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  • Jiaqi Wang, Yue Ding, Yinfeng Li, Xintong Gao, Xiangming Kong, Feng Long, Yishan Feng, Yan Zhang, Yu Li, Zijian Yu, Tianyu Lei, Li Wang, Xiu‐Qing Li, and Jinpeng Wang
    Online available: 2024-07-01
    Oleaceae, a eudicot family with great species diversity, has attracted much attention from botanists because it contains many plants with important economic, medicinal, and ornamental values. However, the history of polyploidization and ancestral genome reshuffling of Oleaceae remains unclear. Here, we clarified an Oleaceae-common hexaploidization (OCH) event occurring at ~53–61 million years ago (Ma) common in all Oleaceae plants and an Oleaceae-recent tetraploidization (ORT) event occurring at ~18–21 Ma shared by the lineages of Syringa, Olea, Osmanthus, and Fraxinus. We found that high-frequency polyploidization events drove the frequency of gene loss in Oleaceae genomes and extended the size of regions containing adjacent gene loss, thereby promoting the degree of genome fragmentation. We revealed that biased fractionation between the OCH- and ORT-produced subgenomes is likely attributed to the origin of allopolyploidization in the OCH and ORT events. Significantly, through paleochromosome rearrangement comparisons, we proposed a "two-step" genome duplication model for OCH and determined the duplicated orders of OCH tripled genome. We reconstructed 11 protochromosomes of the most recent ancestral Oleaceae karyotype (AOK) and elucidated the trajectories of immense paleochromosome reorganization of Oleaceae species from ancestral eudicot karyotype. Notably, we tracked the diversification history of secondary metabolite synthesis genes in the Oleaceae and explored the effects of paleogenome evolution on specialized metabolite synthesis. Our findings provide new insights into the polyploidization and paleogenomic evolution of Oleaceae and have important scientific significance for understanding the genetic basis of species and secondary metabolic diversity in Oleaceae.
  • Enzo Jugieau, Victor Talmot, Cybill Staentzel, Sandra Noir, and Laurent Hardion
    Online available: 2024-05-13
    The two invasive Reynoutria species, Reynoutria japonica var. japonica and Reynoutria sachalinensis, and their hybrid Reynoutria x bohemica are often misidentified by managers and nonspecialists. The taxonomic confusions are all the more exacerbated by the infraspecific variability of introduced populations in terms of morphology, genetic diversity, and ploidy level. We resolved the identity of North-Eastern French invasive populations using 4582 single-nucleotide polymorphisms (SNPs) from a RADseq analysis, DNA contents estimated by flow cytometry, and 12 vegetative morphometric variables. The SNPs supported only one single genotype for R. japonica over 11 localities, while the nine localities of Reynoutria x bohemica were represented by one genotype each. Estimation of genome size using DAPI staining and flow cytometry revealed only octoploid cytotypes for R. japonica and hexaploid cytotypes for R. x bohemica, whereas R. sachalinensis was represented by tetraploid and hexaploid cytotypes. Among morphometric variables, no single one allows for a clear differentiation of the three taxa. We propose a combination of characters to easily and quickly identify these three invasive taxa based on six vegetative criteria including leaf and apex length, as well as leaf shape, leaf base, and apex shape, and the extrafloral nectaries on the node.
  • Ryan A. Folk, Aliasghar A. Maassoumi, Carolina M. Siniscalchi, Heather R. Kates, Douglas E. Soltis, Pamela S. Soltis, Michael B. Belitz, and Robert P. Guralnick
    Online available: 2024-05-13
    Astragalus (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of environmental challenges. Here, we identify the spatial distribution of diversity and endemism in Astragalus using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD) and used randomization approaches to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo- and neoendemism. Phylogenetic regionalization recovered an east-west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.
  • Qiang He, Yuqing Miao, Xinyuan Zheng, Yaru Wang, Yitao Wang, Zheng Jia, Hongyu Zhang, Yu Wang, Yao Xiao, Cailian Du, Wei Li, Longsheng Xing, and Huilong Du
    Online available: 2024-04-01
    Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti‐aging, anti‐inflammatory and anti‐oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near‐complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of long terminal repeats (LTRs) contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole‐genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with disease tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in roost, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.
  • Roser Vilatersana, Juan Antonio Calleja, Sonia Herrando‐Moraira, Núria Garcia‐Jacas, and Alfonso Susanna
    Online available: 2024-02-24
    Understanding the richness and diversification processes in the Mediterranean basin requires both knowledge of the current environmental complexity and paleogeographic and paleoclimate events and information from studies that introduce the temporal dimension. The Carthamus–Carduncellus complex (Cardueae, Compositae) constitutes a good case study to investigate the biogeographic history of this region because it evolved throughout the basin. We performed molecular dating, ancestral area estimation, and diversification analyses based on previous phylogenetic studies of a nearly complete taxon sampling of the complex. The main aims were to determine the role of tectonic and climatic events in the disjunction of the complex and the expansion route of the two main lineages, Carduncellus s.l. and Carthamus. Our results suggest that the main lineages in the complex originated during the Miocene. Later, all main paleogeographic and paleoclimatic events during the Neogene and Pleistocene in the Mediterranean basin had an important imprint on the evolutionary history of the complex. The Messinian Salinity Crisis facilitated the dispersion of the genus Carduncellus from North Africa to the Iberian Peninsula and the split of the genera Phonus and Femeniasia from the Carduncellus lineage. The onset of the Mediterranean climate in the Pliocene together with some orogenic processes could be the main causes of the diversification of the genus Carduncellus. In contrast, Pleistocene glaciations played a key role in the species diversification of Carthamus. In addition, we emphasize the problems derived from secondary dating and the existing differences between two previous dating analyses of the tribe Cardueae.
  • Ana M. Bossa‐Castro, Matheus Colli‐Silva, José R. Pirani, Barbara A. Whitlock, Laura T. Morales Mancera, Natalia Contreras‐Ortiz, Martha L. Cepeda‐Hernández, Federica Di Palma, Martha Vives, and James E. Richardson
    Online available: 2024-02-18
    Crop wild relatives (CWRs) of cultivated species may provide a source of genetic variation that can contribute to improving product quantity and quality. To adequately use these potential resources, it is useful to understand how CWRs are related to the cultivated species and to each other to determine how key crop traits have evolved and discover potentially usable genetic information. The chocolate industry is expanding and yet is under threat from a variety of causes, including pathogens and climate change. Theobroma cacao L. (Malvaceae), the source of chocolate, is a representative of the tribe Theobromateae that consists of four genera and c. 40 species that began to diversify over 25 million years ago. The great diversity within the tribe suggests that its representatives could exhibit advantageous agronomic traits. In this study, we present the most taxonomically comprehensive phylogeny of Theobromateae to date. DNA sequence data from WRKY genes were assembled into a matrix that included 56 morphological characters and analyzed using a Bayesian approach. The inclusion of a morphological data set increased resolution and support for some branches of the phylogenetic tree. The evolutionary trajectory of selected morphological characters was reconstructed onto the phylogeny. This phylogeny provides a framework for the study of morphological and physiological trait evolution, which can facilitate the search for agronomically relevant traits.
  • Michael D. Crisp, Bui Q. Minh, Bokyung Choi, Robert D. Edwards, James Hereward, Carsten Kulheim, Yen Po Lin, Karen Meusemann, Andrew H. Thornhill, Alicia Toon, and Lyn G. Cook
    Online available: 2024-01-23
    Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally, Eucalyptus was defined by its operculum, but when phylogenies placed Angophora, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, Corymbia. Yet, generic delimitation in the tribe Eucalypteae remains uncertain. Here, we address these problems using phylogenetic analysis with the largest molecular data set to date. We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multispecies coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among Arillastrum, Angophora, Eucalyptus, and Corymbia using Shimodaira's approximately unbiased test. Phylogenetic mapping was used to explore the evolution of perianth traits. Monophyly of Corymbia relative to Angophora was decisively rejected. All alternative relationships among the seven currently recognized Eucalypteae genera imply homoplasy in the evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades, except that the expression of separate sepals and petals in Angophora, which is nested within the operculate genus Corymbia, appears to be a reversal to the plesiomorphic perianth structure. Here, we formally raise Corymbia subg. Blakella to genus rank and make the relevant new combinations. We also define and name three sections within Blakella (Blakella sect. Blakella, Blakella sect. Naviculares, and Blakella sect. Maculatae), and two series within Blakella sect. Maculatae (Blakella ser. Maculatae and Blakella ser. Torellianae). Corymbia is reduced to the red bloodwoods.
