101
|
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.
Collapse
Affiliation(s)
- Nobuaki Nagata
- Department of Anthropology, National Museum of Nature and Science, Ibaraki 305-0005, Japan,
| |
Collapse
|
102
|
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.
Collapse
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.
| |
Collapse
|
103
|
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.
Collapse
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)
Collapse
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.
| |
Collapse
|
104
|
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.
Collapse
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
| |
Collapse
|
105
|
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.
Collapse
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
| |
Collapse
|
106
|
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.
Collapse
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
| |
Collapse
|
107
|
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.
Collapse
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.
| |
Collapse
|
108
|
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.].
Collapse
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
| |
Collapse
|
109
|
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.
Collapse
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
| |
Collapse
|
110
|
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.
Collapse
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
| |
Collapse
|
111
|
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.
Collapse
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.)
| |
Collapse
|
112
|
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.
Collapse
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
| |
Collapse
|
113
|
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.
Collapse
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
| |
Collapse
|
114
|
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.
Collapse
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.
| |
Collapse
|
115
|
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.
Collapse
|
116
|
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.
Collapse
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.
| |
Collapse
|
117
|
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.
Collapse
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
| |
Collapse
|
118
|
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.
Collapse
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
| |
Collapse
|
119
|
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.
Collapse
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
| |
Collapse
|
120
|
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.
Collapse
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
| |
Collapse
|
121
|
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.
Collapse
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
| |
Collapse
|
122
|
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.
Collapse
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
| |
Collapse
|
123
|
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.
Collapse
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
| |
Collapse
|
124
|
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.
Collapse
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
| |
Collapse
|
125
|
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.
Collapse
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.)
| |
Collapse
|
126
|
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.
Collapse
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
| |
Collapse
|
127
|
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.
Collapse
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
| |
Collapse
|
128
|
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.
Collapse
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
| |
Collapse
|
129
|
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.
Collapse
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.
| |
Collapse
|
130
|
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.
Collapse
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
| |
Collapse
|
131
|
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.
Collapse
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.
| |
Collapse
|
132
|
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.
Collapse
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
| |
Collapse
|
133
|
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.
Collapse
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
| |
Collapse
|
134
|
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.
Collapse
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
| |
Collapse
|
135
|
King B, Greenhill SJ, Reid LA, Ross M, Walworth M, Gray RD. Bayesian phylogenetic analysis of Philippine languages supports a rapid migration of Malayo-Polynesian languages. Sci Rep 2024; 14:14967. [PMID: 38942799 PMCID: PMC11213883 DOI: 10.1038/s41598-024-65810-x] [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: 08/09/2023] [Accepted: 06/24/2024] [Indexed: 06/30/2024] Open
Abstract
The Philippines are central to understanding the expansion of the Austronesian language family from its homeland in Taiwan. It remains unknown to what extent the distribution of Malayo-Polynesian languages has been shaped by back migrations and language leveling events following the initial Out-of-Taiwan expansion. Other aspects of language history, including the effect of language switching from non-Austronesian languages, also remain poorly understood. Here we apply Bayesian phylogenetic methods to a core-vocabulary dataset of Philippine languages. Our analysis strongly supports a sister group relationship between the Sangiric and Minahasan groups of northern Sulawesi on one hand, and the rest of the Philippine languages on the other, which is incompatible with a simple North-to-South dispersal from Taiwan. We find a pervasive geographical signal in our results, suggesting a dominant role for cultural diffusion in the evolution of Philippine languages. However, we do find some support for a later migration of Gorontalo-Mongondow languages to northern Sulawesi from the Philippines. Subsequent diffusion processes between languages in Sulawesi appear to have led to conflicting data and a highly unstable phylogenetic position for Gorontalo-Mongondow. In the Philippines, language switching to Austronesian in 'Negrito' groups appears to have occurred at different time-points throughout the Philippines, and based on our analysis, there is no discernible effect of language switching on the basic vocabulary.
