Journal of Systematics and Evolution

Comparative phylogeography provides a powerful framework to identify the historical processes shaping biodiversity hotspots by testing whether co-distributed species exhibit shared patterns of diversification. Southeast Asia harbors exceptional biodiversity, yet the extent to which common paleogeographic and climatic drivers have structured diversification across taxa remains poorly understood. Here, we investigated the evolutionary history of five widespread Microhyla species complexes distributed across the Indochinese Peninsula and adjacent regions using dense mitochondrial sampling (1,388 individuals) combined with genome-scale ddRAD sequencing (280 individuals). Across all complexes, both approaches recovered multiple lineages and remarkably congruent phylogeographic breaks and contact/intergradation zones associated with major Indochinese regions, including Myanmar, the Tenasserim-Malay Peninsula, southern Vietnam, and northern Vietnam-southern China, supporting the hypothesis that Indochina functions as a mosaic of stable biogeographic units. However, lineage divergence varied substantially among complexes, suggesting that common biogeographic drivers interacted with species-specific demographic histories. Phylogenomic analyses and cyto-nuclear discordance further revealed historical introgression in every complex, indicating that diversification involved both long-term allopatric isolation and reticulate evolution. These findings portray the Indochinese biodiversity hotspot as a dynamic evolutionary system where cycles of fragmentation and reconnection have repeatedly reshaped lineage boundaries. Moreover, the complex phylogeographic structure recovered exemplifies the urgent need for taxonomic revisions, for which genome-scale data provide an essential framework to validate mitochondrial hypotheses and assess admixture patterns for species delimitation. Finally, regions such as the southern Annamites and Tenasserim Hills emerged as recurrent hotspots of genetic diversity across independent lineages, highlighting their importance for conserving not only species/lineage richness but also the evolutionary processes and adaptive potential that sustain biodiversity.

Phylogeny and taxonomy are related but not identical: phylogeny estimates common ancestry, whereas taxonomy must also provide diagnosable, stable, informative, and useful classifications. We examine this distinction using turtle and whale barnacles of the superfamily Coronuloidea, a group with an extensive fossil record, marked ecological specialization, a long history of morphology-based classification, and a recent topology-driven reclassification that merged recognized higher taxa to preserve monophyly. These changes reduced diagnosability and biological coherence, weakened historical continuity, and relied on placements insufficiently tested against morphological and phylogenetic evidence. Our reanalysis of published molecular datasets shows that critical relationships are sensitive to marker composition and taxon sampling. Together with morphological considerations on extant and fossil forms, these results indicate that topology alone is insufficient for coherent higher classification. We argue that higher taxa should be evaluated using complementary criteria: diagnosability, stability, utility, and monophyly, rather than by mechanically translating a preferred tree into Linnaean ranks.

Although Cinnamomum includes globally important spice and medicinal plants, genome-scale knowledge of Cinnamomum species native to Japan remains limited. The Nansei Islands are an approximately 1,200-km-long archipelago located between the Pacific Ocean and the East China Sea and represent a key biogeographic region shaped by deep-sea barriers such as the Tokara and Kerama Gaps. Here, we integrated chloroplast and nuclear genome data generated in this study with public datasets to examine the phylogenetic relationships of four Cinnamomum species native to the Nansei Islands and ten related species. Chloroplast genomes showed no major structural differences among the four island species, whereas nuclear genome data resolved two distinct evolutionary lineages in the Nansei Islands: C. yabunikkei, C. x durifruticeticola, and C. daphnoides formed a distinct Nansei Islands lineage separate from Sri Lankan, Indonesian, and Taiwanese lineages, whereas C. sieboldii was placed in a Taiwanese lineage. Ancestry estimation indicated that C. x durifruticeticola and C. daphnoides share a common ancestral component, while C. sieboldii exhibited a single homogeneous ancestral component, suggesting reduced ancestral diversity after divergence from a Taiwanese lineage. These findings reveal previously unrecognized genomic differentiation among Japanese Cinnamomum species and suggest that deep-sea barriers, dispersal, and long-term isolation shaped their diversification.