  • Pablo Aguado‐Ramsay, Tamara Villaverde, Ricardo Garilleti, J. Gordon Burleigh, Stuart F. McDaniel, Maren Flagmeier, Jurgen Nieuwkoop, Arno van der Pluijm, Florian Hans, Francisco Lara, and Isabel Draper
    Online available: 2023-12-19
    Currently, a wide range of genomic techniques is available at a relatively affordable price. However, not all of them have been equally explored in bryophyte systematics. In the present study, we apply next-generation sequencing to identify samples that cannot be assigned to a taxon by morphological analysis or by Sanger sequencing methods. These samples correspond to a moss with an enigmatic morphology that has been found throughout Western Europe over the last two decades. They exhibit several anomalies in the gametophyte and, on the rare occasions that they appear, also in the sporophyte. The most significant alterations are related to the shape of the leaves. Morphologically, all specimens correspond to mosses of the genus Lewinskya, and the least modified samples are potentially attributable to the Lewinskya affinis complex. Specimen identifications were first attempted using up to seven molecular markers with no satisfactory results. Thus, we employed data generated from targeted enrichment using the GoFlag 408 flagellate land plant probe set to elucidate their identity. Our results demonstrate that all the enigmatic samples correspond to a single species, L. affinis s.str. This approach provided the necessary resolution to confidently identify these challenging samples and may be a powerful tool for similar cases, especially in bryophytes.
  • Cai-Xia Wei, Phillip E. Jardine, Li-Mi Mao, Luke Mander, Mao Li, William D. Gosling, Carina Hoorn
    J Syst Evol. 2024, 62(4): 687-701.
    https://doi.org/10.1111/jse.13021
    The grasses are one of the most diverse plant families on Earth. However, their classification and evolutionary history are obscured by their pollen stenopalynous (similar) morphology. A combination of high-resolution imaging of pollen surface ornamentation and computational analysis has previously been proposed as a promising tool to classify grass taxonomic boundaries. In this study, we test this hypothesis by studying Poaceae pollen across the phylogeny from plants collected in northern South America and also from published literature across the globe. We assessed if morphotypes that we establish using descriptive terminology are supported by computational analysis, if they vary along six (a)biotic variables and vary across the phylogeny. Based on this analysis, we constructed a reference framework for pollen surface ornamentation morphotypes. Our results showed that there is a wide variation of grass pollen surface ornamentation. We identified nine new and confirmed six known morphotypes, establishing a data set for 223 species (243 individual plant specimens) that represent 11 subfamilies. Computational analysis showed that our morphotypes are well-supported by two quantitative features of pollen sculptural elements (size and density). The specific data set and mapping of the phylogeny confirmed that pollen morphological sculpture is unrelated to (a)biotic variables and is diverse across the phylogeny.
    Pollen surface ornamentation shows a high diversity across the Poaceae phylogeny. The different colors and the number of symbols (square or circle) in the grid show the distribution of the 15-grass pollen morphotypes identified for each specimen in each subfamily.
  • Dong-Mei Jin, Quan Yuan, Xi-Ling Dai, Gregor Kozlowski, Yi-Gang Song
    J Syst Evol. 2024, 62(4): 677-686.
    https://doi.org/10.1111/jse.13022
    Subtropical evergreen broad-leaved forest (EBLF) is the predominant vegetation type in eastern China. However, the majority of the region it covers in eastern China was an arid area during the Paleogene. The temporal history and essential factors involved in the evolution of subtropical EBLFs in eastern China remain enigmatic. Here we report on the niche evolution of Quercus section Cyclobalanopsis, which appeared in south China and Japan during the Eocene and became a dominant component of subtropical EBLFs since the Miocene in eastern Asia, using integrative analysis of occurrences, climate data and a dated phylogeny of 35 species in Cyclobalanopsis. Species within clades Cyclobalanoides, Lamellosa, and Helferiana mainly exist in the Himalaya–Hengduan region, adapting to a plateau climate, while species within the other clades mainly live in eastern China under the control of the East Asian monsoon. Reconstructed history showed that significant divergence of climatic tolerance in Cyclobalanopsis began around 19 million years ago (Ma) in the early Miocene. Simultaneously, disparities in precipitation of wettest/warmest quarter and annual precipitation were markedly enhanced in Cyclobalanopsis, especially in the recent eastern clades. During the Miocene, the marked radiation of Cyclobalanopsis and many other dominant taxa of subtropical EBLFs strongly suggest the rapid formation and expansion of subtropical EBLFs in eastern China. Our research highlights that the intensification of the East Asian monsoon and subsequent occupation of new niches by the ancient clades already present in the south may have jointly promoted the formation of subtropical EBLFs in eastern China since the early Miocene.
    Subtropical evergreen broad-leaved forest (EBLF) is the predominant vegetation type in eastern China, of which the evolutionary history remains enigmatic. Quercus section Cyclobalanopsis has been dominant component of subtropical EBLFs since the Miocene in eastern Asia. Here we report on the niche evolution of Quercus section Cyclobalanopsis, using integrative analysis of occurrences, climate data and a dated phylogeny of 35 species in Cyclobalanopsis. Species belong to clades Cyclobalanoides, Lamellosa, and Helferiana usually habitat in the Himalaya–Hengduan region, adapting to a plateau climate; while species belonging to Semiserrata, Acuta, Glauca, and Gilva mainly live in eastern China, under the control of the East Asian monsoon. The disparity of tolerance to precipitation of the wettest quarter in Cyclobalanopsis has been markedly enhanced since 19 Ma. Meanwhile, significant divergence of climatic tolerance to precipitation began around the early Miocene. Our research highlights that the intensification of the East Asian monsoon system and subsequent species diversification and occupation of new niches by the ancient clades already present in the south may have jointly promoted the formation of subtropical EBLFs in eastern China since the early Miocene.
  • Jacopo Franzoni, Giovanni Astuti, Gianluigi Bacchetta, Giulio Barone, Fabrizio Bartolucci, Liliana Bernardo, Angelino Carta, Fabio Conti, Gianniantonio Domina, Božo Frajman, Gianpietro Giusso del Galdo, Duilio Iamonico, Mauro Iberite, Luigi Minuto, Marco Sarigu, Ana Terlević, Alessia Turini, Lucia Varaldo, Daniel Volgger, Lorenzo Peruzzi
    J Syst Evol. 2024, 62(4): 589-602.
    https://doi.org/10.1111/jse.13025
    European wild carnations (Dianthus) are represented by a high number of taxa organized in unresolved taxonomies. In particular, taxa belonging to the Dianthus virgineus L. complex in the Central Mediterranean have been delimited mainly with qualitative morphological data and still await quantitative investigations, which are vital to understand boundaries and relations among plant diversity groups. Here, we examine the phenotypic features of nuclear genome organization testing for species boundaries in this complex. We have studied the chromosome number, the total haploid length (THL), and the relative genome size (RGS) in 122 populations belonging to 25 out of 33 taxa of the complex. All the studied populations have 2n = 2x = 30 chromosomes, and the THL ranges from 14.09 to 20.71 μm. Genome size estimations support the absence of polyploidization events, but show a certain degree of variation (0.318–0.423 arbitrary units). The RGS variation is not in agreement with current taxonomic treatment, but rather shows a geographical pattern, with higher values in Sicily and Sardinia. No correlation between the THL and the RGS was detected, possibly due to the stable chromosome number and the small size of chromosomes. A number of evolutionary unique groups lower than the number of currently accepted taxa may be hypothesized.
    Taxa belonging to the Dianthus virgineus L. complex in the Central Mediterranean have been delimited mainly with qualitative morphological data and still await quantitative investigations. Here, we examined phenotypic features of nuclear genome organization testing for species boundaries in this complex. A constant diploid chromosome number, coupled with few relative genome size (RGS) differences, was observed among taxa of the D. virgineus complex in the Central Mediterranean. A geographical, rather than taxonomic, RGS variation allowed speculations on the actual evolutionary relationships within this complex.
  • Jorge Cruz-Nicolás, Norberto Martínez-Méndez, Erika Aguirre-Planter, Luis E. Eguiarte, and Juan P. Jaramillo-Correa
    J Syst Evol. 2024, 62(3): 368-383.
    https://doi.org/10.1111/jse.13000
    Interspecific trait divergence may reflect adaptation and reproductive isolation, particularly after the rapid differentiation that may follow the colonization of new environments. Although new lineages are generally expected to be morphologically and ecologically similar to their ancestors, environmental forces can also drive adaptive differentiation along specific phenotypic axes. We used climate niche models and comparative analyses based on a previously inferred phylogeny to examine the history of ecological and morphological divergence of Neotropical firs (Abies Mill., Pinaceae), a group of conifers that have recently colonized and diversified in the mountains of Mexico and northern Central America. We inferred past secondary contact zones by comparing current and past climate niche projections and looked for evidence of recent interspecific gene flow using genomic data. Neotropical firs have similar niches to each other and show a strong phylogenetic signal for most evaluated morphological traits. Analyses based on individual variables suggested a random walk model of differentiation. However, early adaptation to tropical conditions is inferred in the ancestor of the southernmost firs, as all modern southern taxa are differentiated climatically from Abies concolor, the northernmost species. In addition, observed autapomorphic traits for soil properties and the number of resin ducts in needles are consistent with possible species-specific adaptations. Thus, a combination of nonadaptive and adaptive processes along different phenotypic axes, some related to the environment, likely operated after the southward migration of this plant lineage from North America and its subsequent radiation in the Neotropics.