Collapse
Affiliation(s)
- Benedict King
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Simon J Greenhill
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Lawrence A Reid
- National Museum of the Philippines, 1000, Ermita, Manila, Metro Manila, Philippines
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Malcolm Ross
- School of Culture, History and Language, Australian National University, Canberra, 2601, Australia
| | - Mary Walworth
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
| |
Collapse
|
136
|
Ballestas G, Nobles A, Hwang Y, Kwak M, Yoo MJ. Evolutionary unraveling: new insights into the Persicaria amphibia complex. FRONTIERS IN PLANT SCIENCE 2024; 15:1408810. [PMID: 38988639 PMCID: PMC11233751 DOI: 10.3389/fpls.2024.1408810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024]
Abstract
The Persicaria amphibia complex exhibits significant morphological variation depending on its habitat, existing in either aquatic or terrestrial forms. Traditionally, four distinct elements have been recognized based on morphological features along with their distinct geographical distributions. Recent studies suggest that the Asian element may be genetically distinct from the European and American elements. However, a comprehensive study on the genetic differentiation among all four elements remains lacking. This study aimed to leverage whole plastid genome sequences and ITS2 haplotypes to comprehensively assess the genomic diversity within the P. amphibia complex. Notably, we included multiple individuals from New York State to resolve the ongoing debate regarding the taxonomic status of two American elements - whether they represent a single species or distinct entities. Our analysis revealed a well-supported monophyletic clade encompassing all four elements, endorsing their own section, Amphibia. Notably, the terrestrial form of the American element is sister to all other elements, suggesting it deserves its own species status. This reinstates its historical name, P. coccinea, separating it from the broader P. amphibia. Furthermore, distinct compositions of the ITS2 haplotypes differentiated the four elements, although the European element should be further investigated with more sampling. The most intriguing discovery is the identification of putative hybrids between the two American elements. In one population out of four putative hybrid populations, all three entities - the two parent species and their hybrid offspring - thrive together, showcasing a fascinating microcosm of ongoing evolutionary processes. Unraveling the intricate genetic tapestry within each American species and their hybrid populations remains a compelling next step. By delving deeper into their genetic makeup, we can gain a richer understanding of their evolutionary trajectories and the intricacies of their interactions. Finally, it is estimated that the two species of sect. Amphibia diverged approximately 4.02 million years ago during the Pliocene epoch, when there was a significant global cooling and drying trend.
Collapse
Affiliation(s)
| | - Alexander Nobles
- Chemistry and Biomolecular Science Department, Clarkson University, Potsdam, NY, United States
| | - Yoojeong Hwang
- Biology Department, Clarkson University, Potsdam, NY, United States
| | - Myounghai Kwak
- Strategic Planning Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Mi-Jeong Yoo
- Biology Department, Clarkson University, Potsdam, NY, United States
| |
Collapse
|
137
|
Kartavtsev YP, Masalkova NA. Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae). Int J Mol Sci 2024; 25:6902. [PMID: 39000014 PMCID: PMC11241113 DOI: 10.3390/ijms25136902] [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: 04/30/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species' mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26-27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20-68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae.
Collapse
Affiliation(s)
- Yuri Phedorovich Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology (NSCMB), Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | | |
Collapse
|
138
|
Lecocq de Pletincx N, Cerdà X, Kiran K, Karaman C, Taheri A, Aron S. Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants. iScience 2024; 27:109852. [PMID: 38779477 PMCID: PMC11109030 DOI: 10.1016/j.isci.2024.109852] [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: 11/30/2023] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Biological diversity often arises as organisms adapt to new ecological conditions (i.e., ecological opportunities) or colonize suitable areas (i.e., spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ∼18 million years ago and became a taxon of diverse species specializing in prey of different masses. The genus then colonized the Mediterranean Basin around 9 million years ago. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification preceded geographical expansion, resulting in a clade composed of ecologically homogeneous subclades.
Collapse
Affiliation(s)
- Nathan Lecocq de Pletincx
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
| | - Xim Cerdà
- Department of Ethology and Biodiversity Conservation, Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - Kadri Kiran
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Celal Karaman
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Ahmed Taheri
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences of El Jadida, University Chouaïb Doukkali, El Jadida, Morocco
| | - Serge Aron
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
| |
Collapse
|
139
|
Morales P, Gajardo F, Valdivieso C, Valladares MA, Di Genova A, Orellana A, Gutiérrez RA, González M, Montecino M, Maass A, Méndez MA, Allende ML. Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes. BMC Genomics 2024; 25:614. [PMID: 38890559 PMCID: PMC11184842 DOI: 10.1186/s12864-024-10416-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: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
Collapse
Affiliation(s)
- Pamela Morales
- Millennium Institute Center for Genome Regulation, Santiago, Chile.
