The rise of baobab trees in Madagascar

The rise of baobab trees in Madagascar

Wickens, G. E. The Baobabs: Pachycauls of Africa, Madagascar and Australia (Springer, 2008).

Baum, D. A., Small, R. L. & Wendel, J. F. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Syst. Biol.47, 181–207 (1998).

CAS 
PubMed 

Google Scholar 

Karimi, N. et al. Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Syst. Biol.69, 462–478 (2020).

PubMed 

Google Scholar 

Patrut, A. et al. Radiocarbon dating of a very large African baobab. Tree Physiol.27, 1569–1574 (2007).

PubMed 

Google Scholar 

Gebauer, J., El-Siddig, K. & Ebert, G. Baobab (Adansonia digitata L.): a review on a multipurpose tree with promising future in the Sudan. Eur. J. Hort. Sci.67, 155–160 (2002).

CAS 

Google Scholar 

Duvall, C. S. Human settlement and baobab distribution in south-western Mali. J. Biogeogr.34, 1947–1961 (2007).

Google Scholar 

Rangan, H. et al. New genetic and linguistic analyses show ancient human influence on baobab evolution and distribution in Australia. PLoS ONE10, e0119758 (2015).

PubMed 
PubMed Central 

Google Scholar 

Baum, D. A. The comparative pollination and floral biology of baobabs (Adansonia—Bombacaceae). Ann. Mo. Bot. Gard.82, 322–348 (1995).

Google Scholar 

Baum, D. A. A systematic revision of Adansonia (Bombacaceae). Ann. Mo. Bot. Gard.82, 440–471 (1995).

Google Scholar 

Antonelli, A. et al. Madagascar’s extraordinary biodiversity: evolution, distribution and use. Science378, eabf0869 (2022).

CAS 
PubMed 

Google Scholar 

Baum, D. A. & Oginuma, K. A review of chromosome numbers in Bombacaceae with new counts for Adansonia. Taxon43, 11–20 (1994).

Google Scholar 

Conover, J. L. et al. A Malvaceae mystery: a mallow maelstrom of genome multiplications and maybe misleading methods? J. Integr. Plant Biol.61, 12–31 (2019).

PubMed 

Google Scholar 

Marinho, R. C. et al. Do chromosome numbers reflect phylogeny? New counts for Bombacoideae and a review of Malvaceae s.l. Am. J. Bot.101, 1456–1465 (2014).

PubMed 

Google Scholar 

Cvetković, T. et al. Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l. Genes Genomes Genet.11, jkab136 (2021).

Google Scholar 

Yoder, A. D. & Nowak, M. D. Has vicariance or dispersal been the predominant biogeographic force in Madagascar? Only time will tell. Annu. Rev. Ecol. Evol. Syst.37, 405–431 (2016).

Google Scholar 

Peter, H. et al. Evolution and diversity of copy number variation in the great ape lineage. Genome Res.23, 1373–1382 (2013).

Google Scholar 

Edelman, N. B. et al. Genomic architecture and introgression shape a butterfly radiation. Science366, 594–599 (2019).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Meleshko, O. et al. Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting and not ongoing introgression in a rapidly radiated bryophyte genus. Mol. Biol. Evol.38, 2750–2766 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Wen, D. Q., Yu, Y., Zhu, J. F. & Nakhleh, L. Inferring phylogenetic networks using PhyloNet. Syst. Biol.67, 735–740 (2018).

PubMed 
PubMed Central 

Google Scholar 

Green, R. E. A draft sequence of the Neandertal genome. Science328, 710–722 (2010).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Leong Pock-Tsy, J. M. et al. Nuclear microsatellite variation in Malagasy baobabs (Adansonia, Bombacoideae, Malvaceae) reveals past hybridization and introgression. Ann. Bot.112, 1759–1773 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Whitlock, M. C. Fixation of new alleles and the extinction of small populations: drift load, beneficial alleles and sexual selection. Evolution54, 1855–1861 (2000).

CAS 
PubMed 

Google Scholar 

Barlow, A. et al. Partial genomic survival of cave bears in living brown bears. Nat. Ecol. Evol.2, 1563–1570 (2018).

