Aim: To investigate the ecological and evolutionary mechanisms driving biodiversity in the Indo-Malayan hotspots, with a particular focus on the roles of ancient hybridisation and historical climate in shaping species diversity. Location: The Indo-Malayan realm, particularly the Western Ghats-Sri Lanka and Indo-Burma biodiversity hotspots. Time Period: The Miocene Climatic Optimum (similar to 14 million years ago) to these days. Major Taxa Studied: Curcuma (Zingiberaceae). Methods: The evolutionary history of Curcuma was reconstructed using targeted nuclear loci. This genomic data was integrated with ecological niche modelling, biogeographic reconstruction and diversification dynamic analyses to examine the interplay between historical climate, niche evolution and hybridisation. Results: Curcuma originated in the Indo-Burma region approximately 14 Ma. Its diversification was likely promoted by prolonged periods of high humidity and relatively mild climatic conditions. Dispersal to the Western Ghats occurred during the mid-Pliocene (3.6 Ma). Although ancient hybridisation may have facilitated ecological divergence and local adaptation, it did not have a statistically significant effect on diversification rates. Main Conclusions: Our work provides support that the Indo-Malayan biodiversity might be the result of species persistence enabled by extended periods of humidity and warm temperatures over evolutionary timescales, rather than increased speciation rates. These findings enhance our understanding of the processes shaping paleotropical biodiversity and offer insights relevant to the conservation and improvement of Curcuma, a crop of economic and medicinal value.

Hybridization, polyploidization, and apomixis are evolutionary forces that obscure genetic differentiation and boost morphological variability. These processes have shaped the family Rosaceae, particularly the genus Crataegus, which includes both diploid and polyploid species reproducing sexually or via apomixis. In Central Europe, C. monogyna and C. laevigata are predominantly diploid sexuals, while C. rhipidophylla is mainly a polyploid apomict. These species hybridize to form C.  ×  media, C.  ×  macrocarpa, and C.  ×  subsphaerica. Our aim was to assess how hybridization, apomixis, and polyploidy shape Crataegus diversity by integrating genetic, morphological, and cytological data. Leaves and fruits were collected from ten natural populations where all three species coexist and hybridize. Species identification was performed with novel nuclear microsatellites, marking the first genetic-based Crataegus taxonomy in Central Europe. Ploidy levels were estimated by flow cytometry (FCM), including seed screening to infer reproductive modes. A combined morphological analysis of leaves and fruits was used to distinguish parental species and evaluate hybrid variability. Genotyping identified distinct genetic clusters for parental species and their hybrids, with geographic structuring within C. laevigata and C. rhipidophylla. Morphological data clearly separated genetically defined parental species, although hybrids can be difficult to distinguish from parents due to a big overlap in morphology. FCM indicated that C.  ×  media is predominantly a diploid sexual hybrid like its diploid parents, while other tri- or tetraploid hybrids with polyploid C. rhipidophylla as a parent are apomictic. Ploidy rather than hybridization dictates the mode of reproduction.

Understanding the proximate and ultimate causes of genome size variation has been the focus of considerable research. However, the extent and cause of intraspecific variation in genome size are debated and poorly understood. This study aimed to test the role of genome size in adaptation through variations in intraspecific genome size. Genome size was measured in 53 Roscoea tibetica populations from the Hengduan Mountains using flow cytometry. Stomatal size and density data were collected from wild and common garden populations. Associations among genome size, environmental factors, and stomatal traits were explored. We found that high genome size variability was positively correlated with most environmental factors but negatively correlated with solar radiation during the growing season. The environment, rather than geography, significantly influenced variations in genome size. Stomatal traits measured in the wild were significantly correlated with genome size, but no such correlations were detected in the common garden. Populations in the common garden had larger stomatal sizes and lower stomatal densities. Populations with smaller genome size presented a larger degree of stomatal trait variation from the wild to the common garden. Our findings suggest that intraspecific genome size has undergone adaptive evolution driven by environmental stress. A smaller genome size is more advantageous for the alpine ginger to adapt to and thrive in changing alpine habitats.

