Figure 1 - uploaded by Matheus Bianconi
Content may be subject to copyright.
Origin and dispersal of Alloteropsis semialata in Africa. The time-calibrated phylogenetic tree based on mitochondrial genomes is shown, with letters on nodes (A-G) indicating the organelle lineages (see electronic supplementary material, figure S2 for details). White dots indicate nodes with posterior probabilities of 0.95 or above and grey bars represent 95% HPD intervals around estimated ages. For each sample, the photosynthetic type is indicated with a coloured square and the ploidy level by the number of black dots. All sampled African populations are shown on the map, with circles coloured based on the group indicated on the right of the phylogeny. Arrows indicate putative dispersal events. (Online version in colour.)
Source publication
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photo- synthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the...
Contexts in source publication
Context 1
... organelle phylogenetic trees recovered the seven major lineages reported in previous studies, as well as a clear incongruence between the two organelles ( figure 1 and electronic supplementary material, figure S2 [10][11][12]). Indeed, six individuals, including one hexaploid and one dodecaploid, from Cameroon, Democratic Republic of Congo (DRC) and Zambia form a monophyletic group within plastid lineage DE, but form a paraphyletic group within mitochondrial lineage FG (electronic supplementary material, figure S2). ...
Context 2
... from the B and C clades are spread across northern areas of the Central Zambezian region (Burundi, DRC, and Tanzania), with Zambian accessions derived from within part of clade B (figure 1 and electronic supplementary material, figure S2). Within clade A covering southern Africa, early divergence from accessions from Mozambique and Zimbabwe likely represents the footprint of a gradual migration to South Africa between 1.4 and 0.3 Ma ( figure 1 and electronic supplementary material, figure S2). ...
Context 3
... s i a -O c e a n i a photosynthetic type (PT) Within the C 4 organelle lineage D, accessions from Asia, Oceania and Madagascar are sister to a sample from Angola ( figure 1 and electronic supplementary material, figure S2). The sister lineage E contains a subgroup spread east of the Central Zambezian region (Tanzania, Malawi and Mozambique) and South Africa, while the other subgroup contains one accession from Ethiopia that is sister to samples spread from Kenya to Sierra Leone with very little divergence (figure 1 and electronic supplementary material, figure S2). ...
Context 4
... the order of splits within group FG is compatible with an origin west of the Rift Valley lakes, while the wellsupported relationships within lineages B and C support their origin to the east of the lakes (figure 1). The present-day co-occurrence of FG and BC organelle groups probably follows a migration beyond their refugia after the re-expansion of miombo woodlands ( figure 1) [47,49,50]. ...
Context 5
... directionality of this exchange is unknown, but repeated, unidirectional gene flow mediated by pollen must have occurred in a region where only monoparentally inherited organelles persisted [56], as previously reported for other taxa [57]. One of these organelle lineages originates from the Central Zambezian highlands (lineage FG), while the other originates from the lowlands of eastern Africa (lineage DE; figure 1). Differences in elevation along with predominantly easterly winds could have restricted organelle transport via seed migration but favoured nuclear gene flow via pollen movements from the lowlands to the west. ...
Similar publications
Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within‐species studies based on high‐resolution markers are entirely lacking. The genus...
The budding yeast, Saccharomyces cerevisiae, has served as a model for nearly a century to understand the principles of the eukaryotic life cycle. The canonical life cycle of S. cerevisiae comprises a regular alternation between haploid and diploid phases. Haploid gametes generated by sporulation are expected to quickly restore the diploid phase ma...
Citations
... In another study, genes encoding C 4 PEPCs were investigated in two phylogenetically distant C 4 species, Eleocharis baldwinii and E. vivipara (Besnard et al., 2009). Unexpectedly, C 4 PEPC genes have recently diverged between the two Eleocharis species, supporting the idea that one of them has borrowed this core C 4 gene from the other lineage by hybridization or by a horizontal transfer event, as widely reported in grasses (Bianconi et al., 2020). As E. vivipara belongs to a monotypic C 4 lineage, the C 4 PEPC genes were probably obtained from the more diverse E. baldwinii clade (Roalson et al., 2010;Larridon et al., 2021). ...
