Plant Diversification Research Articles

Dispersal and adaptive radiation of Bidens (Compositae) across the remote archipelagoes of Polynesia

AbstractThe genus Bidens (Compositae) comprises c. 230 species distributed across five continents, with the 41 Polynesian species displaying the greatest ecomorphological variation in the group. However, the genus has had a long and complicated taxonomic history, and its phylogenetic and biogeographic history are poorly understood. To resolve the evolutionary history of the Polynesian Bidens, 152 individuals representing 91 species were included in this study, including 39 of the 41 described species from Polynesia. Four chloroplast and two nuclear DNA markers were utilized to estimate phylogenetic relationships, divergence times, and biogeographic history. Bidens was found to be polyphyletic within Coreopsis, consistent with previous assessments. The Polynesian radiation was resolved as monophyletic, with the initial dispersal into the Pacific possibly from South America to either the Hawaiian or Marquesas Islands. From the Marquesas, Bidens dispersed to the Society Islands, and ultimately to the Austral Islands. The initial diversification of the crown group in the Pacific is estimated to have occurred ~1.63 mya (0.74–2.72, 95% HPD), making Polynesian Bidens among the youngest and most rapid plant diversification events documented in the Pacific. Our findings suggest that relatively rare long‐distance dispersal and founder‐event speciation, coupled with subsequent loss of dispersal potential and within‐island speciation, can explain the repeated and explosive adaptive radiation of Bidens throughout the archipelagoes of Polynesia.

The contribution of the edaphic factor as a driver of recent plant diversification in a Mediterranean biodiversity hotspot

Abstract The high diversification rates of plant lineages in the Mediterranean Basin hotspot have been linked to a complex interaction of climatic stressors, geographic isolation and soil type, but the question remains as to which of these factors has been the most significant environmental driver of recent speciation. Here, we draw on distributional data for the entire endemic flora of the Iberian Peninsula, together with DNA‐based phylogenies and spatial phylogenetic methods, to explore the patterns of relative phylogenetic endemism at different spatial resolutions and phylogenetic scales (superclades) and assess how environmental factors contribute to explain these patterns. We found that recent diversification of angiosperms as a whole, and particularly of eudicots, has been boosted by environmental stressors including high values of soil pH and dry‐seasonal climatic conditions, while diversification of monocots has not been associated with soil conditions but with high elevation and less seasonal climate. Synthesis. These results provide robust insights into the environmental factors driving recent plant diversification in the Mediterranean Basin, including a role of soil properties that had not been quantified before. The contrasting environmental drivers of diversification in eudicots and monocots highlight the importance of analysing spatial phylogenetic patterns at multiple phylogenetic scales to get a better understanding of the processes that shape biodiversity.

Plant genomes: Markers of evolutionary history and drivers of evolutionary change

Societal Impact StatementPlant genomes hold the key to understanding the evolutionary history of plants, a lineage that goes back nearly a billion years and contains nearly half a million living species. This history—or phylogeny—is both a record of life now past and a powerful predictive tool for both basic and applied plant science. Coupled phylogenetic and genomic studies can reveal the processes by which new species arise and go extinct, and phylogenies can guide our efforts to improve crop plants, discover new medicines, and develop effective conservation strategies.SummaryPlant genomes exhibit spectacular diversity in size, composition, and complexity, and although we suspect that this diversity is related to the equally spectacular diversity of plant form and function, this link is still poorly understood. Plant genomes carry signatures of evolutionary history, whole‐genome duplication, population processes, and more, and we are just learning how to read this historical information from appropriate genetic markers. But plant genomes are not merely chroniclers of past evolutionary change: they are dynamic, evolving entities in their own right, driving changes in plant chemistry, morphology, ecology, and more. Here, we describe how plant genomes have been harnessed for studies of plant phylogeny and diversification, with examples spanning all green plants, a clade of nearly half a million species spanning nearly a billion years of evolutionary time. Then focusing on angiosperms, we suggest how the process of whole‐genome duplication (polyploidy) has driven, and continues to drive, major innovations in morphology, stress response, and more. Together, these perspectives will begin to reveal how genomic change can lead to novelty and diversity at the organismal level. Finally, we review how little we actually know about plant genomes, given that assembled genome sequences exist for fewer than 1% of all plant species—a major shortcoming as we seek to meet societal challenges of food security, the need for new medicines, and conservation of species in response to climate change.

