{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T09:47:54Z","timestamp":1782899274084,"version":"3.54.5"},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T00:00:00Z","timestamp":1782518400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Manipal Academy of Higher Education, Manipal"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Ecol Evo"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Asian hornbills are flagship species of the wet tropics that face significant threats from hunting, habitat loss, and fragmentation. Despite being conservation flagships, whole genome information is available for only two of the 32 Asian hornbill species. In this study, we provide the first de novo genome assemblies for four hornbill species (Bucerotidae) in Asia.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We used a combination of long-read and short-read sequencing data to assemble and annotate de novo hybrid genomes of four species of hornbills. We also assembled and compared mitochondrial genomes of these species. Using a comparative genomics approach, we performed orthology assignment and gene evolution analyses to identify unique gene families in Asian hornbills, gene families that showed significant expansion, their functions and structural variation. Furthermore, using the Pairwise Sequentially Markov Coalescent (PSMC) method, we reconstructed demographic histories of hornbill species to examine changes in their population trajectories in the past.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present hybrid genome assemblies for Great Hornbill (B. bicornis - GH), Rufous-necked Hornbill (A. nipalensis- RNH), Malabar Pied Hornbill (A. coronatus- MPH) and Wreathed Hornbill (R. undulatus- WH). The genome sizes of these hornbills range from 1.1 Gb to 1.3 Gb, with over 95.9% completeness and gene prediction BUSCO. We reported 10,525 orthogroups shared among four Asian hornbill species and identified significant expansion in gene families associated with structural keratin development in Asian hornbills compared to their ancestors. We also provide annotated mitogenomes for each of these species. Furthermore, we found that the WH, a more abundant, widely distributed, and migratory species, showed a higher Ne than the other three hornbill species. However, an overall decline in Ne for all species was recorded during the Pleistocene climatic fluctuations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We present the first-ever, high-quality reference genomes for the threatened hornbill species from Asia. Hornbills have shown significant expansion in genes involved in structural keratin development. Our results indicate that Pleistocene climatic fluctuations have led to dramatic population declines in all four species. We believe that this study provides robust genomic resources to support future comparative and conservation genomics efforts for hornbills.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12862-026-02547-3","type":"journal-article","created":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T05:58:19Z","timestamp":1782712699000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["De novo genome assemblies of threatened Asian hornbills (Bucerotidae) reveal declining population trajectories during the late Pleistocene"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5153-6719","authenticated-orcid":false,"given":"Pooja Yashwant","family":"Pawar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gopi","family":"Krishnan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohit","family":"Naniwadekar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jahnavi","family":"Joshi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,27]]},"reference":[{"key":"2547_CR1","volume-title":"Hornbills of the world. A photographic Guide","author":"P Poonswad","year":"2013","unstructured":"Poonswad P, Kemp A, Strange M. Hornbills of the world. A photographic Guide. Draco Publishing and Distribution Pte Limited; 2013."