The recently published study by Liu et al. (2024) on a high quality, chromosome‐level genome of Eleocharis vivipara provides new insight into the multiple evolution of C4 photosynthesis in Cyperaceae and in particular in Eleocharis. The species studied has the rare feature of alternately using C3 photosynthesis underwater and C4 photosynthesis on land (Ueno et al., 1988), making it an exciting model to better understand the genetic control and evolution of the C4 trait and, in particular, the evolutionary challenge to switch from C3 to C4 photosynthesis from the aquatic to the terrestrial environment. This may imply both the control of genes involved in the C4 pathway and deep cellular anatomical changes. Alternately using C3 or C4 photosynthesis may also lead to evolutionary trade‐offs (e.g., optimization of photosynthetic enzymes in contrasting C3 and C4 biochemical contexts). Maintaining C3 and C4 genes may therefore be necessary; hybridization
(e.g., allopolyploidization) between non‐C4 and C4 taxa could have been involved to favor the emergence of such facultative photosynthetic strategy...
... Genome data, d 13 C values, and population genetic analyses For the genomic analyses, we compiled previously published double digest restriction-site associated DNA sequencing (ddRADSeq) data sets for Alloteropsis semialata (R. Br.) Hitchc. individuals that also had known d 13 C values from field-collected leaves measured using mass spectrometry (Lundgren et al., 2015Bianconi et al., 2020;Olofsson et al., 2021;Alenazi et al., 2023). Depending on the source of the d 13 C values, these were either single measures (Lundgren et al., 2015Bianconi et al., 2020), replicated if the d 13 C values did not match other individuals of the population and genomic group (Olofsson et al., 2021), or medians of triplicate technical replicates if sufficient material was available (Alenazi et al., 2023). ...
... individuals that also had known d 13 C values from field-collected leaves measured using mass spectrometry (Lundgren et al., 2015Bianconi et al., 2020;Olofsson et al., 2021;Alenazi et al., 2023). Depending on the source of the d 13 C values, these were either single measures (Lundgren et al., 2015Bianconi et al., 2020), replicated if the d 13 C values did not match other individuals of the population and genomic group (Olofsson et al., 2021), or medians of triplicate technical replicates if sufficient material was available (Alenazi et al., 2023). In total, the data set comprised 420 individuals collected from 87 populations across Africa and Asia (Supporting Information Table S1), representing the full range of photosynthetic types found in A. semialata (45 9 C 3 ; 132 9 C 3 +C 4 ; 243 9 C 4 ). ...
... Finally, we used whole-genome resequencing data (Bianconi et al., 2020) for 45 A. semialata individuals to determine whether the genes in the GWAS regions were evolving under positive selection. In short, the datasets were downloaded from NCBI sequence read archive and mapped to the reference genome using BOWTIE2, and consensus sequences generated using previously developed methods (Olofsson et al., 2016;Dunning et al., 2022), and a maximum likelihood phylogeny tree for each gene was inferred using RAXML (Stamatakis, 2014) with 100 bootstrap. ...
C4 photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4 is complicated by the fact that variation in photosynthetic type is usually segregated between species that diverged a long time ago.
Here, we perform a genome‐wide association study (GWAS) using the grass Alloteropsis semialata, the only known species to have C3, intermediate, and C4 accessions that recently diverged. We aimed to identify genomic regions associated with the strength of the C4 cycle (measured using δ¹³C), and the development of C4 leaf anatomy.
Genomic regions correlated with δ¹³C include regulators of C4 decarboxylation enzymes (RIPK), nonphotochemical quenching (SOQ1), and the development of Kranz anatomy (SCARECROW‐LIKE). Regions associated with the development of C4 leaf anatomy in the intermediate individuals contain additional leaf anatomy regulators, including those responsible for vein patterning (GSL8) and meristem determinacy (GIF1).
The parallel recruitment of paralogous leaf anatomy regulators between A. semialata and other C4 lineages implies the co‐option of these genes is context‐dependent, which likely has implications for the engineering of the C4 trait into C3 species.
... The inclusion of the mitogenome in phylogenetic analysis has been increasingly applied in the angiosperm [22][23][24]. It is the diversity of genomic data that has brought the discordance of organelle and nuclear signalling into focus [25,26]. Cytonuclear discordance refers to the incongruence between the evolutionary histories of nuclear and cytoplasmic genomes within a species or a group of species. ...
Background
Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.
Results
Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.
Conclusions
The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.
... Our results suggest that Brachystegia evolved recently, as did most African geoxyles, potentially reflecting the development of fire-prone and high-precipitation savannas in Africa (Maurin et al., 2014). Such results challenge previous views on the origin of the miombo because it is usually perceived as much older than our divergence dating analysis suggested (e.g., Senut et al., 2018;Bianconi et al., 2020). Nevertheless, we have to keep in mind that miombolike vegetation sharing the same physiognomy could have existed before the Brachystegia diversification. ...
Premise: Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a dominant genus of trees in miombo woodlands, appears as a key witness of the history of the largest woodland and savanna biome of Africa.