Fast pyrolysis of sugarcane straw and its integration into the conventional ethanol production process through Pinch Analysis

One way to improve the energy and environmental efficiency of an ethanol production process is through product diversification, as well as the use of agricultural residues via thermochemical routes such as fast pyrolysis. Thus, this study assesses the integration of fast pyrolysis of sugarcane straw into the conventional ethanol production process. The fast pyrolysis process was modelled and simulated in the Aspen Plus® software, using the Lumped Reaction kinetic model. The heat integration procedure was performed using the Pinch analysis, utilising the simulation results and assuming different percentages of straw recovery from the field (25%, 50%, and 75%). The straw pyrolysis model was validated with experimental data from other authors of the literature. The assumed configuration presented itself as self-sufficient in energy terms. Among several evaluated cases, those where heat integration was applied showed a significant increase in surplus electricity (Case IV 30.6%, Case VI 34.8%, and Case VIII 46.4%) in comparison to the Base Case (Case I). Thus, heat integration promotes a rise in energy efficiency, as well as product diversification in ethanol production plants.

Angiosperms at the edge: Extremity, diversity, and phylogeny.

A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.

Population Genetics of Polyploid Complex Psidium cattleyanum Sabine (Myrtaceae): Preliminary Analyses Based on New Species-Specific Microsatellite Loci and Extension to Other Species of the Genus.

Polyploidy is a phenomenon that alters the genetic diversity of populations and has been reported as one of the most important evolutionary forces for plant diversification. The Psidium cattleyanum complex comprises a group of wild populations with several ploidy levels reported in the literature. The multiple cytotypes, associated with its wide distribution area, make this species a potential key model for understanding evolutionary processes related to polyploidization. In this study, we isolated and characterized nuclear microsatellite markers of P. cattleyanum and tested their transferability to other nine species of the genus. We performed a preliminary analysis of genetic diversity and population structure in three populations of P. cattleyanum. The three populations analyzed had different chromosome numbers, being polyploid cytotypes (2n = 6x = 66, 2n = 7x = 77 and 2n = 8x = 88). We designed 46 primer pairs and successfully amplified 37 markers, from which the 10 best were selected for analysis. Considering both the PIC and DP values, most of markers were highly informative. The new SSR markers were used to assess the levels of genetic diversity of the populations and detected one population with predominance of sexual reproduction. DAPC analysis pointed the formation of three groups, which corresponded to the populations analyzed. The markers were successfully amplified in related species, with some species presenting 80% transferability. By producing this panel of polymorphic microsatellites, we contribute to the understanding evolution in groups of natural polyploids for future studies.

Overcoming Competition From Intercropped Forages on Upland Rice With Optimized Nitrogen Input to Food Production in Tropical Region

Intercropping forage grasses with upland rice is an alternative cropping system to improve agroecosystem diversification and could potentially enhance sustainability in tropical regions. However, nitrogen (N) immobilization and nutrient competition between rice and forage grasses could reduce rice grain yield and decrease overall productivity. Therefore, fertilizer N requirements of upland rice intercropped with forage grasses needs to be better defined. Field experiments were carried out during three growing seasons on a Typic Haplorthox soil in Sao Paulo state of Brazil. The experimental design was a randomized block design with a 3 × 4 factorial scheme with four replications. Treatments were cropping system [monocropped rice (Oryza sativa L.), rice intercropped with palisadegrass (Urochloa brizantha), and rice intercropped with guineagrass (Megathyrsus maximus) and sidedress N application rate (0, 40, 80, and 120 kg N ha-1). Intercropped grasses were sown between upland rice rows 30 days after rice emergence. On average, intercropping of rice with palisadegrass or guineagrass decreased rice shoot dry matter and grain yield by 11% and milled rice productivity by 10% compared with monocropped rice. Grain yield, grain protein, and milled productivity of rice increased as N application rate increased. Forage dry matter production (first and second cut) and crude protein (second cut) were greatest in the rice + palisadegrass intercropping system. Production of both forage grasses increased with up to 80 kg N ha-1 in the first cut and increased linearly with N in the second cut. Intercropping of rice with palisadegrass or guineagrass with 80 kg N ha-1 application resulted in the greatest land equivalent ratio (1.96 and 1.55, respectively). Relative N yield was greatest at 120 kg N ha-1 (220 and 173%, respectively). Although rice monocropping had greatest grain yield, intercropping systems with forage grasses were more favorable from both economic and environmental perspectives by enhancing plant diversification, nutrient cycling with forage grasses, land use production per unit area, and profitability throughout the year.

Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics

AbstractWe studied the evolutionary history of Chrysobalanaceae with phylogenetic analyses of complete plastid genomes from 156 species to assess the tempo of diversification in the Neotropics and help to unravel the causes of Amazonian plant diversification. These plastid genomes had a mean length of 162 204 base pairs, and the nearly complete DNA sequence matrix, with reliable fossils, was used to estimate a phylogenetic tree. Chrysobalanaceae diversified from 38.9 Mya (95% highest posterior density, 95% HPD: 34.2–43.9 Mya). A single clade containing almost all Neotropical species arose after a single dispersal event from the Palaeotropics into the Amazonian biome c. 29.1 Mya (95% HPD: 25.5–32.6 Mya), with subsequent dispersals into other Neotropical biomes. All Neotropical genera diversified from 10 to 14 Mya, lending clear support to the role of Andean orogeny as a major cause of diversification in Chrysobalanaceae. In particular, the understory genus Hirtella diversified extremely rapidly, producing > 100 species in the last 6 Myr (95% HPD: 4.9–7.4 Myr). Our study suggests that a large fraction of the Amazonian tree flora has been assembled in situ in the last 15 Myr.

The uncinate viscidium and floral setae, an evolutionary innovation and exaptation to increase pollination success in the Telipogon alliance (Orchidaceae: Oncidiinae)

Floral innovations are key for pollinator specialization and play a significant role in plant diversification. Orchidaceae present many examples of floral innovations that allow its high degrees of pollinator specialization and promoted speciation. The rich neotropical genus Telipogon evolved an uncinate (=hook-like) viscidium on the pollinarium and setae-bearing flowers, which are uncommon in Orchidaceae; however, the importance of them on pollination success and whether they are floral innovations or exaptations in Telipogon have not been investigated. Here we investigate the morphology of the viscidium and floral setae within the Telipogon alliance (including the genera Hofmeisterella, Trichoceros and Telipogon), test their significance in pollination, and their occurrence and evolution across the Oncidiinae. We used Telipogon peruvianus as a model species to test whether uncinate viscidium and floral setae increased pollination success compared with a cochleariform (=spoon-like) viscidium and lack of floral setae condition. We show that the uncinate viscidium is a synapomorphy for Telipogon; setae-bearing flowers are not universally found among all species of Telipogon and evolved once in the Telipogon alliance. Furthermore, Telipogon peruvianus flowers with an uncinate viscidium have achieved higher pollinia export than those with cochleariform viscidium (ancestral condition), whereas flowers with setae have both higher success in pollinia removal, although not significant, and pollinia deposition than those lacking of setae (ancestral condition). We demonstrate that uncinate viscidia and floral setae in Telipogon are a key innovation and exaptation, respectively, that enhance pollination success and they might act as drivers of diversification and pollinator specialization in this genus.

Identification of the Key Regulatory Genes Involved in Elaborate Petal Development and Specialized Character Formation in Nigella damascena (Ranunculaceae).

Petals can be simple or elaborate, depending on whether they have lobes, teeth, fringes, or appendages along their margins, or possess spurs, scales, or other types of modifications on their adaxial/abaxial side, or both. Elaborate petals have been recorded in 23 orders of angiosperms and are generally believed to have played key roles in the adaptive evolution of corresponding lineages. The mechanisms underlying the formation of elaborate petals, however, are largely unclear. Here, by performing extensive transcriptomic and functional studies on Nigella damascena (Ranunculaceae), we explore the mechanisms underlying elaborate petal development and specialized character formation. In addition to the identification of genes and programs that are specifically/preferentially expressed in petals, we found genes and programs that are required for elaborate rather than simple petal development. By correlating the changes in gene expression with those in petal development, we identified 30 genes that are responsible for the marginal/ventral elaboration of petals and the initiation of several highly specialized morphological characters (e.g., pseudonectaries, long hairs, and short trichomes). Expression and functional analyses further confirmed that a class I homeodomain-leucine zipper family transcription factor gene, Nigella damascena LATE MERISTEM IDENTITY1 (NidaLMI1), plays important roles in the development of short trichomes and bifurcation of the lower lip. Our results not only provide the first portrait of elaborate petal development but also pave the way to understanding the mechanisms underlying lateral organ diversification in plants.