Understanding the relative roles of vicariance and dispersal in shaping diversity and distribution patterns is central to historical biogeography. In this study, we investigate the historical biogeography of the ancient centipede genus Digitipes Attems, 1930 from South and Southeast Asia. First, we determined the phylogenetic position of the genus Digitipes within the Order Scolopendromorpha (n=414) by assembling primary and published sequences (n=30) for two mtDNA markers (COI, 16S) and one nuclear marker (28S) using Maximum Likelihood and Bayesian inference. We further used single-locus and multi-locus coalescent-based species delimitation methods to identify putative species within the genus Digitipes. We then used three fossil calibrations to estimate divergence times in a Bayesian framework, and used the resulting time-calibrated phylogeny for biogeographic analysis in a likelihood framework (BioGeoBEARS). The genus Digitipes was monophyletic with strong support, with SEA lineages nested within the Indian clade and sister to the D. barnabasi species complex from the Western Ghats. D. pruthii, the Eastern Ghats species, was nested with the Western Ghats species clade. A single-locus mPTP-based species-delimitation method suggested the presence of 24 putative species, far exceeding the number of morphologically described species, indicating an underestimation of species diversity. Divergence time estimates suggest that Digitipes began diversifying around 126 mya (100-159 mya), affirming its Gondwanan origin. Time-stratified ancestral area reconstruction suggested that early vicariance, followed by jump dispersal and range expansion, shaped the distribution of the genus Digitipes in South and Southeast Asia. There was one dispersal event from India to Southeast Asia, following a transient land connection between them, around 50 mya, supporting the Out-of-India hypothesis. Additionally, three jump dispersal events and five range expansions explained diversification within peninsular India. Particularly, D. pruthii originated from a jump dispersal event from the Central Western Ghats to the Eastern Ghats around 37 mya. Our results highlight the importance of an integrative taxonomic framework to delineate hidden diversity and to obtain robust species hypotheses for testing biogeographic hypotheses.

Speciation can be a slow process for long-lived organisms with large populations due to persistent incomplete lineage sorting, while hybridisation can further obscure species boundaries through admixture. In eucalypts, there is tremendous morphological and environmental variation with almost a thousand described species, subspecies, and hybrid taxa falling into multiple subgenera and intermediate sections. Multilocus molecular studies have generated concatenated species trees supporting deeper divergence between the Corymbia + Blakella + Angophora clade with the rest of eucalypts. However, the proportion of gene trees that recover the concatenated tree topology, including the taxonomic relationships among individual subgenera and sections, remains underappreciated. In this study, we assessed the predictive power of current eucalypt taxonomy - represented as a concatenated tree - in explaining topological variation across gene trees. To do this, we first extracted 1,187 BUSCO loci from short-read data of 701 samples representing roughly 500 described species using CAPTUS. We then inferred individual gene trees and a concatenated species tree using IQ-TREE2. Finally, we calculated the concordance factors for every described subgenus and section on the concatenated tree, and developed a taxonomic consistency test that tracks the taxonomic placement of each sample across gene trees. We show that, even though most taxonomic groups are monophyletic on the concatenated tree with 100% bootstrap support, several groups exhibit very low concordance, indicating that most gene trees do not recover their relationships as represented by the concatenated tree. These results highlight important considerations for current eucalypt taxonomic classification and provide a phylogenomic inference pipeline that can be applied not only to future eucalypt studies, but also to other evolutionarily complex groups of taxa.