    Past climate niche projections of Neotropical firs revealed larger past than current distributions, which translated in recent interspecific gene flow, according to genome data analyses. Neotropical firs have similar niches and show strong phylogenetic signals for most traits evaluated, which predominantely fitted the random walk model, as expected for nonadaptive radiations. However, an early adaptation to tropical conditions in the ancestor of southernmost firs was inferred; all modern southern taxa are climatically differentiated from northernmost Abies concolor, suggesting the possible contribution of nonadaptive and adaptive processes to fir differentiation.
  • Han-Jing Liu, Ming-Hui Li, Zhen Wang, Ting Wang, and Ying-Juan Su
    J Syst Evol. 2024, 62(3): 457-474.
    https://doi.org/10.1111/jse.12999
    Having a comprehensive understanding of genetic differentiation, responses to environmental change and demographic history is critical for genetic improvement and conservation efforts. Forest trees are an excellent resource for understanding population differentiation and adaptive genetic variation due to their ability to adapt to different climates and environments. Cephalotaxus oliveri is a relict conifer endemic to China. In this study, we generated transcriptome data and identified 17 728 high-quality single-nucleotide polymorphisms (SNPs) from 18 populations. We found significant negative correlations between expression diversity and nucleotide diversity within and among populations, suggesting that gene expression and nucleotide diversity have a reciprocal relationship when the species adapts to the environment. The analyses of population structure showed that C. oliveri displayed a striking genetic structure with four groups. BayeScEnv and RDA methods detected the signatures of local adaptation, and identified that 738 outlier SNPs were associated with precipitation, temperature and soil conditions across heterogeneous environmental conditions. Approximate Bayesian computation analyses showed that the first and second divergence occurred in the late Miocene (c. 10.075 million years ago [Ma]) and the middle Pleistocene transition (c. 0.815 Ma), respectively. Ecological niche modeling of C. oliveri revealed signs of westward expansion after the last glacial maximum, while it was predicted to experience significant range contractions in future climate change scenarios. Geographical factors and environmental factors in southern China have played a critical role in establishing the current genetic diversity and population structure of C. oliveri. This study provides an important reference for forest resource management and conservation for C. oliveri.
    In this study, we generated transcriptome data and identified 17 728 high-quality single-nucleotide polymorphisms from 18 Cephalotaxus oliveri populations. We found significant negative correlations between expression diversity and nucleotide diversity within and among populations. The analyses of population structure showed that C. oliveri displays a striking genetic structure with four groups. BayeScEnv and RDA methods detected the signatures of local adaptation. Approximate Bayesian computation analyses showed that the first and second divergence occurred in the late Miocene (c. 10.075 million years ago [Ma]) and middle Pleistocene transition (c. 0.815 Ma), respectively. Ecological niche modeling of C. oliveri revealed signs of westward expansion after the last glacial maximum, while it is predicted to experience significant range contractions in the future.
  • Ivón M. Ramírez-Morillo, Laura A. Espinosa-Barrera, Carolina Granados Mendoza, Sandra I. Vera-Paz, Daniel D. Díaz Contreras Díaz, and Katya J. Romero-Soler
    J Syst Evol. 2024, 62(3): 421-437.
    https://doi.org/10.1111/jse.13004
    Full plastomes have recently proven to be a valuable data source for resolving recalcitrant phylogenetic relationships in the flowering plant family Bromeliaceae. The study of complete plastomes has additionally led to the discovery of new structural rearrangements and advanced our understanding of bromeliad plastome diversity and evolution. Here, we focus on the study of full plastomes of the bromeliad subfamily Hechtioideae to assess phylogenetic relationships, marker informativeness, and plastome structure and evolution. Using whole-genome sequencing data, we de novo assembled and annotated new plastid genomes of 19 Hechtioideae species plus one representative each from the Pitcairnioideae and Puyoideae subfamilies and compared them with four additional available plastomes from other bromeliad subfamilies. Our phylogenetic analysis using complete plastome sequences not only recovered the three currently recognized genera of Hechtioideae as monophyletic, strongly supporting Mesoamerantha as sister of Bakerantha and Hechtia, but also improved statistical support at different phylogenetic depths within the subfamily. We identified a set of highly informative loci, some of them explored for the first time in Hechtioideae. Structural rearrangements, including expansions and contractions of the inverted repeats, large inversions, and gene loss and potential pseudogenization were detected mainly within the genus Hechtia. Evolutionary trait rate shifts were associated with the size and guanine–cytosine content of the small single copy and inverted repeats.
    Analysis of complete plastome sequences obtained by whole-genome sequencing improved statistical support across different phylogenetic depths in Hechtioideae and allowed the identification of highly informative loci previously unexplored in this lineage. Our plastome comparative analysis allowed us to identify several structural rearrangements in the subfamily, including expansions and contractions of the inverted repeat, large inversions, gene loss, and potential pseudogenization. Evolutionary trait rate shifts were detected at different Hechtioideae lineages in the size and guanine–cytosine content of the small single copy and inverted repeats.
  • Eva Mikulášková, Tomáš Peterka, Jakub Šmerda, and Michal Hájek
    J Syst Evol. 2024, 62(3): 475-488.
    https://doi.org/10.1111/jse.13005
    The recent development of genetic methods has facilitated the identification of cryptic species across different groups of organisms, including plants. However, next-generation sequencing has rarely been used to study cryptic speciation in plants, especially in bryophytes, organisms with a dominant haploid life phase. The ability to capture variation across the whole genome makes this method an effective tool for distinguishing cryptic lineages. We have focused on the genetic structure of the moss Meesia triquetra along the Alps-to-Scandinavia transect. We detected the presence of the two genetically critically different lineages of M. triquetra in Europe. These lineages overlap in both morphological characters of the gametophyte and distribution ranges. However, they considerably differ in ecological preferences to groundwater pH. While lineage 1 occupied alkaline to subneutral fens, lineage 2 occurred in fens saturated with neutral to acidic water. We consider the entities cryptic species with respect to genetic and ecological differences but the absence of morphological features necessary for determining the entities. We hypothesize that fragmentation of the ancestral population of the moss in geographically isolated refugia differing in the commonness of acidic and alkaline substrates led to consequent long-term adaptation to different environmental conditions, then drove diversification in M. triquetra.
    The recent development of genetic methods has facilitated the identification of cryptic species across different groups of organisms, including plants. However, next-generation sequencing has rarely been used to study cryptic speciation in plants, especially in bryophytes, an organism with a dominant haploid life phase. The ability to capture variation across the whole genome makes this method an effective tool for distinguishing cryptic lineages. We have focused on the genetic structure of the moss Meesia triquetra along the Alps-to-Scandinavia transect. We detected the presence of the two genetically critically different lineages of M. triquetra in Europe. These lineages overlap in both morphological characters of the gametophyte and distribution ranges. However, they considerably differ in ecological preferences to groundwater pH. While lineage 1 occupied alkaline to subneutral fens, lineage 2 occurred in fens saturated with neutral to acidic water. We consider the entities cryptic species with respect to genetic and ecological differences but the absence of morphological features necessary for determining the entities. We hypothesize that fragmentation of the ancestral population of the moss in geographically isolated refugia differing in the commonness of acidic and alkaline substrates led to consequent long-term adaptation to different environmental conditions, then drove diversification in M. triquetra.
  • Andrea C. Westerband, Tiffany M. Knight, and Kasey E. Barton
    J Syst Evol. 2024, 62(2): 233-241.
    https://doi.org/10.1111/jse.13032
    Despite representing a fraction of the global terrestrial surface area, oceanic islands are disproportionately diverse in species, resulting from high rates of endemicity. Island plants are thought to share a unique phenotype—referred to as an island syndrome—which is thought to be driven by convergent evolution in response to selection by shared abiotic and biotic factors. One aspect of the island plant syndrome that has received relatively little research focus is that island plants are expected to have converged on conservative resource use associated with slow growth rates and weak competitive abilities. Here we tested whether native, woody Hawaiian plant species are phenotypically distinct—with more resource-conservative leaf traits—compared to a globally distributed sample of continental species. Using an archipelago-wide trait data set, we detected that on average, native Hawaiian species had lower leaf nutrient concentrations overall, and lower nutrient concentrations at high leaf mass per area, but no other phenotypic differences compared with continental plants. There was also considerable overlap in the trait spaces of native Hawaiian species and continental species. Our findings indicate that an island plant syndrome for leaf traits is not present in the Hawaiian flora, and that island species can demonstrate extensive variation in their resource-use strategies, on a scale that is comparable with that of continental species worldwide.
