Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

doi:10.1016/j.pld.2024.04.001

Abstract

Abstract: Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex (B. liuyanii, B. longgangensis, B. masoniana and B. variegata) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between B. liuyanii and B. longgangensis occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of B. masoniana have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Key words: Conservation genomics, Karst landscape, Demographic history, Inbreeding, Isolated populations, Mutation load

Yiqing Chen, Lina Dong, Huiqin Yi, Catherine Kidner, Ming Kang. Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts[J]. Plant Diversity, 2024, 46(05): 575-584.

References

Agrawal, A.F., Whitlock, M.C., 2012. Mutation load: The fitness of individuals in populations where deleterious alleles are abundant. Annu. Rev. Ecol. Evol. Syst. 43, 115-135.
Alexander, D.H., Lange, K., 2011. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12, 1-6.
Bai, W.N., Yan, P.C., Zhang, B.W., et al., 2018. Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences. New Phytol. 217, 1726-1736.
Beichman, A.C., Phung, T.N., Lohmueller, K.E. 2017. Comparison of single genome and allele frequency data reveals discordant demographic histories. G3-Genes Genom. Genet. 7, 3605-3620.
Bertorelle, G., Raffini, F., Bosse, M., et al., 2022. Genetic load: genomic estimates and applications in non-model animals. Nat. Rev. Genet. 23, 492-503.
Bohonak, A.J., 2002. IBD (Isolation by Distance): a program for analyses of isolation by distance. J. Hered. 93, 153-154.
Bolger, A.M., Lohse, M., Usadel, B., 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.
Bortoluzzi, C., Bosse, M., Derks, M.F.L., et al., 2020. The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations. Evol. Appl. 13, 330-341.
Brennan, A.C., Bridgett, S., Shaukat Ali, M., et al., 2012. Genomic resources for evolutionary studies in the large, diverse, tropical genus, Begonia. Trop. Plant Biol. 5, 261-276.
Charlesworth, B., 2009. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 10, 195-205.
Chen, C., Xu, Y., 2023. Spatial heterogeneity of human activities and its driving factors in karst areas of Southwest China over the past 20 years. Front. Environ. Sci. 11, 1225888.
Chen, D., Kang, H., Liu, C., 2011. An overview on the potential Quaternary glacial refugia of plants in China mainland. Bull. Botanical Res. 31, 623-632.
Chen, S., Zhou, Y., Chen, Y., et al., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890.
Chen, C., Chen, H., Zhang, Y., et al., 2020a. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant. 13, 1194-1202.
Chen, J., Glemin, S., Lascoux, M., 2020b. From drift to draft: How much do beneficial mutations actually contribute to predictions of Ohta's slightly deleterious model of molecular evolution? Genetics 214, 1005-1018.
Chung, K.F., Leong, W.C., Rubite, R.R., et al., 2014. Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora. Bot. Stud. 55, 1.
Cingolani, P., Platts, A., Wang le, L., et al., 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80-92.
Clements, R., Sodhi, N.S., Schilthuizen, M., et al., 2006. Limestone karsts of Southeast Asia: imperiled arks of biodiversity. BioScience 56, 733-742.
Danecek, P., Auton, A., Abecasis, G., et al., 2011. The variant call format and VCFtools. Bioinformatics 27, 2156-2158.
Davey, J.W., Hohenlohe, P.A., Etter, P.D., et al., 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499-510.
DePristo, M.A., Banks, E., Poplin, R., et al., 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498.
Doyle, J., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-13.
Durand, E.Y., Patterson, N., Reich, D., et al., 2011. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239-2252.
Emelianova, K., Kidner, C., 2022. Comparative transcriptome analysis of two closely related Begonia species reveals divergent patterns in key light-regulated pathways. Edinb. J. Bot. 79, 1-18.
Feng, S., Fang, Q., Barnett, R., et al., 2019. The genomic footprints of the fall and recovery of the crested ibis. Curr. Biol. 29, 340-349.e7.
Feng, Y., Comes, H.P., Chen, J., et al., 2024. Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two ‘living fossil’ tree species of Dipteronia. Plant J. 117, 177-192.