Biodiversity aggregators such as GBIF provide unprecedented access to global biodiversity data, yet their representativeness remains uneven across space and taxa. This study examined the spatial and taxonomic structure of global vascular plant data available on GBIF. Six filters were applied to the GBIF vascular plant dataset, resulting in the removal of 54% of all records. Together, the filters explained more than 90% of the identified spatial issues, with duplicate and missing coordinates accounting for most of the variation. A higher number of occurrence records was associated with a greater number of spatial issues. Record distributions became progressively more even at finer taxonomic levels, from orders to species. The time series of occurrences for species, genera, and families increased sharply after 1800 and continued to rise, with no apparent stabilisation. Of the 824 ecoregions covered, 73 accounted for 72% of all occurrence records. These ecoregions spanned all continents but were strongly concentrated in Europe, followed by North America and Oceania. The analyses reveal four key patterns: (1) data volume is positively associated with spatial issues; (2) a small number of taxa account for a large proportion of records, whereas many are represented by relatively few; (3) occurrence data aggregated by GBIF have increased continuously since 1800; and (4) record coverage remains highly uneven across the world's ecoregions. These results highlight the substantial contribution of biodiversity data aggregators to expanding access to biological information while demonstrating the persistent spatial and taxonomic biases that shape their contents. Such biases should be explicitly considered when assessing data completeness and quality and when using aggregated occurrence records to infer global biodiversity patterns.

The Asparagaceae is an economically and ecologically important angiosperm (monocot) clade, containing iconic garden plants such as asparagus, hyacinth and agave, and arid-adapted keystone species like Joshua tree and dragon blood tree. The approximately 2,500 species in the family are spread across seven subfamilies: Agavoideae, Aphyllanthoideae, Asparagoideae, Brodiaeoideae, Lomandroideae, Nolinoideae and Scilloideae. Relationships among the seven subfamilies are generally unresolved and the sources of gene tree-species tree discordance are largely unknown. Investigating the biology underlying such discordance requires a robust sampling of both taxa and molecular markers, due to the extremely short branches that form the backbone of the Asparagaceae phylogeny. Using targeted sequencing of 1,726 low-copy nuclear genes, and a nearly complete sampling of genera, we interrogate relationships among all seven Asparagaceae subfamilies and investigate the underlying sources of discordance across the phylogeny. Analyses using different phylogenomic approaches (multispecies coalescence vs. nuclear gene supermatrix vs. chloroplast gene supermatrix) each revealed extensive discordance across the Asparagaceae backbone, which may be associated with rapid lineage diversifications that occurred in Africa shortly following the origin of the family ~49 Ma. Specifically, we found that two branches, representing ancestors of Aphyllanthoideae and Nolinoideae, may be responsible for much of the backbone discordance. The placement of Aphyllanthoideae, represented by one extant taxon (Aphyllanthes monspeliensis), is controversial with discordant topologies across many studies. However, multispecies coalescence-based analyses from this study strongly support a sister relationship between Aphyllanthoideae and a larger Agavoideae + Scilloideae + Brodiaeoideae clade. According to gene tree quartet frequencies and ABBA-BABA tests, we cannot reject incomplete lineage sorting (ILS) as the main source of discordance for the placement of Aphyllanthoideae; our results leave open the possibility of an ancient reticulation involving an ancestor of Aphyllanthoideae and an extinct basal Asparagaceae lineage. Regarding Nolinoideae, we found that conflicting support for two possible bifurcating clades (Asparagoideae + Nolinoideae vs. Asparagoideae + Lomandroideae) was associated with skewed support for alternative gene tree topologies, suggesting that phenomena other than ILS may explain the observed discordance. A quartet-based ABBA-BABA analysis, used to test for signatures of introgression, revealed a putative ancient hybridization event between two divergent, ancestral lineages which may have contributed to the origin of the Nolinoideae clade in Africa ~45 Ma. In sum, this study elucidates the long-troublesome backbone of the Asparagaceae phylogeny and advances our understanding of the evolutionary and biogeographical origins of all extant subfamilies. More broadly, this study expands our understanding of the various sources of gene tree discordance that may arise from natural processes associated with rapid lineage radiations across the tree of life.