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alex Di Genova
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- DiGenoma-Lab, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- ANID Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Martin Montecino
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, 837001, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Modelamiento Matemático IRL 2807 CNRS, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Universidad de Chile, Santiago, Chile
| | - Marco A Méndez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Ecología Aplicada y Sustentabilidad (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Cape Horn International Center (CHIC), Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| |
Collapse
|
140
|
Faustini G, Poletto F, Baston R, Tucciarone CM, Legnardi M, Dal Maso M, Genna V, Fiorentini L, Di Donato A, Perulli S, Cecchinato M, Drigo M, Franzo G. D for dominant: porcine circovirus 2d (PCV-2d) prevalence over other genotypes in wild boars and higher viral flows from domestic pigs in Italy. Front Microbiol 2024; 15:1412615. [PMID: 38952451 PMCID: PMC11215180 DOI: 10.3389/fmicb.2024.1412615] [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: 04/05/2024] [Accepted: 05/20/2024] [Indexed: 07/03/2024] Open
Abstract
Introduction Porcine circovirus 2 (PCV-2) is a key pathogen for the swine industry at a global level. Nine genotypes, differing in epidemiology and potentially virulence, emerged over time, with PCV-2a, -2b, and -2d being the most widespread and clinically relevant. Conversely, the distribution of minor genotypes appears geographically and temporally restricted, suggesting lower virulence and different epidemiological drivers. In 2022, PCV-2e, the most genetically and phenotypically divergent genotype, was identified in multiple rural farms in North-eastern Italy. Since rural pigs often have access to outdoor environment, the introduction from wild boars was investigated. Methods Through a molecular and spatial approach, this study investigated the epidemiology and genetic diversity of PCV-2 in 122 wild boars across different provinces of North-eastern Italy. Results Molecular analysis revealed a high PCV-2 frequency (81.1%, 99/122), and classified the majority of strains as PCV-2d (96.3%, 78/81), with sporadic occurrences of PCV-2a (1.2%, 1/81) and PCV-2b (2.5%, 2/81) genotypes. A viral flow directed primarily from domestic pigs to wild boars was estimated by phylogenetic and phylodynamic analyses. Discussion These findings attested that the genotype replacement so far described only in the Italian domestic swine sector occurred also in wild boars. and suggested that the current heterogeneity of PCV-2d strains in Italian wild boars likely depends more on different introduction events from the domestic population rather than the presence of independent evolutionary pressures. While this might suggest PCV-2 circulation in wild boars having a marginal impact in the industrial sector, the sharing of PCV-2d strains across distinct wild populations, in absence of a consistent geographical pattern, suggests a complex interplay between domestic and wild pig populations, emphasizing the importance of improved biosecurity measures to mitigate the risk of pathogen transmission.
Collapse
Affiliation(s)
- Giulia Faustini
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Francesca Poletto
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Riccardo Baston
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | | | - Matteo Legnardi
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Mariangela Dal Maso
- AULSS 8 Berica, Dipartimento di Prevenzione, Servizi Veterinari, Vicenza, Italy
| | | | - Laura Fiorentini
- Istituto Zooprofilattico Sperimentale Della Lombardia E Dell'Emilia Romagna (IZSLER), Forlì, Forlì-Cesena, Italy
| | | | - Simona Perulli
- Istituto Zooprofilattico Sperimentale Della Lombardia E Dell'Emilia Romagna (IZSLER), Forlì, Forlì-Cesena, Italy
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Michele Drigo
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| |
Collapse
|
141
|
Zhu S, Zhang N, Zhang J, Shao X, Guo Y, Cai D. Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China. Genes (Basel) 2024; 15:790. [PMID: 38927726 PMCID: PMC11203007 DOI: 10.3390/genes15060790] [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] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.