  • Gunnar Keppel, Francis J. Nge, and Thomas Ibanez
    J Syst Evol. 2024, 62(2): 201-214.
    https://doi.org/10.1111/jse.13026
    Islands in the tropical Pacific Ocean are renowned for high biodiversity and endemism despite having relatively small landmasses. However, our knowledge of how this biodiversity is formed remains limited. The taxon cycle, where well-dispersed, earlier colonizers become displaced from coastal to inland habitats by new waves of colonizers, producing isolated, range-restricted species, has been proposed to explain current biodiversity patterns. Here, we integrate the outcomes of phylogenetic studies in the region to investigate the sources, age, number of colonizations, and diversification of 16 archipelagos in the tropical and subtropical South Pacific. We then evaluate whether the results support the taxon cycle as a plausible mechanism for these observations. We find that most species in the Pacific arrived less than 5 Mya from geographically close sources, suggesting that colonization by new taxa is a frequent and ongoing process. Therefore, our findings are broadly consistent with the theory of the Taxon Cycle, which posits that ongoing colonization results in the gradual displacement of established lineages. Only the oldest archipelagos, New Caledonia and Fiji, do not conform to this trend, having proportionally less recent colonization events, suggesting that the taxon cycle may slow on older islands. This conclusion is further validated by New Caledonia having lower diversification rate estimates than younger islands. We found that diversification rates across archipelagos are negatively correlated with area and age. Therefore, a taxon cycle that slows with island age appears to be a suitable concept for understanding the dynamic nature and biodiversity patterns of the Pacific Islands.
    Biodiversity on islands in the tropical South Pacific has mostly originated through recent colonization events less than 5 Mya from the closest source areas. Only the oldest archipelagos diverge from that pattern, having an older biota and lower diversification rates. These findings correspond to the processes of the taxon cycle slowing down on older islands.
  • Riccardo Testolin, Fabio Attorre, Vanessa Bruzzaniti, Riccardo Guarino, Borja Jiménez-Alfaro, Michele Lussu, Stefano Martellos, Michele Di Musciano, Salvatore Pasta, Francesco Maria Sabatini, Francesco Santi, Piero Zannini, and Alessandro Chiarucci
    J Syst Evol. 2024, 62(2): 242-256.
    https://doi.org/10.1111/jse.13034
    Small islands represent a common feature in the Mediterranean and host a significant fraction of its biodiversity. However, the distribution of plant species richness across spatial scales—from local communities (alpha) to whole islands (gamma)—is largely unknown, and so is the influence of environmental, geographical, and topographical factors. By building upon classic biogeographic theory, we used the species–area relationship and about 4500 vegetation plots in 54 Central Mediterranean small islands to identify hotspots of plant species richness and the underlying spatial determinants across scales. To do so, we fitted and averaged eight species–area models on gamma and alpha richness against island area and plot size, respectively. Based on positive deviations from the fitted curves, we identified 12 islands as cross-scale hotspots. These islands encompassed around 70% of species and habitat richness, as well as almost 50% of the rarest species in the data set, while occupying less than 40% of the total island surface. By fitting generalized linear mixed models, we found that gamma richness was mainly explained by island area and was weakly related to mean annual temperature (positively) and annual precipitation (negatively). As for alpha richness, after accounting for the idiosyncratic effect of habitats and islands, plot size and gamma richness remained the only significant predictors, showing a positive relationship. This work contributes to the understanding of the patterns and drivers of plant diversity in Central Mediterranean small islands and outlines a useful methodology for the prioritization of conservation efforts.
    We used the species–area relationship to identify plant richness hotspots and coldspots at the island and vegetation community scales. The 12 selected cross-scale hotspots were mainly located in Southern Italian archipelagos. Species richness patterns were mainly related to area and the idiosyncratic effect of habitats and islands, with climate and other large-scale processes playing a secondary role.
  • Martha Kandziora, Juan M. Gorospe, Luciana Salomon, Diana L. A. Vásquez, Maria Pinilla Vargas, Filip Kolář, Petr Sklenář, and Roswitha Schmickl
    J Syst Evol. 2024, 62(2): 275-290.
    https://doi.org/10.1111/jse.13048
    Habitat stability is important for maintaining biodiversity by preventing species extinction, but this stability is being challenged by climate change. The tropical alpine ecosystem is currently one of the ecosystems most threatened by global warming, and the flora close to the permanent snow line is at high risk of extinction. The tropical alpine ecosystem, found in South and Central America, Malesia and Papuasia, Africa, and Hawaii, is of relatively young evolutionary age, and it has been exposed to changing climates since its origin, particularly during the Pleistocene. Estimating habitat loss and gain between the Last Glacial Maximum (LGM) and the present allows us to relate current biodiversity to past changes in climate and habitat stability. In order to do so, (i) we developed a unifying climate-based delimitation of tropical alpine regions across continents, and (ii) we used this delimitation to assess the degree of habitat stability, that is, the overlap of suitable areas between the LGM and the present, in different tropical alpine regions. Finally, we discuss the link between habitat stability and tropical alpine plant diversity. Our climate-based delimitation approach can be easily applied to other ecosystems using our developed code, facilitating macro-comparative studies of habitat dynamics through time.
    Using a climate-based delimitation to compare the extent of tropical alpine areas between the present and during the last glacial maximum permits us to estimate the degree of habitat stability. This new approach facilitates macro-comparative studies of habitat dynamics through time.
  • Jay Edneil C. Olivar, Frank Hauenschild, Hannah J. Atkins, Gemma L.C. Bramley, and Alexandra N. Muellner-Riehl
    J Syst Evol. 2024, 62(2): 215-232.
    https://doi.org/10.1111/jse.13049
    The general dynamic model (GDM) of oceanic island biogeography views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, Cyrtandra, and inferred the directionality of dispersal and founder events throughout the four biogeographical units of the Indo-Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area, followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in Cyrtandra follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of Cyrtandra in the Southeast Asian grade showed early bursts followed by a plateau, which is consistent with adaptive radiation. We did not detect signals of diversity-dependent diversification, and this is attributed to Southeast Asian cyrtandras occupying various niche spaces, evident by their wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the island immaturity speciation pulse model (IISP), wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step toward a framework for investigating diversification dynamics as predicted by the GDM in highly successful insular taxa.
    In this study, we showed that dispersing lineages arriving at island maturity have diversification rates following predictions of adaptive radiation and have a wide range of morphological features to occupy remaining niches in an island. On the other hand, dispersing lineages arriving early in the ontogeny of an island have diversification rates following predictions of the island immaturity speciation pulse model and have a limited range of morphological features due to the least action effect.
  • Jean-Yves Dubuisson, Adèle Nivart, Ehoarn Bidault, Vincent Deblauwe, Vincent Droissart, Narcisse G. Kamdem, Germinal Rouhan, Atsushi Ebihara, and Timothée le Péchon
    J Syst Evol. 2024, 62(1): 84-101.
    https://doi.org/10.1111/jse.12951
    The fern genus Didymoglossum (Hymenophyllaceae) is not so diverse in Africa with seven species at most. However, its local taxonomy is surprisingly still strongly debated, in particular within the Didymoglossum erosum complex interpreted either as a single polymorphic species or as a group of at least three distinct but morphologically very close taxa (D. erosum, Didymoglossum chamaedrys, and Didymoglossum benlii). Investigating these taxonomic issues and more generally the diversity of the genus in Africa and its origin, we conducted a complete anatomo–morphological analysis coupled with a molecular phylogenetic work based on rbcL. Our results support the recognition of all seven species, including Didymoglossum robinsonii that is likely distinct from the Neotropical Didymoglossum reptans to which the African populations were traditionally attributed. We here propose new characters and a novel key to distinguish the seven African species which also include Didymoglossum ballardianum, Didymoglossum lenormandii, and Didymoglossum liberiense. Once the taxonomy is clarified with respect to the distinct evolutionary lineages evidenced, the biogeographic history of the genus in Africa is discussed based on a divergence time estimation and the reconstruction of the ancestral geographic areas. These analyses reveal a Mesozoic (Cretaceous) vicariance event within Didymoglossum which is the second one hypothesized for the family Hymenophyllaceae.
    Analyses combining morphology and molecules confirmed the presence in tropical Africa of at least seven species of Didymoglossum ferns (Hymenophyllaceae) and traced the history of the genus in Africa, which would imply numerous multiple dispersals from the Neotropics or the western Indian Ocean and at least one local diversification in the Cenozoic. A new identification key is produced and phylogenetic inferences also suggest a possible Mesozoic vicariance event at the genus scale.
