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Danmaigoro A, Muhammad MA, Abubakar K, Magiri RB, Bakare AG, Iji PA. Morphological and physiological features in small ruminants: an adaptation strategy for survival under changing climatic conditions. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:1497-1505. [PMID: 38700715 DOI: 10.1007/s00484-024-02694-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/04/2024] [Accepted: 04/27/2024] [Indexed: 07/28/2024]
Abstract
Climate change due to natural human activity is a significant global phenomenon affecting the sustainability of most countries' livestock industries. Climate change factors such as ambient temperature, relative humidity, direct and indirect sun radiation, and wind have significant consequences on feed, water, pasture availability, and the re-emergence of diseases in livestock. All these variables have a considerable impact on livestock production and welfare. However, animals' ability to respond and adapt to changes in climate differs within species and breeds. Comparatively, small ruminants are more adaptive to the adverse effects of climate change than large ruminants in terms of reproduction performance, survival, production yield, and resistance to re-emerging diseases. This is mainly due to their morphological features against harsh climate effects. Tropical breeds are more adaptive to the adverse effects of climate change than small temperate ruminants. However, the difference in morphological characteristics towards adaptation to the impact of climate change will guide the development of suitable policies on the selection of breeding stock suitable for different regions in the world. The choice of breeds based on morphological features and traits is an essential strategy in mitigating and minimizing the effects of climate change on small ruminants' production and welfare. This review highlights the adaptive morphological features within and among breeds of small ruminants toward adaptation to climate change.
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Affiliation(s)
- Abubakar Danmaigoro
- Department of Veterinary Sciences, College of Agriculture, Fisheries and Forestry, Fiji National University, Koronivia Campus, P. O. Box 1544, Nausori, Suva, Fiji.
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Kelantan Malaysia, Pengkalan Chepa 16100 Kota Bharu, Kelantan, Malaysia.
| | - Mahmud Abdullahi Muhammad
- Department of Animal Health and Production Technology, Niger State College of Agriculture, Mokwa, Niger State, Nigeria
| | - Kabeer Abubakar
- Institut de Neurosciences des Systemes, Aix-Marselille Uneversite, 27 Bd Jean Moulin, Marseille, 13005, France
| | - Royford Bundi Magiri
- Department of Veterinary Sciences, College of Agriculture, Fisheries and Forestry, Fiji National University, Koronivia Campus, P. O. Box 1544, Nausori, Suva, Fiji
| | - Archibold Garikayi Bakare
- Department of Veterinary Sciences, College of Agriculture, Fisheries and Forestry, Fiji National University, Koronivia Campus, P. O. Box 1544, Nausori, Suva, Fiji
| | - Paul Ade Iji
- Department of Veterinary Sciences, College of Agriculture, Fisheries and Forestry, Fiji National University, Koronivia Campus, P. O. Box 1544, Nausori, Suva, Fiji
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Weng YM, Kavanaugh DH, Schoville SD. Evidence for Admixture and Rapid Evolution During Glacial Climate Change in an Alpine Specialist. Mol Biol Evol 2024; 41:msae130. [PMID: 38935588 PMCID: PMC11247348 DOI: 10.1093/molbev/msae130] [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: 12/05/2023] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype-environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
- Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan
| | - David H Kavanaugh
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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Li J, Jiang H, Xie M, Song C, He C, Bian H, Sheng L. Functional characteristics and habitat suitability of threatened birds in northeastern China. Ecol Evol 2024; 14:e11550. [PMID: 38932959 PMCID: PMC11199129 DOI: 10.1002/ece3.11550] [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: 11/16/2023] [Revised: 04/08/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Northeast China, rich in natural resources and diverse biodiversity, boasts a unique habitat for threatened bird species due to its remote location and perennial cold climate. An analysis assessed the adaptability of these species using data on their geographic distribution and functional traits collected through database queries. The results revealed that threatened bird species share similar functional traits and a stronger phylogenetic signal (Blomberg mean K = 0.39) compared to common species. The Biomod2 model analyzed potentially suitable ranges and environmental drivers under current and future climate scenarios, showing a pattern of larger suitable areas in southern regions and smaller suitable areas in the north. The most critically threatened species faced greater geographical constraints (0.989), with mean annual temperature being a key influence. Altitude and water system distribution were also key factors impacting the distribution of other threatened bird species. Simulated projections under different climate scenarios (RCP 45 and 85) indicated varying degrees of expansion in the suitable range for these species. This research sheds light on the functional traits and distribution of threatened bird species in Northeast China, providing a scientific foundation for future conservation and management efforts.