PubMed 
PubMed Central 

Google Scholar 

del Pozo, J. C. & Ramirez-Parra, E. Whole genome duplications in plants: an overview from Arabidopsis. J. Exp. Bot.66, 6991–7003 (2015).

PubMed 

Google Scholar 

Palkopoulou, E. et al. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr. Biol.25, 1395–1400 (2015).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Ceballos, F. C., Hazelhurst, S. & Ramsay, M. Assessing runs of homozygosity: a comparison of SNP array and whole genome sequence low coverage data. BMC Genomics19, 106 (2018).

PubMed 
PubMed Central 

Google Scholar 

Bell, K. L. et al. Genetic diversity and biogeography of the baobab Adansonia gregorii (Malvaceae: Bombacoideae). Aust. J. Bot.62, 164–174 (2014).

Google Scholar 

Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature475, 493–496 (2011).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Sepkoski, J. J. Jr., McKinney, F. K. & Lidgard, S. Competitive displacement among post-Paleozoic cyclostome and cheilostome bryozoans. Paleobiology26, 7–18 (2000).

PubMed 

Google Scholar 

Roberts, G. G., Paul, J. D., White, N. & Winterbourne, J. Temporal and spatial evolution of dynamic support from river profiles: a framework for Madagascar. Geochem. Geophys. Geosyst.13, Q04004 (2012).

ADS 

Google Scholar 

Stephenson, S. N. et al. Cenozoic dynamic topography of Madagascar. Geochem. Geophys. Geosyst.22, e2020GC009624 (2021).

ADS 

Google Scholar 

Johnson, T. C. et al. A progressively wetter climate in southern East Africa over the past 1.3 million years. Nature537, 220–224 (2016).

ADS 
CAS 
PubMed 

Google Scholar 

Chikhi, L. et al. The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice. Heredity120, 13–24 (2018).

PubMed 

Google Scholar 

Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land area. Int. J. Climatol.37, 4302–4315 (2017).

Google Scholar 

Whittaker, R. H. Dominance and diversity in land plant communities: numerical relations of species express the importance of competition in community function and evolution. Science147, 250–260 (1965).

ADS 
CAS 
PubMed 

Google Scholar 

Aguilar, R. et al. Habitat fragmentation reduces plant progeny quality: a global synthesis. Ecol. Lett.22, 1163–1173 (2019).

PubMed 

Google Scholar 

Phillips, S. J.,erson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model.190, 231–259 (2006).

Google Scholar 

Fernández‐Palacios, J. M. et al. Towards a glacial‐sensitive model of island biogeography. Glob. Ecol. Biogeogr.25, 817–830 (2016).

Google Scholar 

Pico, T., Creveling, J. R. & Mitrovica, J. X. Sea-level records from the US mid-Atlantic constrain Laurentide Ice Sheet extent during Marine Isotope Stage 3. Nat. Commun.8, 15612 (2017).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Borreggine, M. et al. Sea-level rise in Southwest Greenland as a contributor to Viking abandonment. Proc. Natl Acad. Sci. USA120, e2209615120 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Miller, K. G. et al. Cenozoic sea-level and cryospheric evolution from deep-sea geochemical and continental margin records. Sci. Adv.6, eaaz1346 (2020).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Liu, Y., Wang, Y., Willett, S. D., Zimmermann, N. E. & Pellissier, L. Escarpment evolution drives the diversification of the Madagascar flora. Science383, 653–658 (2024).

CAS 
PubMed 

Google Scholar 

Leong Pock-Tsy, J. et al. Chloroplast DNA phylogeography suggests a West African centre of origin for the baobab, Adansonia digitata L. (Bombacoideae, Malvaceae). Mol. Ecol.18, 1707–1715 (2009).

PubMed 

Google Scholar 

Parisod, C., Holderegger, R. & Brochmann, C. Evolutionary consequences of autopolyploidy. New Phytol.186, 5–17 (2010).

CAS 
PubMed 

Google Scholar 

Marques, D. A., Meier, J. I. & Seehausen, O. A combinatorial view on speciation and adaptive radiation. Trends Ecol. Evol.34, 531–544 (2019).