  • Theresa C. Saunders, J. Mark Porter, and Leigh A. Johnson
    J Syst Evol. 2024, 62(1): 55-72.
    https://doi.org/10.1111/jse.13010
    Phylogenetics is crucial in the study of evolutionary processes and events transpiring in the course of species diversification. Phylogenetic studies within kingdom Plantae often reveal hybridization and introgression. Here, we study a subsection rife with historic hybridization and discuss the impacts of such processes on evolutionary trajectories. Aliciella subsection Subnuda comprises seven species of herbaceous plants occurring in Utah, the Navajo Nation, and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of nuclear ITS and chloroplast DNA regions and genome-wide RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from chloroplast and nuclear ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny and multispecies coalescent species tree robustly resolve relationships between six species-level clades. We use STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest that hybridization has occurred among all species in the subsection at some point in their history. Cytonuclear discordance reveals historic chloroplast capture, and we discuss potential causes of the observed discordance. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.
    Phylogenetics is crucial in the study of evolutionary processes and events transpiring in the course of species diversification. Phylogenetic studies within kingdom Plantae often reveal hybridization and introgression. Here, we study a subsection rife with historic hybridization and discuss the impacts of such processes on evolutionary trajectories. Aliciella subsection Subnuda comprises seven species of herbaceous plants occurring in Utah, the Navajo Nation, and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of nuclear ITS and chloroplast DNA regions and genome-wide RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from chloroplast and nuclear ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny and multispecies coalescent species tree robustly resolve relationships between six species-level clades. We use STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest that hybridization has occurred among all species in the subsection at some point in their history. Cytonuclear discordance reveals historic chloroplast capture, and we discuss potential causes of the observed discordance. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.
  • Cristina Ramos-Capón, Pablo Vargas, Fernando Pomeda-Gutiérrez, and Sara Martín-Hernanz
    J Syst Evol. 2024, 62(1): 20-37.
    https://doi.org/10.1111/jse.13018
    The sclerophyllous syndrome is characterized by well-defined traits (evergreen coriaceous leaves, inconspicuous flowers, and fleshy fruits). It has been hypothesized that lineages displaying the sclerophyllous syndrome show lower speciation rates than non-sclerophyllous lineages after the establishment of the mediterranean climate. Daphne gnidium displays sclerophyllous traits and some differentiation into three subspecies (gnidium, mauritanica, maritima), but the spatio-temporal origin of this taxonomic group is unknown due to the lack of a time-calibrated phylogeny of the whole genus. Here, we inferred phylogenetic relationships and divergence times of Daphne (32 species, 238 samples) and other genera of Thymelaeaceae (16 genera, 38 species, 34 samples) using the internal transcribed spacer (ITS), which revealed that the current circumscription of Daphne is profoundly polyphyletic because some species are nested within the genera Wikstroemia and Edgeworthia. In contrast, D. gnidium formed a well-supported clade as recognized in taxonomic accounts (subgenus Spachia). We found morphological and phylogenetic support for Daphne mauritanica as a monophyletic lineage sister to D. gnidium. Divergence between D. gnidium and D. mauritanica appears to have predated the establishment of seasonally dry conditions, which supports a pre-mediterranean temporal origin of the lineage. A phylogeographical analysis within D. gnidium based on 66 nrDNA (ITS) and 84 cpDNA (rps16, trnV) sequences agreed with the low differentiation of the species in the Pleistocene despite its large distribution range. Altogether, D. gnidium illustrates one more example of the sclerophyllous syndrome with no speciation after the onset of the mediterranean climate.
    In this study, we provide evidence to support the historical hypothesis of a pre-Mediterranean origin (more than 2.8 million years ago), followed by low speciation in sclerophyllous lineages of the Mediterranean Floristic Region. This hypothesis is positively tested by inferring the temporal origin and phylogeography of the sclerophyllous Daphne gnidium using the most comprehensive phylogeny of the genus to date.
  • Zhi-Yuan Du, Jin Cheng, and Qiu-Yun (Jenny) Xiang
    J Syst Evol. 2024, 62(1): 1-19.
    https://doi.org/10.1111/jse.13037
    The big-bracted dogwood clade Benthamidia of Cornus is a typical example of the well-known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than in NA. The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective. We generated RAD-seq data, conducted phylogenomic and biogeographic analyses for the clade with sampling of all species (9) and subspecies (10) currently recognized in floras. We also assessed species delineation and calculated phylogenetic diversity to evaluate the diversity unevenness between EA and NA. Finally, we examined variation of diversification rates and ecological niches on the phylogeny to explore potential causes underlying the observed diversity pattern. Our results revealed phylogenetic relationships congruent with previous studies and suggested a trans-Beringian ancestral distribution of the clade Benthamidia in the mid-Oligocene, dispersal from Mexico to eastern United States in the mid-Miocene, and early diversification of the EA clade in SW China. Our results also confirmed greater phylogenetic diversity and diversification rate of the EA clade. Species delimitation analysis suggested 17 species in the clade Benthamidia, including all recognized subspecies. By integrating the results of molecular data with morphology, we proposed to retain the subspecies without changing their ranks. Our data suggested increased diversification rate in EA as an intrinsic factor explaining the greater species diversity in the region driven mainly by biogeographic isolation and partially by niche divergence.
    Phylogeny and biogeographic history of the big-bracted dogwoods, clade Benthamidia of Cornus, based on RAD-seq data. The results support a trans-Beringia distribution of the ancestor across Eurasia and western North America (including Mexico), divergence of the EA and NA clades in the mid-Oligocene, dispersals into Europe from EA and into ENA from Mexico in the mid-Miocene, and early diversification of the EA clade in southwest China. Our data confirmed greater phylogenetic diversity in EA and supported an explanation by greater diversification rate in the clade.
  • Fei Qin, Xiao-Xia Zhang, Yun-Feng Huang, Lei Wu, Wei-Bin Xu, Tian-Tian Xue, Wen-Di Zhang, Qin Liu, Jiang-Hong Yu, Jie-Jing Gao, Rainer W. Bussmann, Juan Wang, and Sheng-Xiang Yu
    J Syst Evol. 2023, 61(6): 967-978.
    https://doi.org/10.1111/jse.12941
    National key protected wild plants (NKPWPs) are species with important conservation value based on genetics, ecology, culture, and/or scientific research, which are also confronted with serious threats. However, their geographical distribution patterns and conservation status remain unclear. In this study, we compiled 1032 species of NKPWPs. We measured the diversity to identify hotspots of NKPWPs based on species richness, weighted range size rarity and a complementarity-based analysis. Comparing the distribution and hotspots of NKPWPs with the coverage of Chinese nature reserves (NRs), we assessed conservation effectiveness and identified conservation gaps. The results identified 13 diversity hotspots; only 9.5% of them were covered by NRs with >30% of the grid cell area, and even 19.5% were not covered at all by NRs. Overall, 44.7% of NKPWPs were effectively protected by national NRs. Despite this success, 571 species in Yunnan, Guizhou, Sichuan, Chongqing, Guangxi, Guangdong, southern Hainan, Taiwan, and northern Xinjiang remain unprotected by NRs. The protected proportion of plants with first-level protection was lower than that of plants with second-level protection. The low overall proportion of protected hotspots indicates that the conservation outlook for NKPWPs is not optimistic. This study identifies priority conservation areas and conservation gaps and provides a scientific reference for the conservation of wild plants in China.
    This study identified hotspots for priority conservation and conservation gaps of national key protected wild plants (NKPWPs) based on species richness, weighted range size rarity and a complementarity-based analysis. The protected proportion of plants with first-level protection is lower than that with second-level protection, and the low proportion of protected hotspots indicates that the conservation status of NKPWPs is not optimistic.
  • Rui-Yun Li, Lin-Hao Cui, Dong-Jing Fu, and Xing-Liang Zhang
    J Syst Evol. 2023, 61(6): 1091-1101.
    https://doi.org/10.1111/jse.12942
    Macroalgae have been a key ecological component of marine ecosystems since the Proterozoic period and are common fossil forms in Cambrian Burgess Shale-type Lagerstätten. However, in most cases, it is difficult to place these early fossil algae into modern groups because little distinctive morphology is preserved. Here, we describe a new form of macroalgae, Qingjiangthallus cystocarpium gen. & sp. nov., from the Qingjiang biota of South China. The new taxon is represented by 546 specimens remarkably preserved with characteristics that allow a phylogenetic placement into crown groups of red algae. Centimeter-sized thalli resemble members of the extant Rhodymeniophycidae (a subclass of the class Florideophyceae), and hence suggest a florideophycean affinity, which indicates that ahnfeltiophycidaen and rhodymeniophycidaen algae may have diverged at least 518Ma, accordant with estimations of molecular studies. The presence of possible cystocarps on Qingjiangthallus thalli suggests that evolutionary innovation of a triphasic life cycle in red algae may have occurred no later than the Early Cambrian. The branching patterns and branch width of Qingjiangthallus are consistent with the coarsely dichotomously branched morphogroup, which was previously present in the Ediacaran, Ordovician, and afterward, but absent in the Cambrian.