Insect pollination of cycads

AbstractMost cycads have intimate associations with their insect pollinators that parallel those of well‐known flowering plants, such as sexually deceptive orchids and the male wasps and bees they deceive. Despite this, the mistaken belief that cycads are mostly wind‐pollinated is still commonly expressed. Perhaps as a consequence, cycad–pollinator systems are rarely exemplified in studies of the role of pollinators in plant evolution and diversification. Although first recognised more than a century ago, specialised associations between cycads and their insect pollinators have been elucidated experimentally only in the past few decades. This review covers the history of understanding pollination in cycads, the advances that have been made since the 1980s using field observations and experiments, and analyses of molecular data from the population to phylum level. We outline areas for future research to address how such interactions might have affected speciation and extinctions. We stress that inclusion of cycads in broader considerations of the role of pollinators in plant diversification is important because they are phylogenetically distant from flowering plants and their pollination systems might have evolved independently of one another. This review is timely because cycads are a globally threatened group that might be vulnerable to co‐extinction with pollinator loss.

Plant growth and dynamics of green mass and dry matter accumulation in crop rotations and monocrops on irrigation

Introduction. In intensive farming, soil fertility is enhanced via sufficient amounts of organic and mineral fertilizers, appropriate ameliorative measures, and providing effective biodiversity in agricultural lands. Crop rotations play an important role in preserving and restoring soil fertility as well as in increasing crop yields.Along with cereals, high potential soybean plays a special role in crop rotations. This crop is important for providing food, improving soil fertility and, as green fodder, for livestock development.Material and methods. Crop rotations were compared with monocrops by the Department of Sustainable Agriculture and Plant Diversification of the Absheron Subsidiary Research Farm in 2015–2017. Weighty results have been obtained with the effective use of organic matter from root and top residues by other plants.Result and discussion. In the bean formation phase, the green mass of soybean increased by 2.15 t/ha, and the dry matter - by 0.69 t ha in the crop rotation compared to the monocrop.The results showed that in the crop rotation the amount of plant residues per hectare collected from the 0-40 cmlayer of soil increased from 2.38 t to 2.68 t in soybean, from 4.38 t to 4.76 t in winter wheat, and from 3.95 t to 4.21 t in barleyConclusions. The results demonstrated that the plant growth and development in monocrops was slowed down. The highest values of height, green mass, dry matter, root weight and yield were recorded in the crop rotation.

En busca de un enfoque preventivo para el manejo del barrenador de las meliáceas (Hypsipyla grandella)

Se sintetizan las experiencias del autor y colaboradores en la búsqueda de métodos preventivos para lidiar con Hypsipyla grandella (Lepidoptera: Pyralidae). Enmarcados en la noción del manejo integrado de plagas (MIP), incluyen el injerto de Cedrela odorata sobre un patrón resistente de cedro australiano (Toona ciliata var. australis); la estructuración de plantaciones ecológicamente robustas, basadas en la diversificación de la vegetación y el control biológico natural; el diseño de un sistema de predicción del riesgo; el abatimiento precoz de la población, usando trampas con feromonas; la evitación mediante la repelencia de adultos o la fagodisuasión de larvas; y la mortalidad de larvas por toxicidad o disrupción de su crecimiento.

<p><strong>The oldest water scorpion discovered in the Early Cretaceous Crato Formation (Hemiptera: Nepidae)</strong></p>

Araripenepa vetussiphonis gen. et sp. nov., the oldest representative of the family Nepidae is described from the Early Cretaceous Crato Formation in Brazil. It is considered as the sister group of all the extant Nepidae, having retained tarsi with three tarsomeres and a transverse pronotum. The general habitus, elongate siphon, and strong grasping legs strongly suggest that its biology was very similar to that of the extant Nepa spp., viz. a predaceous bug living in the mud and/or the abundant aquatic vegetation of the Crato palaeolake. Possibly, the Triassic—Jurassic representatives of the stem group of Nepidae had no elongate siphon and were similar to Cratonepa, an enigmatic Nepoidea previously described from the Crato Formation. The development of the siphon was possibly favoured by the diversification of the lacustrine plants that occurred during the Early Cretaceous.

