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León F, Pizarro E, Noll D, Pertierra LR, Parker P, Espinaze MPA, Luna-Jorquera G, Simeone A, Frere E, Dantas GPM, Cristofari R, Cornejo OE, Bowie RCK, Vianna JA. Comparative Genomics Supports Ecologically Induced Selection as a Putative Driver of Banded Penguin Diversification. Mol Biol Evol 2024; 41:msae166. [PMID: 39150953 PMCID: PMC11371425 DOI: 10.1093/molbev/msae166] [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: 11/21/2023] [Revised: 06/27/2024] [Accepted: 07/10/2024] [Indexed: 08/18/2024] Open
Abstract
The relative importance of genetic drift and local adaptation in facilitating speciation remains unclear. This is particularly true for seabirds, which can disperse over large geographic distances, providing opportunities for intermittent gene flow among distant colonies that span the temperature and salinity gradients of the oceans. Here, we delve into the genomic basis of adaptation and speciation of banded penguins, Galápagos (Spheniscus mendiculus), Humboldt (Spheniscus humboldti), Magellanic (Spheniscus magellanicus), and African penguins (Spheniscus demersus), by analyzing 114 genomes from the main 16 breeding colonies. We aim to identify the molecular mechanism and genomic adaptive traits that have facilitated their diversifications. Through positive selection and gene family expansion analyses, we identified candidate genes that may be related to reproductive isolation processes mediated by ecological thermal niche divergence. We recover signals of positive selection on key loci associated with spermatogenesis, especially during the recent peripatric divergence of the Galápagos penguin from the Humboldt penguin. High temperatures in tropical habitats may have favored selection on loci associated with spermatogenesis to maintain sperm viability, leading to reproductive isolation among young species. Our results suggest that genome-wide selection on loci associated with molecular pathways that underpin thermoregulation, osmoregulation, hypoxia, and social behavior appears to have been crucial in local adaptation of banded penguins. Overall, these results contribute to our understanding of how the complexity of biotic, but especially abiotic, factors, along with the high dispersal capabilities of these marine species, may promote both neutral and adaptive lineage divergence even in the presence of gene flow.
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Affiliation(s)
- Fabiola León
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Eduardo Pizarro
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Daly Noll
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Luis R Pertierra
- Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Patricia Parker
- Department of Biology, University of Missouri St. Louis and Saint Louis Zoo, St. Louis, MO 63121-4400, USA
| | - Marcela P A Espinaze
- Department of Conservation Ecology and Entomology, Faculty of AgriScience, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Guillermo Luna-Jorquera
- Center for Ecology and Sustainable Management of Oceanic Islands (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Universidad Católica del Norte, Coquimbo, Chile
| | - Alejandro Simeone
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Departamento de Ecología y Biodiversidad, Santiago, Chile
| | - Esteban Frere
- Centro de Investigaciones de Puerto Deseado, Universidad Nacional de la Patagonia Austral, Puerto Deseado, Argentina
| | - Gisele P M Dantas
- PPG Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG 30535-901, Brazil
| | - Robin Cristofari
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720-3160, USA
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
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Roca I, Espinoza K, Irigoin-Lovera C, Piquet M, Palomino-Kobayashi LA, Castillo AK, Gonzales-DelCarpio DD, Viñes J, Muñoz L, Ymaña B, Oporto R, Zavalaga C, Pons MJ, Ruiz J. Clonal dissemination of Acinetobacter radioresistens among Humboldt penguins (Spheniscus humboldti) inhabiting a barren northern Peruvian island. Eur J Microbiol Immunol (Bp) 2024; 14:210-218. [PMID: 38483509 PMCID: PMC11097781 DOI: 10.1556/1886.2023.00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/27/2024] [Indexed: 05/16/2024] Open
Abstract
Acinetobacter spp. are often isolated from natural sources, but knowledge about their presence in wild animals is fragmented and uncomplete. The present study aimed to characterize a series of Acinetobacter radioresistens isolated from Humboldt penguins (Spheniscus humboldti). Fifteen Humboldt penguins from an inhabited northern Peruvian island were sampled. Microorganisms were identified by MALDI-TOF MS. Antibiotic susceptibility to 12 antimicrobial agents was established, and clonal relationships were determined. A representative isolate was selected for whole genome sequencing (WGS). A. radioresistens were isolated from the feces of 12 (80%) Humboldt penguins, being susceptible to all the antimicrobial agents tested, except eight cefotaxime-intermediate isolates. All A. radioresistens were clonally related. WGS showed that the isolate belonged to ST1972, the presence of two chromosomal encoded carbapenemases (blaOXA-23 and a putative subclass B3 metallo-β-lactamase), and a series of point mutations in antibiotic-resistance related chromosomal genes, which were considered as polymorphisms. In addition, a few virulence factors, including a capsule-encoding operon, superoxide dismutases, catalases, phospholipases and a siderophore receptor were identified. The present results suggest that A. radioresistens may be a common member of the gut microbiota of Humboldt penguins, but further studies in other geographical areas are needed to establish this finding.
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Affiliation(s)
- Ignasi Roca
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Kathya Espinoza
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos – “One Health”, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación en Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Cinthia Irigoin-Lovera
- Unidad de Investigación de Ecosistemas Marinos-Grupo Aves Marinas, Universidad Científica del Sur, Lima, Peru
| | - Maria Piquet
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Luciano A. Palomino-Kobayashi
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos – “One Health”, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación en Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Angie K. Castillo
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos – “One Health”, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación en Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Diego D. Gonzales-DelCarpio
- Unidad de Investigación de Ecosistemas Marinos-Grupo Aves Marinas, Universidad Científica del Sur, Lima, Peru
| | - Joaquim Viñes
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- Servei Veterinari de Genètica Molecular (SVGM), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Muñoz
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Barbara Ymaña
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos – “One Health”, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación en Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Rosario Oporto
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos – “One Health”, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación en Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Carlos Zavalaga
- Unidad de Investigación de Ecosistemas Marinos-Grupo Aves Marinas, Universidad Científica del Sur, Lima, Peru
| | - Maria J. Pons
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos – “One Health”, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación en Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Joaquim Ruiz
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos – “One Health”, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación en Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
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Strong Philopatry, Isolation by Distance, and Local Habitat Have Promoted Genetic Structure in Heermann’s Gull. DIVERSITY 2022. [DOI: 10.3390/d14020108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Philopatry can promote genetic differentiation among populations but remains undescribed in many seabirds. Hence, we explored such associations in Heermann’s Gull. Philopatry was observed monitoring 998 gulls in Rasa Island, while genetic differences were examined in the Cardonosa, Rasa, and Isabel islands using the cytochrome b of 296 gulls. Adults returned repeatedly to its natal valley or to a very close distance from it under different modelled hypotheses. Likewise, the interaction between sex and distance indicated significant male-biased philopatry. Besides, low to high genetic differentiation was observed between the Rasa and Cardonosa islands (ΦST = 0–0.22) (both in the Midriff Islands Region), but higher genetic differentiation against Isabel Island (ΦST > 0.25) (in the Mexican Province region). Consistently, genetic structure among regions was observed using different approaches (AMOVA: ΦCT = 0.49; SAMOVA: FCT = 0.49; and BAPS: K = 2). Similarly, a pattern of isolation by distance (rM = 0.82, p = 0.03), agrees with lower estimates of scaled migration rates between regions than among islands of the same region. Overall, it is suggested that the genetic structure found in Heermann’s Gull has been promoted by physical and behavioral barriers.
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