},{"key":"2547_CR2","volume-title":"The Ecology and conservation of Asian hornbills: farmers of the forest","author":"MF Kinnaird","year":"2007","unstructured":"Kinnaird MF, O\u2019Brien TG. The Ecology and conservation of Asian hornbills: farmers of the forest. University of Chicago Press; 2007."},{"key":"2547_CR3","doi-asserted-by":"publisher","unstructured":"Naniwadekar R, Shukla U, Isvaran K, Datta A. Reduced hornbill abundance associated with low seed arrival and altered recruitment in a hunted and logged tropical forest. PLoS ONE. 2015;10(3):e0120062. https:\/\/doi.org\/10.1371\/journal.pone.0120062.","DOI":"10.1371\/journal.pone.0120062"},{"key":"2547_CR4","first-page":"20","volume":"4","author":"CR Shepherd","year":"2023","unstructured":"Shepherd CR, Shepherd L, Rathore D, Mendiratta U. Recent seizures of hornbills trafficked to India. Hornbill Nat Hist Conserv. 2023;4:20\u201324.","journal-title":"Hornbill Nat Hist Conserv"},{"issue":"4","key":"2547_CR5","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1046\/j.1365-3008.1998.d01-58.x","volume":"32","author":"A Datta","year":"1998","unstructured":"Datta A. Hornbill abundance in unlogged forest, selectively logged forest and a forest plantation in Arunachal Pradesh, India. Oryx. 1998;32(4):285\u201394. https:\/\/doi.org\/10.1046\/j.1365-3008.1998.d01-58.x.","journal-title":"Oryx"},{"key":"2547_CR6","doi-asserted-by":"publisher","unstructured":"Sitompul AF, Kinnaird MF, O\u2019Brien TG. Size matters: the effects of forest fragmentation and resource availability on the endemic Sumba hornbill Aceros everetti. Bird Conserv Int. 2004;14(S1):S23\u201337. https:\/\/doi.org\/10.1017\/S0959270905000201.","DOI":"10.1017\/S0959270905000201"},{"issue":"2","key":"2547_CR7","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1111\/ibi.12895","volume":"163","author":"PY Pawar","year":"2021","unstructured":"Pawar PY, Mudappa D, Raman TRS. Hornbill abundance and breeding incidence in relation to habitat modification and fig fruit availability. Ibis (Lond 1859). 2021;163(2):473\u201385. https:\/\/doi.org\/10.1111\/ibi.12895.","journal-title":"Ibis (Lond 1859)"},{"key":"2547_CR8","unstructured":"Dharapuram B, Pawar P, Joshi J, Naniwadekar R. Low mitochondrial genetic diversity in the Narcondam hornbill (Rhyticeros narcondami), an island endemic frugivore of ecological importance. Report Submitted To Br Ornithologists\u2019 Union. 2023."},{"issue":"2","key":"2547_CR9","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1016\/j.ympev.2013.02.012","volume":"67","author":"JCT Gonzalez","year":"2013","unstructured":"Gonzalez JCT, Sheldon BC, Collar NJ, Tobias JA. A comprehensive molecular phylogeny for the hornbills (Aves: Bucerotidae). Mol Phylogenet Evol. 2013;67(2):468\u201383. https:\/\/doi.org\/10.1016\/j.ympev.2013.02.012.","journal-title":"Mol Phylogenet Evol"},{"issue":"1","key":"2547_CR10","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1186\/1471-2148-12-203","volume":"12","author":"S Sammler","year":"2012","unstructured":"Sammler S, Ketmaier V, Havenstein K, Krause U, Curio E, Tiedemann R. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss. BMC Evol Biol. 2012;12(1):203. https:\/\/doi.org\/10.1186\/1471-2148-12-203.","journal-title":"BMC Evol Biol"},{"key":"2547_CR11","doi-asserted-by":"publisher","unstructured":"Jansamut P, Gale GA, Sukmak M, Wajjwalku W, Punkong C, Kaolim N, et al. Mitogenome-based genetic management of captive Great hornbill in Thailand: implications for reintroduction. Global Ecol Conserv. 