An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

BackgroundThe New World Tropics has experienced a dynamic landscape across evolutionary history and harbors a high diversity of flora and fauna. While there are some studies addressing diversification in Neotropical vertebrates and plants, there is still a lack of knowledge in arthropods. Here we examine temporal and spatial diversification patterns in the damselfly family Polythoridae, which comprises seven genera with a total of 58 species distributed across much of Central and South America.ResultsOur time-calibrated phylogeny for 48 species suggests that this family radiated during the late Eocene (~ 33 Ma), diversifying during the Miocene. As with other neotropical groups, the Most Recent Common Ancestor (MRCA) of most of the Polythoridae genera has a primary origin in the Northern Andes though the MRCA of at least one genus may have appeared in the Amazon Basin. Our molecular clock suggests correlations with some major geographical events, and our biogeographical modeling (with BioGeoBEARS and RASP) found a significant influence of the formation of the Pebas and Acre systems on the early diversification of these damselflies, though evidence for the influence of the rise of the different Andean ranges was mixed. Diversification rates have been uniform in all genera except one—Polythore—where a significant increase in the late Pliocene (~ 3 mya) may have been influenced by recent Andean uplift.ConclusionThe biogeographical models implemented here suggest that the Pebas and Acre Systems were significant geological events associated with the diversification of this damselfly family; while diversification in the tree shows some correlation with mountain building events, it is possible that other abiotic and biotic changes during our study period have influenced diversification as well. The high diversification rate observed in Polythore could be explained by the late uplift of the Northern Andes. However, it is possible that other intrinsic factors like sexual and natural selection acting on color patterns could be involved in the diversification of this genus.

Testing hypotheses of hybrid origins for two seashore species ofCarexsectionPhacocystis(Cyperaceae)

AbstractTaxonomists have proposed numerous hybrid species in plants, but to gain a better understanding of the role that hybridization may play in plant diversification, such taxonomic hypotheses must be tested using genomic data. In this study, we employ ddRAD sequence data to test taxonomic hypotheses of hybrid origins in Carex salina and C. ramenskii (Carex section Phacocystis). Sequence data from multiple Norwegian and Icelandic populations of the putative hybrid and parental species were generated for hundreds of ddRAD loci. These data were used to estimate geographical structuring of genetic diversity and admixture and to explicitly test for hybrid origins using several analytical approaches. Our results indicate recurrent hybrid origins for the populations of C. salina and C. ramenskii sampled in our study and show that these populations are characterized by high interspecific heterozygosity. Our results support the idea that hybridization may indeed play an important role in the diversification of lineages of Carex and highlight the important role that clonal propagation might play in maintaining hybrid populations. Future studies focusing on a broader geographical sampling would be needed to assess if the genetic structuring in these Nordic populations reflects range-wide patterns in these hybrid lineages.

Endophytic microbes: biodiversity, plant growth-promoting mechanisms and potential applications for agricultural sustainability.

Endophytic microbes are known to live asymptomatically inside their host throughout different stages of their life cycle and play crucial roles inthe growth, development, fitness, and diversification of plants. The plant-endophyte association ranges from mutualism to pathogenicity. These microbes help the host to combata diverse array of biotic and abiotic stressful conditions. Endophytic microbes play a major role in the growth promotion of their host by solubilizing of macronutrients such as phosphorous, potassium, and zinc; fixing of atmospheric nitrogen, synthesizing of phytohormones, siderophores, hydrogen cyanide, ammonia, and act as a biocontrol agent against wide array of phytopathogens. Endophytic microbes are beneficial to plants by directly promoting their growth or indirectly by inhibiting the growth of phytopathogens. Over a long period of co-evolution, endophytic microbes have attained the mechanism of synthesis of various hydrolytic enzymes such as pectinase, xylanases, cellulase, and proteinase which help in the penetration of endophytic microbes into tissues of plants. The effective usage of endophytic microbes in the form of bioinoculants reduce the usage of chemical fertilizers. Endophytic microbes belong to different phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Deinococcus-thermus, Firmicutes, Proteobacteria, and Verrucomicrobia. The most predominant and studied endophytic bacteria belonged to Proteobacteria followed by Firmicutes and then by Actinobacteria. The most dominant among reported genera in most of the leguminous and non-leguminous plants are Bacillus, Pseudomonas, Fusarium, Burkholderia, Rhizobium, and Klebsiella. In future, endophytic microbes have a wide range of potential for maintaining health of plant as well as environmental conditions for agricultural sustainability. The present review is focused on endophytic microbes, their diversity in leguminous as well as non-leguminous crops, biotechnological applications, and ability to promote the growth of plant for agro-environmental sustainability.