Asian Passifloraceae occupy a distinctive evolutionary and ecological position within the family despite their relatively low species diversity compared with the Neotropics. Many Asian representatives are highly localized, small and often ephemeral climbers that persist seasonally through rhizomes, tuberous stems or dormant seeds, while considerable morphological plasticity may obscure species limits and evolutionary relationships. Xishuangbanna, southwestern China, lies at the convergence of Southeast Asian, Indian-Himalayan and southern Chinese floristic elements and represents an important regional centre of Passifloraceae diversity, with two species of Adenia and five species of Passiflora, including the recently described P. xishuangbannaensis and P. menghaiensis. We investigate the evolutionary relationships, plastome evolution and population genomics of these taxa using complete plastome assemblies, a concatenated dataset of 68 selected plastid protein-coding genes, 356 reconstructed nuclear Coding Sequences (CDS), and Genotyping-By-Sequencing (GBS) across the known wild distribution of P. xishuangbannaensis. Plastid, concatenated nuclear and nuclear coalescent phylogenies were strongly incongruent and differed from published classifications based on morphology and earlier phylogenies (ITS, ncpGS, ctyGS, ndhF and trnL-F). Gene-tree discordance and phylogenetic-network inference indicated widespread incomplete lineage sorting together with introgression. The two statistically best-supported network models placed P. menghaiensis, which showed high genetic similarity to the Indian P. napalensis, as a sister lineage involved in independent reticulation events associated with P. altebilobata, P. xishuangbannaensis and P. sumatrana. A pronounced biogeographic pattern was evident within Passiflora supersection Disemma, particularly in the P. siamica-P. cochinchinensis lineage across the Hua Line, whereas relationships among other Asian Passiflora blurred this boundary. This pattern suggests that diversification and reticulation within the Asian lineage may have overlapped temporally with the development of the biogeographic divide represented by the Hua Line. The concentration of early-diverging lineages around Xishuangbanna and the eastern Himalayan-Indian region further points to this area as an important centre in the early diversification of Asian Passiflora. Within this context, the highly localized P. xishuangbannaensis may represent either a relictual of an early Asian lineage or the surviving product of an ancient reticulate complex, contrasting with lineages such as P. siamica that subsequently expanded farther across Southeast Asia. Comparative plastome analyses revealed extensive structural and gene-content evolution within subgenus Decaloba, including pseudogenization, gene and intron losses, and repeated Inverted-Repeat (IR) expansions and contractions; substantial plastome modification also characterized supersection Disemma. Passiflora sumatrana exhibited a particularly distinctive IR expansion extending into the accD-pafII region, potentially characterizing this lineage. Adenia plastomes were generally more structurally conservative, although A. penangiana displayed an IR-boundary contraction involving the rps19-rpl2 region. Mitochondrial CDS and non-coding regions provided the best-resolved phylogenetic signal and revealed strong discordance with the chloroplast phylogeny, consistent with maternal mitochondrial inheritance and variable plastid transmission, potentially involving paternal or biparental inheritance and heteroplasmy. GBS analyses of P. xishuangbannaensis using complementary distant-reference, de novo and closely related-reference approaches showed that mapping to P. organensis provided the clearest SNP distribution and population resolution. ADMIXTURE, PCA and FST analyses revealed two strongly geographically structured populations with additional substructure and substantial differentiation (FST = 0.112). Linkage disequilibrium based demographic reconstruction using GONE2 indicated declining effective population size (Ne) toward the present in both populations, with a particularly abrupt recent decline in Pop1 and a more gradual decline in Pop2. Few candidate Self-Incompatibility (SI) genes could be confidently reconstructed, including limited recovery of highly variable docking regions. However, the intracellular region of an S-locus Receptor Kinases (SRK) contained a distinctive non-synonymous substitution predicted to alter protein configuration without major disruption of overall folding, potentially contributing to compatibility differences between populations. Together, these results reveal a complex evolutionary history combining historical dispersal, incomplete lineage sorting, reticulation, morphological plasticity, plastome structural evolution and strong population differentiation. The narrow distributions and recent demographic decline of these newly recognized Xishuangbanna taxa emphasize their conservation importance, while broader Asian taxon sampling and deeper genomic sequencing will be essential to resolve the evolutionary history of this discreet and poorly known Passifloraceae radiation.