Societal Impact Statement The primarily neotropical plant genus Heliconia has been cultivated commercially in gardens and nurseries for hundreds of years. Many of these same species are ecological keystones in their native habitats as important resources for herbivorous insects and pollinating hummingbirds, yet they face threats of habitat loss and degradation, competition with invasive species, poaching from the wild, and impacts of climate change. Only a handful have been assessed to date for their conservation status. We show that nearly half of the species are threatened with extinction, many are not protected, and conserving priority species may reduce overall threats to the genus. Summary Heliconia is a charismatic genus containing 181 neotropical species and six paleotropical species, which play critical ecological roles in natural habitats and are widely cultivated as ornamentals with significant horticultural value. To date little data on the conservation status of these species have been available. To conduct conservation assessments, specimen data were assembled from herbarium collections, species distributions were mapped across biomes and ecoregions, the extent of occurrence and area of occupancy were calculated, and land‐cover vegetation loss from human activities was plotted. The number of botanical gardens holding ex situ specimens was also determined. Finally, phylogenomic patterns were used to evaluate the evolutionary conservation status across the genus. Eighty‐seven species (47%) of Heliconia are threatened with extinction. Among threatened species, all but one are in five or fewer protected localities; most non‐threatened species (61%) are in five or more protected localities. The majority of species maintained in ex situ collections (70 of 118 species) are of least conservation concern. Conservation status and protection are not evenly distributed with some evolutionary lineages more threatened and less protected than others. Previously less than 10% of Heliconia were in the IUCN Red List. Current results indicate that nearly half of species are threatened, but that many species are minimally protected through in situ and ex situ conservation. Forty‐five species are considered top priorities for additional protection. Extinction threat also extends to major lineages within the genus. Recommendations are made to concentrate conservation efforts in specific lineages to insure the survival of Heliconia.

AimThe outstanding Andean biodiversity has been linked to the occurrence of evolutionary radiations that are common among high-elevation plant lineages. One of the most iconic examples is found in the species-rich genus Senecio, with an impressive variation in growth forms and habitat preference. Here, we use Hyb-Seq to overcome the lack of phylogenetic resolution found in previous studies with the aim of disentangling the processes shaping Senecio's hyper-diversity in the Andes, including the evolution of woodiness, growth form and habitat preference.LocationCentral and Northern Andes.TaxonSenecio ser. Culcitium.MethodsHyb-Seq data for 104 accessions of Senecio were newly generated and analysed using a data analysis workflow that utilises paralogs for phylogenetic reconstruction. The robustness of the species tree under different missing data treatments was investigated, and the phylogeny was dated. The role of hybridisation in the diversification of this lineage was addressed. The evolution of morphological key features and changes in habitat preferences were evaluated. In addition, the association of these features with diversification rate heterogeneity was tested.ResultsSenecio ser. Culcitium is a monophyletic lineage, likely of a Pleistocene origin. Hybridisation, possibly promoted by altitudinal range shifts during the Pleistocene climatic oscillations, played an important role in its evolution. We found evidence for several events of south-to-north migration from the puna on the Central Andes to the p & aacute;ramo on the Northern Andes. One of these migrations to the p & aacute;ramo resulted in a dramatic species diversification. Habitat changes from the p & aacute;ramo to the montane forest occurred multiple times and were associated with growth form shifts.Main ConclusionsWith a net diversification rate of 2 species per million years, high-elevation Andean Senecio is among the fastest diversifying lineages documented so far in the region. Frequent shifts in woodiness, growth form, and habitat played a crucial role in the diversification of this lineage.

Members of the genus Heliconia L. (Heliconiaceae) have evolved complex interactions with both insect herbivores and hummingbird pollinators in tropical forests and secondary growth where they are abundant and diverse. Many of these same species have also been cultivated as ornamentals around the world for hundreds of years because of their extraordinary colors and forms. Because of the large size, fleshy nature, and tropical distribution, and despite a long taxonomic history, the classification and phylogenetic relationships of species of Heliconia have not received sufficient attention to date. No complete classification has been published for the entire genus, although some preliminary attempts have been offered. In this paper we used tissue sampled from field and herbarium collections of 136 species for genomic sequencing to determine the phylogenetic patterns within Heliconia, which then served as the basis for a new evolutionary classification of the genus. This new classification, which is based on extensive field work and the phylogenomic insights provided here, includes 187 currently recognized species. The new classification of Heliconia is composed of 17 sections in five subgenera with all groups well-supported in the phylogenomic analysis. Four subgenera are each composed of two sections and one subgenus includes nine sections. One subgenus and 10 sections are described as new.