Collapse
Affiliation(s)
- Siqi Zhu
- Department of Archaeology, School of History, Wuhan University, Wuhan 430072, China;
| | - Naifan Zhang
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
- National Centre for Archaeology, Beijing 100013, China
| | - Jie Zhang
- Xinjiang Institute of Cultural Relics and Archaeology, Ürümqi 830011, China;
| | - Xinyue Shao
- Department of Archaeology, University of Southampton, Avenue Campus, Southampton SO17 1BF, UK;
| | - Yaqi Guo
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
| | - Dawei Cai
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
| |
Collapse
|
142
|
Valencia M P, Baeza JA, López-Cuamatzi IL, Ortega J. Characterization of the mitochondrial genomes of the Mexican endemic bats Corynorhinus mexicanus and Corynorhinus leonpaniaguae (Chiroptera: Vespertilionidae). Mol Biol Rep 2024; 51:760. [PMID: 38874795 DOI: 10.1007/s11033-024-09700-5] [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: 03/19/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The genus Corynorhinus is composed of four recognized species: C. rafinesquii, C. townsendii, C. mexicanus, and C. leonpaniaguae, the latter two being endemic to Mexico. According to the IUCN, C. mexicanus is considered "Near Threatened", as its populations are dwindling and habitats are affected by anthropogenic disturbance. Corynorhinus leonpaniaguae has not been assigned to an IUCN Red List risk category due to its recent description. METHODS AND RESULTS In this study, the mitochondrial genomes of C. mexicanus and C. leonpaniaguae were assembled and characterized in detail. The mitochondrial genomes (mtDNA) of C. mexicanus and C. leonpaniaguae have lengths of 16,470 and 16,581 bp respectively, with a predominant nucleotide usage of adenine (31.670% and 31.729%, respectively) and thymine (26.15% and 26.18%, respectively). The mtDNA of C. mexicanus and C. leonpaniaguae is composed of 37 coding and non-coding elements: 22 transfer RNAs (tRNA), 13 protein-coding genes (PCGs), two ribosomal RNAs and a non-coding region, the control region, which has a length of 933 bp and 1,149 bp, respectively. All tRNAs exhibited a cloverleaf secondary structure, with the exception of trn-Ser1 which showed a deletion of the dihydrouridine arm in the two species. All PCGs are subjected to purifying selection, with atp8 being the gene showing the highest Ka/Ks value. CONCLUSIONS These are the first whole mitogenomic resources developed for C. mexicanus and C. leonpaniaguae and enhance our knowledge of the ecology of these species and aid in their conservation.
Collapse
Affiliation(s)
- Pablo Valencia M
- Laboratorio de Bioconservación y Manejo, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Manuel Carpio y Plan de Ayala s/n, Col. Santo Tomás C.P. 11340 Alcaldía Miguel Hidalgo, Ciudad de México, México
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile
| | - Issachar L López-Cuamatzi
- Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos 44, Zona Centro, Centro, Xalapa-Enríquez, 91000, México
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Manuel Carpio y Plan de Ayala s/n, Col. Santo Tomás C.P. 11340 Alcaldía Miguel Hidalgo, Ciudad de México, México.
| |
Collapse
|
143
|
Brownstein CD, Near TJ. Colonization of the ocean floor by jawless vertebrates across three mass extinctions. BMC Ecol Evol 2024; 24:79. [PMID: 38867201 PMCID: PMC11170801 DOI: 10.1186/s12862-024-02253-y] [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: 01/16/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The deep (> 200 m) ocean floor is often considered to be a refugium of biodiversity; many benthic marine animals appear to share ancient common ancestry with nearshore and terrestrial relatives. Whether this pattern holds for vertebrates is obscured by a poor understanding of the evolutionary history of the oldest marine vertebrate clades. Hagfishes are jawless vertebrates that are either the living sister to all vertebrates or form a clade with lampreys, the only other surviving jawless fishes. RESULTS We use the hagfish fossil record and molecular data for all recognized genera to construct a novel hypothesis for hagfish relationships and diversification. We find that crown hagfishes persisted through three mass extinctions after appearing in the Permian ~ 275 Ma, making them one of the oldest living vertebrate lineages. In contrast to most other deep marine vertebrates, we consistently infer a deep origin of continental slope occupation by hagfishes that dates to the Paleozoic. Yet, we show that hagfishes have experienced marked body size diversification over the last hundred million years, contrasting with a view of this clade as morphologically stagnant. CONCLUSION Our results establish hagfishes as ancient members of demersal continental slope faunas and suggest a prolonged accumulation of deep sea jawless vertebrate biodiversity.
Collapse
Affiliation(s)
- Chase Doran Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA.
