diverse gecko genus Cyrtodactylus is one such group where delimitation using mtDNA remains the paradigm. In this study, we use genomic data to test putative species boundaries established using mtDNA within three recognized species of Cyrtodactylus on the island of Borneo. We predict that multi-locus genomic data will estimate fewer species than mtDNA, which could have important ramifications for the species diversity within the genus. We aim to (i) investigate the correspondence between species delimitations using mtDNA and genomic data, (ii) infer species trees for each target species, and (iii) quantify gene flow and identify migration patterns to assess population connectivity. We find that species diversity is overestimated and that species boundaries differ between mtDNA and nuclear data. This underscores the value of using genomic data to reassess mtDNA-based species delimitations for taxa lacking clear species boundaries. We expect the number of recognized species within Cyrtodactylus to continue increasing, but, when possible, genomic data should be included to inform more accurate species boundaries.
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Affiliation(s)
- Hayden R. Davis
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, WA98195, USA
| | - Henry T. Sanford
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, WA98195, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti of Malaysia, Sarawak, Kota Samarahan, Malaysia
| | - Izneil Nashriq
- Institute of Biodiversity and Environmental Conservation, Universiti of Malaysia, Sarawak, Kota Samarahan, Malaysia
| | - Adam D. Leaché
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington, Seattle, WA98195, USA
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60
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Hurtado-Gómez JP, Vargas-Ramírez M, Iverson JB, Joyce WG, McCranie JR, Paetzold C, Fritz U. Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae). Mol Phylogenet Evol 2024; 197:108083. [PMID: 38679303 DOI: 10.1016/j.ympev.2024.108083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/02/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.
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Affiliation(s)
| | - Mario Vargas-Ramírez
- Grupo Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia; Estación de Biología Tropical Roberto Franco (EBTRF), Universidad Nacional de Colombia, Villavicencio, Colombia
| | - John B Iverson
- Department of Biology, Earlham College, Richmond, IN 47374, USA
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, 1700 Fribourg, Switzerland
| | - James R McCranie
- Smithsonian Research Associate, 10770 SW 164th Street, Miami, FL 33157, USA
| | - Claudia Paetzold
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany.
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61
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Burriel-Carranza B, Mochales-Riaño G, Talavera A, Els J, Estarellas M, Al Saadi S, Urriago Suarez JD, Olsson PO, Matschiner M, Carranza S. Clinging on the brink: Whole genomes reveal human-induced population declines and severe inbreeding in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus). Mol Ecol 2024; 33:e17451. [PMID: 38970417 DOI: 10.1111/mec.17451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/08/2024]
Abstract
Human-mediated habitat destruction has had a profound impact on increased species extinction rates and population declines worldwide. The coastal development in the United Arab Emirates (UAE) over the last two decades, serves as an example of how habitat transformation can alter the landscape of a country in just a few years. Here, we study the genomic implications of habitat transformation in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus), the only endemic vertebrate of the UAE. We generate a high-quality reference genome for this gecko, representing the first reference genome for the family Phyllodactylidae, and produce whole-genome resequencing data for 23 specimens from 10 different species of leaf-toed geckos. Our results show that A. caudivolvulus has consistently lower genetic diversity than any other Arabian species of Asaccus, suggesting a history of ancient population declines. However, high levels of recent inbreeding are recorded among populations in heavily developed areas, with a more than 50% increase in long runs of homozygosity within a 9-year period. Moreover, results suggest that this species does not effectively purge deleterious mutations, hence making it more vulnerable to future stochastic threats. Overall, results show that A. caudivolvulus is in urgent need of protection, and habitat preservation must be warranted to ensure the species' survival.
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Affiliation(s)
- Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Museu de Ciències Naturals de Barcelona, Barcelona, Spain
| | | | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Maria Estarellas
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | | | | | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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62
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Burgess SC, Turner AM, Johnston EC. Niche breadth and divergence in sympatric cryptic coral species ( Pocillopora spp.) across habitats within reefs and among algal symbionts. Evol Appl 2024; 17:e13762. [PMID: 39100752 PMCID: PMC11294925 DOI: 10.1111/eva.13762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/05/2024] [Accepted: 07/10/2024] [Indexed: 08/06/2024] Open
Abstract
While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co-occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbA ncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth-Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine-scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.
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Affiliation(s)
- Scott C. Burgess
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Alyssa M. Turner
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Erika C. Johnston
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
- Present address:
Hawai‘i Institute of Marine BiologyKāne‘oheHawaiiUSA
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63
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Wang M, Zhu M, Qian J, Yang Z, Shang F, Egan AN, Li P, Liu L. Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes. Mol Phylogenet Evol 2024; 197:108093. [PMID: 38740145 DOI: 10.1016/j.ympev.2024.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Mulberries (genus Morus), belonging to the order Rosales, family Moraceae, are important woody plants due to their economic values in sericulture, as well as for nutritional benefits and medicinal values. However, the taxonomy and phylogeny of Morus, especially for the Asian species, remains challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of Morus, we combined plastomes and a large-scale nuclear gene analyses to investigate their phylogenetic relationships. We assembled the plastomes and screened 211 single-copy nuclear genes from 13 Morus species and related taxa. The plastomes of Morus species were relatively conserved in terms of genome size, gene content, synteny, IR boundary and codon usage. Using nuclear data, our results elucidated identical topologies based on coalescent and concatenation methods. The genus Morus was supported as monophyletic, with M. notabilis as the first diverging lineage and the two North American Morus species, M. microphylla and M. rubra, as sister to the other Asian species. In the Asian Morus species, interspecific relationships were completely resolved. However, cyto-nuclear discordances and gene tree-species tree conflicts were detected in the phylogenies of Morus, with multiple evidences supporting hybridization/introgression as the main cause of discordances between nuclear and plastid phylogenies, while gene tree-species tree conflicts were mainly caused by ILS.
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Affiliation(s)
- Meizhen Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453000, China; Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mengmeng Zhu
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Jiayi Qian
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhaoping Yang
- College of Life Sciences and Technologies, Tarim University, Alar 843300, China
| | - Fude Shang
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng 475001, China; College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, UT 84058, United States.
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Luxian Liu
- College of Life Sciences, Henan Normal University, Xinxiang 453000, China; Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng 475001, China.
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64
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Becker FS, Alexander GJ, Tolley KA. Substrate specialisation drives an unexpectedly diverse radiation in barking geckos (Ptenopus: Gekkonidae). Mol Phylogenet Evol 2024; 197:108104. [PMID: 38750676 DOI: 10.1016/j.ympev.2024.108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/25/2024] [Accepted: 05/12/2024] [Indexed: 06/06/2024]
Abstract
Barking geckos (genus Ptenopus) are terrestrial, burrowing lizards endemic to southern Africa, currently with three recognised species. Two species are range-restricted (P. kochi and P. carpi) and display clear differences in substrate preference (soft sand vs. hard gravel). The third and most widespread species, P. garrulus, occurs on a variety of substrates of differing hardness, across potential geographic barriers, and over a steep climatic gradient. Variations in morphology and advertisement calls indicates that P. garrulus may be a species complex. Two subspecies of P. garrulus are currently recognised: P. g. maculatus and P. g. garrulus. To investigate species boundaries, we produced the first comprehensive phylogeny for the genus. We used a novel application of multiple regression on matrices models to assess multiple environmental drivers of diversification, as contrasted to isolation by distance. We show that P. kochi, P. carpi, and P. g. garrulus are valid species, but that P. g. maculatus is a paraphyletic complex of five previously unrecognised taxa. Specialisation onto different substrates was likely the main driver of divergence, with parapatric occurrence of two to four clades occurring at each of the three substrate transition zones identified a priori. The region encompasses diverse bioclimatic regions and potential geographic barriers, and these likely played a role in some divergence events.
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Affiliation(s)
- Francois S Becker
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P.O. Wits, 2050 Johannesburg, South Africa; South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, Cape Town, South Africa; National Museum of Namibia, Ministry of Education, Arts and Culture, Private Bag 13186, Windhoek, Namibia; Gobabeb Namib Research Institute, PO Box 953, Walvis Bay 13103, Namibia.
