Philippa Kaur

Authors and AffiliationsJacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, IsraelGopal MuraliMitrani Department of Desert Ecology, The Swiss Institute for Dryland Environments and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, IsraelGopal Murali & Uri RollDepartment F.-A. Forel for Aquatic and Environmental Sciences, Faculty of Science, University of Geneva, Geneva, SwitzerlandTakuya IwamuraDepartment of Forest Ecosystems and Society, College of Forestry, Oregon State University, Corvallis, OR, USATakuya IwamuraSchool of Zoology, Tel Aviv University, Tel Aviv, IsraelShai MeiriThe Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, IsraelShai MeiriAuthorsGopal MuraliTakuya IwamuraShai MeiriUri RollCorresponding authorCorrespondence to
Gopal Murali. More

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Oil palm plantations can supplant once biodiverse tropical forests. As planted areas expand, it is vital to plan landscapes to better balance biodiversity and oil palm production. Strategic ‘set-asides’ offer a key approach.In recent decades, oil palm has expanded spectacularly in some of the most biodiverse areas of the tropics, especially in Indonesia and Malaysia. This expansion has caused extensive deforestation (including loss of more than 2.1 million ha of primary forests in Borneo2, as well as other forests and agroforests), and management of plantations often relies heavily on clearing, herbicides and pesticides. This has generated many direct and indirect impacts on wildlife, ecosystems, climate and human communities3. Further expansion is ongoing, and global demand continues to rise4. More

Genetic and morphological delineation between G. huxleyi strainsWe first assessed genetic variability through analysis of genomic polymorphism to determine whether distinct genetic lineages exist in G. huxleyi and to test whether these relate to morphotypes. We used 2,086,643 high-quality biallelic single nucleotide polymorphisms (SNPs) retrieved from the 47 clonal culture strains with the best genome sequence coverage ( >20×). A principal component analysis (PCA) and a discriminant analysis in principal component (DAPC) both delineate three well-defined genetic groups, with the distribution of strains being unequal and with no overlap on the principal components (Fig. 1a; Supplementary Fig. S3a,b). With regards to population structure, the DAPC analysis suggested that 3 clusters (K = 3) can be used to depict a genotype membership matrix for each strain (Fig. 1b; Supplementary Fig. S4). As such, it confirmed the three-lineage delineation proposed by the PCA, while illustrating no admixture between lineages.Fig. 1: Relationship between genetic structure and morphotypes in G. huxleyi.a Principal component analysis (PCA) based on 2,086,643 SNPs recovered from 47 G. huxleyi genomes; b Relationship between coalescent species phylogeny (ASTRAL tree based on 1000 supergenes) and DAPC clustering; c Correspondence between morphotypes and lineages within G. huxleyi, and sub-lineages within A1 (scale bar = 4 μm). Variable elements in relation to genotypes are highlighted in the schematics under the SEM pictures; d Distribution of coccolith length for 5 randomly chosen strains representing each clade and sub-clade, with a jittered box-plot on the left and a half-violin plot on the right for each group; e Matrix plot of Bonferroni corrected p-value corresponding to the Dunn-test for the comparison of coccolith length measurements between groups.Full size imagePhylogenetic inference based on alignments with higher mapping coverage only (47 strains) or including sequences with lower mapping coverage (59 strains) all supported segregation of strains into three main lineages, which we term clades A1, A2 and B, with A1 and A2 being more closely related to each other than to B (Fig. 1b; Supplementary Fig. S5a, b). This delineation is congruent with previous studies on the phylogeny of the Gephyrocapsa genus [17, 46, 65]. These clades also correspond to differences in morphotypes (Fig. 1b, c). All strains in clade A1 produce unambiguous A-group coccolith morphotypes (type A and type R). Similarly, all strains in clade B produce unambiguous B-group coccolith morphotypes (type B and type O). Clade A2 is less distinctive, with strains producing lightly calcified type A coccoliths. Some of these strains could be classified as type B/C [66] or C (both regarded as B-group morphotypes), but distinctive by the lower elevation of distal shield elements and by greater degree of calcification of the central area grid (which is reduced and sometimes absent in morphotypes B/C and C). At a finer level, clade A1 is composed of four sub-clades, which we term A1a, A1b, A1c, and A1d. Strains in sub-clades A1a, A1c and A1d all produce coccoliths with type A morphologies and distinctive degrees of calcification: strains in the sub-clade A1a form relatively lightly calcified coccoliths with regular elements, while strains in sub-clades A1c and A1d produce similar moderately calcified coccoliths, sometimes with conspicuous irregularities (inner tube elements overlapping into the central area). Strains in clade A1b produce distinct coccoliths exhibiting A-group morphology but with heavy calcification, including forms with heavily calcified shields which have been termed type R and also forms with heavily calcified central areas which have been referred to as “type A overcalcified”. Some clade A2 strains produce coccoliths with a similar morphology to strains in A1a, indicative of partially cryptic lineages (Supplementary Fig. S2; Supplementary Table S4).The congruence between morphotypes and clades is also supported by significant differences in the length of coccoliths measured between some of the clades (Fig. 1d, e). The morphogroups A and B differ significantly, and insignificant comparison relates to the comparison of sub-clades against the clade A2, which reinforces the closest relationship between A1 and A2. We denote also that the case of A1a and A2 demonstrating no significant difference in coccolith length concurs with the cryptic delineation mentioned above.Based on the clustering analyses and the phylogenetic reconstructions, we tested whether different groupings are distinct species with regards to the null hypothesis “G. huxleyi is a single species”, which correspond to the current state of taxonomy. Species delimitation based on comparison of Marginal Likelihood Estimators (MLE) with Bayes Factors (BF) supported the hypothesis that the three lineages depicted by ordination and phylogenetic reconstructions are distinct species as the best model (Table 1).Table 1 Species delimitation based on Bayes Factor Delimitation (BDF).Full size tableD-statistics calculated to estimate gene flow reveal a non-significant excess of alleles shared between the three lineages (Fig. 2a; Supplementary Table S5). Fbranch statistics, (fb) revealed significant signatures of gene-flow between sub-lineages within A1 associated with correlated estimates in relation to A1a, A2 and B (Fig. 2a) [60]. Signatures on the basal branch of diversification in A1 may correspond to genetic exchanges between A1 and B, with gene-flow signatures attributed to A2 corresponding to correlated estimates due to common ancestry. Recent signatures of gene-flow throughout the evolution of A1 are thus likely associated to the common ancestry between A1a, A2 and B during gene-flow events between the sub-lineages, as supported by the non-significant D statistics between the three lineages. Moreover, the phylogenetic network revealed similar convolutions between A1 sub-lineages but clear separation of the main lineages and longer branches in the A2 lineage (Fig. 2b).Fig. 2: Excess of allele sharing and differentiation in G. huxleyi.a f-branch (fb) statistics between lineages and sub-lineages. The gradient represents the fb score, grey blocks represents tests not consistent with the species tree (for each branch on the topology of the y axis, having itself or a sister taxon as donor on the topology of the x axis); asterisks denote block jack-knifing significance at p  More

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