    The new form of macroalgae, Qingjiangthallus cystocarpium gen. et sp. nov., is placed in the crown-group Rhodophyta, and probably has an affinity with the Florideophyceae. Its comparability with Rhodymeniophycidae and early age indicate that ahnfeltiophycidaen and rhodymeniophycidaen algae may have diverged at least 518Ma. The presence of possible cystocarps on Qingjiangthallus thalli suggests that evolutionary innovations of triphasic life history in red algae may have occurred no later than the Early Cambrian. Morphologically, Qingjiangthallus fills the Cambrian gap in the fossil record of the coarsely dichotomously branched morphogroup.
  • Meng-Ting Wang, Zhen-Yu Hou, Chao Li, Jia-Peng Yang, Zhi-Tao Niu, Qing-Yun Xue, Wei Liu, and Xiao-Yu Ding
    J Syst Evol. 2023, 61(5): 790-805.
    https://doi.org/10.1111/jse.12912
    Reconstructing mitochondrial genomes of angiosperms is extremely intricate due to frequent recombinations which give rise to varied sized in Dendrobium mitogenomes and their structural variations, even in most orchid species. In this study, we first sequenced two complete and five draft mitochondrial genomes of Dendrobium using next-generation and third-generation sequencing technologies. The mitochondrial genomes were 420 538-689 048 bp long, showing multipartite (multichromosomal) structures that consisted of variably sized circular or linear-mapping isoforms (chromosomes). The comparison of mitochondrial genomes showed frequent gene losses in Dendrobium species. To explore structure variations of mitochondrial genomes in vivo, we quantified copy numbers of five mitochondrial genes and DNA contents per mitochondrion. The gene copy numbers and the DNA contents showed extreme differences during Dendrobium development, suggesting dynamic structures of mitochondrial genomes. Furthermore, phylogenetic relationships of 97 accessions from 39 Dendrobium species were constructed based on 12 nuclear single-copy genes and 15 mitochondrial genes. We discovered obvious discordance between the nuclear and mitochondrial trees. Reticulate evolution was inferred from the species network analysis in Dendrobium. Our findings revealed the rapid structural evolution of Dendrobium mitochondrial genomes and the existence of hybridization events in Dendrobium species, which provided new insights into in vivo structural variations of plant mitochondrial genomes and the strong potential of mitochondrial genes in deciphering plant evolution history.
    Mitochondrial genomes of Dendrobium showed multichromosomal structures with variably sized circular or linear isoforms. Mitochondrial protein-coding genes underwent frequent lost events in Dendrobium species. The structures of mitochondrial genomes were dynamic during Dendrobium development. The mitochondrial tree and the nuclear tree displayed obvious phylogenetic discordances in Dendrobium.
  • Sergio Castro, Audrey Muratet, Magdalena Szczepaniak, Julie Nguefack, and Laurent Hardion
    J Syst Evol. 2023, 61(5): 764-775.
    https://doi.org/10.1111/jse.12940
    Melica (Poaceae) consist of about 92 species distributed across temperate regions of the world. Within section Dalycum, Melica ciliata sensu lato forms a taxonomic complex of several species and subspecies with clinal morphological variation causing conflicting identifications. To resolve taxonomic confusion, we used three complementary approaches, through molecular, morphological, and phytoecological analyses. The double-digest restriction-associated DNA markers significantly support the monophyly of three taxa: (i) the Mediterranean Melica magnolii, (ii) the Eurasian Melica transsilvanica subsp. transsilvanica, and (iii) the west-European M. ciliata subsp. glauca. This differentiation is corroborated by the analysis of 22 morphometric variables. Furthermore, phytoecological analysis of 221 floristic inventories revealed habitat distinctions among these taxa. Our approach of integrative taxonomy argues for a specific distinction for these three taxa, and we include a key to separate these forms. These new molecular data on the section Dalycum, subsection Ciliatae, call for further phylogenetic analyses including samples of M. ciliata subsp. ciliata and other East-Mediterranean and South African taxa.
    Three types of markers were used to clarify the taxonomic status of Melica magnolii, Melica ciliata subsp. glauca, and Melica transsilvanica subsp. transsilvanica. RAD sequencing-based phylogenetic analyses reveal the monophyletic nature of each taxon, which is congruent with morphometric clustering and habitat distinctions. Useful information for field recognition is presented. More work is needed to fully understand the evolution and diversification of this intricate taxonomic complex.
  • Li‐Jun Yan, Zhi‐Guo Zhu, Pei Wang, Chao‐Nan Fu, Xi‐Jin Guan, Philip Kear, Chun‐Zhi Zhang, and Guang‐Tao Zhu
    J Syst Evol. 2023, 61(4): 599-612.
    https://doi.org/10.1111/jse.12898
    Common potato (Solanum tuberosum L.) and its wild relatives belong to Solanum section Petota. This section's phylogeny and species delimitation are complicated due to various ploidy levels, high heterozygosity, and frequent interspecific hybridization. Compared to the nuclear genome, the plastid genome is more conserved, has a haploid nature, and has a lower nucleotide substitution rate, providing informative alternative insights into the phylogenetic study of section Petota. Here, we analyzed 343 potato plastid genomes from 53 wild and four cultivated species. The diversity of sequences and genomes was comprehensively analyzed. A total of 24 species were placed in a phylogenetic tree based on genomic data for the first time. Overall, our results not only confirmed most existing clades and species boundaries inferred by nuclear evidence but also provided some distinctive species clade belonging and the maternally inherited evidence supporting the hybrid origin of some species. Furthermore, the divergence times between the major potato clades were estimated. In addition, the species discriminatory power of universal barcodes, nuclear ribosomal DNA, and whole and partial plastid genomes and their combinations were thoroughly evaluated; the plastid genome performed best but had limited discriminatory power for all survey species (40%). Overall, our study provided not only new insights into phylogeny and DNA barcoding of potato but also provided valuable genetic data resources for further systematical research of Petota.
    Potato and its wild relatives belong to Solanum section Petota. In this study, the phylogeny of Petota was confirmed on clade level based on 343 plastid genomes. The species identification rates of universal barcodes, nuclear ribosomal DNA, whole plastid genomes, and hypervariable regions were thoroughly evaluated.
  • Marie Claire Veranso‐Libalah, Hannah Mertes, Robert Douglas Stone, Luo Chen, Tariq Stévart, Frank Almeda, Xander M. van der Burgt, and Gudrun Kadereit
    J Syst Evol. 2023, 61(4): 657-681.
    https://doi.org/10.1111/jse.12921
    The tribe Sonerileae in tropical Africa and Madagascar is a morphologically diverse lineage that consists of 239 species in 10 genera. In this study, we present the first in-depth phylogenetic analysis of African Sonerileae to test monophyly of the currently recognized genera. Phylogenetic analyses were performed using sequence data from two nuclear (nrITS and nrETS) and three plastid loci (accD-psaI, ndhF and psbK-psbL). Sampling consisted of 140 accessions including 64 African, 27 Malagasy, 46 Asian, and three neotropical Sonerileae together with a broad outgroup sampling (105 spp.). Phylogenetic relationships were inferred using maximum likelihood and Bayesian inference approaches, and a careful reassessment of morphological characters was carried out. Our results neither support the monophyly of the Old World nor African Sonerileae. The monospecific African genus Benna is partially supported as sister to Phainantha, one of the basal neotropical lineages, while African and Malagasy Medinilla are nested among the SE Asian genera. Gravesia (116 spp.), the most species-rich and morphologically diverse genus in Madagascar, is recovered as monophyletic. The African genera of Sonerileae Calvoa, Dicellandra, and Preussiella form well-supported clades. In contrast, Amphiblemma (including Amphiblemma molle) and Cincinnobotrys s.l. (including Cincinnobotrys felicis) are not monophyletic. To accommodate the caulescent C. felicis we propose reinstatement of the monospecific genus Bourdaria. For the distinctive A. molle a new genus Mendelia is described. Calvoa hirsuta is designated here as the type of genus Calvoa, lectotypes are designated for Medinilla engleri and Veprecella lutea, and a neotype is designated for Preussiella kamerunensis.
    The first in-depth phylogenetic analysis of African Sonerileae to test monophyly of the currently recognized genera is here presented. Phylogenetic analyses neither support monophyly of the Old World nor African Sonerileae. The genera Calvoa, Dicellandra, Gravesia, and Preussiella form well-supported clades while Amphiblemma and Cincinnobotrys are not monophyletic. The monospecific genus Bourdaria is reinstated and a new genus Mendelia is described to accommodate Cincinnobotrys felicis and Amphiblemma molle, respectively.