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P.O. Wits, 2050 Johannesburg, South Africa
| | - Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, Cape Town, South Africa; Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
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65
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Nagata N. Phylogeography of Parnassius citrinarius Based on Mitochondrial DNA Reveals Large Differences in Genetic Structure between the Eastern and Western Japan. Zoolog Sci 2024; 41:385-391. [PMID: 39093284 DOI: 10.2108/zs230072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/01/2024] [Indexed: 08/04/2024]
Abstract
The Japanese Archipelago hosts a rich butterfly fauna, and elucidating the genetic structures of multiple species is necessary to clarify their formation processes. This study aimed to reveal the genetic structure and distribution formation process of Parnassius citrinarius, which is widely distributed across the Japanese Archipelago from Hokkaido to Shikoku, through phylogeographic analysis based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Thirty haplotypes were revealed from 311 individuals from 47 sites, indicating significant differences in the genetic structures between the eastern and western parts of the Japanese Archipelago. In Eastern Japan, multiple genetic clusters were found, with some sites harboring two clusters. The divergence times among populations in Eastern Japan were relatively recent, and no genetic differentiation was observed between regions, including between Hokkaido and Honshu, which are separated by a narrow strait. In contrast, in Western Japan, including Shikoku, unique genetic clusters were observed in each region. The phylogenetic relationships among populations were regionally clustered, and the divergence times were relatively ancient. The distribution and genetic structure of P. citrinarius in the Japanese Archipelago have been significantly influenced by temperature fluctuations and the presence of geographical barriers during the Pleistocene glacial-interglacial cycles, including the potential formation of refugia in Western Japan.
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Affiliation(s)
- Nobuaki Nagata
- Department of Anthropology, National Museum of Nature and Science, Ibaraki 305-0005, Japan,
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66
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Andrade P, Alves JM, Pereira P, Rubin CJ, Silva E, Sprehn CG, Enbody E, Afonso S, Faria R, Zhang Y, Bonino N, Duckworth JA, Garreau H, Letnic M, Strive T, Thulin CG, Queney G, Villafuerte R, Jiggins FM, Ferrand N, Andersson L, Carneiro M. Selection against domestication alleles in introduced rabbit populations. Nat Ecol Evol 2024; 8:1543-1555. [PMID: 38907020 DOI: 10.1038/s41559-024-02443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
| | - Joel M Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Paulo Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Bergen, Norway
| | - Eugénio Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Yexin Zhang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Never Bonino
- Estación Experimental Bariloche, Instituto Nacional de Tecnología Agropecuaria, Casilla de Correo Bariloche, Argentina
| | - Janine A Duckworth
- Wildlife Ecology and Management Group, Manaaki Whenua - Landcare Research, Lincoln, New Zealand
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Hervé Garreau
- GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Mike Letnic
- Centre for Ecosystem Science, School of BEES, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, School of BEES, University of New South Wales, Sydney, New South Wales, Australia
| | - Tanja Strive
- Centre for Invasive Species Solutions, University of Canberra, Bruce, Australian Capital Territory, Australia
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Carl-Gustaf Thulin
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Guillaume Queney
- ANTAGENE, Wildlife Genetics Laboratory, La Tour de Salvagny, France
| | | | | | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
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67
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Nielsen BF, Berrig C, Grenfell BT, Andreasen V. One hundred years of influenza A evolution. Theor Popul Biol 2024; 159:25-34. [PMID: 39094981 DOI: 10.1016/j.tpb.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 07/05/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Leveraging the simplicity of nucleotide mismatch distributions, we provide an intuitive window into the evolution of the human influenza A 'nonstructural' (NS) gene segment. In an analysis suggested by the eminent Danish biologist Freddy B. Christiansen, we illustrate the existence of a continuous genetic "backbone" of influenza A NS sequences, steadily increasing in nucleotide distance to the 1918 root over more than a century. The 2009 influenza A/H1N1 pandemic represents a clear departure from this enduring genetic backbone. Utilizing nucleotide distance maps and phylogenetic analyses, we illustrate remaining uncertainties regarding the origin of the 2009 pandemic, highlighting the complexity of influenza evolution. The NS segment is interesting precisely because it experiences less pervasive positive selection, and departs less strongly from neutral evolution than e.g. the HA antigen. Consequently, sudden deviations from neutral diversification can indicate changes in other genes via the hitchhiking effect. Our approach employs two measures based on nucleotide mismatch counts to analyze the evolutionary dynamics of the NS gene segment. The rooted Hamming map of distances between a reference sequence and all other sequences over time, and the unrooted temporal Hamming distribution which captures the distribution of genotypic distances between simultaneously circulating viruses, thereby revealing patterns of nucleotide diversity and epi-evolutionary dynamics.
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Affiliation(s)
- Bjarke Frost Nielsen
- High Meadows Environmental Institute, Princeton University, Princeton, NJ, United States of America; Department of Science and Environment, Roskilde University, Roskilde, Denmark; Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Christian Berrig
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States of America.
| | - Viggo Andreasen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.
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68
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Jaito W, Singchat W, Patta C, Thatukan C, Kumnan N, Chalermwong P, Budi T, Panthum T, Wongloet W, Wattanadilokchatkun P, Thong T, Muangmai N, Han K, Duengkae P, Phatcharakullawarawat R, Srikulnath K. Shared alleles and genetic structures in different Thai domestic cat breeds: the possible influence of common racial origins. Genomics Inform 2024; 22:12. [PMID: 39085978 PMCID: PMC11292921 DOI: 10.1186/s44342-024-00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
Over hundreds of years, cats have been domesticated and selectively bred, resulting in numerous pedigreed breeds expedited by recent cat shows and breeding associations. Concerns have been raised about the limited breeding options and the genetic implications of inbreeding, indicating challenges in maintaining genetic diversity and accurate identification in purebred cats. In this study, genetic variability and structure were examined in 5 Thai domestic cat breeds using 15 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequencing. In total, 184 samples representing the Wichien Maat (WCM), Suphalak (SL), Khao-Manee (KM), Korat (KR), and Konja (KJ) breeds were analyzed. High genetic diversity (Ho and He > 0.5) was observed in all breeds, and mtDNA analysis revealed two primary haplogroups (A and B) that were shared among all domestic cat breeds in Thailand and globally. However, minor differences were observed between Thai domestic cat breeds based on clustering analyses, in which a distinct genetic structure was observed in the WCM breed. This suggests that allele fixation for distinctive morphological traits has occurred in Thai domestic cat breeds that emerged in isolated regions with shared racial origins. Analysis of relationships among individuals within the breed revealed high identification efficiency in Thai domestic cat breeds (P(ID)sibs < 10-4). Additionally, diverse and effective individual identification can be ensured by optimizing marker efficiency by using only nine loci. This comprehensive genetic characterization provides valuable insights into conservation strategies and breeding practices for Thai domestic cat breeds.
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Grants
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- Higher Education for Industry Consortium (Hi–FI)
- International SciKU Branding (ISB), Faculty of Science, Kasetsart University
- High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA)
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Affiliation(s)
- Wattanawan Jaito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
| | - Chananya Patta
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Chadaphon Thatukan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand.
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69
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Ahlawat B, Dewangan H, Pasupuleti N, Dwivedi A, Rajpal R, Pandey S, Kumar L, Thangaraj K, Rai N. Investigating linguistic and genetic shifts in East Indian tribal groups. Heliyon 2024; 10:e34354. [PMID: 39082022 PMCID: PMC11284423 DOI: 10.1016/j.heliyon.2024.e34354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
South Asia is home to almost a quarter of the world's total population and is home to significant ethnolinguistic diversity. Previous studies of linguistic and genetic affiliations of Indian populations suggest that the formation of these distinct groups was a protracted and complex phenomenon involving multiple waves of migration, cultural assimilation, and genetic admixture. The evolutionary processes of migration, mixing and merging of populations thus impact the culture and linguistic diversity of different groups, some of which may retain their linguistic affinities despite genetic admixture with other groups, or vice versa. Our study examines the relationship of genetic and linguistic affinities between Austroasiatic and Indo-European speakers in adjacent geographical regions of Eastern India. We analyzed 224 mitogenomes and 0.65 million SNP genotypes from 40 unrelated individuals belonging to the Bathudi, Bhumij, Ho, and Mahali ethnic groups from the Eastern Indian state of Odisha. These four groups are speakers of Austroasiatic languages who have adopted elements from Indo-European languages spoken in neighbouring regions. Our results suggest that these groups have the greatest maternal genetic affinity with other Austroasiatic-speaking groups in India. Allele frequency-based analyses, genome-wide SNPs, haplotype-based methods and IBD sharing further support the genetic similarity of these East Indian groups to Austroasiatic speakers of South Asia rather than regional populations speaking Indo-European and Dravidian languages. Our study shows that these populations experienced linguistic mixing, likely due to industrialization and modernization that brought them into close cultural contact with neighbouring Indo-European-speaking groups. However, linguistic change in these groups is not reflected in genetic mixing in these populations, as they appear to maintain strict genetic boundaries while simultaneously experiencing cultural mixing.