Methods: We reconstructed the evolutionary history of the genus using targeted-enrichment sequencing on 60 Brachystegia specimens for a nearly complete species sampling. Phylogenomic inferences used supermatrix (RAxML‐NG) and summary-method
(ASTRAL‐III) approaches. Conflicts between species and gene trees were assessed, and the phylogeny was time‐calibrated in BEAST. Introgression between species was explored using Phylonet.
Results: The phylogenies were globally congruent regardless of the method used. Most of the species were recovered as monophyletic, unlike previous plastid phylogenetic reconstructions where lineages were shared among geographically close individuals independently of species identity. Still, most of the individual gene trees had low levels of phylogenetic information and, when informative, were mostly in conflict with the reconstructed species trees. These results suggest incomplete lineage sorting and/or reticulate evolution, which was supported by network analyses. The BEAST analysis supported a Pliocene origin for current Brachystegia lineages, with most of the diversification events dated to the Pliocene‐Pleistocene.
Conclusions: These results suggest a recent origin of species of the miombo, congruently with their spatial expansion documented from plastid data. Brachystegia species appear to behave potentially as a syngameon, a group of interfertile but still relatively well-delineated species, an aspect that deserves further investigations.
... A notable example of introgression, potentially explained by gene flow through polyploid bridges, pertains to genes encoding the C 4 photosynthetic pathway in Alloteropsis semialata, which have been laterally acquired from the polyploid Setaria palmifolia complex, most likely in tropical Africa, where both species co-occur (46). Most of the non-C 4 individuals in A. semialata are diploids, with C 4 individuals ranging from diploid to dodecaploid levels (45,75). Although triploid hybrids have not been reported so far for A. semialata, the most plausible path through which genetic information coding for C 4 biochemistry could have introgressed into the diploid level of the species would be through compatible crosses that required the presence of a triploid intermediate, from which a cross of the type 3x × 2x would allow the information to spread down to the diploid level. ...
... An alternative hypothesis may relate the presence of C 4 diploid individuals to the process of diploidization. However, despite the fact that diploidization is a slow process measured at macroevolutionary scales (33), there is direct experimental evidence that crosses between photosynthetic types in diploid A. semialata are viable (75). That is, following introgression from polyploid S. palmifolia, information coding for C 4 biochemistry had to necessarily travel through the different ploidy levels in A. semialata to reach the diploid level, where C 4 and non-C 4 individuals are then capable of exchanging genetic material. ...
Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.
... The photosynthetic types of A. semialata correspond to distinct genetic lineages that probably evolved during the Plio-Pleistocene (Lundgren et al., 2015;Bianconi et al., 2020a) from a common ancestor that used a weak C 4 cycle (Dunning et al., 2017;Fig. 1). ...
... The initial divergence between A. semialata C 4 and non-C 4 types most likely happened in the Central Zambezian miombo woodlands of Africa, where the species originated c. 3 Ma (Lundgren et al., 2015;Bianconi et al., 2020a). The C 3 lineage (clade I) later migrated to Southern Africa and a single C 4 lineage (clade IV) spread across Africa, Madagascar, Southeast Asia, and Oceania. ...
... The Central Zambezian region remained occupied by another C 4 lineage (clade III) and by C 3 + C 4 populations (clade II). The lineages evolved largely in isolation, but repeated episodes of genetic exchange might have contributed to the expansion of the different photosynthetic types (Lundgren et al., 2015;Olofsson et al., 2016Olofsson et al., , 2021Bianconi et al., 2020a). Currently, C 4 plants overlap with C 3 plants in Southern Africa and with C 3 + C 4 ones in the Central Zambezian region, but when they appear mixed (growing close to each other), the C 4 are polyploids and the non-C 4 are diploids, and this ploidy difference probably prevents gene flow between them (Olofsson et al., 2021). ...
C4 photosynthesis is a key innovation in land plant evolution, but its immediate effects on population demography are unclear. We explore the early impact of the C4 trait on the trajectories of C4 and non‐C4 populations of the grass Alloteropsis semialata.
We combine niche models projected into paleoclimate layers for the last 5 million years with demographic models based on genomic data.
The initial split between C4 and non‐C4 populations was followed by a larger expansion of the ancestral C4 population, and further diversification led to the unparalleled expansion of descendant C4 populations. Overall, C4 populations spread over three continents and achieved the highest population growth, in agreement with a broader climatic niche that rendered a large potential range over time. The C4 populations that remained in the region of origin, however, experienced lower population growth, rather consistent with local geographic constraints. Moreover, the posterior transfer of some C4‐related characters to non‐C4 counterparts might have facilitated the recent expansion of non‐C4 populations in the region of origin.