2024;51:e02932. https:\/\/doi.org\/10.1016\/j.gecco.2024.e02932.","DOI":"10.1016\/j.gecco.2024.e02932"},{"issue":"10","key":"2547_CR12","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1016\/j.cub.2015.03.047","volume":"25","author":"K Nadachowska-Brzyska","year":"2015","unstructured":"Nadachowska-Brzyska K, Li C, Smeds L, Zhang G, Ellegren H. Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences. Curr Biol. 2015;25(10):1375\u201380. https:\/\/doi.org\/10.1016\/j.cub.2015.03.047.","journal-title":"Curr Biol"},{"issue":"1","key":"2547_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-12-35","volume":"12","author":"S Sammler","year":"2011","unstructured":"Sammler S, Bleidorn C, Tiedemann R. Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination. BMC Genomics. 2011;12(1):1\u201310. https:\/\/doi.org\/10.1186\/1471-2164-12-35.","journal-title":"BMC Genomics"},{"issue":"3","key":"2547_CR14","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1007\/s12686-017-0803-4","volume":"10","author":"Y Chen","year":"2018","unstructured":"Chen Y, Li C, Yan H, Xiao H, Chen S. The complete mitochondrial genome sequence of Buceros bicornis (bucerotiformes: bucerotidae). Conserv Genet Resour. 2018;10(3):287\u201390. https:\/\/doi.org\/10.1007\/s12686-017-0803-4.","journal-title":"Conserv Genet Resour"},{"issue":"1","key":"2547_CR15","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/s12686-017-0957-0","volume":"11","author":"Y Chen","year":"2019","unstructured":"Chen Y, Yan H, Sun J, Li C, Xiao H, Chen S. Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Rhyticeros undulatus (bucerotiformes: bucerotidae). Conserv Genet Resour. 2019;11(1):27\u201330. https:\/\/doi.org\/10.1007\/s12686-017-0957-0.","journal-title":"Conserv Genet Resour"},{"issue":"4","key":"2547_CR16","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1017\/S0266467418000202","volume":"34","author":"RJ Morley","year":"2018","unstructured":"Morley RJ. Assembly and division of the South and South-east Asian flora in relation to tectonics and climate change. J Trop Ecol. 2018;34(4):209\u201334. https:\/\/doi.org\/10.1017\/S0266467418000202.","journal-title":"J Trop Ecol"},{"key":"2547_CR17","doi-asserted-by":"publisher","unstructured":"Hamilton R, Amano N, Bradshaw CJA, Saltr\u00e9 F, Patalano R, Penny D, et al. Forest mosaics, not savanna corridors, dominated in Southeast Asia during the last glacial maximum. Proc Natl Acad Sci USA. 2024;121(1):e2311280120. https:\/\/doi.org\/10.1073\/pnas.2311280120.","DOI":"10.1073\/pnas.2311280120"},{"issue":"1","key":"2547_CR18","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/s41597-025-04412-2","volume":"12","author":"J Patel","year":"2025","unstructured":"Patel J, Botes A, Mollett J, De Maayer P. Whole genome sequencing, assembly and annotation of the Southern Ground hornbill \u2013 Bucorvus leadbeateri. Sci DataSci Data. 2025;12(1):58. https:\/\/doi.org\/10.1038\/s41597-025-04412-2.","journal-title":"Sci DataSci Data"},{"key":"2547_CR19","doi-asserted-by":"publisher","unstructured":"Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. Imeta. 2023;2(2):e107. https:\/\/doi.org\/10.1002\/imt2.107.","DOI":"10.1002\/imt2.107"},{"issue":"5","key":"2547_CR20","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722\u201336. https:\/\/doi.org\/10.1101\/gr.215087.116.","journal-title":"Genome Res"},{"issue":"9","key":"2547_CR21","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1038\/s41587-022-01261-x","volume":"40","author":"H Cheng","year":"2022","unstructured":"Cheng H, Jarvis ED, Fedrigo O, Koepfli KP, Urban L, Gemmell NJ, et al. Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol. 2022;40(9):1332\u201335. https:\/\/doi.org\/10.1038\/s41587-022-01261-x.","journal-title":"Nat Biotechnol"},{"key":"2547_CR22","doi-asserted-by":"publisher","unstructured":"Zimin AV, Salzberg SL. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS Comput Biol. 2020;16(6):e1007981. https:\/\/doi.org\/10.1371\/journal.pcbi.1007981.","DOI":"10.1371\/journal.pcbi.1007981"},{"issue":"10","key":"2547_CR23","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","volume":"38","author":"M Manni","year":"2021","unstructured":"Manni M, Berkeley MR, Seppey M, Sim\u00e3o FA, Zdobnov EM. BUSCO Update: novel and Streamlined Workflows along with broader and deeper phylogenetic coverage for scoring of Eukaryotic, Prokaryotic, and Viral genomes. Mol Biol Evol. 2021;38(10):4647\u201354. https:\/\/doi.org\/10.1093\/molbev\/msab199.","journal-title":"Mol Biol Evol"},{"issue":"4","key":"2547_CR24","doi-asserted-by":"publisher","first-page":"1361","DOI":"10.1534\/g3.119.400908","volume":"10","author":"R Challis","year":"2020","unstructured":"Challis R, Richards E, Rajan J, Cochrane G, Blaxter BM. BlobToolKit \u2013 interactive quality assessment of genome assemblies. G3 Genes|Genomes|Genet. 2020;10(4):1361\u201374. https:\/\/doi.org\/10.1534\/g3.119.400908.","journal-title":"G3 Genes|Genomes|Genet"},{"issue":"1","key":"2547_CR25","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","volume":"21","author":"A Rhie","year":"2020","unstructured":"Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21(1):245. https:\/\/doi.org\/10.1186\/s13059-020-02134-9.","journal-title":"Genome Biol"},{"key":"2547_CR26","volume-title":"RepeatMasker 4.0","author":"A Smit","year":"2013","unstructured":"Smit A, Hubley R, Green P. RepeatMasker 4.0. Seattle, WA: Institute for Systems Biology; 2013."},{"issue":"1","key":"2547_CR27","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/s13100-020-00230-y","volume":"12","author":"J Storer","year":"2021","unstructured":"Storer J, Hubley R, Rosen J, Wheeler TJ, Smit AF. The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob DNA. 2021;12(1):2. https:\/\/doi.org\/10.1186\/s13100-020-00230-y.","journal-title":"Mob DNA"},{"issue":"1","key":"2547_CR28","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1186\/s12859-023-05449-z","volume":"24","author":"T Br\u016fna","year":"2023","unstructured":"Br\u016fna T, Li H, Guhlin J, Honsel D, Herbold S, Stanke M, et al. Galba: genome annotation with miniprot and AUGUSTUS. BMC Bioinf. 2023;24(1):327. https:\/\/doi.org\/10.1186\/s12859-023-05449-z.","journal-title":"BMC Bioinf"},{"issue":"18","key":"2547_CR29","doi-asserted-by":"publisher","first-page":"2866","DOI":"10.1093\/bioinformatics\/btab219","volume":"37","author":"V Rossier","year":"2021","unstructured":"Rossier V, Warwick Vesztrocy A, Robinson-Rechavi M, Dessimoz C. Omamer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. Bioinformatics. 2021;37(18):2866\u201373. https:\/\/doi.org\/10.1093\/bioinformatics\/btab219.","journal-title":"Bioinformatics"},{"issue":"1","key":"2547_CR30","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):238. https:\/\/doi.org\/10.1186\/s13059-019-1832-y.","journal-title":"Genome Biol"},{"key":"2547_CR31","doi-asserted-by":"publisher","unstructured":"Sun J, Lu F, Luo Y, Bie L, Xu L, Wang Y. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 2023;51(W1):W397\u2013403. https:\/\/doi.org\/10.1093\/nar\/gkad313.","DOI":"10.1093\/nar\/gkad313"},{"issue":"22\u201323","key":"2547_CR32","doi-asserted-by":"publisher","first-page":"5516","DOI":"10.1093\/bioinformatics\/btaa1022","volume":"36","author":"FK Mendes","year":"2021","unstructured":"Mendes FK, Vanderpool D, Fulton B, Hahn MW. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics. 2021;36(22\u201323):5516\u201318. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa1022.","journal-title":"Bioinformatics"},{"key":"2547_CR33","doi-asserted-by":"publisher","unstructured":"Kumar S, Suleski M, Craig JM, Kasprowicz AE, Sanderford M, Li M, et al. TimeTree 5: an expanded resource for species divergence times. Mol Biol Evol. 2022;39(8):msac174. https:\/\/doi.org\/10.1093\/molbev\/msac174.","DOI":"10.1093\/molbev\/msac174"},{"issue":"12","key":"2547_CR34","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38(12):5825\u201329. https:\/\/doi.org\/10.1093\/molbev\/msab293.","journal-title":"Mol Biol Evol"},{"key":"2547_CR35","doi-asserted-by":"publisher","unstructured":"Mar\u00e7ais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018;14(1):e1005944. https:\/\/doi.org\/10.1371\/journal.pcbi.1005944.","DOI":"10.1371\/journal.pcbi.1005944"},{"issue":"19","key":"2547_CR36","doi-asserted-by":"publisher","first-page":"3021","DOI":"10.1093\/bioinformatics\/btw369","volume":"32","author":"M Nattestad","year":"2016","unstructured":"Nattestad M, Schatz MC. Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics. 2016;32(19):3021\u201323. https:\/\/doi.org\/10.1093\/bioinformatics\/btw369.","journal-title":"Bioinformatics"},{"key":"2547_CR37","doi-asserted-by":"publisher","unstructured":"Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. https:\/\/doi.org\/10.1093\/gigascience\/giab008.","DOI":"10.1093\/gigascience\/giab008"},{"issue":"15","key":"2547_CR38","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156\u201358. https:\/\/doi.org\/10.1093\/bioinformatics\/btr330.","journal-title":"Bioinformatics"},{"issue":"1","key":"2547_CR39","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1186\/s13059-020-02154-5","volume":"21","author":"JJ Jin","year":"2020","unstructured":"Jin JJ, Yu WB, Yang JB, Song Y, DePamphilis CW, Yi T-S, et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020;21(1):241. https:\/\/doi.org\/10.1186\/s13059-020-02154-5.","journal-title":"Genome Biol"},{"issue":"2","key":"2547_CR40","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.ympev.2012.08.023","volume":"69","author":"M Bernt","year":"2013","unstructured":"Bernt M, Donath A, J\u00fchling F, Externbrink F, Florentz C, Fritzsch G, et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69(2):313\u201319. https:\/\/doi.org\/10.1016\/j.ympev.2012.08.023.","journal-title":"Mol Phylogenet Evol"},{"key":"2547_CR41","doi-asserted-by":"publisher","unstructured":"Meng G, Li Y, Yang C, Liu S. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 2019;47(11):e63. https:\/\/doi.org\/10.1093\/nar\/gkz173.","DOI":"10.1093\/nar\/gkz173"},{"issue":"1","key":"2547_CR42","doi-asserted-by":"publisher","first-page":"3358","DOI":"10.1038\/s41598-024-52979-4","volume":"14","author":"V Muhala","year":"2024","unstructured":"Muhala V, Guimar\u00e3es-Costa A, Bessa-Silva AR, Rabelo LP, Carneiro J, Macate IE, et al. Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species. Sci Rep. 2024;14(1):3358. https:\/\/doi.org\/10.1038\/s41598-024-52979-4.","journal-title":"Sci Rep"},{"issue":"7357","key":"2547_CR43","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/nature10231","volume":"475","author":"H Li","year":"2011","unstructured":"Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011;475(7357):493\u201396. https:\/\/doi.org\/10.1038\/nature10231.","journal-title":"Nature"},{"issue":"20","key":"2547_CR44","doi-asserted-by":"publisher","first-page":"2678","DOI":"10.1093\/bioinformatics\/bts503","volume":"28","author":"F Garc\u00eda-Alcalde","year":"2012","unstructured":"Garc\u00eda-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, G\u00f6tz S, Tarazona S, et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics. 2012;28(20):2678\u201379. https:\/\/doi.org\/10.1093\/bioinformatics\/bts503.","journal-title":"Bioinformatics"},{"key":"2547_CR45","doi-asserted-by":"publisher","first-page":"608339","DOI":"10.3389\/fevo.2020.608339","volume":"8","author":"M Natesh","year":"2020","unstructured":"Natesh M, Vinay KL, Ghosh S, Jayapal R, Mukherjee S, Vijay N, et al. Contrasting trends of population size change for two eurasian owlet species\u2014Athene brama and glaucidium radiatum from South Asia over the Late Quaternary. Front Ecol Evol. 2020;8:608339. https:\/\/doi.org\/10.3389\/fevo.2020.608339.","journal-title":"Front Ecol Evol"},{"key":"2547_CR46","doi-asserted-by":"crossref","unstructured":"Br\u00fcniche-Olsen A, Kellner KF, Belant JL, DeWoody JA. Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation. Proceedings of the Royal Society B: Biological Sciences. 2021: 1961, 288.","DOI":"10.1098\/rspb.2021.1441"},{"issue":"5","key":"2547_CR47","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1111\/cobi.13486","volume":"34","author":"JP Bird","year":"2020","unstructured":"Bird JP, Martin R, Ak\u00e7akaya HR, Gilroy J, Burfield IJ, Garnett ST, et al. Generation lengths of the world\u2019s birds and their implications for extinction risk. Conserv Biol. 2020;34(5):1252\u201361. https:\/\/doi.org\/10.1111\/cobi.13486.","journal-title":"Conserv Biol"},{"issue":"7833","key":"2547_CR48","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/s41586-020-2873-9","volume":"587","author":"S Feng","year":"2020","unstructured":"Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, et al. Dense sampling of bird diversity increases power of comparative genomics. Nature. 2020;587(7833):252\u201357. https:\/\/doi.org\/10.1038\/s41586-020-2873-9.","journal-title":"Nature"},{"key":"2547_CR49","doi-asserted-by":"publisher","unstructured":"Kapusta A, Suh A, Feschotte C. Dynamics of genome size evolution in birds and mammals. Proc Natl Acad Sci USA. 2017;114(8):E1460\u201369. https:\/\/doi.org\/10.1073\/pnas.1616702114.","DOI":"10.1073\/pnas.1616702114"},{"issue":"6215","key":"2547_CR50","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1126\/science.1251385","volume":"346","author":"G Zhang","year":"2014","unstructured":"Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014, Dec, 12;346(6215):1311\u201320. https:\/\/doi.org\/10.1126\/science.1251385.","journal-title":"Science"},{"issue":"1","key":"2547_CR51","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1111\/nyas.13295","volume":"1389","author":"A Kapusta","year":"2017","unstructured":"Kapusta A, Suh A. Evolution of bird genomes\u2014a transposon\u2019s-eye view. Ann New Y Acad Sci. 2017, Feb;1389(1):164\u201385. https:\/\/doi.org\/10.1111\/nyas.13295.","journal-title":"Ann New Y Acad Sci"},{"issue":"6","key":"2547_CR52","doi-asserted-by":"publisher","first-page":"1537","DOI":"10.1111\/mec.14794","volume":"28","author":"L Schrader","year":"2019","unstructured":"Schrader L, Schmitz J. The impact of transposable elements in adaptive evolution. Mol Ecol. 2019, Mar;28(6):1537\u201349. https:\/\/doi.org\/10.1111\/mec.14794.","journal-title":"Mol Ecol"},{"issue":"6","key":"2547_CR53","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1177\/194008291300600603","volume":"6","author":"R Naniwadekar","year":"2013","unstructured":"Naniwadekar R, Datta A. Spatial and temporal variation in hornbill densities in Namdapha Tiger Reserve, Arunachal Pradesh, north-east India. Trop Conserv Sci. 2013, Dec;6(6):734\u201348. https:\/\/doi.org\/10.1177\/194008291300600603.","journal-title":"Trop Conserv Sci"},{"key":"2547_CR54","unstructured":"Germain RR, Feng S, Buffan L, Carmona CP, Chen G, Graves GR, et al. Changes in the functional diversity of modern bird species over the last million years. Proceedings of the National Academy of Sciences. 2023: (7): e2201945119, 120."},{"issue":"3","key":"2547_CR55","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/j.pld.2022.12.003","volume":"45","author":"MA Khan","year":"2023","unstructured":"Khan MA, Mahato S, Spicer RA, Spicer TEV, Ali A, Hazra T, et al. Siwalik plant megafossil diversity in the Eastern Himalayas: a review. Plant Divers. 