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Affiliation(s)
- Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Department of Anthropology, Panjab University, Chandigarh, 160014, India
| | - Hemlata Dewangan
- Shreyanshi Health Care Private Limited, Raipur, Chattisgarh, 492001, India
| | - Nagarjuna Pasupuleti
- CSIR—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Aparna Dwivedi
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Richa Rajpal
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Saurabh Pandey
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Kumarasamy Thangaraj
- CSIR—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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70
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Wong TKF, Cherryh C, Rodrigo AG, Hahn MW, Minh BQ, Lanfear R. MAST: Phylogenetic Inference with Mixtures Across Sites and Trees. Syst Biol 2024; 73:375-391. [PMID: 38421146 PMCID: PMC11282360 DOI: 10.1093/sysbio/syae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/18/2023] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST). This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of ILS in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of 4 Platyrrhine species for which standard concatenated maximum likelihood (ML) and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e., the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyze a concatenated alignment using ML while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.
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Affiliation(s)
- Thomas K F Wong
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Caitlin Cherryh
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Allen G Rodrigo
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Bui Quang Minh
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Robert Lanfear
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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71
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Smith K, Ayres D, Neumaier R, Wörheide G, Höhna S. Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI. Syst Biol 2024; 73:455-469. [PMID: 38284268 DOI: 10.1093/sysbio/syae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 01/30/2024] Open
Abstract
Phylogenies are central to many research areas in biology and commonly estimated using likelihood-based methods. Unfortunately, any likelihood-based method, including Bayesian inference, can be restrictively slow for large datasets-with many taxa and/or many sites in the sequence alignment-or complex substitutions models. The primary limiting factor when using large datasets and/or complex models in probabilistic phylogenetic analyses is the likelihood calculation, which dominates the total computation time. To address this bottleneck, we incorporated the high-performance phylogenetic library BEAGLE into RevBayes, which enables multi-threading on multi-core CPUs and GPUs, as well as hardware specific vectorized instructions for faster likelihood calculations. Our new implementation of RevBayes+BEAGLE retains the flexibility and dynamic nature that users expect from vanilla RevBayes. In addition, we implemented native parallelization within RevBayes without an external library using the message passing interface (MPI); RevBayes+MPI. We evaluated our new implementation of RevBayes+BEAGLE using multi-threading on CPUs and 2 different powerful GPUs (NVidia Titan V and NVIDIA A100) against our native implementation of RevBayes+MPI. We found good improvements in speedup when multiple cores were used, with up to 20-fold speedup when using multiple CPU cores and over 90-fold speedup when using multiple GPU cores. The improvement depended on the data type used, DNA or amino acids, and the size of the alignment, but less on the size of the tree. We additionally investigated the cost of rescaling partial likelihoods to avoid numerical underflow and showed that unnecessarily frequent and inefficient rescaling can increase runtimes up to 4-fold. Finally, we presented and compared a new approach to store partial likelihoods on branches instead of nodes that can speed up computations up to 1.7 times but comes at twice the memory requirements.
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Affiliation(s)
- Killian Smith
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Daniel Ayres
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - René Neumaier
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Gert Wörheide
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Sebastian Höhna
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
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72
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de Jonge PA, van den Born BJH, Zwinderman AH, Nieuwdorp M, Dutilh BE, Herrema H. Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage. Nat Commun 2024; 15:6346. [PMID: 39068184 PMCID: PMC11283538 DOI: 10.1038/s41467-024-50777-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in various human populations. Based on a phylogeny using sequences from six viral genome databases, we propose the Candidatus order Heliusvirales. We identify heliusviruses in 82% of 5441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1000 and 5000 years ago. We show that a large lineage started to diversify when Homo sapiens first appeared some 300,000 years ago. Ancient peoples and modern hunter-gatherers have distinct Ca. Heliusvirales populations with lower richness than modern urbanized people. Urbanized people suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles.
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Affiliation(s)
- Patrick A de Jonge
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Bert-Jan H van den Born
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology; Biostatistics and Bioinformatics; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics; Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity; Faculty of Biological Sciences; Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
| | - Hilde Herrema
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands.
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands.
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73
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Wolfe JM, Ballou L, Luque J, Watson-Zink VM, Ahyong ST, Barido-Sottani J, Chan TY, Chu KH, Crandall KA, Daniels SR, Felder DL, Mancke H, Martin JW, Ng PKL, Ortega-Hernández J, Palacios Theil E, Pentcheff ND, Robles R, Thoma BP, Tsang LM, Wetzer R, Windsor AM, Bracken-Grissom HD. Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments. Syst Biol 2024; 73:247-262. [PMID: 37941464 PMCID: PMC11282366 DOI: 10.1093/sysbio/syad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/15/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].
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Affiliation(s)
- Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Lauren Ballou
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Javier Luque
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | | | - Shane T Ahyong
- Australian Museum, 1 William St, Sydney, NSW 2010, Australia
- School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Joëlle Barido-Sottani
- Institut de Biologie de l’École Normale Supérieure (IBENS), ENS, CNRS, INSERM, Université PSL (Paris Sciences & Lettres), Paris, France
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan, ROC
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Darryl L Felder
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Harrison Mancke
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Joel W Martin
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore, Singapore
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Emma Palacios Theil
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, ul. Banacha 12/16, 90-237 Łódź, Poland
| | - N Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Rafael Robles
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Campeche, San Francisco de Campeche, Campeche, México
| | - Brent P Thoma
- Department of Biology, Jackson State University, P.O. Box 18540, Jackson, MS 39217, USA
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Amanda M Windsor
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- United States Food and Drug Administration, Office of Regulatory Science, 5001 Campus Dr. College Park, MD 20740, USA
| | - Heather D Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
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74
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Santos BF, Colombo WD, Murray EA, Brady SG, Azevedo CO. Insights from the first phylogenomic analysis of flat wasps (Hymenoptera, Bethylidae) reveal two new subfamilies. Cladistics 2024. [PMID: 39056213 DOI: 10.1111/cla.12594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 06/14/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Despite significant advances in alpha level taxonomy in the past few decades, the higher-level phylogeny of flat wasps (Hymenoptera, Bethylidae) remains poorly explored. Herein we provide the first phylogenomic assessment of the family based on data from ultraconserved elements for 96 species in 61 genera of the family, with material from 29 countries and all biogeographic regions. Dataset cutoffs including ultraconserved element loci recovered for 50 and 70% of terminals resulted in matrices with 1513 and 451 loci, which were analysed in both parsimony and maximum likelihood frameworks. We also provide the first analyses of divergence dating for the family based on the calibration of 12 nodes. All analyses recovered the Bethylidae as a monophyletic group and estimated the origin of the family at around 143 Ma. The results suggest that all extant subfamilies had already diversified by the Late Cretaceous. All topologies suggest that Glenosema and Chilepyris form a clade separate from other Scleroderminae; owing to the morphological distinctiveness of each genus, we propose that they are accommodated in two new subfamilies, Glenoseminae subf. nov. and Chilepyrinae subf. nov. The monotypic sclerodermine genus Galodoxa was consistently recovered within Epyrinae and is transferred to the latter subfamily.
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Affiliation(s)
- Bernardo F Santos
- Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Invalidenstraße 43, Berlin, 10115, Germany
| | - Wesley D Colombo
- Depto de Ciências Biológicas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari 514, Goiabeiras, Vitória, 29075-010, ES, Brazil
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, 10th and Constitution Ave. NW, Washington, DC, USA
| | - Celso O Azevedo
- Depto de Ciências Biológicas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari 514, Goiabeiras, Vitória, 29075-010, ES, Brazil
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75
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Yan ZT, Tang XY, Yang D, Fan ZH, Luo ST, Chen B. Phylogenetic and Comparative Genomics Study of Papilionidae Based on Mitochondrial Genomes. Genes (Basel) 2024; 15:964. [PMID: 39062743 PMCID: PMC11275471 DOI: 10.3390/genes15070964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/19/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024] Open
Abstract
Most species of Papilionidae are large and beautiful ornamental butterflies. They are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. Complete mitochondrial genomes (mitogenomes) have been widely used in phylogenetic studies of butterflies, but mitogenome knowledge within the family Papilionidae is limited, and its phylogeny is far from resolved. In this study, we first report the mitogenome of Byasa confusa from the subfamily Papilioninae of Papilionidae. The mitogenome of B. confusa is 15,135 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region (CR), closely mirroring the genomic structure observed in related butterfly species. Comparative analysis of 77 Papilionidae mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, Ka/Ks, and relative synonymous codon usage (RSCU) are all consistent with that of other reported butterfly mitogenomes. We conducted phylogenetic analyses using maximum-likelihood (ML) and Bayesian-inference (BI) methods, with 77 Papilionidae species as ingroups and two species of Nymphalidae and Lycaenidae as outgroups. The phylogenetic analysis indicated that B. confusa were clustered within Byasa. The phylogenetic trees show the monophyly of the subfamily Papilioninae and the tribes Leptocircini, Papilionini, and Troidini. The data supported the following relationships in tribe level on Papilioninae: (((Troidini + Papilionini) + Teinopalpini) + Leptocircini). The divergence time analysis suggests that Papilionidae originated in the late Creataceous. Overall, utilizing the largest number of Papilionidae mitogenomes sequenced to date, with the current first exploration in a phylogenetic analysis on Papilionidae (including four subfamilies), this study comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of the Papilionidae family.