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
- Yale Peabody Museum, Yale University, New Haven, CT, 06511, USA
| |
Collapse
|
144
|
Goedderz S, Clements MA, Bent SJ, Nicholls JA, Patel VS, Crayn DM, Schlüter PM, Nargar K. Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genus Dipodium and provides insights into plastid gene degeneration. FRONTIERS IN PLANT SCIENCE 2024; 15:1388537. [PMID: 38938632 PMCID: PMC11210000 DOI: 10.3389/fpls.2024.1388537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/13/2024] [Indexed: 06/29/2024]
Abstract
The orchid genus Dipodium R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. Dipodium. This study examined plastome degeneration in Dipodium in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 Dipodium samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. Dipodium. Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found that sect. Leopardanthus is the sister lineage to sect. Dipodium. Dipodium ensifolium, the only leafy autotrophic species in sect. Dipodium, was found to be a sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence-time estimations found that Dipodium arose ca. 33.3 Ma near the lower boundary of the Oligocene and that crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. Dipodium. The comparative assessment of plastome structure and gene degradation in Dipodium revealed that plastid ndh genes were pseudogenised or physically lost in all Dipodium species, including in leafy autotrophic species of both Dipodium sections. Levels of plastid ndh gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. Dipodium exhibits an early stage of plastid genome degradation, as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context.
Collapse
Affiliation(s)
- Stephanie Goedderz
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Mark A. Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia
| | - Stephen J. Bent
- Data61, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Brisbane, QLD, Australia
| | - James A. Nicholls
- Australian National Insect Collection, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Vidushi S. Patel
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Darren M. Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Philipp M. Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| |
Collapse
|
145
|
Magalhaes ILF, Martins PH, Faleiro BT, Vidigal THDA, Santos FR, Carvalho LS, Santos AJ. Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands and landmasses, and indicates that Andean orogeny promotes speciation. Cladistics 2024. [PMID: 38861251 DOI: 10.1111/cla.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/24/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
The Neotropical region is the most diverse on the planet, largely owing to its mosaic of tropical rainforests. Multiple tectonic and climatic processes have been hypothesized to contribute to generating this diversity, including Andean orogeny, the closure of the Isthmus of Panama, the GAARlandia land bridge and historical connections among currently isolated forests. Micrathena spiders are diverse and widespread in the region, and thus a complete phylogeny of this genus allows the testing of hypotheses at multiple scales. We estimated a complete, dated phylogeny using morphological data for 117 Micrathena species and molecular data of up to five genes for a subset of 79 species. Employing eventc-based approaches and biogeographic stochastic mapping while considering phylogenetic uncertainty, we estimated ancestral distributions, the timing and direction of dispersal events and diversification rates among areas. The phylogeny is generally robust, with uncertainty in the position of some of the species lacking sequences. Micrathena started diversifying around 25 Ma. Andean cloud forests show the highest in-situ speciation, while the Amazon is the major dispersal source for adjacent areas. The Dry Diagonal generated few species and is a sink of diversity. Species exchange between Central and South America involved approximately 23 dispersal events and started ~20 Ma, which is consistent with a Miocene age for the Isthmus of Panama closure. We inferred four dispersal events from Central America to the Antilles in the last 20 Myr, indicating the spiders did not reach the islands through the GAARlandia land bridge. We identified important species exchange routes among the Amazon, Andean cloud forests and Atlantic forests during the Plio-Pleistocene. Sampling all species of the genus was fundamental to the conclusions above, especially in identifying the Andean forests as the area that generated the majority of species. This highlights the importance of complete taxonomic sampling in biogeographic studies.
Collapse
Affiliation(s)
- Ivan L F Magalhaes
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Pedro H Martins
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Bárbara T Faleiro
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Teofânia H D A Vidigal
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Fabrício R Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Leonardo S Carvalho
- Universidade Federal do Piauí, Campus Amílcar Ferreira Sobral, BR 343, KM 3.5, Bairro Meladão, s/no. CEP 6, 64808-660, Floriano, Piauí, Brazil
| | - Adalberto J Santos
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
146
|
Li Y, Bollen N, Hong SL, Brusselmans M, Gámbaro F, Suchard MA, Rambaut A, Lemey P, Dellicour S, Baele G. spread.gl: visualising pathogen dispersal in a high-performance browser application. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.04.24308447. [PMID: 38883783 PMCID: PMC11177906 DOI: 10.1101/2024.06.04.24308447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Phylogeographic analyses are able to exploit the location data associated with sampled molecular sequences to reconstruct the spatio-temporal dispersal history of a pathogen. Visualisation software is commonly used to facilitate the interpretation of the accompanying estimation results, as these are not always easily interpretable. spread.gl is a powerful, open-source and feature-rich browser application that enables smooth, intuitive and user-friendly visualisation of both discrete and continuous phylogeographic inference results, enabling the animation of pathogen geographic dispersal through time. spread.gl can render and combine the visualisation of several data layers, including a geographic layer (e.g., a world map), multiple layers that contain information extracted from the input phylogeny, and different types of layers that represent environmental data. As such, users can explore which environmental data may have shaped pathogen dispersal patterns, that can subsequently be formally tested through more principled statistical analyses. We showcase the visualisation features of spread.gl on several representative pathogen dispersal examples, including the smooth animation of a phylogeny encompassing over 17,000 genomic sequences resulting from a large-scale SARS-CoV-2 analysis.