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Affiliation(s)
- Jianwei Li
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of EnvironmentNortheast Normal UniversityChangchunChina
| | - Haibo Jiang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of EnvironmentNortheast Normal UniversityChangchunChina
| | - Mingjun Xie
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of EnvironmentNortheast Normal UniversityChangchunChina
| | - Chuantao Song
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of EnvironmentNortheast Normal UniversityChangchunChina
| | - Chunguang He
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of EnvironmentNortheast Normal UniversityChangchunChina
| | - Hongfeng Bian
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of EnvironmentNortheast Normal UniversityChangchunChina
| | - Lianxi Sheng
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of EnvironmentNortheast Normal UniversityChangchunChina
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Williamson JL, Gyllenhaal EF, Bauernfeind SM, Bautista E, Baumann MJ, Gadek CR, Marra PP, Ricote N, Valqui T, Bozinovic F, Singh ND, Witt CC. Extreme elevational migration spurred cryptic speciation in giant hummingbirds. Proc Natl Acad Sci U S A 2024; 121:e2313599121. [PMID: 38739790 PMCID: PMC11126955 DOI: 10.1073/pnas.2313599121] [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: 08/11/2023] [Accepted: 03/19/2024] [Indexed: 05/16/2024] Open
Abstract
The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.
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Affiliation(s)
- Jessie L. Williamson
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM87131
- Department of Biology, University of New Mexico, Albuquerque, NM87131
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY14850
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY14850
| | - Ethan F. Gyllenhaal
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM87131
- Department of Biology, University of New Mexico, Albuquerque, NM87131
| | | | - Emil Bautista
- Centro de Ornitología y Biodiversidad, Lima15064, Peru
| | - Matthew J. Baumann
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM87131
| | - Chauncey R. Gadek
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM87131
- Department of Biology, University of New Mexico, Albuquerque, NM87131
- Environmental Stewardship, Los Alamos National Laboratory, Los Alamos, NM87545
| | - Peter P. Marra
- The Earth Commons Institute, Department of Biology, McCourt School of Public Policy, Georgetown University, Washington, DC20057
| | - Natalia Ricote
- Facultad de Artes Liberales, Departamento de Ciencias, Universidad Adolfo Ibáñez, Santiago7941169, Chile
| | - Thomas Valqui
- Centro de Ornitología y Biodiversidad, Lima15064, Peru
- Facultad de Ciencias Forestales, Universidad Nacional Agraria La Molina, Lima15024, Peru
| | - Francisco Bozinovic
- Departamento de Ecología, Center of Applied Ecology and Sustainability, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago3542000, Chile
| | - Nadia D. Singh
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Christopher C. Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM87131
- Department of Biology, University of New Mexico, Albuquerque, NM87131
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Li H, Peng Y, Wu C, Li Z, Zou L, Mao K, Ping J, Buck R, Monahan S, Sethuraman A, Xiao Y. Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens. INSECT SCIENCE 2024. [PMID: 38204333 DOI: 10.1111/1744-7917.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan-Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine-rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest.
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Affiliation(s)
- Hongran Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Zhimin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Luming Zou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Kaikai Mao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Junfen Ping
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Ryan Buck
- Department of Biology, San Diego State University, CA, USA
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Scott Monahan
- Department of Biology, San Diego State University, CA, USA
| | | | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
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6
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Zhao Y, Su C, He B, Nie R, Wang Y, Ma J, Song J, Yang Q, Hao J. Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome. Nat Commun 2023; 14:8190. [PMID: 38081828 PMCID: PMC10713551 DOI: 10.1038/s41467-023-44023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.
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Affiliation(s)
- Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Ruie Nie
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Junye Ma
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jingyu Song
- College of Animal Science, Shandong Agricultural University, Taian, 271000, China
| | - Qun Yang
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China.
- Nanjing College, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
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Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. J Evol Biol 2023; 36:1226-1241. [PMID: 37485603 DOI: 10.1111/jeb.14200] [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: 12/14/2022] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ13 C, δ15 N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed amarked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Mercè Palacios
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Oscar Frías
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Keith Hobson
- Biology Department, Western University, London, Ontario, Canada
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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Spies I, Tarpey C, Kristiansen T, Fisher M, Rohan S, Hauser L. Genomic differentiation in Pacific cod using
P
ool‐
S
eq. Evol Appl 2022; 15:1907-1924. [PMID: 36426128 PMCID: PMC9679252 DOI: 10.1111/eva.13488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/05/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Abstract
Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod (Gadus macrocephalus) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence (FST) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence (dXY) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence (dXY) but roughly double the relative divergence (FST) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species.
