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View article: Genome‐wide patterns of local adaptation associated with transposable elements in <i>Tetrastigma hemsleyanum</i> (Vitaceae)
Genome‐wide patterns of local adaptation associated with transposable elements in <i>Tetrastigma hemsleyanum</i> (Vitaceae) Open
Summary The mobility of transposable elements (TEs) partly drives genome evolution, potentially leading to either adaptive or deleterious effects. However, it remains far from clear whether and how TEs contribute to adaptation to changing …
View article: Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics
Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics Open
We failed to reconstruct a reliable and unambiguous evolutionary history among Amana, Erythronium, and Tulipa due to especially pervasive ILS and reticulate evolution, likely caused either by obscured minority phylogenetic signal or differ…
View article: Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics
Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics Open
Background: Phylogenetic research in Tulipa (Liliaceae), a genus of significant economic and horticultural value, has relied on limited nuclear (mostly nrITS) and plastid gene sequences, resulting in low-resolution phylogenetic trees and u…
View article: BERTPhylo: An Efffcient Method to Accelerate Phylogenetic Inference Using a Pretrained DNA Language Model
BERTPhylo: An Efffcient Method to Accelerate Phylogenetic Inference Using a Pretrained DNA Language Model Open
Understanding the phylogenetic relationships among species is crucial for comprehending major evolutionary transitions, serving as the foundation for many biological studies. Despite the ever-growing volume of sequence data providing a sig…
View article: Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization
Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization Open
Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., di…
View article: Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two ‘living fossil’ tree species of <i>Dipteronia</i>
Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two ‘living fossil’ tree species of <i>Dipteronia</i> Open
SUMMARY ‘Living fossils’, that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long‐term su…
View article: Issue Information
Issue Information Open
On the Cover: Centre: Papuan frogmouth (Podargus papuensis) is a large nocturnal insectivorous bird living in Papua New Guinea and Cape York Peninsula in Australia; photograph by Katerina Sam; pp.1803-1816.Top right: Lupinus montanus (Faba…
View article: Did Late Quaternary climate change trigger shifts in mating system in temperate plant species of the Sino-Japanese Floristic Region? A commentary on ‘Genetic and demographic signatures accompanying the evolution of the selfing syndrome in <i>Daphne kiusiana</i>, an evergreen shrub’
Did Late Quaternary climate change trigger shifts in mating system in temperate plant species of the Sino-Japanese Floristic Region? A commentary on ‘Genetic and demographic signatures accompanying the evolution of the selfing syndrome in <i>Daphne kiusiana</i>, an evergreen shrub’ Open
This article comments on: Eun-Kyeong Han, Ichiro Tamaki, Sang-Hun Oh, Jong-Soo Park, Won-Bum Cho, Dong-Pil Jin, Bo-Yun Kim, Sungyu Yang, Dong Chan Son, Hyeok-Jae Choi, Amarsanaa Gantsetseg, Yuji Isagi, and Jung-Hyun Lee. Genetic and demogr…
View article: Variation in scent amount but not in composition correlates with pollinator visits within populations of deceptive Arum maculatum L. (Araceae)
Variation in scent amount but not in composition correlates with pollinator visits within populations of deceptive Arum maculatum L. (Araceae) Open
Floral scent is vital for pollinator attraction and varies among and within plant species. However, little is known about how inter-individual variation in floral scent affects the abundance and composition of floral visitor assemblages wi…
View article: Plant speciation in the Namib Desert: potential origin of a widespread derivative species from a narrow endemic
Plant speciation in the Namib Desert: potential origin of a widespread derivative species from a narrow endemic Open
Funding: This research was funded in part by the award of a Natural Environment Research Council (NERC) CASE research studentship to J.J.M.
View article: Evidence for an evo‐devo‐derived hypothesis on three‐dimensional flower shape modularity in a tropical orchid clade
Evidence for an evo‐devo‐derived hypothesis on three‐dimensional flower shape modularity in a tropical orchid clade Open
Covarying suites of phenotypic traits, or modules, are increasingly recognized to promote morphological evolution. However, information on how modularity influences flower diversity is rare and lacking for Orchidaceae. Here, we combine hig…
View article: Plio-Pleistocene climatic change drives allopatric speciation and population divergence within the Scrophularia incisa complex (Scrophulariaceae) of desert and steppe subshrubs in Northwest China
Plio-Pleistocene climatic change drives allopatric speciation and population divergence within the Scrophularia incisa complex (Scrophulariaceae) of desert and steppe subshrubs in Northwest China Open
Numerous temperate plants and animals on the Qinghai-Tibet Plateau (QTP) are hypothesized to have differentiated due to vicariant allopatric speciation associated with the geologic uplifts. However, this hypothesis has rarely been tested t…
View article: A Comparative Study of Genetic Responses to Short- and Long-Term Habitat Fragmentation in a Distylous Herb Hedyotis chyrsotricha (Rubiaceae)
A Comparative Study of Genetic Responses to Short- and Long-Term Habitat Fragmentation in a Distylous Herb Hedyotis chyrsotricha (Rubiaceae) Open
The genetic effects of habitat fragmentation are complex and are influenced by both species traits and landscape features. For plants with strong seed or pollen dispersal capabilities, the question of whether the genetic erosion of an isol…
View article: Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae)
Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae) Open
Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats deriv…
View article: Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae)
Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae) Open
Subfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and ca. 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents…
View article: An overlooked dispersal route of Cardueae (Asteraceae) from the Mediterranean to East Asia revealed by phylogenomic and biogeographical analyses of<i>Atractylodes</i>
An overlooked dispersal route of Cardueae (Asteraceae) from the Mediterranean to East Asia revealed by phylogenomic and biogeographical analyses of<i>Atractylodes</i> Open
Background and Aims The East Asian–Tethyan disjunction pattern and its mechanisms of formation have long been of interest to researchers. Here, we studied the biogeographical history of Asteraceae tribe Cardueae, with a particular focus on…
View article: Local Insect Availability Partly Explains Geographical Differences in Floral Visitor Assemblages of Arum maculatum L. (Araceae)
Local Insect Availability Partly Explains Geographical Differences in Floral Visitor Assemblages of Arum maculatum L. (Araceae) Open
Geographical variation in abundance and composition of pollinator assemblages may result in variable selection pressures among plant populations and drive plant diversification. However, there is limited knowledge on whether differences in…
View article: Plant speciation in the Namib Desert: origin of a widespread derivative species from a narrow endemic
Plant speciation in the Namib Desert: origin of a widespread derivative species from a narrow endemic Open
Background Parapatric (or ‘budding’) speciation is increasingly recognized as an important phenomenon in plant evolution but its role in extreme (e.g. desert) environments is poorly documented. Aims To test this speciation model in a hypot…
View article: Plant speciation in the Namib Desert: potential origin of a widespread derivative species from a narrow endemic
Plant speciation in the Namib Desert: potential origin of a widespread derivative species from a narrow endemic Open
Parapatric (or ‘budding’) speciation is increasingly recognised as an important phenomenon in plant evolution but its role in extreme (e.g. desert) environments is poorly documented. To test this speciation model in a hypothesised sister p…
View article: Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (<i>Trapa</i> spp., Lythraceae)
Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (<i>Trapa</i> spp., Lythraceae) Open
Summary Humans have domesticated diverse species from across the plant kingdom; however, our current understanding of plant domestication is largely founded on major cereal crops. Here, we examine the evolutionary processes and genetic bas…
View article: Floral Scents of a Deceptive Plant Are Hyperdiverse and Under Population-Specific Phenotypic Selection
Floral Scents of a Deceptive Plant Are Hyperdiverse and Under Population-Specific Phenotypic Selection Open
Floral scent is a key mediator in plant-pollinator interactions. However, little is known to what extent intraspecific scent variation is shaped by phenotypic selection, with no information yet in deceptive plants. In this study, we collec…
View article: Evidence for selectively constrained 3D flower shape evolution in a Late Miocene clade of Malagasy <i>Bulbophyllum</i> orchids
Evidence for selectively constrained 3D flower shape evolution in a Late Miocene clade of Malagasy <i>Bulbophyllum</i> orchids Open
Summary Questions concerning the evolution of complex biological structures are central to the field of evolutionary biology. Yet, still little information is known about the modes and temporal dynamics of three‐dimensional (3D) flower sha…
View article: Evolution of crassulacean acid metabolism (CAM) as an escape from ecological niche conservatism in Malagasy <i>Bulbophyllum</i> (Orchidaceae)
Evolution of crassulacean acid metabolism (CAM) as an escape from ecological niche conservatism in Malagasy <i>Bulbophyllum</i> (Orchidaceae) Open
Summary Despite growing evidence that niche shifts are more common in flowering plants than previously thought, little is known of whether such shifts are promoted by changes in photosynthetic pathways. Here we combine the most complete ph…
View article: Floral scents of a deceptive plant are hyperdiverse and under population-specific phenotypic selection
Floral scents of a deceptive plant are hyperdiverse and under population-specific phenotypic selection Open
Floral scent is a key mediator in plant-pollinator interactions; however, little is known to what extent intraspecific scent variation is shaped by phenotypic selection, with no information yet in deceptive plants. We recorded 291 scent co…
View article: Primary hybrid zone formation in<i>Tephroseris helenitis</i>(Asteraceae), following postglacial range expansion along the central Northern Alps
Primary hybrid zone formation in<i>Tephroseris helenitis</i>(Asteraceae), following postglacial range expansion along the central Northern Alps Open
Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental‐selective) processes are distinguis…
View article: Evolution of Crassulacean Acid Metabolism (CAM) as an escape from ecological niche conservatism in Malagasy<i>Bulbophyllum</i>(Orchidaceae)
Evolution of Crassulacean Acid Metabolism (CAM) as an escape from ecological niche conservatism in Malagasy<i>Bulbophyllum</i>(Orchidaceae) Open
Introductory paragraph Despite growing evidence that niche shifts are more common in flowering plants than previously thought, still little is known about the key physiological (e.g. photosynthesis) traits underlying such niche shifts. To …
View article: Genomic insights on the contribution of balancing selection and local adaptation to the long‐term survival of a widespread living fossil tree, <i>Cercidiphyllum japonicum</i>
Genomic insights on the contribution of balancing selection and local adaptation to the long‐term survival of a widespread living fossil tree, <i>Cercidiphyllum japonicum</i> Open
Summary ‘Living fossils’ are testimonies of long‐term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations…