Exploring potentialities of avian genomic research in Nepalese Himalayas

Prashant Ghimire; Nishma Dahal; Ajit K. Karna; Surendra Karki; Sangeet Lamichhaney

doi:10.1186/s40657-021-00290-5

Volume 12 Issue 1

Jul. 2021

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Avian Research > 2021 > 12(1): 57. > DOI: 10.1186/s40657-021-00290-5

Prashant Ghimire, Nishma Dahal, Ajit K. Karna, Surendra Karki, Sangeet Lamichhaney. 2021: Exploring potentialities of avian genomic research in Nepalese Himalayas. Avian Research, 12(1): 57. DOI: 10.1186/s40657-021-00290-5

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Exploring potentialities of avian genomic research in Nepalese Himalayas

1.
Department of Biological Sciences, Kent State University, Kent, OH, USA
2.
Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP, India
3.
Center for Health and Disease Studies-Nepal, Kathmandu, Nepal
4.
Institute of Agriculture and Animal Sciences, Tribhuvan University, Kathmandu, Nepal
5.
Emergency Centre for Transboundary Animal Diseases, Food & Agricultural Organization of the UN, Kathmandu, Nepal
6.
School of Biomedical Sciences, Kent State University, Kent, OH, USA

Funds:

the Department of Biological Sciences

Govt. of India for DST INSPIRE DST/INSPIRE/04/2018/001587

More Information

Corresponding author:
Sangeet Lamichhaney, slamichh@kent.edu
Received Date: 03 May 2021
Accepted Date: 18 Oct 2021
Available Online: 24 Apr 2022
Publish Date: 29 Oct 2021

Graphical Abstract

Abstract

Abstract

Nepal, a small landlocked country in South Asia, holds about 800 km of Himalayan Mountain range including the Earth's highest mountain. Within such a mountain range in the north and plain lowlands in the south, Nepal provides a habitat for about 9% of global avian fauna. However, this diversity is underrated because of the lack of enough studies, especially using molecular tools to quantify and understand the distribution patterns of diversity. In this study, we reviewed the studies in the last two decades (2000‒2019) that used molecular methods to study the biodiversity in Nepal to examine the ongoing research trend and focus. Although Nepalese Himalaya has many opportunities for cutting-edge molecular research, our results indicated that the rate of genetic/genomic studies is much slower compared to the regional trends. We found that genetic research in Nepal heavily relies on resources from international institutes and that too is mostly limited to research on species monitoring, distribution, and taxonomic validations. Local infrastructures to carry out cutting-edge genomic research in Nepal are still in their infancy and there is a strong need for support from national/international scientists, universities, and governmental agencies to expand such genomic infrastructures in Nepal. We particularly highlight avian fauna as a potential future study system in this region that can be an excellent resource to explore key biological questions such as understanding eco-physiology and molecular basis of organismal persistence to changing environment, evolutionary processes underlying divergence and speciation, or mechanisms of endemism and restrictive distribution of species.
- Avian fauna,
- Evolutionary Process,
- Genomics,
- Himalayas,
- Nepal

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Correction to: Avian Res (2021) 12:19

https://doi.org/10.1186/s40657-021-00254-9

Following publication of the original article (Hou et al. 2021), the authors identified an error in Fig. 1. The correct figure is given below.

Figure 1. The experiment design in this study

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The original article (Hou et al. 2021) has been updated.

References (60)

References

Abbott RJ, Brennan AC. Altitudinal gradients, plant hybrid zones and evolutionary novelty. Philos Trans R Soc Lond B Biol Sci. 2014;369: 20130346.

Amiot C, Lorvelec O, Mandon-Dalger I, Sardella A, Lequilliec P, Clergeau P. Rapid morphological divergence of introduced Red-whiskered Bulbuls Pycnonotus jocosus in contrasting environments. Ibis. 2007;149: 482–9.

Arnaiz-Villena A, Guillén J, Ruiz-del-Valle V, Lowy E, Zamora J, Varela P, et al. Phylogeography of crossbills, bullfinches, grosbeaks, and rosefinches. Cell Mol Life Sci. 2001;58: 1159–66.

Baral HS, Inskipp C. Birds of Nepal: their status and conservation especially with regards to watershed perspectives. In: Regmi GR, Huettmann F, editors. Hindu Kush—Himalaya watersheds downhill: landscape ecology and conservation perspective. Cham: Springer; 2020. p. 435–58.

Baral H, Regmi U, Poudyal L, Acharya R. Status and Conservation of Birds in Nepal. Biodiversity conservation in Nepal: a success story; 2012. p. 69–90.

Basnet D, Kandel P, Chettri N, Yang Y, Lodhi M, Htun N, et al. Biodiversity research trends and gaps from the confluence of three global biodiversity hotspots in the Far-Eastern Himalaya. Int J Ecol. 2019;2019: 1323419.