PubMed 

Google Scholar 

Carvalho-Sobrinho, J. G. et al. Revisiting the phylogeny of Bombacoideae (Malvaceae): novel relationships, morphologically cohesive clades and a new tribal classification based on multilocus phylogenetic analyses. Mol. Phylogenet. Evol.101, 56–74 (2016).

PubMed 

Google Scholar 

Vieilledent, G. et al. Vulnerability of baobab species to climate change and effectiveness of the protected area network in Madagascar: towards new conservation priorities. Biol. Conserv.166, 11–22 (2013).

Google Scholar 

Goodman, S. M. The New Natural History of Madagascar (Princeton Univ. Press, 2022).

Masters, J. C. et al. Biogeographic mechanisms involved in the colonization of Madagascar by African vertebrates: rifting, rafting and runways. J. Biogeogr.48, 492–510 (2021).

Google Scholar 

Ali, J. R. & Hedges, S. B. A review of geological evidence bearing on proposed Cenozoic land connections between Madagascar and Africa and its relevance to biogeography. Earth Sci. Rev.232, 104103 (2022).

Google Scholar 

Xin, H. P. et al. A genome for Cissus illustrates features underlying the evolutionary success in dry savannas. Hort. Res.9, uhac208 (2022).

Google Scholar 

Chen, Y. et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience7, gix120 (2018).

Marcais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics27, 764–770 (2011).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics33, 2202–2204 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun.11, 1432 (2020).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods13, 1050–1054 (2016).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE9, e112963 (2014).

ADS 
PubMed 
PubMed Central 

Google Scholar 

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods18, 170–175 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst.3, 95–98 (2016).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science356, 92–95 (2017).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile DNA6, 11 (2015).

Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA117, 9451–9457 (2020).

ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res.35, W265–W268 (2007).

PubMed 
PubMed Central 

Google Scholar 

Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res.27, 573–580 (1999).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol.37, 907–915 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Kovaka, S. et al. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol.20, 278 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Cheng, C. Y. et al. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J.89, 789–804 (2017).

CAS 
PubMed 

Google Scholar 

Du, X. et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat. Genet.50, 796–802 (2018).

CAS 
PubMed 

Google Scholar 

Teh, B. T. et al. The draft genome of tropical fruit durian (Durio zibethinus). Nat. Genet.49, 1633–1641 (2017).

CAS 
PubMed 

Google Scholar 

Argout, X. et al. The cacao Criollo genome v2. 0: an improved version of the genome for genetic and functional genomic studies. BMC Genomics18, 730 (2017).

Udall, J. A. et al. De novo genome sequence assemblies of Gossypium raimondii and Gossypium turneri. Genes Genomics Genet.9, 3079–3085 (2019).

CAS 

Google Scholar 

Keilwagen, J. et al. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res.44, e89–e89 (2016).

PubMed 
PubMed Central 

Google Scholar 

Stanke, M., Schöffmann, O., Morgenstern, B. & Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinf.7, 62 (2006).

Korf, I. Gene finding in novel genomes. BMC Bioinf.5, 59 (2004).

Campbell, M. S., Holt, C., Moore, B. & Yandell, M. Genome annotation and curation using MAKER and MAKER‐P. Curr. Protoc. Bioinform.48, 4–11 (2014).

Google Scholar 

Gremme, G., Steinbiss, S. & Kurtz, S. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Trans. Comput. Biol. Bioinform.10, 645–656 (2013).

PubMed 

Google Scholar 

Zhang, R. G. et al. TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes. Hort. Res.9, uhac017 (2022).

Google Scholar 

Neumann, P., Novak, P., Hostakova, N. & Macas, J. Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA10, 1 (2019).

PubMed 
PubMed Central 

Google Scholar 

Ou, S. & Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiol.176, 1410–1422 (2018).

CAS 
PubMed 

Google Scholar 

Tang, H. et al. Synteny and collinearity in plant genomes. Science320, 486–488 (2008).

ADS 
CAS 
PubMed 

Google Scholar 

Hasegawa, M., Kishino, H. & Yano, T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol.22, 160–174 (1985).