Collapse
Affiliation(s)
- Yimin Li
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nena Bollen
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Samuel L. Hong
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marius Brusselmans
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Fabiana Gámbaro
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrew Rambaut
- Institute for Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| |
Collapse
|
147
|
Dey P, Ray SD, Kochiganti VHS, Pukazhenthi BS, Koepfli KP, Singh RP. Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails. Genes (Basel) 2024; 15:742. [PMID: 38927678 PMCID: PMC11202683 DOI: 10.3390/genes15060742] [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: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau's geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.
Collapse
Affiliation(s)
- Prateek Dey
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
- Bharathiar University, Coimbatore 641046, Tamil Nadu, India
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Swapna Devi Ray
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
| | | | - Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya 824236, Bihar, India
| |
Collapse
|
148
|
Oyarzún-Ruiz P, Thomas R, Santodomingo A, Zamorano-Uribe M, Moroni M, Moreno L, Muñoz-Leal S, Flores V, Brant S. Systematics and life cycles of four avian schistosomatids from Southern Cone of South America. J Helminthol 2024; 98:e47. [PMID: 38828707 DOI: 10.1017/s0022149x2400035x] [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] [Indexed: 06/05/2024]
Abstract
Relative to the numerous studies focused on mammalian schistosomes, fewer include avian schistosomatids particularly in the southern hemisphere. This is changing and current research emerging from the Neotropics shows a remarkable diversity of endemic taxa. To contribute to this effort, nine ducks (Spatula cyanoptera, S.versicolor, Netta peposaca), 12 swans (Cygnus melancoryphus) and 1,400 Physa spp. snails from Chile and Argentina were collected for adults and larval schistosomatids, respectively. Isolated schistosomatids were preserved for morphological and molecular analyses (28S and COI genes). Four different schistosomatid taxa were retrieved from birds: Trichobilharzia sp. in N. peposaca and S. cyanoptera that formed a clade; S.cyanoptera and S. versicolor hosted Trichobilharzia querquedulae; Cygnus melancoryphus hosted the nasal schistosomatid, Nasusbilharzia melancorhypha; and one visceral, Schistosomatidae gen. sp., which formed a clade with furcocercariae from Argentina and Chile from previous work. Of the physid snails, only one from Argentina had schistosomatid furcocercariae that based on molecular analyses grouped with T. querquedulae. This study represents the first description of adult schistosomatids from Chile as well as the elucidation of the life cycles of N.melancorhypha and T. querquedulae in Chile and Neotropics, respectively. Without well-preserved adults, the putative new genus Schistosomatidae gen. sp. could not be described, but its life cycle involves Chilina spp. and C. melancoryphus. Scanning electron microscopy of T. querquedulae revealed additional, undescribed morphological traits, highlighting its diagnostic importance. Authors stress the need for additional surveys of avian schistosomatids from the Neotropics to better understand their evolutionary history.