Bouverot P. Adaptation to altitude-hypoxia in vertebrates. Berlin: Springer-Verlag; 1985.

Brown JH. Why are there so many species in the tropics? J Biogeogr. 2014;41: 8–22.

Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, et al. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet. 2020;16: e1008274.

Chen Y, Li F, Zhang Q, Wang Q. Complete mitochondrial genome of the Himalayan Monal Lophophorus impejanus (Phasianidae), with phylogenetic implication. Conserv Genet Resour. 2018;10: 877–80.

Cibois A, Gelang M, Alström P, Pasquet E, Fjeldså J, Ericson PGP, et al. Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy. Zool Scr. 2018;47: 428–40.

Cocker PM, Inskipp C. A Himalayan ornithologist: the life and work of Brian Houghton Hodgson. Oxford: Oxford University Press; 1988.

Cui K, Li W, James JG, Peng C, Jin J, Yan C, et al. The first draft genome of Lophophorus: a step forward for Phasianidae genomic diversity and conservation. Genomics. 2019;111: 1209–15.

Dahal N, Lamichhaney S, Kumar S. Climate change impacts on Himalayan biodiversity: evidence-based perception and current approaches to evaluate threats under climate change. J Indian Inst Sci. 2021;101: 195–210.

DFSC. CITIES convention and related laws in Nepal. Babarmahal, Kathmandu: Department of Forest and Soil Conservation; 2019.

DNPWC. Vulture conservation action plan for Nepal (2015‒2019). Department of National Parks and Wildlife Conservation. Kathmandu: Ministry of Forests and Soil Conservation, Government of Nepal; 2015.

DNPWC. Bengal florican conservation action plan. Babarmahal: Department of National Parks and Wildlife Conservation; 2016.

DNPWC, BCN. Birds of Nepal: an official checklist. Kathmandu: Department of National Parks and Wildlife Conservation; 2018.

DNPWC, DFSC. Pheasant conservation action plan for Nepal (2019‒2023). Kathmandu: Department of National Parks and Wildlife Conservation and Department of Forests and Soil Conservation; 2018.

DNPWC, DFSC. Owl conservation action plan for Nepal 2020‒2029. Kathmandu, Nepal: Department of National Parks and Wildlife Conservation and Department of Forests and Soil Conservation; 2020.

Dong F, Hung CM, Li SH, Yang XJ. Potential Himalayan community turnover through the Late Pleistocene. Clim Change. 2021;164: 6.

Fleming RL Sr, Fleming RL Jr, Bangdel LS. Birds of Nepal. Flemings Sr and Jr.; 1976.

Gill FB, Slikas B, Sheldon FH. Phylogeny of Titmice (Paridae): Ⅱ. Species relationships based on sequences of the mitochondrial cytochrome-B gene. Auk. 2005;122: 121–43.

GON. National Parks and Wildlife Conservation Regulation (Fifth amendment). Government of Nepal; 2019.

Huang Z, Liu N, Xiao Y, Cheng Y, Mei W, Wen L, et al. Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control-region genes. Mol Phylogenet Evol. 2009;53: 378–83.

Inskipp C, Baral HS, Phuyal S, Bhatt TR, Khatiwada M, Inskipp T, et al. The status of Nepal's Birds: the national red list series. London: Zoological Society of London; 2016.

Ivy CM, Lague SL, York JM, Chua BA, Alza L, Cheek R, et al. Control of breathing and respiratory gas exchange in high-altitude ducks native to the Andes. J Exp Biol. 2019;222: jeb198622.

Johnsgard P. Review of the pheasants of the world. 1978. .

Kimball RT, Hosner PA, Braun EL. A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths. Mol Phylogenet Evol. 2021;158: 107091.

Laguë SL. High-altitude champions: birds that live and migrate at altitude. J Appl Physiol. 2017;123: 942–50.

Laguë SL, Ivy CM, York JM, Chua BA, Alza L, Cheek R, et al. Cardiovascular responses to progressive hypoxia in ducks native to high altitude in the Andes. J Exp Biol. 2020;223: jeb211250.

Laine VN, Gossmann TI, Schachtschneider KM, Garroway CJ, Madsen O, Verhoeven KJF, et al. Evolutionary signals of selection on cognition from the great tit genome and methylome. Nat Commun. 2016;7: 10474.

Lamichhaney S, Barrio MA, Rafati N, Sundström G, Rubin CJ, Gilbert ER, et al. Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. P Natl Acad Sci USA. 2012;109: 19345–50.

Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, et al. Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature. 2015;518: 371–5.

Lamichhaney S, Fan G, Widemo F, Gunnarsson U, Thalmann DS, Hoeppner MP, et al. Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nat Genet. 2016;48: 84–8.