  • Chapa Manawaduge, Gillian Brown, Catherine L. Simmons, Matthew J. Phillips, and Susan Fuller
    J Syst Evol. 2023, 61(4): 643-656.
    https://doi.org/10.1111/jse.12922
    Conservation decision-making and prioritization of management actions for taxa at high risk of extinction require a clear understanding of systematic relationships and species boundaries. Taxonomic uncertainty surrounds two threatened species of native olive (genus Notelaea) endemic to Australia. Notelaea ipsviciensis is known from only one small population and is listed as critically endangered under Australian and Queensland legislation, while Notelaea lloydii is listed as vulnerable due to its restricted distribution in south-east Queensland, Australia. Notelaea ipsviciensis occurs in sympatry with N. lloydii, at the only site where it is found, and exhibits intermediate morphology between N. lloydii and Notelaea ovata raising speculation that it is a natural hybrid of the two. To address this uncertainty, we have reconstructed the molecular phylogeny of the genus Notelaea using both single-gene sequencing and single nucleotide polymorphism (SNP) data. While the chloroplast DNA markers were not found to be informative, the genome-wide SNPs used in this study have unequivocally resolved the long-standing question of the hybrid origin of N. ipsviciensis. Results of the phylogenetics and hybrid analyses of SNP data show that N. ipsviciensis is a natural hybrid of N. lloydii and N. ovata, and the taxon's circumscription needs to be re-evaluated. Our results also revealed unclear species boundaries among numerous other Notelaea species, including the threatened N. lloydii, indicating that further investigation and taxonomic revision may be necessary.
    Threatened species conservation relies on having knowledge of the systematic relationships between species and clearly resolved species boundaries. This study investigated the systematics of the two least studied threatened native olive species (Notelaea ipsviciensis and Notelaea lloydii) in Australia. Results of the phylogenetics and hybrid analyses of genomic data confirm that N. ipsviciensis is a natural hybrid of N. lloydii and Notelaea ovata, and the taxon's circumscription needs to be re-evaluated. Furthermore, the molecular phylogeny consequently raises doubts about the current circumscription of some other species of Notelaea, including the threatened species N. lloydii.
  • Peng-Juan Zu, Reinaldo García-García, Meredith C. Schuman, Serguei Saavedra, and Carlos J. Melián
    J Syst Evol. 2023, 61(3): 445-453.
    https://doi.org/10.1111/jse.12841
    Cross-species communication, where signals are sent by one species and perceived by others, is one of the most intriguing types of communication that functionally links different species to form complex ecological networks. Global change and human activity can affect communication by increasing fluctuations in species composition and phenology, altering signal profiles and intensity, and introducing noise. So far, most studies on cross-species communication have focused on a few specific species isolated from ecological communities. Scaling up investigations of cross-species communication to the community level is currently hampered by a lack of conceptual and practical methodologies. Here, we propose an interdisciplinary framework based on information theory to investigate mechanisms shaping cross-species communication at the community level. We use plants and insects, the cornerstones of most ecosystems, as a showcase and focus on chemical communication as the key communication channel. We first introduce some basic concepts of information theory, then we illustrate information patterns in plant-insect chemical communication, followed by a further exploration of how to integrate information theory into ecological and evolutionary processes to form testable mechanistic hypotheses. We conclude by highlighting the importance of community-level information as a means to better understand the maintenance and workings of ecological systems, especially during rapid global change.
  • Witold Wachowiak, Weronika B. Żukowska, Annika Perry, Andrzej Lewandowski, Stephen Cavers, and Bartosz Łabiszak
    J Syst Evol. 2023, 61(2): 315-327.
    https://doi.org/10.1111/jse.12907
    We analyzed mitochondrial DNA polymorphisms to search for evidence of the genetic structure and patterns of admixture in 124 populations (N = 1407 trees) across the distribution of Scots pine in Europe and Asia. The markers revealed only a weak population structure in Central and Eastern Europe and suggested postglacial expansion to middle and northern latitudes from multiple sources. Major mitotype variants include the remnants of Scots pine at the north-western extreme of the distribution in the Scottish Highlands; two main variants (western and central European) that contributed to the contemporary populations in Norway and Sweden; the central-eastern European variant present in the Balkan region, Finland, and Russian Karelia; and a separate one common to most eastern European parts of Russia and western Siberia. We also observe signatures of a distinct refugium located in the northern parts of the Black Sea basin that contributed to the patterns of genetic variation observed in several populations in the Balkans, Ukraine, and western Russia. Some common haplotypes of putative ancient origin were shared among distant populations from Europe and Asia, including the most southern refugial stands that did not participate in postglacial recolonization of northern latitudes. The study indicates different genetic lineages of the species in Europe and provides a set of genetic markers for its finer-scale population history and divergence inference.
    The distribution of various mitochondrial DNA haplotypes (marked in different colors) of Scots pine in Europe and Asia has been studied. Major mitotype variants include the remnants of Scots pine at the most western distribution of the species that colonized the Scottish Highlands, the main variants (western and central European) that contributed to the contemporary populations in Norway and Sweden, the central-eastern European variant that colonized Baltic countries, Finland, and Russian Karelia, and a separate one common to most eastern European parts of Russia and western Siberia. The study highlights the complex population history of the species that influenced the distribution of genetic variations across the species range.
  • Fernando Pomeda‐Gutiérrez, María Begoña García, María Leo, Mario Fernández‐Mazuecos, Mostafa Lamrani Alaoui, Anass Terrab, and Pablo Vargas
    J Syst Evol. 2023, 61(2): 253-272.
    https://doi.org/10.1111/jse.12917
    The current distribution of most species results from ecological niche, past distribution, and migrations during glacial–interglacial periods and in situ evolution. Here, we disentangle the colonization history of Saxifraga longifolia Lapeyr., a limestone plant abundant in the Pyrenees and rare in other Iberian mountains and the African Atlas. Our working hypothesis is that the current distribution results from the shrinkage of a more extensive distribution in previous cold periods. We sampled 160 individuals of 32 populations across the whole distribution range and sequenced four DNA regions (rpl32-trnL, rps16-trnQ, trnS-trnG, and ITS). Ecological conditions were modeled to identify factors promoting high genetic diversity and long-term persistence areas for S. longifolia. In addition, we inferred phylogenetic relationships, phylogeographic divergence, genetic diversity, and migration routes. Seven plastid haplotypes were found, of which six occur in the Pyrenees and one in the High Atlas (Morocco). Discrete phylogeographic analysis (DPA) estimated migration routes predominantly from the Pyrenees to the other areas. Colonization events to those areas appear to have taken place recently given that the rest of the Iberian mountains do not harbor exclusive haplotypes. Iberian–Northern African distribution was inferred to be the result of long-distance dispersal because the split between Iberian and High Atlas haplotypes is estimated to have taken place in the last 4 million years ago when the Strait of Gibraltar was already open. Migrations from the Pyrenees to the south may have been favored by a corridor of predominant limestone rocks along Eastern Iberia, followed by successful overcoming the Strait of Gibraltar to reach northern Africa.
    The colonization history of Saxifraga longifolia begins in the Pyrenees, a cradle of plant diversity. Continues along the Eastern Iberian limestone corridor reaching the morrocan High Atlas by a long-distance dispersal event after the opening of the Strait of Gibraltar. However, this pattern appears to have been blurred during the Quaternary when S. longifolia colonized and recolonized the Iberian mountains.
  • Jeprianto Manurung, Blanca M. Rojas Andrés, Christopher D. Barratt, Jan Schnitzler, Bror F. Jönsson, Ruliyana Susanti, Walter Durka, and Alexandra N. Muellner‐Riehl
    J Syst Evol. 2023, 61(2): 299-314.
    https://doi.org/10.1111/jse.12923
    The Indonesian Archipelago accommodates the largest mangrove area in Southeast Asia and possesses the world's richest composition of mangrove species. The archipelago comprises areas of the biogeographic regions Sunda and Wallacea, separated by Wallace's line. Here, we used the true mangrove species Lumnitzera littorea and Lumnitzera racemosa as a study case for understanding the effects of phylogeographic history, sea surface currents, and geographical distance on genetic diversity and genetic structure. We sampled 14 populations of L. littorea (N = 106) and 21 populations of L. racemosa (N = 152) from Indonesia and used 3122 and 3048 SNP loci, respectively, genotyped using the ddRADseq approach. We assessed genetic diversity, genetic structure, and effective dispersal of the populations and related them to geographical distance and sea surface currents. Our study revealed low levels of genetic variation at the population level in Lumnitzera. Pronounced genetic differentiation between populations indicated two phylogroups in both species. While in L. littorea the two phylogroups were largely separated by Wallace's line, L. racemosa showed a northwest vs. southeast pattern with strong mixture in Wallacea. Our findings provide novel insights into the phylogeography of the mangrove genus Lumnitzera and the role of sea surface currents in the Indonesian Archipelago.
    Our population genomic data show pronounced genetic differentiation among populations, indicating two phylogroups in both species. While in Lumnitzera littorea the two phylogroups are largely separated by Wallace's line, Lumnitzera racemosa shows a northwest vs. southeast pattern with strong mixture in Wallacea.