Forrest, L.L., Hughes, M., Hollingsworth, P.M., 2005. A phylogeny of Begonia using nuclear ribosomal sequence data and morphological characters. Syst. Bot. 30, 671-682.
Funk, W.C., McKay, J.K., Hohenlohe, P.A., et al., 2012. Harnessing genomics for delineating conservation units. Trends Ecol. Evol. 27, 489-496.
Goodall-Copestake, W.P., PERez-Espona, S., Harris, D.J., et al., 2010. The early evolution of the mega-diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies. Biol. J. Linn. Soc. 101, 243-250.
Grantham, R., 1974. Amino acid difference formula to help explain protein evolution. Science 185, 862-864.
Grossen, C., Guillaume, F., Keller, L.F., et al., 2020. Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nat. Commun. 11, 1001.
Gutenkunst, R.N., Hernandez, R.D., Williamson, S.H., et al., 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5, e1000695.
Hao, Z., Kuang, Y., Kang, M., 2015. Untangling the influence of phylogeny, soil and climate on leaf element concentrations in a biodiversity hotspot. Funct. Ecol. 29, 165-176.
Hohenlohe, P.A., Funk, W.C., Rajora, O.P., 2021. Population genomics for wildlife conservation and management. Mol. Ecol. 30, 62-82.
Hu, J.Y., Hao, Z.Q., Frantz, L., et al., 2020. Genomic consequences of population decline in critically endangered pangolins and their demographic histories. Natl. Sci. Rev. 7, 798-814.
Hughes, M., Hollingsworth, P.M., 2008. Population genetic divergence corresponds with species-level biodiversity patterns in the large genus Begonia. Mol. Ecol. 17, 2643-2651.
Humble, E., Stoffel, M.A., Dicks, K., et al., 2023. Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx. Proc. Natl. Acad. Sci. U.S.A. 120, e2210756120.
Jangjoo, M., Matter, S.F., Roland, J., et al., 2016. Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network. Proc. Natl. Acad. Sci. U.S.A. 113, 10914-10919.
Kang, M., Wang, J., Huang, H., 2015. Nitrogen limitation as a driver of genome size evolution in a group of karst plants. Sci. Rep. 5, 11636.
Kardos, M., Zhang, Y., Parsons, K.M., et al., 2023. Inbreeding depression explains killer whale population dynamics. Nat. Ecol. Evol. 7, 675-686.
Ke, F., Vasseur, L., Yi, H., et al., 2022. Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists. Mol. Ecol. 31, 104-118.
Khan, A., Patel, K., Shukla, H., et al., 2021. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc. Natl. Acad. Sci. U.S.A. 118, e2023018118.
Kong, H., Condamine, F.L., Harris, A.J., et al., 2017. Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China. Mol. Ecol. 26, 6414-6429.
Korneliussen, T.S., Albrechtsen, A., Nielsen, R., 2014. ANGSD: Analysis of next generation sequencing data. BMC Bioinformatics 15, 356.
Korunes, K.L., Samuk, K., 2021. pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Mol. Ecol. Resour. 21, 1359-1368.
LaBar, T., Adami, C., 2017. Evolution of drift robustness in small populations. Nat. Commun. 8, 1012.
Li, H., 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: Genomics.
Li, H., Durbin, R., 2011. Inference of human population history from individual whole-genome sequences. Nature 475, 493-496.
Li, W.H., Wu, C.I., Luo, C.C., 1984. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21, 58-71.
Li, H., Handsaker, B., Wysoker, A., et al., 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079.
Li, C., Tian, D., Li, X., et al., 2015. Morphological and molecular identification of natural hybridization between Begonia hemsleyana and B. macrotoma. Sci. Hortic. 192, 357-360.
Li, J., Milne, R.I., Ru, D., et al., 2020. Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China. Mol. Ecol. 29, 1250-1266.
Li, L., Chen, X., Fang, D., et al., 2022. Genomes shed light on the evolution of Begonia, a mega-diverse genus. New Phytol. 234, 295-310.
Liu, D., Zhang, L., Wang, J., et al., 2020. Conservation genomics of a threatened Rhododendron: contrasting patterns of population structure revealed from neutral and selected SNPs. Front. Genet. 11, 757.
Ma, H., Liu, Y., Liu, D., et al., 2021a. Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation. Plant J. 107, 1533-1545.
Ma, Y., Liu, D., Wariss, H.M., et al., 2021b. Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple. Mol. Ecol. 31, 767-779.
Malinsky, M., Matschiner, M., Svardal, H., 2021. Dsuite-Fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584-595.