Oceanic islands are natural laboratories for investigating the processes that generate, maintain, and redistribute biodiversity through time. An ideal flowering plant system to investigate these processes is Grewia L. (Malvaceae, Grewioideae), comprising ca. 283 species, of which nearly 30% are endemic to Madagascar, where they display considerable morphological diversity. Using Angiosperms353 target-capture sequencing for 171 accessions (119 Grewia spp.), we reconstructed the first densely sampled phylogeny of Grewia and performed divergence-time estimation, diversification analyses, and ancestral-range reconstruction. Our results support a Malagasy origin of the crown group around 27 million years ago, followed by extensive in situ diversification of Grewia. Repeated dispersal events from Madagascar to continental Africa subsequently contributed to the establishment of new African lineages, whereas colonization of the western Indian Ocean islands was more recent and resulted in anagenetic dispersals. Africa acted as the principal source of dispersal toward Arabia and into tropical Asia, suggesting the presence of a Miocene Afro-Arabian migration corridor under warm and humid conditions. Subsequent eastward dispersal from Asia to Australia is consistent with the stepping stone pathway provided by the Sunda and Sahul regions during the Miocene. This complex dispersal history was likely aided by fleshy fruits adapted for endozoochory. Our new evolutionary framework provides a robust basis for future taxonomic revision of this morphologically and ecologically diverse genus, and for identifying which characters have contributed to its exceptional diversification.

Hybridization and introgression are thought to play key roles in the formation of biodiversity. However, detecting gene flow between species and understanding reticulation patterns remain challenging, especially in species-rich lineages with complex evolutionary histories. Adiantum is a large fern genus, and ecological studies in Amazonia have found that species identification is often difficult due to morphological similarity and overlapping characteristics among species. Although several hybrids have been described in tropical America, comprehensive studies investigating genetic exchanges in this genus are still lacking. We used chloroplast and nuclear phylogenomic data to examine evolutionary relationships among tropical American Adiantum species. By combining traditional phylogenetic analyses with advanced bioinformatic methods such as HybSeq-based target capture, reference-guided phasing (HybPhaser), and network-based analyses, we found widespread reticulate evolution involving both recent and ancient hybridization events. These were especially common among those species that have been difficult to delineate morphologically. Our findings indicate that reticulate evolution has played an important role in shaping the diversity of neotropical Adiantum, especially within the tetraphyllum lineage. Such widespread hybridization has no doubt contributed to morphological ambiguity and taxonomic challenges. Our integrated analytical approach provides a first attempt at untangling the reticulate evolutionary history in this group, and future studies with additional sampling can be expected to clarify the evolutionary processes further.

The Himalayan-Tibetan-Hengduan (HTH) region is the richest biodiversity hotspot for high-elevation plants. However, owing to its remote and physically challenging topography as well as the trans-national nature of the region, many taxonomic problems in the area remain unresolved, particularly in the Himalaya. This, in turn, has impeded our understanding of the assembly of its extraordinary high-elevation flora. Here, we resolve phylogenetic relationships and delimit species in a distinctive clade of honeysuckles that is endemic to the HTH, the Isoxylosteum clade of Lonicera, using restriction-site associated DNA sequencing (RADseq) and morphological data. Five species complexes of Isoxylosteum have standardly been recognized. Three of these complexes are highly variable and have been divided into several varieties or species each. Phylogenetic, population structure, and morphological analyses of leaf and floral traits from samples collected across the range of the clade support the recognition of five species, including a species that has most often been recognized as a variety of L. rupicola (L. rupicola var. minuta). Instead, we find that it is sister to L. spinosa. This is surprising because the geographic range of L. minuta is contiguous with the other varieties of L. rupicola in the northern Hengduan region but widely separated from L. spinosa whose range lies mainly to the west of the Tibetan plateau. On close examination we find that several morphological and ecological traits also support a closer relation of L. minuta to L. spinosa. None of the other eight previously recognized varieties and species were supported. Floral traits showed high discriminatory power, correctly classifying 89% of samples to species. By comparison, leaf dimensions classified species with 59% accuracy. Our results identify diagnostic morphological apomorphies for each recognized species and major clade and provide a revised taxonomic framework for Isoxylosteum.