Altogether, our findings support that C4 photosynthesis provided an immediate demographic advantage to A. semialata populations, but its effect might be masked by geographic contingencies.
... A notable example of introgression, potentially explained by gene flow through polyploid bridges, pertains to genes encoding the 4 phosynthetic pathway in Alloteropsis semialata, which have been laterally acquired from the polyploid Setaria palmifolia complex, most likely in tropical Africa, where both species co-occur(42). Most of the non-4 individuals in A. semialata are diploids, with 4 individuals ranging from diploid to dodecaploid levels(41,70). Although triploid hybrids have not been reported so far for A. semialata, the most plausible path through which genetic information coding for 4 biochemistry could have introgressed into the diploid level of the species would be through compatible crosses that required the presence of a triploid intermediate, from which a cross of the type 3 × 2 would allow the information to spread down to the diploid level. ...
... An alternative hypothesis may relate the presence of 4 diploid individuals to the process of diploidization. However, despite the fact that diploidization is a slow process measured at macroevolutionary scales(11), there is direct experimental evidence that crosses between photosynthetic types in A. semialata are viable(70). That is, following introgression from polyploid S. palmifolia, information coding for 4 biochemistry had to necessarily travel through the different ploidy levels in A. semialata to reach the diploid level, where 4 and non-4 individuals are then capable of exchanging genetic material. ...
Many organisms have more than two sets of chromosomes, due to whole genome duplication (WGD), and are thus polyploid. Despite usually being an ephemeral state in the history of life, polyploidy is widely recognized as an important source of genetic novelty over macroevolutionary scales. More recently, polyploidy has also been shown to facilitate interspecific gene flow, circumventing reproductive barriers between their diploid ancestors. Yet, the implications of WGD-linked introgression on community-level evolutionary dynamics remain unknown. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of viability, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents WGD-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, which allows a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with non-zero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on evolutionary change within and between mixed-ploidy populations.
... These genes were acquired from at least nine different donors separated by 20-40 Myr of evolution and multiple speciation events that gave rise to thousands of descendant species Hibdige et al., 2021). Alloteropsis semialata originated in tropical Africa, where divergent genetic lineages and the sister species Alloteropsis angusta still occur (Bianconi et al., 2020). Previous analyses have identified laterally acquired genes that are present in multiple Alloteropsis species, that were either acquired before the divergence of the species or that were subsequently introgressed after their speciation (Olofsson et al., 2016Dunning et al., 2019). ...
... This includes three A. semialata (R. Br.) Hitchc. assemblies that, together with the previously sequenced genome from an Australian individual (accession AUS1; Clade IV; Dunning et al., 2019), encompass the four main nuclear clades within this species ( Fig. 1; Bianconi et al., 2020): one individual from South Africa (accession RSA5-3; Clade I), one from Tanzania (accession TAN1-04B; Clade II) and one from Zambia (accession ZAM1505-10; Clade III). We also generated an assembly for A. angusta Stapf from a Ugandan accession (AANG_UGA4). ...
... In all but two cases, a single reference gene was sufficient to recover all loci in the laterally acquired clade, with two nonoverlapping annotated sequences used as references where this was not possible. We then determined the presence of each of these representative genes in whole-genome short-read datasets belonging to 45 diploid Alloteropsis accessions (including the five individuals with reference genomes; Bianconi et al., 2020), using a combination of BLASTN searches (minimum alignment length 100 bp) and phylogenetic analyses. For each of the 45 datasets, putative reads corresponding to each laterally acquired gene were identified via a BLASTN analysis with default parameters. ...
Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics.
We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses.
We detect 168 laterally acquired genes in the five reference genomes (32–100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6–28 per Ma) and subsequent losses (11–24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02–0.8% per Ma).
This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.
... The photosynthetic variation existing in A. semialata was discovered based on leaf anatomical surveys and measurements of carbon isotopes independently by Ellis (1974) and Brown (1975). The differences between photosynthetic types within this species have been repeatedly studied since then, focusing on the ecological (Ripley et al., 2007(Ripley et al., , 2010bIbrahim et al., 2008;Osborne et al., 2008;Bateman and Johnson, 2011;Lundgren et al., 2015), cytogenetic (Frean and Marks, 1988;Liebenberg and Fossey, 2001;Lundgren et al., 2015;Bianconi et al., 2020;Olofsson et al., 2021), physiological (Frean et al., 1980(Frean et al., , 1983aLundgren et al., 2016) and biochemical variation (Ueno and Sentoku, 2006;Phansopa et al., 2020), and more recently, on evolutionary and genomic aspects of C 4 photosynthesis (Ibrahim et al., 2009;Christin et al., 2012;Lundgren et al., 2015Olofsson et al., 2016Olofsson et al., , 2021Dunning et al., 2017Dunning et al., , 2019aBianconi et al., 2018Bianconi et al., , 2020Curran et al., 2022). In this review, we consolidate the knowledge accumulated on this study system. ...