Marsden, C.D., Ortega-Del Vecchyo, D., O'Brien, D.P., et al., 2016. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proc. Natl. Acad. Sci. U.S.A. 113, 152-157.
Matolweni, L.O., Balkwill, K., McLellan, T., 2000. Genetic diversity and gene flow in the morphologically variable, rare endemics Begonia dregei and Begonia homonyma (Begoniaceae). Am. J. Bot. 87, 431-439.
McKenna, A., Hanna, M., Banks, E., et al., 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.
Molina, J., Sikora, M., Garud, N., et al., 2011. Molecular evidence for a single evolutionary origin of domesticated rice. Proc. Natl. Acad. Sci. U.S.A. 108, 8351-8356.
Moonlight, P.W., Reynel, C., Tebbitt, M., 2017. Begonia elachista Moonlight & Tebbitt sp. nov., an enigmatic new species and a new section of Begonia (Begoniaceae) from Peru. Eur. J. Taxon. 281, 1-13.
Mussmann, S.M., Douglas, M.R., Chafin, T.K., et al., 2019. BA3-SNPs: Contemporary migration reconfigured in BayesAss for next-generation sequence data. Methods Ecol. Evol. 10, 1808-1813.
Nguyen, L.T., Schmidt, H.A., von Haeseler, A., et al., 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268-274.
Oginuma, K., Peng, C.I., 2022. Karyomorphology of Taiwanese Begonia (Begoniaceae): taxonomic implications. J. Plant. Res. 115, 225-235.
Paez, S., Kraus, R.H.S., Shapiro, B., et al., 2022. Reference genomes for conservation. Science 377, 364-366.
Peng, C.I., Ku, S.M., Leong, W.C., 2005. Begonia liuyanii (sect. Coelocentrum, Begoniaceae), a new species from limestone areas in Guangxi, China. Bot. Bull. Acad. Sinica 46, 245-245.
Peng, C.I., Yang, H.A., Kono, Y., et al., 2013. Novelties in Begonia sect. Coelocentrum: B. longgangensis and B. ferox from limestone areas in Guangxi, China. Bot. Stud. 54, 44.
Poon, A., Otto, S.P., 2000. Compensating for our load of mutations: freezing the meltdown of small populations. Evolution 54, 1467-1479.
Portik, D.M., Leache, A.D., Rivera, D., et al., 2017. Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection. Mol. Ecol. 26, 5245-5263.
Provan, J., Bennett, K.D., 2008. Phylogeographic insights into cryptic glacial refugia. Trends Ecol. Evol. 23, 564-571.
Pu, G., Lv, Y., Xu, G., et al., 2017. Research progress on karst Tiankeng ecosystems. Bot. Rev. 83, 5-37.
Qin, H.N., Yang, Y, Dong, S.Y., et al., 2017. Threatened species list of China’s higher plants. Biodiv. Sci. 25, 696-744.
Robinson, J.A., Raikkonen, J., Vucetich, L.M., et al., 2019. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. Sci. Adv. 5, eaau0757.
Robinson, J., Kyriazis, C.C., Yuan, S.C., et al., 2023. Deleterious variation in natural populations and implications for conservation genetics. Annu. Rev. Anim. Biosci. 11, 93-114.
Rodger, Y.S., Pavlova, A., Sinclair, S., et al., 2021. Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy. Heredity 126, 846-858.
Sarthou, C., Samadi, S., Boisselier-Dubayle, M.-C., 2001. Genetic structure of the saxicole Pitcairnia geyskesii (Bromeliaceae) on inselbergs in French Guiana. Am. J. Bot. 88, 861-868.
Setoguchi, H., Mitsui, Y., Ikeda, H., et al., 2010. Genetic structure of the critically endangered plant Tricyrtis ishiiana (Convallariaceae) in relict populations of Japan. Conserv. Genet. 12, 491-501.
Spielman, D., Brook, B.W., Frankham, R., 2004. Most species are not driven to extinction before genetic factors impact them. Proc. Natl. Acad. Sci. U.S.A. 101, 15261-15264.
Tao, T., Milne, R.I., Li, J., et al., 2024. Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load. Plant Divers. 46, 78-90.
Thomas, D.C., Hughes, M., Phutthai, T., et al., 2012. West to east dispersal and subsequent rapid diversification of the mega-diverse genus Begonia (Begoniaceae) in the Malesian archipelago. J. Biogeogr. 39, 98-113.
Tian, D., Li, C., Xiao, Y., et al., 2017. Occurrence and characteristics of natural hybridization in Begonia in China. Biodiv. Sci. 25: 654-674.
Tian, D., Xiao, Y., Tong, Y., et al., 2018. Diversity and conservation of Chinese wild begonias. Plant Divers. 40, 75-90.
Tsai, M.Y., Kuan, C., Guo, Z.L., et al., 2022. Stomatal clustering in Begonia improves water use efficiency by modulating stomatal movement and leaf structure. Plant Environ. Interact. 3, 141-154.
Tseng, Y.H., Huang, H.Y., Xu, W.B., et al., 2019. Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure. Bot. Stud. 60, 20.