The palaeogeographic history of the Neotropics has inspired multiple diversification models, emphasizing either the Andes or Amazonia as primary drivers of biodiversity. However, the extensive Pebas wetland system that covered western Amazonia during the Miocene has gained attention as a potential barrier to dispersal and diversification. This system may have contributed to the modern diversity imbalance between the Andes and Amazonia, known as the Gentry pattern. Most evidence for this hypothesis comes from isolated case studies and fossils. Here, we conduct a meta-analysis including 1,361 species of Neotropical butterflies to evaluate the role of the Pebas wetland on the dynamics of dispersal and diversification. We found that Andean- and Amazonian-centred clades show complementary but temporarily distinct biogeographic patterns. High Andean diversity reflects an Andean origin, with early occupancy and diversification occurring within the Andes, followed by post-Pebas dispersal into Amazonia. By contrast, Amazonian-centred clades, reflect an Amazonian origin, with an early diversification in Amazonia and subsequent post-Pebas colonization of the Andes. While several clades show little evidence of Pebas influence, our study suggests that the Pebas wetland did not uniformly restrict diversification, but rather selectively constrained dispersal between the Andes and Amazonia, preventing simultaneous diversification in both regions and thereby creating a diversity imbalance that characterizes the modern Neotropic.

Myricaria Desv. (Tamaricaceae) is a genus of shrubs that play a keystone role in montane riparian ecosystems across Eurasia, shaping riverine habitats and supporting ecological function. The genus has a centre of origin in the Qinghai-Tibetan Plateau and exhibits a broad distribution, but many species boundaries are unresolved. Here, we present the first phylogenomic analysis of Myricaria using the Angiosperms353 target enrichment bait set, with sampling across its full geographic range. Off-target plastid loci were extracted from next-generation sequencing data using the CAPTUS bioinformatics pipeline. We infer species relationships using ASTRAL-IV and network analysis with SplitsTree, in conjunction with morphology. We also provide a taxonomic treatment of the genus, integrating our morphological observations and phylogenomic analyses for species delimitations. Based on our analyses, recognise two infrageneric sections: sect. Parallelantherae (containing only M. elegans) and sect. Myricaria (the remainder of the genus, with type species M. germanica). We also propose synonymising M. davurica, M. bracteata and M. squamosa with M. germanica. Although species boundaries in the Asian highlands remain unresolved, we conclude that the species M. elegans, M. germanica, M. laxiflora, M. longifolia, M. platyphylla, and M. pulcherrima are well-supported both phylogenomically and morphologically.

Hybridization is a powerful process in plant evolution generating reticulate patterns of speciation, introgression, and chloroplast capture. In the Petota clade of Solanum, which spans cultivated and wild potatoes, these processes cause much of the taxonomic complexity of the group. We examined the evolutionary history of the Commersoniana group (Solanum commersonii and S. malmeanum) relative to S. chacoense (Tuberosa Group) using an integrative framework of phylogenomics and morphology. With target-capture sequencing (Angiosperms353) of nuclear and plastid loci recovered from herbarium specimens, together with data mining we built nuclear and plastome phylogenies and ran symmetry tests, gene concordance analyses, and coalescent simulations to weigh incomplete lineage sorting against chloroplast capture. The data reveal cytonuclear discordance and events consistent with chloroplast capture from S. chacoense into Commersoniana lineages supported by both empirical and simulated results. Phylogenetic networks confirm repeated historical and recent reticulation, especially involving S. malmeanum. Non-metric Multidimensional Scaling (NMDS) of morphological traits did not recover clear species boundaries but was consistent with a hybrid origin for the group. These results indicate that recurrent hybridization and event consistent with chloroplast capture are strongly influencing evolution in the examined wild potatoes, complicating classical taxonomy and informing conservation and breeding. They also underscore the value of combining genomic and phenotypic data to resolve species boundaries in plant groups with tangled hybrid histories.