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Affiliation(s)
- Zhen-Tian Yan
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Xiao-Ya Tang
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Dong Yang
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Zhen-Huai Fan
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Si-Te Luo
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Bin Chen
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
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76
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Bankamp B, Kim G, Hart D, Beck A, Ben Mamou M, Penedos A, Zhang Y, Evans R, Rota PA. Global Update on Measles Molecular Epidemiology. Vaccines (Basel) 2024; 12:810. [PMID: 39066448 PMCID: PMC11281501 DOI: 10.3390/vaccines12070810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Molecular surveillance of circulating measles variants serves as a line of evidence for the absence of endemic circulation and provides a means to track chains of transmission. Molecular surveillance for measles (genotyping) is based on the sequence of 450 nucleotides at the end of the nucleoprotein coding region (N450) of the measles genome. Genotyping was established in 1998 and, with over 50,000 sequence submissions to the Measles Nucleotide Surveillance database, has proven to be an effective resource for countries attempting to trace pathways of transmission. This review summarizes the tools used for the molecular surveillance of measles and describes the challenge posed by the decreased number of circulating measles genotypes. The Global Measles and Rubella Laboratory Network addressed this challenge through the development of new tools such as named strains and distinct sequence identifiers that analyze the diversity within the currently circulating genotypes. The advantages and limitations of these approaches are discussed, together with the need to generate additional sequence data including whole genome sequences to ensure the continued utility of strain surveillance for measles.
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Affiliation(s)
- Bettina Bankamp
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
| | - Gimin Kim
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
| | | | - Andrew Beck
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
| | - Myriam Ben Mamou
- World Health Organization Regional Office for Europe, 2100 Copenhagen, Denmark;
| | - Ana Penedos
- United Kingdom Health Security Agency, London NW9 5EQ, UK;
| | - Yan Zhang
- WHO Western Pacific Regional Measles/Rubella Reference Laboratory, National Institute for Viral Disease Control and Prevention, Beijing 100013, China;
| | - Roger Evans
- World Health Organization Western Pacific Regional Office, Manila 1000, Philippines;
| | - Paul A. Rota
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
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77
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Gyllenhaal EF, Brady SS, DeCicco LH, Naikatini A, Hime PM, Manthey JD, Kelly J, Moyle RG, Andersen MJ. Waves of Colonization and Gene Flow in a Great Speciator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.603796. [PMID: 39091784 PMCID: PMC11291091 DOI: 10.1101/2024.07.18.603796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones-where reproductive isolation can further develop via reinforcement or phenotypic displacement-or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr's foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.
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Affiliation(s)
- Ethan F. Gyllenhaal
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Serina S. Brady
- Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, USA
| | - Lucas H. DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | | | - Paul M. Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Present Address: McDonnell Genome Institute and Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Joseph D. Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - John Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
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78
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Zhou Y, Osborne CP. Stomatal dynamics in Alloteropsis semialata arise from the evolving interplay between photosynthetic physiology, stomatal size and biochemistry. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39037305 DOI: 10.1111/pce.15047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
C4 plants are expected to have faster stomatal movements than C3 species because they tend to have smaller guard cells. However, little is known about how the evolution of C4 photosynthesis influences stomatal dynamics in relation to guard cell size and environmental factors. We studied photosynthetically diverse populations of the grass Alloteropsis semialata, showing that the origin of C4 photosynthesis in this species was associated with a shortening of stomatal guard and subsidiary cells. However, for a given cell size, C4 and C3-C4 intermediate individuals had similar or slower light-induced stomatal opening speeds than C3 individuals. Conversely, when exposed to decreasing light, stomata in C4 plants closed as fast as those in non-C4 plants. Polyploid formation in some C4 plants led to larger stomatal cells and was associated with slower stomatal opening. Conversely, diversification of C4 diploid plants into wetter environments was associated with an acceleration of stomatal opening. Overall, there was significant relationship between light-saturated photosynthesis and stomatal opening speed in the C4 plants, implying that photosynthetic energy production was limiting for stomatal opening. Stomatal dynamics in this wild grass therefore arise from the evolving interplay between photosynthetic physiology and the size and biochemical function of stomatal complexes.
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Affiliation(s)
- Yanmin Zhou
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
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79
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L'Hôte L, Light I, Mattiangeli V, Teasdale MD, Halpin Á, Gourichon L, Key FM, Daly KG. An 8000 years old genome reveals the Neolithic origin of the zoonosis Brucella melitensis. Nat Commun 2024; 15:6132. [PMID: 39033187 PMCID: PMC11271283 DOI: 10.1038/s41467-024-50536-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Brucella melitensis is a major livestock bacterial pathogen and zoonosis, causing disease and infection-related abortions in small ruminants and humans. A considerable burden to animal-based economies today, the presence of Brucella in Neolithic pastoral communities has been hypothesised but we lack direct genomic evidence thus far. We report a 3.45X B. melitensis genome preserved in an ~8000 year old sheep specimen from Menteşe Höyük, Northwest Türkiye, demonstrating that the pathogen had evolved and was circulating in Neolithic livestock. The genome is basal with respect to all known B. melitensis and allows the calibration of the B. melitensis speciation time from the primarily cattle-infecting B. abortus to approximately 9800 years Before Present (BP), coinciding with a period of consolidation and dispersal of livestock economies. We use the basal genome to timestamp evolutionary events in B. melitensis, including pseudogenization events linked to erythritol response, the supposed determinant of the pathogen's placental tropism in goats and sheep. Our data suggest that the development of herd management and multi-species livestock economies in the 11th-9th millennium BP drove speciation and host adaptation of this zoonotic pathogen.
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Affiliation(s)
- Louis L'Hôte
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ian Light
- Max Planck Institute for Infection Biology, Evolutionary Pathogenomics, 10117, Berlin, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Áine Halpin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Felix M Key
- Max Planck Institute for Infection Biology, Evolutionary Pathogenomics, 10117, Berlin, Germany
| | - Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
- School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.
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80
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Scheepers M, Bragança PHN, Chakona A. Naming the other cousin: A new goldie barb (Cyprinidae: Smiliogastrininae) from the northeast escarpment in South Africa, with proposed taxonomic rearrangement of the goldie barb group in southern Africa. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39021263 DOI: 10.1111/jfb.15870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
A growing body of evidence indicates that the global diversity of freshwater fishes has not been fully documented. Studies of freshwater fishes that were previously thought to be morphologically variable have revealed the existence of deeply divergent lineages, with many distinct species. In southern Africa a number of Enteromius species exhibit either exceedingly wide or divided distribution patterns that should be rare for freshwater fishes with limited dispersal opportunities between river systems. One such species is the sidespot barb, Enteromius neefi. As currently defined, E. neefi has a disjunct distribution that is divided between rivers in the northeast escarpment in South Africa and Eswatini, and tributaries of the Upper Zambezi in Zambia and southern Congo in the Democratic Republic of Congo, with a large geographic gap between these two populations. With the use of molecular and morphological methods, the level of divergence between the two populations was examined, and a new species was described from the Steelpoort River in the Limpopo River system of South Africa. Findings from this study provide further evidence for a number of taxonomic problems within the goldie barbs of southern Africa, and some taxonomic rearrangements are proposed for this group.
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Affiliation(s)
- Martinus Scheepers
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
| | - Pedro H N Bragança
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
| | - Albert Chakona
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
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81
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Jelley L, Douglas J, O'Neill M, Berquist K, Claasen A, Wang J, Utekar S, Johnston H, Judy B, Allais M, de Ligt J, Tan CE, Seeds R, Wood T, Aminisani N, Jennings T, Welch D, Turner N, McIntyre P, Dowell T, Trenholme A, Byrnes C, Webby R, French N, Winter D, Huang QS, Geoghegan JL. Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24310412. [PMID: 39072023 PMCID: PMC11275701 DOI: 10.1101/2024.07.15.24310412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.