Lamichhaney S, Han F, Webster MT, Andersson L, Grant BR, Grant PR. Rapid hybrid speciation in Darwin's finches. Science. 2018;359: 224–8.

Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, et al. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. Phil Trans R Soc B Biol Sci. 2019;374: 20180248.

Lamichhaney S, Han F, Webster MT, Grant BR, Grant PR, Andersson L. Female-biased gene flow between two species of Darwin's finches. Nat Ecol Evol. 2020;4: 979–86.

Mittermeier RA, Turner WR, Larsen F, Brooks TM, Gascon C. Global biodiversity conservation: the critical role of hotspots. In: Zachos F, Habel J, editors. Biodiversity hotspots. Heidelberg: Springer; 2011. p. 3–22.

Päckert M, Martens J, Sun Y-H, Veith M. The radiation of the Seicercus burkii complex and its congeners (Aves: Sylviidae): molecular genetics and bioacoustics. Org Divers Evol. 2004;4: 341–64.

Päckert M, Martens J, Sun Y-H. Phylogeny of long-tailed tits and allies is inferred from mitochondrial and nuclear markers (Aves: Passeriformes, Aegithalidae). Mol Phylogenet Evol. 2010;55: 952–67.

Päckert M, Martens J, Sun Y-H, Severinghaus LL, Nazarenko AA, Ting J, et al. Horizontal and elevational phylogeographic patterns of Himalayan and Southeast Asian forest passerines (Aves: Passeriformes). J Biogeogr. 2012;39: 556–73.

Päckert M, Martens J, Liang W, Hsu Y-C, Sun Y-H. Molecular genetic and bioacoustic differentiation of Pnoepyga Wren-babblers. J Ornithol. 2013;154: 329–37.

Päckert M, Sun Y-H, Fischer BS, Tietze DT, Martens J. A phylogeographic break and bioacoustic intraspecific differentiation in the Buff-barred Warbler (Phylloscopus pulcher) (Aves: Passeriformes, Phylloscopidae). Avian Res. 2014;5: 2.

Paudel PK, Bhattarai BP, Kindlmann P. An overview of the biodiversity in Nepal. In: Kindlmann P, editor. Himalayan biodiversity in the changing world. Dordrecht: Springer; 2011. p. 1–40.

Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature. 2015;526: 569–73.

Rana SK, Rawal RS, Dangwal B, Bhatt ID, Price TD. 200 years of research on Himalayan biodiversity: trends, gaps, and policy implications. Front Ecol Evol. 2021;8: 603422.

Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, et al. Convergent regulatory evolution and loss of flight in paleognathous birds. Science. 2019;364: 74–8.

Santure AW, Cauwer ID, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Mol Ecol. 2013;22: 3949–62.

Scott GR. Elevated performance: the unique physiology of birds that fly at high altitudes. J Exp Biol. 2011;214: 2455–62.

Sharma E, Chettri N, Tshe-ring K, Shrestha A, Jing F, Mool P, et al. Climate change impacts and vulnerability in the Eastern Himalayas. 2009. .

Shen Y-Y, Liang L, Sun Y-B, Yue B-S, Yang X-J, Murphy RW, et al. A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol. 2010;10: 132.

Shen Y-Y, Dai K, Cao X, Murphy RW, Shen X-J, Zhang Y-P. The updated phylogenies of the Phasianidae based on combined data of nuclear and mitochondrial DNA. PLoS ONE. 2014;9: e95786.

Srinivasan U, Tamma K, Ramakrishnan U. Past climate and species ecology drive nested species richness patterns along an east-west axis in the Himalaya. Global Ecol Biogeogr. 2014;23: 52–60.

Thapa K, Manandhar S, Bista M, Shakya J, Sah G, Dhakal M, et al. Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape. PLoS ONE. 2018;13: e0193495.

Tribsch A, Schönswetter P. Patterns of endemism and comparative phylogeography confirm palaeo-environmental evidence for Pleistocene refugia in the Eastern Alps. Taxon. 2003;52: 477–97.

Wang N, Hosner PA, Liang B, Braun EL, Kimball RT. Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data. Mol Phylogenet Evol. 2017;109: 217–25.

Witt KE, Huerta-Sánchez E. Convergent evolution in human and domesticate adaptation to high-altitude environments. Phil Trans R Soc B Biol Sci. 2019;374: 20180235.

Zhang ZW, Ding CQ, Ding P, Zheng GM. The current status and a conservation strategy for species of Galliformes in China. Biodivers Sci. 2003;11: 414–21.

Zou Y, Sang W, Hausmann A, Axmacher JC. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages. Sci Rep. 2016;6: 23045.

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Exploring potentialities of avian genomic research in Nepalese Himalayas