Determining the correct donor species/lineages of grass-to-grass lateral gene transfer (LGT) is vital for deducing specific donor features that could help inform the mechanism of transfer. This requires a dataset spanning a broad range of species to achieve the phylogenetic resolution necessary for precise donor inference. As grass-to-grass LGT often involves the transfer of multi-gene DNA fragments, they can contain additional sequences that allow for accurate orthologous comparisons, such as nuclear DNA of plastid origin (NUPTs). Here we systematically scan for NUPTs in the genomes of four Alloteropsis semialata accessions, whose LGTs have previously been characterised. Using the abundant Panicoideae chloroplast sequences, we reconstruct NUPT phylogenies and infer two lateral acquisitions: one from Paniceae/Digitaria and another from Andropogoneae/Eremochloa adjacent to a previously identified LGT. We then assembled and included an additional 12 Eremochloa chloroplast genomes in the analysis and showed the likely donor was Eremochloa attenuata. Subsequent short-read mapping from E. attenuata to the nuclear region flanking this NUPT showed consistent coverage across the region, including the previously identified LGT, supporting co-transfer. Overall this study highlights the potential for NUPTs to better identify the donors of grass-to-grass LGT.

Rapid diversification can generate regional biodiversity through ancestral polymorphism, admixture, and ecological differentiation, while leaving complex genomic signals. We analysed whole-genome variation in 325 butterflies, including 166 individuals of the Papilio bianor species complex and six outgroup species, to reconstruct lineage relationships and demographic history. Nuclear genomic analyses recovered three major clades corresponding to the recognized species and placed the island lineage as sister to continental P. bianor. Analyses of 18,635 autosomal window trees revealed extensive genealogical discordance, with incomplete lineage sorting predominating among continental lineages and the strongest introgression signals involving island related ancestry. Demographic modelling supported early island continental divergence followed by continental diversification and ancient admixture. The best fitting fastsimcoal2 model inferred an admixed origin of the Eastern China lineage, while BPP analyses supported ancient island-related introgression into the Eastern China ancestor, Western Himalaya and southwestern Thailand. Peripheral populations exhibited pronounced genetic differentiation and distinct demographic histories; Western Himalaya additionally showed mitochondrial affinity with Yaeyama despite its placement within the Himalayan nuclear lineage. Together, these findings suggest that introgression among deeply differentiated ancestral populations and incomplete lineage sorting during rapid divergence jointly shaped lineage diversity in the P. bianor complex. This study provides an empirical framework for investigating how lineage diversity emerges rapidly during the early stages of speciation, particularly in groups with deep ancestral population structure.

Understanding the evolutionary history of recent rapidly radiating groups remains a major challenge in systematics, especially when incomplete reproductive isolation and rampant interspecific gene flow obscure phylogenetic signal. Here, we present a comprehensive phylogenomic study of the genus Castilleja (the paintbrushes, Orobanchaceae), integrating nuclear and chloroplast data to investigate patterns of diversification, hybridization, and geographic structure across its range. Our results provide the first evidence that Castilleja functions as a multicompartmentalized syngameon-a network of closely related species with ongoing or historical gene flow among non-sister lineages within and between geographically structured compartments. High nuclear gene tree discordance, coupled with strong cpDNA geographic compartment structuring and nuclear network analysis, supports the hypothesis that recent rapid radiation and Plio-Pleistocene climatic fluctuations created alternating periods of range expansion and contraction. These dynamics likely promoted localized hybridization within isolated compartments during contraction and further introgression between compartments during range expansion. Our findings not only clarify the evolutionary relationships within Castilleja but also demonstrate the importance of genome-scale data and syngameon theory in understanding diversification in lineages where hybridization is rampant.