Twyford, A.D., Ennos, R.A., Kidner, C.A., 2013. Development and characterization of microsatellite markers for Central American Begonia sect. Gireoudia (Begoniaceae). Appl Plant Sci. 1, apps.1200499.
Twyford, A.D., Kidner, C.A., Ennos, R.A., 2014. Genetic differentiation and species cohesion in two widespread Central American Begonia species. Heredity 112, 382-390.
Twyford, A.D., Kidner, C.A., Ennos, R.A., 2015. Maintenance of species boundaries in a Neotropical radiation of Begonia. Mol. Ecol. 24, 4982-4993.
van der Valk, T., Diez-Del-Molino, D., Marques-Bonet, T., et al., 2019. Historical genomes reveal the genomic consequences of recent population decline in eastern gorillas. Curr. Biol. 29, 165-170.e6.
Villanueva, R.A.M., Chen, Z.J., 2019. ggplot2: Elegant graphics for data analysis. Taylor & Francis, Beijing.
Wang, J., Kang, M., Huang, H., 2014. Long-distance pollen dispersal ensures genetic connectivity of the low-density tree species, Eurycorymbus cavaleriei, in a fragmented karst forest landscape. Conserv. Genet. 15, 1163-1172.
Wang, J., Ai, B., Kong, H., et al., 2017a. Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot. Evol. Appl. 10, 919-934.
Wang, J., Feng, C., Jiao, T., et al., 2017b. Genomic signature of adaptive divergence despite strong nonadaptive forces on edaphic islands: A case study of Primulina juliae. Genome Biol. Evol. 9, 3495-3508.
Wang, P., Burley, J.T., Liu, Y., et al., 2021. Genomic consequences of long-term population decline in brown eared pheasant. Mol. Biol. Evol. 38, 263-273.
Wang, Q., Lan, T., Li, H., et al., 2022. Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation. Commun. Biol. 5, 821.
Whitlock, M.C., 2000. Fixation of new alleles and the extinction of small populations: drift load, beneficial alleles, and sexual selection. Evolution 54, 1855-1861.
Willi, Y., Van Buskirk, J., Hoffmann, A.A., 2006. Limits to the adaptive potential of small populations. Annu. Rev. Ecol. Evol. Syst. 37, 433-458.
Wilson, G.A., Rannala, B., 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163, 1177-1191.
Wu, F.Q., Shen, S.K., Zhang, X.J., et al., 2014. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron. AoB Plants 7, plu082.
Wu, G.L., Ye, Q., Liu, H., et al., 2022. The evolutionary rate of leaf osmotic strength drives diversification of Primulina species in karst regions. J. Systemat. Evol. 51, 843-851.
Xiao, Y., Li, X.J., Jiang, X.L., et al., 2023. Spatial genetic patterns and distribution dynamics of Begonia grandis (Begoniaceae), a widespread herbaceous species in China. Front Plant Sci. 14, 1178245.
Yang, Y., Ma, T., Wang, Z., et al., 2018. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat. Commun. 9, 5449.
Zachos, J.C., Dickens, G.R., Zeebe, R.E., 2008. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451, 279-283.
Zhang, J.G., Chen, H.S., Su, Y.R., et al., 2011. Spatial variability and patterns of surface soil moisture in a field plot of karst area in southwest China. Plant Soil Environ. 57, 409-417.
Zhang, X.J., Liu, X.F., Liu, D. T., et al., 2021. Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations. Plant Divers. 43, 472-479.
Zheng, B., Xu, Q., Shen, Y., 2001. The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau: Review and speculation. Quat. Int. 97-98, 93-101.
Zhu, X., Liang, H., Jiang, H., et al., 2022. Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China. Front. Plant Sci. 13, 999964.

[1]	Zhen Yang, Lisong Liang, Weibo Xiang, Lujun Wang, Qinghua Ma, Zhaoshan Wang. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis [J]. Plant Diversity, 2024, 46(03): 294-308.
[2]	Tongzhou Tao, Richard I. Milne, Jialiang Li, Heng Yang, Shiyang Wang, Sihan Chen, Kangshan Mao. Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load [J]. Plant Diversity, 2024, 46(01): 78-90.
[3]	Xue Li, Markus Ruhsam, Yi Wang, Hong-Ying Zhang, Xiao-Yan Fan, Lei Zhang, Jing Wang, Kang-Shan Mao. Wind-dispersed seeds blur phylogeographic breaks: The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin [J]. Plant Diversity, 2023, 45(02): 156-168.
[4]	ysajan Abdusalam, Qing Jun Li. Elevation-related variation in the population characteristics of distylous Primula nivalis affects female fitness and inbreeding depression [J]. Plant Diversity, 2019, 41(04): 250-257.
[5]	LI Jing - Xiu GUAN Kai - Yun LI Zhi - Jian GUO Rui - Xian. A Preliminary Studies on Resistance Breeding of Begonia [J]. Plant Diversity, 2001, 23(04): 1-3.