The importance of plant diversity in the ecological management of insects in agroecosystems: a review

The objective of this study is to evaluate the importance of plant diversity in insect management in agroecosystems.The conventional management of agroecosystems is based on monoculture, with exploitation of plant genotypes susceptible to pests and diseases, with intense use of agrochemicals and soil mechanization. The impact on agroecosystem biodiversity by intensifying agronomic practices results in losses of important ecological functions: decomposition, nutrient cycling, predation and parasitism. The potential of plant diversity in the sustainability of agroecosystems is recommended through practices such as intercropping, agroforestry systems, management of cover crops, spontaneous herbs and the use of plants attractive to natural enemies and as pest traps. Farm planning should take into account some level of plant diversification to avoid pest insect outbreaks. Thus, it will be possible to reduce pesticides in conventional system, and reduce the number of interventions with alternative substances in farm in agroecological systems.

Diversified floral provisioning enhances performance of the generalist predator, Orius insidiosus (Hemiptera: Anthocoridae)

Providing nectar and pollen through the establishment of insectary plants is one approach to conserving natural enemies and enhancing biological control of arthropod pests. Recent studies show that natural enemy performance may be influenced by the diversity of insectary plant species and the resources they provide. We conducted laboratory assays to investigate the influence of buckwheat (Fagopyrum esculentum Moench.) and cowpea (Vigna unguiculata (L.) Walp.) alone and in a mixture on the performance of the insidious flower bug, Orius insidiosus (Say, 1832). We measured performance as longevity, fecundity and predation of O. insidiosus reared on a laboratory diet of Ephestia kuehniella or its field prey, Ostrinia nubilalis (Hübner). O. insidiosus survived on average 20–25% longer and oviposited 67–88% more eggs when provided with either insectary species compared to a water only control. However, when provided with a biculture of cowpea and buckwheat, O. insidiosus survived 35% longer and laid 111% more eggs compared to the water only control, with a strong preference for cowpea as an oviposition host. This study provides novel empirical evidence that cowpea, a plant anecdotally cited for its insectary properties, functions as a preferred oviposition sites compared to buckwheat and laboratory standard green beans. The presence of insectary resources, however, did not significantly influence predation on O. nubilalis sentinel prey by O. insidiosus as we anticipated. These results indicate that the performance of beneficial insects like O. insidious may be differentially influenced by the resources provided by insectary species and should be screened for potential benefits before establishing in field settings. Further implications of plant diversification for conservation biological control are discussed.

The genome of a cave plant, Primulina huaijiensis, provides insights into adaptation to limestone karst habitats.

Although whole genome duplication (WGD) has been suggested to facilitate adaptive evolution and diversification, the role of specific WGD events in promoting diversification and adaptation in angiosperms remains poorly understood. Primulina, a species-rich genus with >180 species associated with limestone karst habitat, constitutes an ideal system for studying the impact of WGD events on speciation and evolutionary adaptation. We sequenced and assembled a chromosome-level genome of the cave-dwelling species P.huaijiensis to study gene family expansion and gene retention following WGDs. We provide evidence that P.huaijiensis has undergone two WGDs since the γ triplication event shared by all eudicots. In addition to a WGD shared by almost all Lamiales (L event), we identified a lineage-specific WGD (D event) that occurred in the early Miocene around 20.6-24.2Myr ago and that is shared by almost the entire subtribe Didymocarpinae. We found that gene retentions following the D event led to gene family proliferation (e.g. WRKYs) that probably facilitated adaptation to the high salinity and drought stress in limestone karst. Our study highlights the role of lineage-specific WGD in species diversification and adaptation of plants from special habitats.