The Mediterranean Basin is recognized as one of the world's most prominent biodiversity hotspots, where past climatic changes have driven range shifts, secondary contact between populations, and gene exchange. This study investigates the impact of historical introgression on the diversification of diploid members of the genus Picris (Compositae). Using nuclear and plastid genome data obtained through the Hyb-Seq approach, we assess whether introgression contributed to the evolution of the Mediterranean Picris, potentially giving rise to multiple regional endemics. We also test whether introgression was associated with the transfer of traits such as life strategy and fruit morphology, which are involved in habitat-specific adaptation. Phylogenetic network analysis revealed two major introgression events that shaped evolutionary trajectories within the genus. The earliest and most complex events involved the Turkish endemic P. campylocarpa, which hybridized with the most recent common ancestor (MRCA) of the P. cyprica-P. pauciflora lineage and with the MRCA of the B1 subclade, comprising the P. hieracioides group and the P. scaberrima-P. strigosa lineage. The latter introgression preceded shifts from iteroparity to semelparity and from heterocarpy to homocarpy, ruling out an adaptive introgression origin for these traits. Nevertheless, all detected historical introgression events contributed to the diversification of diploid Picris taxa.

European larch (Larix decidua Mill.) is a common deciduous conifer tree species naturally occurring in the Alps and in scattered populations in Central-Eastern Europe, including the Jeseníky region (NE Czechia). It is commonly planted in forests and especially some of its traditionally described regional types are highly valued in forestry for outstanding form and wood properties. Here we present the results of the first research to date focused on the genetic structure of a larger number of larch populations from the Jeseníky region using analysis of nuclear DNA microsatellite markers in the context of the variability throughout the whole range of the species. The region is traditionally considered to be a part of the native distribution range of larch and a specific local type of larch, called ‘Sudety’ or ‘Jeseníky’ type, has been described there. We confirm a common presence of the ‘Sudety’ type in a form of a genetic lineage closely related to larch populations from northern Carpathians and lowlands of Poland. However, we found notable levels of artificial admixture of genetic material from the Alps in many of the populations, including the populations specifically protected to preserve the local type of larch. The admixture is either low or absent in the core protected populations but in the periphery, including some of the protected areas, and commonly managed forests, the Alpine genotypes can reach up to 50

The overarching aim of the present study is to sort out the taxonomy of a group of gingers that include the useful and worldwide economically important green cardamom, Elettaria cardamomum, and its wild relatives, to highlight potentially overlooked genetic resources. These species occur naturally in India and Sri Lanka, and our study facilitates more appropriate management priorities for the remaining forest fragments in which they occur. We used NGS Hyb-Seq methods and sampled four species of the Alpinia I (Fax) clade, six representatives of Aframomum and Renealmia as well as two other basally flowering Sri Lankan species. This is the only pantropically distributed lineage within the entire family, and our result shows that the Alpinia I clade in fact is simply the genus Elettaria (confined to India and Sri Lanka), which is sister to the genera Aframomum (Africa) and Renealmia (Africa and Neotropics). The taxonomic implications are: (1) a recircumscription of Elettaria comprising seven species (E. cardamomum, E. ensal, E. floribunda, E. involucrata, E. rufescens as well as two new species, E. facifera and E. tulipifera described here); (2) the Sri Lankan endemic genus Cyphostigma should be retained; (3) the new monotypic genus, Srilankanthus endemic in Sri Lanka, is described with S. nemoralis, formerly Amomum nemorale, as type. A key is provided to the seven species of Elettaria and lectotypifications are made for five species (Cyphostigma pulchellum, Elettaria floribunda, E. involucrata, E. nemoralis, E. rufescens).

Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analyzed repeat dynamics, and identified potential hybridization events within the genus. Our analysis confirmed the presence of four major infrageneric clades (A–D) within Amomum, with clades A–C exclusively comprising diploid species (2n = 48) and clade D encompassing both diploid and tetraploid species (2n = 48 and 96). We observed an increase in the repeat content within the genus, ranging from 84% to 89%, compared to outgroup species with 75% of the repeatome. The SIRE lineage of the Ty1-Copia repeat superfamily was prevalent in most analyzed ingroup genomes. We identified significant difference in repeatome structure between the basal Amomum clades (A, B, C) and the most diverged clade D. Our investigation revealed evidence of ancient hybridization events within Amomum, coinciding with a substantial proliferation of multiple repeat groups. This finding supports the hypothesis that ancient hybridization is a driving force in the genomic evolution of Amomum. Furthermore, we contextualize our findings within the broader context of genome size variations and repeatome dynamics observed across major monocot lineages. This study enhances our understanding of evolutionary processes within monocots by highlighting the crucial roles of repetitive elements in shaping genome size and suggesting the mechanisms that drive these changes.

The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for "inappropriate" names. It is evident that such proposals come from very deep feelings, but we show how they can irreparably damage the foundation of biological communication and, in turn, the sciences that depend on it. There are four essential consequences of objective codes of nomenclature: universality, stability, neutrality, and transculturality. These codes provide fair and impartial guides to the principles governing biological nomenclature and allow unambiguous universal communication in biology. Accordingly, no subjective proposals should be allowed to undermine them.

European larch (Larix decidua Mill.) is an important tree species commonly used in managed forests of central Europe. However, its genetic structure, post-glacial range dynamics, and consequent nativity status are poorly understood. Here we provide the first study focusing on the genetic structure of in situ larch populations in the north-eastern Czech Republic using molecular genetics. Most of the studied area is traditionally considered to be a part of the autochthonous native range of the Jeseníky lineage of larch and some of the included populations are protected as belonging to this type. We confirm a common presence of the Jeseníky type and its close evolutionary relation with larch populations from both the Carpathians and Poland. However, we also found important levels of admixture of genetic material from the Alps in all of the analyzed populations. The highest amount of Alpine admixture was found in the populations of intensively managed forests, the proportion of non-native material in the protected areas was relatively lower but still significant. Our results show the importance of populationgenetic research for practical conservation of local populations and lineages even for common species.

Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored. Here, we present an account of several events of ancient hybridization in turmeric, the economically important plant genus Curcuma (Zingiberaceae), which harbors about 130 known species. We analyzed 1094 targeted low-copy genes and plastomes obtained by next-generation sequencing of 37 species of Curcuma, representing the known genetic diversity and spanning the geographical distribution of the genus. Using phylogenetic network analysis, we show that the entire genus Curcuma as well as its most speciose lineage arose via introgression from the genus Pyrgophyllum and one of the extinct lineages, respectively. We also document a single event of ancient hybridization, with C. vamana as a product, that represents an evolutionary dead end. We further discuss distinct circumstances of those hybridization events that deal mainly with (in)congruence in chromosome counts of the parental lineages.

The monocot family Costaceae Nakai consists of seven genera but their mutual relationships have not been satisfactorily resolved in previous studies employing classical molecular markers. Phylogenomic analyses of 365 nuclear genes and nearly-complete plastome data provide almost fully resolved insights into their diversification. Paracostus is identified as sister to all other taxa, followed by several very short branches leading to discrete lineages, suggesting an ancient rapid radiation of these early lineages and leaving the exact relationships among them unresolved. Relationships among Chamaecostus, Dimerocostus and Monocostus confirmed earlier findings that these genera form a monophyletic group. The Afro-American Costus is also monophyletic. By contrast, Tapeinochilos appeared as a well-supported crown lineage of Cheilocostus rendering it paraphyletic. As these two genera differ morphologically from one another owing to a shift from insect- to bird-pollination, we propose to keep both names. The divergence time within Costaceae was estimated using penalized likelihood utilizing two fossils within Zingiberales, †Spirematospermum chandlerae and †Ensete oregonense, indicated a relatively recent diversification of Costaceae, between 18 and 9 Mya. Based on these data, the current pantropical distribution of the family is hypothesized to be the result of several long-distance intercontinental dispersal events, which do not correlate with global geoclimatic changes.