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82
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Oróstica KY, Mohr SB, Dehning J, Bauer S, Medina-Ortiz D, Iftekhar EN, Mujica K, Covarrubias PC, Ulloa S, Castillo AE, Daza-Sánchez A, Verdugo RA, Fernández J, Olivera-Nappa Á, Priesemann V, Contreras S. Early mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants in Chile. Sci Rep 2024; 14:16000. [PMID: 38987406 PMCID: PMC11237036 DOI: 10.1038/s41598-024-66885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/05/2024] [Indexed: 07/12/2024] Open
Abstract
Genomic surveillance (GS) programmes were crucial in identifying and quantifying the mutating patterns of SARS-CoV-2 during the COVID-19 pandemic. In this work, we develop a Bayesian framework to quantify the relative transmissibility of different variants tailored for regions with limited GS. We use it to study the relative transmissibility of SARS-CoV-2 variants in Chile. Among the 3443 SARS-CoV-2 genomes collected between January and June 2021, where sampling was designed to be representative, the Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, and B.1.1 lineages were predominant. We found that Lambda and Gamma variants' reproduction numbers were 5% (95% CI: [1%, 14%]) and 16% (95% CI: [11%, 21%]) larger than Alpha's, respectively. Besides, we observed a systematic mutation enrichment in the Spike gene for all circulating variants, which strongly correlated with variants' transmissibility during the studied period (r = 0.93, p-value = 0.025). We also characterised the mutational signatures of local samples and their evolution over time and with the progress of vaccination, comparing them with those of samples collected in other regions worldwide. Altogether, our work provides a reliable method for quantifying variant transmissibility under subsampling and emphasises the importance of continuous genomic surveillance.
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Affiliation(s)
| | - Sebastian B Mohr
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Jonas Dehning
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Simon Bauer
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - David Medina-Ortiz
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Emil N Iftekhar
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Karen Mujica
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Paulo C Covarrubias
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Soledad Ulloa
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Andrés E Castillo
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | | | - Ricardo A Verdugo
- Facultad de Medicina, Universidad de Talca, Talca, Chile
- Departamento de Oncología Básico-Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jorge Fernández
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Santiago, Chile
| | - Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Seba Contreras
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany.
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83
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Luong NN, Ha HTT, Huy NX, Loi BV, Van NH, Quang HT, Loc NH. Characterizing the Phan Rang Sheep: A First Look at the Y Chromosome, Mitochondrial DNA, and Morphometrics. Animals (Basel) 2024; 14:2020. [PMID: 39061482 PMCID: PMC11274324 DOI: 10.3390/ani14142020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/24/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country's sheep population. These provinces are known for their high temperatures and frequent droughts. The long-standing presence of the Phan Rang sheep in these regions suggests their potential resilience to heat stress-a trait of increasing interest in the face of global climate change. Despite the breed's significance, a critical knowledge gap hinders conservation and breeding programs. To address this, our study employed a two-pronged approach. First, we collected body conformational data to aid in breed identification. Second, we analyzed mitochondrial DNA (D-loop) and Y chromosome markers (SRY and SRYM18) to elucidate the maternal and paternal lineages. Among the 68 Phan Rang sheep analyzed for their D-loop, 19 belonged to mitochondrial haplogroup A, while 49 belonged to haplogroup B. The haplogroups can be subdivided into 16 unique haplotypes. All 19 rams surveyed for their paternal lineages belonged to haplotypes H5 and H6. These findings strongly support the hypothesis of dual origins for the Phan Rang sheep. This study presents the first genetic data for the Phan Rang breed, providing crucial insights for future research and conservation efforts.
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Affiliation(s)
- Nguyen Ngoc Luong
- College of Sciences, Hue University, 77 Nguyen Hue, Hue 530000, Vietnam
| | - Huynh Thi Thu Ha
- College of Sciences, Hue University, 77 Nguyen Hue, Hue 530000, Vietnam
| | - Nguyen Xuan Huy
- Department of Science, Technology and International Relations, Hue University, 4 Le Loi, Hue 530000, Vietnam;
- Faculty of Biology, University of Education, Hue University, 34 Le Loi, Hue 530000, Vietnam
| | - Bui Van Loi
- Presidential Board, Hue University, 3 Le Loi, Hue 530000, Vietnam;
| | - Nguyen Huu Van
- University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam;
| | - Hoang Tan Quang
- Institute of Biotechnology, Hue University, Tinh Lo 10, Phu Thuong, Phu Vang 536801, Vietnam;
| | - Nguyen Hoang Loc
- College of Sciences, Hue University, 77 Nguyen Hue, Hue 530000, Vietnam
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84
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Rose JP, Kriebel R, Sytsma KJ, Drew BT. Phylogenomic perspectives on speciation and reproductive isolation in a North American biodiversity hotspot: an example using California sages (Salvia subgenus Audibertia: Lamiaceae). ANNALS OF BOTANY 2024; 134:295-310. [PMID: 38733329 PMCID: PMC11232522 DOI: 10.1093/aob/mcae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND AND AIMS The California Floristic Province (CA-FP) is the most species-rich region of North America north of Mexico. One of several proposed hypotheses explaining the exceptional diversity of the region is that the CA-FP harbours myriad recently diverged lineages with nascent reproductive barriers. Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple sympatric and compatible species. METHODS Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyse contemporaneous patterns of gene flow and mechanical reproductive isolation. KEY RESULTS Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades, indicating that reproductive barriers arise with increasing genetic divergence. Species are generally not mechanically isolated, suggesting that it is unlikely to be the primary factor leading to reproductive isolation. CONCLUSIONS Rapid, recent speciation with some interspecific gene flow in conjunction with the onset of a Mediterranean-like climate is the underlying cause of extant diversity in Salvia subgenus Audibertia. Speciation has largely not been facilitated by gene flow. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different instances of historical gene flow, probably characteristic of many CA-FP lineages. Mechanical reproductive isolation appears to be only part of a mosaic of factors limiting gene flow.
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Affiliation(s)
- Jeffrey P Rose
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
- California Academy of Sciences, San Francisco, CA 94118, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Bryan T Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
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85
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Avrahami HM, Makovicky PJ, Tucker RT, Zanno LE. A new semi-fossorial thescelosaurine dinosaur from the Cenomanian-age Mussentuchit Member of the Cedar Mountain Formation, Utah. Anat Rec (Hoboken) 2024. [PMID: 38979930 DOI: 10.1002/ar.25505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/18/2024] [Accepted: 05/06/2024] [Indexed: 07/10/2024]
Abstract
Thescelosaurines are a group of early diverging, ornithischian dinosaurs notable for their conservative bauplans and mosaic of primitive features. Although abundant within the latest Cretaceous ecosystems of North America, their record is poor to absent in earlier assemblages, leaving a large gap in our understanding of their evolution, origins, and ecological roles. Here we report a new small bodied thescelosaurine-Fona herzogae gen. et sp. nov.-from the Mussentuchit Member of the Cedar Mountain Formation, Utah, USA. Fona herzogae is represented by multiple individuals, representing one of the most comprehensive skeletal assemblages of a small bodied, early diverging ornithischian described from North America to date. Phylogenetic analysis recovers Fona as the earliest member of Thescelosaurinae, minimally containing Oryctodromeus, and all three species of Thescelosaurus, revealing the clade was well-established in North America by as early as the Cenomanian, and distinct from, yet continental cohabitants with, their sister clade, Orodrominae. To date, orodromines and thescelosaurines have not been found together within a single North American ecosystem, suggesting different habitat preferences or competitive exclusion. Osteological observations reveal extensive intraspecific variation across cranial and postcranial elements, and a number of anatomical similarities with Oryctodromeus, suggesting a shared semi-fossorial lifestyle.
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Affiliation(s)
- Haviv M Avrahami
- North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
| | - Peter J Makovicky
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ryan T Tucker
- Department of Earth Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Lindsay E Zanno
- North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
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86
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Daza JD, Stanley EL, Heinicke MP, Leah C, Doucet DS, Fenner KL, Arias JS, Smith RDA, Peretti AM, Aung NN, Bauer AM. Compound osteoderms preserved in amber reveal the oldest known skink. Sci Rep 2024; 14:15662. [PMID: 38977836 PMCID: PMC11231356 DOI: 10.1038/s41598-024-66451-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
Scincidae is one of the most species-rich and cosmopolitan clades of squamate reptiles. Abundant disarticulated fossil material has also been attributed to this group, however, no complete pre-Cenozoic crown-scincid specimens have been found. A specimen in Burmite (99 MYA) is the first fossil that can be unambiguously referred to this clade. Our analyses place it as nested within extant skinks, supported by the presence of compound osteoderms formed by articulated small ostedermites. The specimen has a combination of dorsal and ventral compound osteoderms and overlapping cycloid scales that is limited to skinks. We propose that this type of osteoderm evolved as a response to an increased overlap of scales, and to reduced stiffness of the dermal armour. Compound osteoderms could be a key innovation that facilitated diversification in this megadiverse family.