ADS 
CAS 
PubMed 

Google Scholar 

Huang, S. et al. The genome of the cucumber, Cucumis sativus L. Nat. Genet.41, 1275–1281 (2009).

CAS 
PubMed 

Google Scholar 

Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol.24, 1586–1591 (2007).

CAS 
PubMed 

Google Scholar 

Li, L., Stoeckert, C. J. Jr. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res.13, 2178–2189 (2003).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res.32, 1792–1797 (2004).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics17, 754–755 (2001).

CAS 
PubMed 

Google Scholar 

Hernández-Gutiérrez, R. & Magallón, S. The timing of Malvales evolution: incorporating its extensive fossil record to inform about lineage diversification. Mol. Phylo. Evol.140, 106606 (2019).

Google Scholar 

Mirarab, S. et al. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics30, i541–i548 (2014).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res.14, 708–715 (2004).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Shimodaira, H. & Hasegawa, M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics17, 1246–1247 (2001).

CAS 
PubMed 

Google Scholar 

Dierckxsens, N., Mardulyn, P. & Smits, G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res.45, e18 (2017).

PubMed 

Google Scholar 

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics25, 1754–1760 (2009).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience10, giab008 (2021).

PubMed 
PubMed Central 

Google Scholar 

Broad Institute. Picard Toolkit. GitHub https://broadinstitute.github.io/picard/ (2019).

van der Auwera, G. A. From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinform.43, 11.10.1–11.10.33 (2013).

Google Scholar 

Gao, Y. et al. De novo genome assembly of the red silk cotton tree (Bombax ceiba). Gigascience7, giy051 (2018).

PubMed 
PubMed Central 

Google Scholar 

Suvakov, M., Panda, A., Diesh, C., Holmes, I. & Abyzov, A. CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. GigaScience10, giab074 (2021).

Malinsky, M., Matschiner, M. & Svardal, H. Dsuite—fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour.21, 584–595 (2021).

PubMed 

Google Scholar 

Than, C., Ruths, D. & Nakhleh, L. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinf.9, 322 (2008).

Google Scholar 

Yu, Y. & Nakhleh, L. A maximum pseudo-likelihood approach for phylogenetic networks. BMC Genomics16, S10 (2015).

PubMed 
PubMed Central 

Google Scholar 

Haubold, B., Pfaffelhuber, P. & Lynch, M. mlRho—a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Mol. Ecol.19, 277–284 (2010).

PubMed 
PubMed Central 

Google Scholar 

Liu, S. et al. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell184, 4874–4885 (2021).

CAS 
PubMed 

Google Scholar 

Wan, J. N. et al. Modeling impacts of climate change on the potential distribution of six endemic baobab species in Madagascar. Plant Divers.43, 117–124 (2021).

PubMed 

Google Scholar 

Pearson, K. Notes on the history of correlation. Biometrika13, 25e45 (1920).

Google Scholar 

Vargas-Jaimes, J. et al. Impact of climate and land cover changes on the potential distribution of four endemic salamanders in Mexico. J. Nat. Conserv.64, 126066 (2021).

Google Scholar 

Broennimann, O. et al. Measuring ecological niche overlap from occurrence and spatial environmental data. Glob. Ecol. Biogeogr.21, 481–497 (2012).

Google Scholar 

Wang, Y. et al. Plants maintain climate fidelity in the face of dynamic climate change. Proc. Natl Acad. Sci. USA120, e2201946119 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Di Cola, V. et al. ecospat: an R package to support spatial analyses and modeling of species niches and distributions. Ecography40, 774–787 (2017).

ADS 

Google Scholar 

Chen, T. et al. The Genome Sequence Archive family: toward explosive data growth and diverse data types. Genom. Proteom. Bioinform.19, 578–583 (2021).

Google Scholar 

CNCB-NGDC Members and Partners. Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. Nucleic Acids Res.51, D18–D28 (2023).

Google Scholar 

Wan, J. N. Genome sequencing of baobabs. figshare https://doi.org/10.6084/m9.figshare.25422502.v2 (2024).

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