European larch (Larix decidua Mill.) is an important tree species commonly used in managed forests of central Europe. However, its genetic structure, post-glacial range dynamics, and consequent nativity status are poorly understood. Here we provide the first study focusing on the genetic structure of in situ larch populations in the north-eastern Czech Republic using molecular genetics. Most of the studied area is traditionally considered to be a part of the autochthonous native range of the Jeseniky lineage of larch and some of the included populations are protected as belonging to this type. We confirm a common presence of the Jeseniky type and its close evolutionary relation with larch populations from both the Carpathians and Poland. However, we also found important levels of admixture of genetic material from the Alps in all of the analyzed populations. The highest amount of Alpine admixture was found in the populations of intensively managed forests, the proportion of non-native material in the protected areas was relatively lower but still significant. Our results show the importance of population -genetic research for practical conservation of local populations and lineages even for common species.

Plant species with large genomes tend to be excluded from climatically more extreme environments with a shorter growing season. Species that occupy such environments are assumed to be under natural selection for more rapid growth and smaller genome size (GS). However, evidence for this is available only for temperate organisms. Here, we study the evolution of GS in two subfamilies of the tropical family Zingiberaceae to find out whether species with larger genomes are confined to environments where the vegetative season is longer. We tested our hypothesis on 337 ginger species from regions with contrasting climates by correlating their GS with an array of plant traits and environmental variables. We revealed 16-fold variation in GS which was tightly related to shoot seasonality. Negative correlations of GS with latitude, temperature and precipitation emerged in the subfamily Zingiberoidae, demonstrating that species with larger GS are excluded from areas with a shorter growing season. In the subfamily Alpinioideae, GS turned out to be correlated with the type of stem and light requirements and its members cope with seasonality mainly by adaptation to shady and moist habitats. The Ornstein-Uhlenbeck models suggested that evolution in regions with humid climates favoured larger GS than in drier regions. Our results indicate that climate seasonality exerts an upper constraint on GS not only in temperate regions but also in the tropics, unless species with large genomes find alternative ways to escape from that constraint.

Background and Aims: A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated.Methods: In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted.Key Results: Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum.Conclusions: Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.

A molecular systematic study of Globba section Nudae (Zingiberaceae) using ITS and matK sequences identifies three major clades, Globba subsection Nudae, G. subsection Mediocalcaratae and a new subsection, Globba subsection Pelecantherae, which is described here. The two species belonging in this subsection, Globba pelecanthera and Globba securifer, which are both new, are described. Rectangular anther appendages are reported in Globba for the first time. Evidence of hybridisation is given. The morphological characters of the flowers, which are likely to be important in pollination, are discussed.

Premise Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. Methods To evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony‐informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance. Results Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony‐informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. Discussion A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large‐scale systematic studies, where financially possible.

Ochagavia (four species) and Fascicularia (one species) form a well-supported clade of the early-diverging Bromelioideae. The two genera are morphologically similar, but they can be easily discerned on the basis of generative characters. Besides the species distributed on the Chilean mainland, the group includes O. elegans, endemic to the Robinson Crusoe Island of the Juan Fernandez Islands. In previous molecular phylogenetic studies, O. elegans formed a sister clade to the remainder of Fascicularia and Ochagavia. A phylogenomic approach, including nearly complete and, in five cases, full plastomes (c. 160 kbp) and the nuclear rDNA cistron (c. 6 kbp), and scanning electron microscope (SEM) images of pollen were used to analyse relationships in the Fascicularia-Ochagavia group. Plastome and nuclear trees were largely congruent and supported previous phylogenetic analyses of O. elegans being sister to the remainder of the group. A divergent phylogenetic position was suggested for O. carnea using different organellar trees. SEM analysis of pollen supported the division of Fascicularia and Ochagavia. Evolutionary and taxonomic implications of our results are discussed.