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Affiliation(s)
- Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, 77341, USA.
| | - Edward L Stanley
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | | | - Chuck Leah
- Houston Museum of Natural Sciences, Houston, TX, 77030, USA
| | - Daniel S Doucet
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, 77341, USA
| | - Kelsey L Fenner
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - J Salvador Arias
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical, CONICET-Universidad Nacional de Misiones, and Facultad de Ciencias Exactas, Químicas y Naturales, 3300, Posadas, Misiones, Argentina
| | - Ru D A Smith
- Jabatan Geologi, University Malaya, 50603, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Adolf M Peretti
- Peretti Museum Foundation, Baumschulweg, 13, 6045, Meggen, Switzerland
| | - Nyi Nyi Aung
- Peretti Museum Foundation, Baumschulweg, 13, 6045, Meggen, Switzerland
- Myanmar Geosciences Society, Department of Geology, University of Yangon, Yangon, 11041, Myanmar
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, Villanova, PA, 19085, USA
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87
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Ghimire P, Palacios C, Trimble J, Lamichhaney S. Museum genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens. G3 (BETHESDA, MD.) 2024; 14:jkae081. [PMID: 38626302 DOI: 10.1093/g3journal/jkae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/16/2024] [Accepted: 04/05/2024] [Indexed: 04/18/2024]
Abstract
The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia spp.) and examine their genetic composition and taxonomic status and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences; however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollynecks are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies Ciconia episcopus neglecta and Ciconia episcopus episcopus, suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.
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Affiliation(s)
- Prashant Ghimire
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Jeremiah Trimble
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
- School of Biomedical Sciences, Kent State University, Kent, OH 44240, USA
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88
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Przelomska NAS, Diaz RA, Ávila FA, Ballen GA, Cortés-B R, Kistler L, Chitwood DH, Charitonidou M, Renner SS, Pérez-Escobar OA, Antonelli A. Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy. Mol Biol Evol 2024; 41:msae114. [PMID: 38982580 PMCID: PMC11233275 DOI: 10.1093/molbev/msae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 07/11/2024] Open
Abstract
South American coca (Erythroxylum coca and E. novogranatense) has been a keystone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half-century, global demand for its alkaloid cocaine has driven intensive agriculture of this plant and placed it in the center of armed conflict and deforestation. To monitor the changing landscape of coca plantations, the United Nations Office on Drugs and Crime collects annual data on their areas of cultivation. However, attempts to delineate areas in which different varieties are grown have failed due to limitations around identification. In the absence of flowers, identification relies on leaf morphology, yet the extent to which this is reflected in taxonomy is uncertain. Here, we analyze the consistency of the current naming system of coca and its four closest wild relatives (the "coca clade"), using morphometrics, phylogenomics, molecular clocks, and population genomics. We include name-bearing type specimens of coca's closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the statistical analyses illuminate that rounder and more obovate leaves of certain varieties could be associated with the subtle domestication syndrome of coca. Our phylogenomic data indicate extensive gene flow involving E. gracilipes which, combined with morphometrics, supports E. gracilipes being retained as a single species. Establishing a robust evolutionary-taxonomic framework for the coca clade will facilitate the development of cost-effective genotyping methods to support reliable identification.
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Affiliation(s)
- Natalia A S Przelomska
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Rudy A Diaz
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | | | - Gustavo A Ballen
- Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Rocío Cortés-B
- Herbario Forestal Universidad Distrital, Campus El Vivero, CR 5E 15-82 Bogotá, Colombia
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Martha Charitonidou
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, SE 41319 Göteborg, Sweden
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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89
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Singer B, Di Nardo A, Hein J, Ferretti L. Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes. Mol Biol Evol 2024; 41:msae126. [PMID: 38922185 PMCID: PMC11251493 DOI: 10.1093/molbev/msae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterize their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterize the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete "trait" independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission.
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Affiliation(s)
- Benjamin Singer
- Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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90
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Pereira AC, Lourenço J, Themudo G, Botelho A, Cunha MV. Population structure and history of Mycobacterium bovis European 3 clonal complex reveal transmission across ecological corridors of unrecognized importance in Portugal. Microbiol Spectr 2024; 12:e0382923. [PMID: 38771094 PMCID: PMC11218495 DOI: 10.1128/spectrum.03829-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Mycobacterium bovis causes animal tuberculosis in livestock and wildlife, with an impact on animal health and production, wildlife management, and public health. In this work, we sampled a multi-host tuberculosis community from the official hotspot risk area of Portugal over 16 years, generating the largest available data set in the country. Using phylogenetic and ecological modeling, we aimed to reconstruct the history of circulating lineages across the livestock-wildlife interface to inform intervention and the implementation of genomic surveillance within the official eradication plan. We find evidence for the co-circulation of M. bovis European 1 (Eu1), Eu2, and Eu3 clonal complexes, with Eu3 providing sufficient temporal signal for further phylogenetic investigation. The Eu3 most recent common ancestor (bovine) was dated in the 1990s, subsequently transitioning to wildlife (red deer and wild boar). Isolate clustering based on sample metadata was used to inform phylogenetic inference, unravelng frequent transmission between two clusters that represent an ecological corridor of previously unrecognized importance in Portugal. The latter was associated with transmission at the livestock-wildlife interface toward locations with higher temperature and precipitation, lower agriculture and road density, and lower host densities. This is the first analysis of M. bovis Eu3 complex in Iberia, shedding light on background ecological factors underlying long-term transmission and informing where efforts could be focused within the larger hotspot risk area of Portugal. IMPORTANCE Efforts to strengthen surveillance and control of animal tuberculosis (TB) are ongoing worlwide. Here, we developed an eco-phylodynamic framework based on discrete phylogenetic approaches informed by M. bovis whole-genome sequence data representing a multi-host transmission system at the livestock-wildlife interface, within a rich ecological landscape in Portugal, to understand transmission processes and translate this knowledge into disease management benefits. We find evidence for the co-circulation of several M. bovis clades, with frequent transmission of the Eu3 lineage among cattle and wildlife populations. Most transition events between different ecological settings took place toward host, climate and land use gradients, underscoring animal TB expansion and a potential corridor of unrecognized importance for M. bovis maintenance. Results stress that animal TB is an established wildlife disease without ecological barriers, showing that control measures in place are insufficient to prevent long-distance transmission and spillover across multi-host communities, demanding new interventions targeting livestock-wildlife interactions.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Lourenço
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Gonçalo Themudo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Botelho
- INIAV, I.P.—National Institute for Agrarian and Veterinary Research, Oeiras, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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91
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Cavallini M, Lombardo G, Cantini C, Gerosa M, Binelli G. Genetic Insights into the Historical Attribution of Variety Names of Sweet Chestnut ( Castanea sativa Mill.) in Northern Italy. Genes (Basel) 2024; 15:866. [PMID: 39062645 PMCID: PMC11276188 DOI: 10.3390/genes15070866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The sweet chestnut (Castanea sativa Mill.) is subject to the progressive disappearance of its traditional chestnut groves. In the northern part of Italy, where distribution of the sweet chestnut is fragmented, many local varieties continue to be identified mostly by oral tradition. We characterised by SSRs eleven historically recognised varieties of sweet chestnut in the area surrounding Lake Como, with the goal of giving a genetic basis to the traditional classification. We performed classical analysis about differentiation and used Bayesian approaches to detect population structure and to reconstruct demography. The results revealed that historical and genetic classifications are loosely linked when chestnut fruits are just "castagne", that is, normal fruits, but increasingly overlap where "marroni" (the most prized fruits) are concerned. Bayesian classification allowed us to identify a homogeneous gene cluster not recognised in the traditional assessment of the varieties and to reconstruct possible routes used for the propagation of sweet chestnut. We also reconstructed ancestral relationships between the different gene pools involved and dated ancestral lineages whose results fit with palynological data. We suggest that conservation strategies based on a genetic evaluation of the resource should also rely on traditional cultural heritage, which could reveal new sources of germplasm.