2023;45(3):243\u201364. https:\/\/doi.org\/10.1016\/j.pld.2022.12.003.","journal-title":"Plant Divers"},{"key":"2547_CR56","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.quascirev.2014.07.008","volume":"101","author":"A Bhattacharyya","year":"2014","unstructured":"Bhattacharyya A, Mehrotra N, Shah SK, Basavaiah N, Chaudhary V, Singh IB. Analysis of vegetation and climate change during Late Pleistocene from Ziro Valley, Arunachal Pradesh, Eastern Himalaya region. Quaternary Sci Rev. 2014;101:111\u201323. https:\/\/doi.org\/10.1016\/j.quascirev.2014.07.008.","journal-title":"Quaternary Sci Rev"},{"issue":"2","key":"2547_CR57","doi-asserted-by":"publisher","first-page":"195","DOI":"10.18520\/cs\/v119\/i2\/195-218","volume":"119","author":"R Kar","year":"2020","unstructured":"Kar R, Quamar MF. Late Pleistocene\u2013Holocene vegetation and climate change from the Western and Eastern Himalaya (india): palynological perspective. Curr Sci. 2020;119(2):195\u2013218. https:\/\/doi.org\/10.18520\/cs\/v119\/i2\/195-218.","journal-title":"Curr Sci"},{"key":"2547_CR58","doi-asserted-by":"publisher","unstructured":"Meijer HJM. The avian fossil record in insular Southeast Asia and its implications for avian biogeography and palaeoecology. PeerJ. 2014;2:e295. https:\/\/doi.org\/10.7717\/peerj.295.","DOI":"10.7717\/peerj.295"},{"issue":"8","key":"2547_CR59","doi-asserted-by":"publisher","first-page":"1708","DOI":"10.1016\/j.jas.2009.03.027","volume":"36","author":"H Barton","year":"2009","unstructured":"Barton H, Piper PJ, Rabett R, Reeds I. Composite hunting technologies from the terminal Pleistocene and early Holocene, Niah Cave, Borneo. J Archaeolog Sci. 2009;36(8):1708\u201314. https:\/\/doi.org\/10.1016\/j.jas.2009.03.027.","journal-title":"J Archaeolog Sci"},{"key":"2547_CR60","doi-asserted-by":"publisher","first-page":"88","DOI":"10.7152\/bippa.v28i0.12021","volume":"28","author":"PJ Piper","year":"2008","unstructured":"Piper PJ, Rabett RJ, Kurui EB. Late pleistocene and early holocene forager organizations in Southeast Asia using community, composition and structural variation in terminal Pleistocene vertebrate assemblages to identify human hunting behaviour at the Niah caves, Borneo. BIPPA. 2008;2888\u201398. https:\/\/doi.org\/10.7152\/bippa.v28i0.12021.","journal-title":"BIPPA"},{"key":"2547_CR61","first-page":"249","volume":"7","author":"T Tyrberg","year":"2008","unstructured":"Tyrberg T. The Late Pleistocene continental avian extinction - an evaluation of the fossil evidence. Oryctos. 2008;7:249\u201369.","journal-title":"Oryctos"},{"key":"2547_CR62","first-page":"902","volume":"138","author":"S Dasgupta","year":"2012","unstructured":"Dasgupta S, Hilaluddin. Differential effects of hunting on populations of hornbills and imperial pigeons in the rainforests of the Eastern Indian Himalaya. Indian For. 2012;138:902\u201309.","journal-title":"Indian For"}],"container-title":["BMC Ecology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12862-026-02547-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12862-026-02547-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12862-026-02547-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T09:05:50Z","timestamp":1782896750000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12862-026-02547-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,27]]},"references-count":62,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["2547"],"URL":"https:\/\/doi.org\/10.1186\/s12862-026-02547-3","relation":{},"ISSN":["2730-7182"],"issn-type":[{"value":"2730-7182","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,27]]},"assertion":[{"value":"7 October 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"PYP obtained the approval (- NCF-EC-01\/12\/2022-(73)) from the Ethics Committee, Nature Conservation Foundation to conduct this study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"54"}}