  • Jing‐Fang Guo, Baosheng Wang, Zhan‐Lin Liu, Jian‐Feng Mao, Xiao‐Ru Wang, and Wei Zhao
    J Syst Evol. 2023, 61(1): 143-156.
    https://doi.org/10.1111/jse.12821

    Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.

    Increasing variability of future climate imposes challenges for the persistence of endangered relict species. This study infers the evolutionary history and the impacts of demography and landscape factors on population structure and diversity of the red list pine Pinus bungeana. We show that drastic bottlenecks during the Pliocene and Pleistocene and long-term isolation in fragmented habitats resulted in extremely low genetic diversity in P. bungeana, which exposes the species to high risk of decline under future climate, particularly in marginal and relict populations.
  • Cathucia F. Andriamihaja, Alemao Botomanga, Chantal Misandeau, Aro V. Ramarosandratana, Michel Grisoni, Denis Da Silva, Thierry Pailler, Vololoniaina H. Jeannoda, and Pascale Besse
    J Syst Evol. 2023, 61(1): 80-98.
    https://doi.org/10.1111/jse.12858

    The leafless Vanilla species complex from the South-West Indian Ocean (SWIO) region has long been a taxonomic challenge, due to limited patterns of morphological differentiation and an absence of variation within chloroplast sequences. This complex includes seven known morphospecies: V. madagascariensis, V. bosseri, V. decaryana, and V. perrieri endemic to Madagascar, V. humblotii presumed as endemic to the Comoros Archipelago, but also present in Madagascar, V. roscheri from the East African coast, and V. phalaenopsis endemic to Seychelles. A previous population genetic study using microsatellite markers allowed us to distinguish, in addition to the five recognized Malagasy taxa, two other genetic clusters present in the East of the island. An integrative taxonomy approach was therefore conducted by combining microsatellite and morphological data used in the previous study with new data sets, and by adding ITS sequencing data, to validate the taxonomic level of these Malagasy genetic clusters and unravel phylogenetic relationships between SWIO species. As a result, based on phylogenetic, genotypic and morphological evidence, nine species were discriminated in the SWIO region, including seven in Madagascar, with two new eastern species. The leafless Vanilla group originated and diversified in Madagascar, from an ancestor of African descent, with three subsequent independent colonization events from Madagascar to the other territories of SWIO within the two main lineages (white versus yellow flower species). The new Malagasy species, V. allorgeae Andriamihaja & Pailler sp. nov., and V. atsinananensis Andriamihaja & Pailler sp. nov., are described and a new identification key is proposed.

    An integrative taxonomy approach (ITS phylogeny, population-based microsatellite study, and floral traits morphological characterization) revealed nine species in the recent leafless Vanilla species complex in the South-West Indian Ocean region, including two new species from Madagascar described in the present paper. This leafless species group originated from Madagascar (of African descent) and its subsequent diversification involved three transoceanic dispersal events to the Comoros archipelago islands, Seychelles islands, and back to East Africa.
  • María Teresa Boquete, Zulema Varela, José Angel Fernández, Juan Antonio Calleja, Cristina Branquinho, Antonina Chilà, Nils Cronberg, Ricardo Cruz de Carvalho, Cristiana Aleixo, Belén Estébanez‐Pérez, Verónica Fernández‐González, Andrés Baselga, Carola Gómez‐Rodríguez, Juana María González‐Mancebo, Sebastien Leblond, Javier Martínez‐Abaigar, Nagore G. Medina, Encarnación Núñez‐Olivera, Jairo Patiño, Rubén Retuerto, Antón Vázquez‐Arias, Alain Vanderpoorten, Harald G. Zechmeister, and Jesús Ramón Aboal
    J Syst Evol. 2023, 61(1): 213-226.
    https://doi.org/10.1111/jse.12897
    Unisexual bryophytes provide excellent models to study the mechanisms that regulate the frequency of sexual versus asexual reproduction in plants, and their ecological and evolutionary implications. Here, we determined sex expression, phenotypic sex ratio, and individual shoot traits in 242 populations of the cosmopolitan moss Pseudoscleropodium purum spanning its whole distributional range. We tested whether niche differentiation, sex-specific differences in shoot size, and biogeographical history explained the spatial variation of reproductive traits. We observed high levels of sex expression and predominantly female-biased populations, although both traits showed high intraspecific variation among populations. Sex expression and sex ratio were partly explained by current macroscale environmental variation, with male shoots being less frequent at the higher end of the environmental gradients defined by the current distribution of the species. Female bias in population sex ratio was significantly lower in areas recolonized after the last glacial maximum (recent populations) than in glacial refugia (long-term persistent populations). We demonstrated that reproductive trait variation in perennial unisexual mosses is partially driven by macroscale and historical environmental variation. Based on our results, we hypothesize that sexual dimorphism in environmental tolerance and vegetative growth contribute to sex ratio bias over time, constraining the chances of sexual reproduction, especially in long-term persistent populations. Further studies combining genetic analyses and population monitoring should improve our understanding of the implications of the intraspecific variation in the frequency of sexual versus asexual reproduction in bryophyte population fitness and eco-evolutionary dynamics.
    In this study, we showed that both current environmental and historical factors contribute to intraspecific variation in reproductive traits in the unisexual perennial moss Pseudoscleropodium purum across its large distributional range. The observed patterns were explained by differences in environmental optima as well as in the cost of reproduction between males and females linked to the probability to find each sex within a specific environment, as well as their vegetative growth capacity.
  • Mario Martínez‐Azorín, Manuel B. Crespo, María Ángeles Alonso‐Vargas, Michael Pinter, Neil R. Crouch, Anthony P. Dold, Ladislav Mucina, Martin Pfosser, and Wolfgang Wetschnig
    J Syst Evol. 2023, 61(1): 42-63.
    https://doi.org/10.1111/jse.12905

    The taxonomy and systematics of Urgineoideae (Hyacinthaceae) have been controversial in recent decades, with contrasting taxonomic treatments proposed based on preliminary and partial studies that have focused on morphology and/or solely plastid DNA sequence data. Some authors have recognized only two genera, with a very broadly conceived Drimia, while others have accepted several genera that, although better defined morphologically, were doubtfully monophyletic. Here, we present phylogenetic analyses involving four plastid DNA regions (trnL intron, trnL-F spacer, matK, and the trnCGCA-ycf6 intergenic region), a nuclear region (Agt1), and a selection of 40 morphological characters. Our study covers 293 samples and ca. 160 species of Urgineoideae (ca. 80% of its global diversity). Bayesian inference, maximum likelihood, and maximum parsimony analyses were performed to derive the phylogenetic patterns. The combination of data yielded phylogenetic trees with 31 well-defined clades or lineages, most corresponding to previously described genera, although some have required description or revised circumscription. As with other monocot families, a considerable degree of homoplasy was observed in morphological characters, especially in those groups with unspecialized flowers; nonetheless, consistent syndromes of traditional and novel characters are shown to support clade recognition at genus rank. The forthcoming revised classification of Urgineoideae is outlined here.

    Floral variation in the genera of Urgineoideae
  • Charles Pouchon, Jérémy Gauthier, Camille Pitteloud, Cyrille Claudel, and Nadir Alvarez
    J Syst Evol. 2023, 61(1): 64-79.
    https://doi.org/10.1111/jse.12910

    Encompassing ca. 200 species distributed in paleotropical Africa and Asia, Amorphophallus is one of the largest genera of Araceae. In spite of the great economic interest in its glucomannan production, only a few studies have attempted to grasp the evolutionary history of this genus. In the current state of knowledge, four main clades, mostly linked to biogeographical delineation, have been identified from phylogenies based on a few genes. However, relationships among and within these clades still remain unclear, due to the rapid radiation that occurred during the early evolutionary history of the genus. Here, we generated genome skimming libraries for 43 specimens from 36 species distributed across the 4 clades, which allowed us to produce a phylogenetic matrix for a set of 71 plastid genes. Our phylogenies confirm the monophyly of these clades but show a new and well-resolved arrangement among these clades. Our analyses therefore provide a new scenario and timeline for the evolution of the main Amorphophallus clades, consistent with the morphological characteristics of the clades. The inferred scenario is also in agreement with climate dynamics and the onset of long-distance dispersal by the earliest migratory birds near the Oligocene/Miocene transition around 23 million years ago. Our study provides an up-to-date baseline to understand biogeographic and ecological processes that shaped the current diversity and distribution of Amorphophallus, paving the way for larger-scale phylogenomic studies based on plastid and nuclear genomes.

    A phylogenomic study of Amorphophallus from plastid DNA revealed a new scenario and timeline for the evolution of the main clades, consistent with their morphological characteristics, past climate dynamics, and long-distance dispersal events across the genus.