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Affiliation(s)
- Marta Cavallini
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (G.L.)
| | - Gianluca Lombardo
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (G.L.)
| | - Claudio Cantini
- Institute of Bioeconomy (IBE), Consiglio Nazionale Ricerche (CNR), 58022 Follonica, Italy;
| | - Mauro Gerosa
- Associazione Castanicoltori Lario Orientale, 23851 Sala al Barro, Italy;
| | - Giorgio Binelli
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (G.L.)
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92
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Parakkunnel R, K BN, Vanishree G, George A, Kv S, Yr A, K UB, Anandan A, Kumar S. Exploring selection signatures in the divergence and evolution of lipid droplet (LD) associated genes in major oilseed crops. BMC Genomics 2024; 25:653. [PMID: 38956471 PMCID: PMC11218257 DOI: 10.1186/s12864-024-10527-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Oil bodies or lipid droplets (LDs) in the cytosol are the subcellular storage compartments of seeds and the sites of lipid metabolism providing energy to the germinating seeds. Major LD-associated proteins are lipoxygenases, phospholipaseD, oleosins, TAG-lipases, steroleosins, caleosins and SEIPINs; involved in facilitating germination and enhancing peroxidation resulting in off-flavours. However, how natural selection is balancing contradictory processes in lipid-rich seeds remains evasive. The present study was aimed at the prediction of selection signatures among orthologous clades in major oilseeds and the correlation of selection effect with gene expression. RESULTS The LD-associated genes from the major oil-bearing crops were analyzed to predict natural selection signatures in phylogenetically close-knit ortholog clusters to understand adaptive evolution. Positive selection was the major force driving the evolution and diversification of orthologs in a lineage-specific manner. Significant positive selection effects were found in 94 genes particularly in oleosin and TAG-lipases, purifying with excess of non-synonymous substitution in 44 genes while 35 genes were neutral to selection effects. No significant selection impact was noticed in Brassicaceae as against LOX genes of oil palm. A heavy load of deleterious mutations affecting selection signatures was detected in T-lineage oleosins and LOX genes of Arachis hypogaea. The T-lineage oleosin genes were involved in mainly anther, tapetum and anther wall morphogenesis. In Ricinus communis and Sesamum indicum > 85% of PLD genes were under selection whereas selection pressures were low in Brassica juncea and Helianthus annuus. Steroleosin, caleosin and SEIPINs with large roles in lipid droplet organization expressed mostly in seeds and were under considerable positive selection pressures. Expression divergence was evident among paralogs and homeologs with one gene attaining functional superiority compared to the other. The LOX gene Glyma.13g347500 associated with off-flavor was not expressed during germination, rather its paralog Glyma.13g347600 showed expression in Glycine max. PLD-α genes were expressed on all the tissues except the seed,δ genes in seed and meristem while β and γ genes expressed in the leaf. CONCLUSIONS The genes involved in seed germination and lipid metabolism were under strong positive selection, although species differences were discernable. The present study identifies suitable candidate genes enhancing seed oil content and germination wherein directional selection can become more fruitful.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India.
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Anjitha George
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sripathy Kv
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Aruna Yr
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - A Anandan
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, 275103, Uttar Pradesh, India
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93
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Moreno-Contreras I, Jokimäki J, Kaisanlahti-Jokimäki ML, Leveau LM, Suhonen J, Tobias JA, Tryjanowski P. Disentangling the drivers of urban bird diversity in the non-breeding season: A general synthesis. GLOBAL CHANGE BIOLOGY 2024; 30:e17421. [PMID: 39034889 DOI: 10.1111/gcb.17421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/19/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024]
Abstract
Current knowledge about the impacts of urbanisation on bird assemblages is based on evidence from studies partly or wholly undertaken in the breeding season. In comparison, the non-breeding season remains little studied, despite the fact that winter conditions at higher latitudes are changing more rapidly than other seasons. During the non-breeding season, cities may attract or retain bird species because they offer milder conditions or better feeding opportunities than surrounding habitats. However, the range of climatic, ecological and anthropogenic mechanisms shaping different facets of urban bird diversity in the non-breeding season are poorly understood. We explored these mechanisms using structural equation modelling to assess how urbanisation affects the taxonomic, phylogenetic and functional diversity of avian assemblages sampled worldwide in the non-breeding season. We found that minimum temperature, elevation, urban area and city age played a critical role in determining taxonomic diversity while a range of factors-including productivity, precipitation, elevation, distance to coasts and rivers, socio-economic (as a proxy of human facilitation) and road density-each contributed to patterns of phylogenetic and functional diversity. The structure and function of urban bird assemblages appear to be predominantly shaped by temperature, productivity and city age, with effects of these factors differing across seasons. Our results underline the importance of considering multiple hypotheses, including seasonal effects, when evaluating the impacts of urbanisation on biodiversity.
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Affiliation(s)
- Israel Moreno-Contreras
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jukka Jokimäki
- Nature Inventory and EIA-Services, Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Lucas M Leveau
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-IEGEBA (CONICET-UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Jukka Suhonen
- Department of Biology, University of Turku, Turku, Finland
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Piotr Tryjanowski
- Department of Zoology, Poznań University of Life Sciences, Poznań, Poland
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94
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Sewell TR, van Dorp L, Ghosh PN, Wierzbicki C, Caroe C, Lyakurwa JV, Tonelli E, Bowkett AE, Marsden S, Cunningham AA, Garner TWJ, Gilbert TP, Moyer D, Weldon C, Fisher MC. Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild. Proc Biol Sci 2024; 291:20241157. [PMID: 39081176 PMCID: PMC11289635 DOI: 10.1098/rspb.2024.1157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 06/19/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
Outbreaks of emerging infectious diseases are influenced by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Deterioration in the population of the micro-endemic Tanzanian Kihansi spray toad (Nectophrynoides asperginis) occurred after the construction of a hydropower dam, implicating habitat modification in this species decline. Population recovery followed habitat augmentation; however, a subsequent outbreak of chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) led to the spray toad's extinction in the wild. We show using spatiotemporal surveillance and mitogenome assembly of Bd from archived toad mortalities that the outbreak was caused by invasion of the BdCAPE lineage and not the panzootic lineage BdGPL. Molecular dating reveals an emergence of BdCAPE across southern Africa overlapping with the timing of the spray toad's extinction. That our post-outbreak surveillance of co-occurring amphibian species in the Udzungwa Mountains shows widespread infection by BdCAPE yet no signs of ill-health or decline suggests these other species can tolerate Bd when environments are stable. We conclude that, despite transient success in mitigating the impact caused by dams' construction, invasion by BdCAPE caused the ultimate die-off that led to the extinction of the Kihansi spray toad.
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Affiliation(s)
- Thomas R. Sewell
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution & Environment, UCL Genetics Institute, University College London, LondonWC1E 6BT, UK
| | - Pria N. Ghosh
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
| | - Claudia Wierzbicki
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
- Institute of Zoology, Zoological Society of London, LondonNW1 4RY, UK
| | - Christian Caroe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen1353, Denmark
| | - John V. Lyakurwa
- Department of Zoology and Wildlife Conservation, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Elena Tonelli
- Department of Natural Sciences, Manchester Metropolitan University, ManchesterM1 5GD, UK
| | | | - Stuart Marsden
- Department of Natural Sciences, Manchester Metropolitan University, ManchesterM1 5GD, UK
| | | | - Trenton W. J. Garner
- Institute of Zoology, Zoological Society of London, LondonNW1 4RY, UK
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Tom P. Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen1353, Denmark
| | - David Moyer
- Integrated Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, White City, Imperial, LondonW12 0BZ, UK
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95
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Fernandez JE, Egli A, Overesch G, Perreten V. Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution. Nat Commun 2024; 15:5526. [PMID: 38951499 PMCID: PMC11217367 DOI: 10.1038/s41467-024-49644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.