... The photosynthetic variation existing in A. semialata was discovered based on leaf anatomical surveys and measurements of carbon isotopes independently by Ellis (1974) and Brown (1975). The differences between photosynthetic types within this species have been repeatedly studied since then, focusing on the ecological (Ripley et al., 2007(Ripley et al., , 2010bIbrahim et al., 2008;Osborne et al., 2008;Bateman and Johnson, 2011;Lundgren et al., 2015), cytogenetic (Frean and Marks, 1988;Liebenberg and Fossey, 2001;Lundgren et al., 2015;Bianconi et al., 2020;Olofsson et al., 2021), physiological (Frean et al., 1980(Frean et al., , 1983aLundgren et al., 2016) and biochemical variation (Ueno and Sentoku, 2006;Phansopa et al., 2020), and more recently, on evolutionary and genomic aspects of C 4 photosynthesis (Ibrahim et al., 2009;Christin et al., 2012;Lundgren et al., 2015Olofsson et al., 2016Olofsson et al., , 2021Dunning et al., 2017Dunning et al., , 2019aBianconi et al., 2018Bianconi et al., , 2020Curran et al., 2022). In this review, we consolidate the knowledge accumulated on this study system. ...
... It has been suggested that A. papillosa is a possible hybrid, because the linear leaf-blades resemble A. semialata while the inflorescence and spikelet characters are reminiscent of A. cimicina (Clayton and Renvoize, 1982). The divergence of samples assigned to A. cimicina and A. paniculata was estimated as ~2.5 Ma (Olofsson et al., 2016;Bianconi et al., 2020), and these two species will be discussed jointly as 'A. cimicina' in this review. ...
Background:
Numerous groups of plants have adapted to CO2 limitations by independently evolving C4 photosynthesis. This trait relies on concerted changes in anatomy and biochemistry to concentrate CO2 within the leaf and thereby boost productivity in tropical conditions. The ecological and economical importance of C4 photosynthesis has motivated intense research, often relying on comparisons between distantly related C4 and non-C4 plants. The photosynthetic type is fixed in most species, with the notable exception of the grass Alloteropsis semialata. This species includes populations exhibiting the ancestral C3 state in southern Africa, intermediate populations in the Zambezian region and C4 populations spread around the paleotropics.
Scope:
We compile here the knowledge on the distribution and evolutionary history of the Alloteropsis genus as a whole and discuss how this has furthered our understanding of C4 evolution. We then present a chromosome-level reference genome for a C3 individual and compare the genomic architecture to that of a C4 accession of A. semialata.
Conclusions:
Alloteropsis semialata represents one of the best systems to investigate the evolution of C4 photosynthesis as the genetic and phenotypic variation provides a fertile ground for comparative and population-level studies. Preliminary comparative genomic investigations show the C3 and C4 genomes are highly syntenic, and have undergone a modest amount of gene duplication and translocation since the different photosynthetic groups diverged. The background knowledge and publicly available genomic resources make Alloteropsis semialata a great model for further comparative analyses of photosynthetic diversification.
... Landscape effects on the genetic diversity of Noronhia spinifolia A strong continuous spatial structure Beyond revealing surprisingly high levels of genetic diversity, our results also show complementary signals of a strong continuous structure in space (PCA, clustering and IBD), from both organelles and the nucleus, in contrast to generally expected incongruent patterns among genomes (Bianconi et al., 2020;Olofsson et al., 2019). While the northwest-southeast differentiation cline represented as much as ~15% of the variance of the PCA on nuclear data, the geographic Euclidean distance alone explained up to ~55% of the nuclear genetic variance using IBD tests. ...
Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human‐driven deforestation is intense throughout Madagascar, exceptions in areas like the Loky‐Manambato region (North) raise questions. Such regions also harbor a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong‐Wa) to better understand the vegetation dynamic in the Loky‐Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction associated sequencing data (RADseq) and chloroplast microsatellites (cpSSR). Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long‐standing habitat mosaic in the region. This sustains a major and long‐term role of riparian corridors in maintaining connectivity across those antique mosaic‐habitats, calling for the study of organismal interactions that promote gene flow.