Collapse
Affiliation(s)
- P Oyarzún-Ruiz
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción4030000, Chile
| | - R Thomas
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán3780000, Chile
| | - A Santodomingo
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán3780000, Chile
| | - M Zamorano-Uribe
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán3780000, Chile
| | - M Moroni
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia5090000, Chile
| | - L Moreno
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción4030000, Chile
| | - S Muñoz-Leal
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán3780000, Chile
| | - V Flores
- Laboratorio de Parasitología, INIBIOMA (CONICET-Universidad Nacional del Comahue), San Carlos de Bariloche, Río Negro, Argentina
| | - S Brant
- Museum of Southwestern Biology Parasite Division, University of New Mexico, 167 Castetter MSCO3 2020, Albuquerque, NM 87131, USA
| |
Collapse
|
149
|
Brownstein CD, Zapfe KL, Lott S, Harrington R, Ghezelayagh A, Dornburg A, Near TJ. Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean. Curr Biol 2024; 34:2541-2550.e4. [PMID: 38788708 DOI: 10.1016/j.cub.2024.04.066] [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: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
Major ecological transitions are thought to fuel diversification, but whether they are contingent on the evolution of certain traits called key innovations1 is unclear. Key innovations are routinely invoked to explain how lineages rapidly exploit new ecological opportunities.1,2,3 However, investigations of key innovations often focus on single traits rather than considering trait combinations that collectively produce effects of interest.4 Here, we investigate the evolution of synergistic trait interactions in anglerfishes, which include one of the most species-rich vertebrate clades in the bathypelagic, or "midnight," zone of the deep sea: Ceratioidea.5 Ceratioids are the only vertebrates that possess sexual parasitism, wherein males temporarily attach or permanently fuse to females to mate.6,7 We show that the rapid transition of ancestrally benthic anglerfishes into pelagic habitats occurred during a period of major global warming 50-35 million years ago.8,9 This transition coincided with the origins of sexual parasitism, which is thought to increase the probability of successful reproduction once a mate is found in the midnight zone, Earth's largest habitat.5,6,7 Our reconstruction of the evolutionary history of anglerfishes and the loss of immune genes support that permanently fusing clades have convergently degenerated their adaptive immunity. We find that degenerate adaptive immune genes and sexual body size dimorphism, both variably present in anglerfishes outside the ceratioid radiation, likely promoted their transition into the bathypelagic zone. These results show how traits from separate physiological, morphological, and reproductive systems can interact synergistically to drive major transitions and subsequent diversification in novel environments.
Collapse
Affiliation(s)
- Chase D Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Katerina L Zapfe
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Spencer Lott
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
| | - Richard Harrington
- Department of Natural Resources, Marine Resources Division, 217 Ft. Johnson Road, Charleston, SC 29412-9110, USA
| | - Ava Ghezelayagh
- Department of Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA; Peabody Museum, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
| |
Collapse
|
150
|
Anoma S, Bhattarakosol P, Kowitdamrong E. Characteristics and evolution of hemagglutinin and neuraminidase genes of Influenza A(H3N2) viruses in Thailand during 2015 to 2018. PeerJ 2024; 12:e17523. [PMID: 38846750 PMCID: PMC11155671 DOI: 10.7717/peerj.17523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024] Open
Abstract
Background Influenza A(H3N2) virus evolves continuously. Its hemagglutinin (HA) and neuraminidase (NA) genes have high genetic variation due to the antigenic drift. This study aimed to investigate the characteristics and evolution of HA and NA genes of the influenza A(H3N2) virus in Thailand. Methods Influenza A positive respiratory samples from 2015 to 2018 were subtyped by multiplex real-time RT-PCR. Full-length HA and NA genes from the positive samples of influenza A(H3N2) were amplified and sequenced. Phylogenetic analysis with the maximum likelihood method was used to investigate the evolution of the virus compared with the WHO-recommended influenza vaccine strain. Homology modeling and N-glycosylation site prediction were also performed. Results Out of 443 samples, 147 (33.18%) were A(H1N1)pdm09 and 296 (66.82%) were A(H3N2). The A(H3N2) viruses circulating in 2015 were clade 3C.2a whereas sub-clade 3C.2a1 and 3C.2a2 dominated in 2016-2017 and 2018, respectively. Amino acid substitutions were found in all antigenic sites A, B, C, D, and E of HA but the majority of the substitutions were located at antigenic sites A and B. The S245N and N329S substitutions in the NA gene affect the N-glycosylation. None of the mutations associated with resistance to NA inhibitors were observed. Mean evolutionary rates of the HA and NA genes were 3.47 × 10 -3 and 2.98 × 10-3 substitutions per site per year. Conclusion The influenza A(H3N2) virus is very genetically diverse and is always evolving to evade host defenses. The HA and NA gene features including the evolutionary rate of the influenza A(H3N2) viruses that were circulating in Thailand between 2015 and 2018 are described. This information is useful for monitoring the genetic characteristics and evolution in HA and NA genes of influenza A(H3N2) virus in Thailand which is crucial for predicting the influenza vaccine strains resulting in high vaccine effectiveness.
Collapse
Affiliation(s)
- Sasiprapa Anoma
- Interdisciplinary Program in Medical Microbiology, Graduated School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Parvapan Bhattarakosol
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Division of Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ekasit Kowitdamrong
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Division of Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|