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Affiliation(s)
- Javier Eduardo Fernandez
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gudrun Overesch
- Center for Zoonoses, Animal Bacterial Diseases and Antimicrobial Resistance, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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96
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Xu H, Guo Y, Xia M, Yu J, Chi X, Han Y, Li X, Zhang F. An updated phylogeny and adaptive evolution within Amaranthaceae s.l. inferred from multiple phylogenomic datasets. Ecol Evol 2024; 14:e70013. [PMID: 39011133 PMCID: PMC11246835 DOI: 10.1002/ece3.70013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 06/17/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
Amaranthaceae s.l. is a widely distributed family consisting of over 170 genera and 2000 species. Previous molecular phylogenetic studies have shown that Amaranthaceae s.s. and traditional Chenopodiaceae form a monophyletic group (Amaranthaceae s.l.), however, the relationships within this evolutionary branch have yet to be fully resolved. In this study, we assembled the complete plastomes and full-length ITS of 21 Amaranthaceae s.l. individuals and compared them with 38 species of Amaranthaceae s.l. Through plastome structure and sequence alignment analysis, we identified a reverse complementary region approximately 5200 bp long in the genera Atriplex and Chenopodium. Adaptive evolution analysis revealed significant positive selection in eight genes, which likely played a driving role in the evolution of Amaranthaceae s.l., as demonstrated by partitioned evolutionary analysis. Furthermore, we found that about two-thirds of the examined species lack the ycf15 gene, potentially associated with natural selection pressures from their adapted habitats. The phylogenetic tree indicated that some genera (Chenopodium, Halogeton, and Subtr. Salsolinae) are paraphyletic lineages. Our results strongly support the clustering of Amaranthaceae s.l. with monophyletic traditional Chenopodiaceae (Clades I and II) and Amaranthaceae s.s. After a comprehensive analysis, we determined that cytonuclear conflict, gene selection by adapted habitats, and incomplete lineage sorting (ILS) events were the primary reasons for the inconsistent phylogeny of Amaranthaceae s.l. During the last glacial period, certain species within Amaranthaceae s.l. underwent adaptations to different environments and began to differentiate rapidly. Since then, these species may have experienced morphological and genetic changes distinct from those of other genera due to intense selection pressure.
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Affiliation(s)
- Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuqin Guo
- Qinghai National Park Research Monitoring and Evaluation CenterXiningChina
| | - Mingze Xia
- School of PharmacyWeifang Medical UniversityWeifangChina
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Yun Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoping Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
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97
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Inès D, Courty PE, Wendehenne D, Rosnoblet C. CDC48 in plants and its emerging function in plant immunity. TRENDS IN PLANT SCIENCE 2024; 29:786-798. [PMID: 38218650 DOI: 10.1016/j.tplants.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
Protein homeostasis, namely the balance between protein synthesis and degradation, must be finely controlled to ensure cell survival, notably through the ubiquitin-proteasome system (UPS). In all species, including plants, homeostasis is disrupted by biotic and abiotic stresses. A key player in the maintenance of protein balance, the protein CDC48, shows emerging functions in plants, particularly in response to biotic stress. In this review on CDC48 in plants, we detail its highly conserved structure, describe a gene expansion that is only present in Viridiplantae, discuss its various functions and regulations, and finally highlight its recruitment, still not clear, during the plant immune response.
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Affiliation(s)
- Damien Inès
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Institut Agro, Université de Bourgogne, Université Bourgogne-Franche-Comté, Dijon, France.
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98
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Wu M, Cheng Y, Jiang C, Zhang M, Shi T, Zhao C. Phylogeography of Morella nana: The Wumeng Mountains as a natural geographical isolation boundary on the Yunnan-Guizhou Plateau. Ecol Evol 2024; 14:e11566. [PMID: 38983704 PMCID: PMC11232048 DOI: 10.1002/ece3.11566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/25/2024] [Accepted: 05/30/2024] [Indexed: 07/11/2024] Open
Abstract
The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of the limestone Karst Islands and features the Wumeng Mountains, which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aimed to assess the effects of geographic isolation and past climate fluctuation on the distribution of flora in the YGP. To achieve this, we carried out the phylogeographical pattern and genetic structure based on chloroplast and nuclear ribosomal DNA sequence in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modeling for Morella nana, an important wild plant resource and endemic to the YGP once considered a vulnerable species. The results suggest that the genetic and chlorotype network structures of M. nana are divided into at least two groups: cpDNA chlorotype H2 (or dominant nrDNA haplotypes h1 and h2), distributed primarily to the east of the Wumeng Mountains, and cpDNA chlorotypes H1 and H3-H10 (or dominant nrDNA haplotype h2 and h3), distributed to the west of the Wumeng Mountains. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. This east-west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mountains, and supports the existence of at least two glacial refuges during the Quaternary glacial period, along with two genetic diversity center, and at least two large geographic protection units for the important species of M. nana. This study indicates that the phylogeographical pattern of M. nana can be attributed to geographic/environmental isolation caused by the Wumeng Mountains and climate fluctuation during the last glacial maximum, and proposes an effective strategy to protecting this important plant resource.
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Affiliation(s)
- Min Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Yu Cheng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Chunxue Jiang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Mingsheng Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Tian Shi
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
| | - Cai Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro‐Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro‐BioengineeringGuizhou UniversityGuiyangChina
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99
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Probst RS, Longino JT, Branstetter MG. Evolutionary déjà vu? A case of convergent evolution in an ant-plant association. Proc Biol Sci 2024; 291:20241214. [PMID: 38981524 PMCID: PMC11334994 DOI: 10.1098/rspb.2024.1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here, we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, Myrmelachista species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within Myrmelachista are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstructions, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.
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Affiliation(s)
- Rodolfo S. Probst
- Science Research Initiative (SRI), College of Science, University of Utah, Salt Lake City, UT84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112, USA
| | - John T. Longino
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112, USA
| | - Michael G. Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT84322, USA
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100
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White RT, Bakker S, Burton M, Castro ML, Couldrey C, Dyet K, Eustace A, Harland C, Hutton S, Macartney-Coxson D, Tarring C, Velasco C, Voss EM, Williamson J, Bloomfield M. Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing. Microb Genom 2024; 10:001273. [PMID: 38967541 PMCID: PMC11316549 DOI: 10.1099/mgen.0.001273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) are well described in the neonatal intensive care unit (NICU) setting. Genomics has revolutionized the investigation of such outbreaks; however, to date, this has largely been completed retrospectively and has typically relied on short-read platforms. In 2022, our laboratory established a prospective genomic surveillance system using Oxford Nanopore Technologies sequencing for rapid outbreak detection. Herein, using this system, we describe the detection and control of an outbreak of sequence-type (ST)97 MRSA in our NICU. The outbreak was identified 13 days after the first MRSA-positive culture and at a point where there were only two known cases. Ward screening rapidly defined the extent of the outbreak, with six other infants found to be colonized. There was minimal transmission once the outbreak had been detected and appropriate infection control measures had been instituted; only two further ST97 cases were detected, along with three unrelated non-ST97 MRSA cases. To contextualize the outbreak, core-genome single-nucleotide variants were identified for phylogenetic analysis after de novo assembly of nanopore data. Comparisons with global (n=45) and national surveillance (n=35) ST97 genomes revealed the stepwise evolution of methicillin resistance within this ST97 subset. A distinct cluster comprising nine of the ten ST97-IVa genomes from the NICU was identified, with strains from 2020 to 2022 national surveillance serving as outgroups to this cluster. One ST97-IVa genome presumed to be part of the outbreak formed an outgroup and was retrospectively excluded. A second phylogeny was created using Illumina sequencing, which considerably reduced the branch lengths of the NICU isolates on the phylogenetic tree. However, the overall tree topology and conclusions were unchanged, with the exception of the NICU outbreak cluster, where differences in branch lengths were observed. This analysis demonstrated the ability of a nanopore-only prospective genomic surveillance system to rapidly identify and contextualize an outbreak of MRSA in a NICU.
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Affiliation(s)
- Rhys T. White
- Institute of Environmental Science and Research, Health Group, Porirua 5022, New Zealand
| | - Sarah Bakker
- Institute of Environmental Science and Research, Health Group, Porirua 5022, New Zealand
| | - Megan Burton
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington 6021, New Zealand
| | - M. Leticia Castro
- Institute of Environmental Science and Research, Health Group, Porirua 5022, New Zealand
| | - Christine Couldrey
- Livestock Improvement Corporation, Research and Development, Newstead 3286, New Zealand
| | - Kristin Dyet
- Institute of Environmental Science and Research, Health Group, Porirua 5022, New Zealand
| | - Alexandra Eustace
- Institute of Environmental Science and Research, Health Group, Porirua 5022, New Zealand
| | - Chad Harland
- Livestock Improvement Corporation, Research and Development, Newstead 3286, New Zealand
| | - Samantha Hutton
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington 6021, New Zealand
| | - Donia Macartney-Coxson
- Institute of Environmental Science and Research, Health Group, Porirua 5022, New Zealand
| | - Claire Tarring
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington 6021, New Zealand
| | - Charles Velasco
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington 6021, New Zealand
| | - Emma M. Voss
- Livestock Improvement Corporation, Research and Development, Newstead 3286, New Zealand
- University of Otago, Department of Microbiology and Immunology, Dunedin 9016, New Zealand
| | - John Williamson
- University of Otago, Department of Microbiology and Immunology, Dunedin 9016, New Zealand
| | - Max Bloomfield
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington 6021, New Zealand
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast & Hutt Valley, Wellington 6021, New Zealand
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