Telomeres have the crucial role of protecting chromosome ends and its length varies significantly between organisms. What evolutionary factor shapes this natural variation has been a long standing question, with answers providing insights into chromosome function and evolution. In animals life-history variation relating to senescence or tumorigenesis explains telomere length variation. For plants, however, we lack knowledge of what factor is driving their length variation in nature. Is life-history differences also driving telomere length variation among plant species? We answer this question by analyzing the telomeres of 257 plant species spanning the major orders of the green plant kingdom. Telomere lengths were estimated for species that vary significantly in their life-history, geographical distribution, and trait characters. Results showed telomere length increased with the evolution of terrestrialization, where Chlorophytes had the shortest telomeres and Spermatophytes had the longest telomeres. Surprisingly, plants with different life-histories had minimal telomere length differences, but biogeographic clines had significant effect on telomere length variation. Plant telomere length increases closer to the equator, while telomere length decreases at higher altitude. Domestication was previously proposed to lengthen telomeres, but we found no consistent domestication effect on telomere lengths comparing crops and their wild progenitors. From our results we conclude plant telomere length contrasts with animal telomeres, in that life-history has minimal effect on length variation. Instead we propose the ecological adaptation hypothesis, where telomere length in plants is determined by selection from abiotic conditions, and suggest temperature is a major factor shaping telomere length in plants.

Annual versus perennial life histories represent a fundamental axis of plant strategy, with empirical evidence showing that the proportion of annuals is greater in hot, arid, or variable climates. Crucially, introduced species, a group that disproportionately includes annuals, are expanding in number and range across the globe. Whether introduced richness is governed by the same climatic controls as native richness remains untested at continental scales. For 19,299 native (12% annual) and 2,802 introduced (34% annual) Australian plant species, we show that native annual richness tracks climate far more tightly than introduced annual richness. Both floras largely follow the global pattern: the annual fraction rises in dry and seasonal climates. However, hotspots of native and introduced annual richness are completely different. Introduced annuals (28% of all annual species) concentrate in wet, populated areas with low precipitation seasonality, whereas native annual richness is fairly evenly distributed, with the highest diversity in the seasonal tropics. The current continental-scale pattern is thus the sum of a long interaction between the native floras life histories and in situ climate, with dynamic, path-dependent introductions layered on top. As introductions and range expansions continue, they will reshape the annual-to-perennial balance along pathways of human influence.

Partition models are widely used in phylogenomic analyses to account for heterogeneous evolutionary processes across different regions or loci of a sequence alignment. How alignment regions are grouped into partitions (the partitioning scheme) affects both the degree of over- or under-parameterization and the accuracy of downstream phylogenetic inferences. PartitionFinder is a widely adopted framework for selecting an optimal partitioning scheme. Using Akaike information criterion (AIC) and Bayesian information criterion (BIC), PartitionFinder merges partitions with similar evolutionary processes to avoid model overfitting. However, AIC and BIC are based on conditional likelihoods that treat partition assignments as fixed, whereas the recently introduced marginal AIC (mAIC) averages site likelihoods over the models of all partitions, providing a more appropriate criterion for inferring global parameters such as tree topology and branch lengths (Susko et al. 2026). Here, we implement mAIC for partition models in IQ-TREE 3 and integrate it into the PartitionFinder algorithms. Using a range of simulated and empirical DNA and protein datasets, we show that PartitionFinder-mAIC yields partitioning schemes with fewer partitions than those selected by AIC or BIC, and additionally improves phylogenetic inference at most key branches of the green plant evolution. The new PartitionFinder-mAIC is available in IQ-TREE version 3.1.4 with the command-line option -merit mAIC.