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Affiliation(s)
- Ingrid Spies
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | | | - Mary Fisher
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Sean Rohan
- Resource Assessment and Conservation Engineering Division Alaska Fisheries Science Center Seattle Washington USA
| | - Lorenz Hauser
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA
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Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota. Appl Microbiol Biotechnol 2022; 106:6701-6711. [PMID: 36097173 DOI: 10.1007/s00253-022-12171-y] [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: 06/29/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/02/2022]
Abstract
Highland birds evolve multiple adaptive abilities to cope with the harsh environments; however, how they adapt to the high-altitude habitats via the gut microbiota remains understudied. Here we integrated evidences from comparative analysis of gut microbiota to explore the adaptive mechanism of black-necked crane, a typical highland bird in the Qinghai-Tibet Plateau. Firstly, the gut microbiota diversity and function was compared among seven crane species (one high-altitude species and six low-altitude species), and then among three populations of contrasting altitudes for the black-necked crane. Microbiota community diversity in black-necked crane was significantly lower than its low-altitude relatives, but higher microbiota functional diversity was observed in black-necked crane, suggesting that unique bacteria are developed and acquired due to the selection pressure of high-altitude environments. The functional microbial genes differed significantly between the low- and high-altitude black-necked cranes, indicating that altitude significantly impacted microbial communities' composition and structure. Adaptive changes in microbiota diversity and function are observed in response to high-altitude environments. These findings provide us a new insight into the adaptation mechanism to the high-altitude environment for birds via the gut microbiota. KEY POINTS: • The diversity and function of gut microbiota differed significantly between the low- and high-altitude crane species. • Black-necked crane adapts to the high-altitude environment via specific gut microbiota. • Altitude significantly impacted microbial communities' composition and structure.
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10
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Chen Y, Tan S, Fu J. Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans). J Mol Evol 2022; 90:389-399. [PMID: 36029325 DOI: 10.1007/s00239-022-10070-4] [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: 04/02/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
High-elevation adaptation provides an excellent system for examining adaptive evolution, and adaptive variations may manifest at gene expression or any other phenotypic levels. We examined gene expression profiles of Asiatic toads (Bufo gargarizans) along an elevational gradient from both wild and common-garden acclimated populations. Asiatic toads originated from high altitudes have distinctive gene expression patterns. We identified 18 fixed differentially expressed genes (DEGs), which are different in both wild and acclimated samples, and 1217 plastic DEGs, which are different among wild samples. The expression levels of most genes were linearly correlated with altitude gradient and down-regulated in high-altitude populations. Expression variations of several genes associated with metabolic process are fixed, and we also identified a co-expression module that is significantly different between acclimated populations and has functions related to DNA repair. The differential expression of the vast majority genes, however, are due to phenotypic plasticity, revealing the highly plastic nature of gene expression variations. Expression modification of some specific genes related to metabolism and response to UV radiation play crucial role in adaptation to high altitude for Asiatic toads. Common-garden experiments are essential for evaluating adaptive evolution of natural populations.
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Affiliation(s)
- Ying Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
- The University of Chinese Academy of Science, Beijing, China.
| | - Song Tan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The University of Chinese Academy of Science, Beijing, China
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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11
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Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation. iScience 2022; 25:103899. [PMID: 35243257 PMCID: PMC8873613 DOI: 10.1016/j.isci.2022.103899] [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: 10/11/2021] [Revised: 12/12/2021] [Accepted: 02/07/2022] [Indexed: 11/20/2022] Open
Abstract
The phenotypic plasticity in responses to short-term stress can provide clues for understanding the adaptive fixation mechanism of genetic variation during long-term exposure to extreme environments. However, few studies have compared short-term stress responses with long-term evolutionary patterns; in particular, no interactions between the two processes have been evaluated in high-altitude environment. We performed RNA sequencing in embryo fibroblasts derived from great tits and mice to explore transcriptional responses after exposure to simulated high-altitude environmental stresses. Transcriptional changes of genes associated with metabolic pathways were identified in both bird and mice cells after short-term stress responses. Genomic comparisons among long-term highland tits and mammals and their lowland relatives revealed similar pathways (e.g., metabolic pathways) with that initiated under short-term stress transcriptional responses in vitro. These findings highlight the indicative roles of short-term stress in the long-term adaptation, and adopt common paths to molecular adaptation in mouse and bird cells. Short-term stress and long-term adaptations share the common metabolic pathways Phenotypic plasticity can promote adaptive evolution Adopt common paths to molecular adaptation in mouse and bird cells
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