Abstract Over the past two decades, advances in high‐throughput‐sequencing technology platforms and in the recovery of highly degraded DNA have ushered ancient DNA research into the era of deep‐time paleogenomics, expanding sample ages from no more than 100 ka to the Early Pleistocene (~2 Ma). These developments have resolved long‐standing phylogenetic controversies, refined reconstructions of the dispersal and population history across diverse taxa (including humans), and enabled direct investigation of molecular response to Quaternary climate change. Paleogenomics in China developed later than in Europe and North America, with early landmark breakthroughs largely focused on ancient human remains. However, China preserves one of the richest and most distinctive records of Quaternary megafauna, many lineages of which are morphologically and genetically differentiated from their western Eurasian counterparts. Here, we synthesize recent paleogenomic advances across major megafauna clades, including Proboscidea, Perissodactyla, Artiodactyla, and large Carnivora, to evaluate how time‐resolved genomic data are reshaping systematics, phylogeography, and evolutionary interpretation of the Chinese Quaternary fauna. Current megafauna paleogenomic coverage remains taxonomically and geographically biased toward northern assemblages and mitochondrial datasets. We therefore outline key methodological and sampling priorities, including coordinated recovery of nuclear genomes and improved approaches for southern contexts with poor preservation, to position Chinese megafaunal paleogenomics as a platform for testing general models of megafauna responses to Quaternary climatic oscillations. These efforts refine the systematics and evolutionary history of Chinese Quaternary megafauna and provide a conceptual model for understanding how megafauna respond to Quaternary climate oscillations worldwide.
Abstract Marmota represents a genus of relatively large‐bodied, fossorial rodents widely distributed across grassland and alpine meadow ecosystems in the Northern Hemisphere. This study integrates paleontological data with molecular phylogenetics from extant species to reconstruct the spatiotemporal dynamics of Marmota distribution, elucidating its origins, biogeographic dispersal patterns, phylogenetic relationships, and species divergence times. Results indicate that the genus likely originated in North America, with the earliest fossil occurrences dated to ~16.3 million years ago (Mya). The radiation of extant Marmota commenced approximately 6.09 Mya, marked by elevated speciation rates during the Late Miocene and Pliocene. Throughout the late Miocene to the early Pleistocene, the extinction rate was maintained at a relatively stable level. At around 1 Mya, both the speciation rate and the extinction rate increased synchronously, leading to a slight increase in the net diversification rate. These shifts in net diversification rate showed strong correlations with global environmental transformations, particularly the expansion of grasslands since the Late Miocene and climatic oscillations associated with the Last Glacial Maximum. Within the context of contemporary anthropogenic climate warming, Marmota species face significant survival challenges, with certain taxa potentially at risk of extinction due to maladaptation to rapidly altering environments.
Abstract As genomics moves from multilocus data sets to pangenomes and graph genome representations, the main challenge is no longer only to detect variation but also to explain how genomic features are distributed across lineages. Pangenomes and graph genomes reveal structural variants, alternative haplotypes, lineage‐specific sequences, and complex patterns of lineage sharing. These signals, however, do not by themselves show whether a pattern reflects common ancestry, retained ancestral polymorphism, introgression, recurrent origin, or analytical artifact. This problem is especially acute in clades shaped by hybridization, introgression, and polyploidy, where a single bifurcating tree may be useful for some questions but misleading for others. Here, we argue that the pangenome era increases the need for explicit macroevolutionary coordinates. We propose a conservative evidence ladder that treats conflict first as an observation, evaluates incomplete lineage sorting and analytical artifacts before stronger process claims are made, and then considers introgression, backbone‐level reticulation, and, when necessary, polyploid‐aware interpretation. For many downstream questions, the output may be a compressed reticulate backbone rather than a fully elaborated network. Such a backbone should be auditable and retain only those departures from treeness that change comparative, functional, breeding‐oriented, or taxonomic interpretation. Examples from crop pangenomes, Rosaceae, and other conflict‐rich systems illustrate how macroevolutionary reasoning can improve the interpretation of micro‐scale genomic signals in the pangenome era.
Abstract Mountain regions of the Northern Hemisphere harbor exceptional biodiversity, yet the processes underlying species diversification and migration among these regions remain poorly understood. This study investigates the macroevolutionary dynamics of Androsace s.l ., a genus widely distributed across temperate regions of the Northern Hemisphere, with notable diversity in the Alps and the Hengduan–Himalaya regions. Although previous phylogenetic studies have advanced understanding of the evolutionary history of Androsace , its biogeographic origins and diversification history have remained unresolved due to limited species sampling and low statistical support. Here, we revisited the inter‐ and infrageneric taxonomic controversies. Using chloroplast genome (cpDNA) and nuclear ribosomal ITS (nrDNA) sequences from 101 species representing four related genera and seven infrageneric sections, we reconstructed the most comprehensively sampled phylogeny of Androsace to date and established a spatiotemporal framework for its biogeographic and diversification history. Phylogenetic analyses based on cpDNA revealed four well‐supported clades corresponding to distinct ecological, geographic, and morphological traits. A similar four‐clade structure was recovered in the ITS phylogeny, albeit with lower statistical support. Divergence time estimation and biogeographic analyses traced the origin of Androsace s.l . to the Pan‐Tibetan Highlands in the early Oligocene (~33 Ma), identifying this region as the source for other mountain systems. The genus underwent asynchronous diversification across different mountain systems and clades, driven by distinct tectonic events, environmental changes, and trait innovations. These results provide a spatiotemporal framework for understanding the evolution of alpine plants in the Northern Hemisphere.
Abstract Co‐flowering species in sympatry sharing a common pollinator can mitigate potential reproductive interference through a combination of ethological and mechanical barriers. However, empirical studies integrating both sex‐specific foraging behavior and mechanical trait divergence within a specialized pollination system have been rarely conducted. To bridge this gap, the floral rewards, floral visitors, foraging behavior, visitation frequency, pollen‐transfer efficiency, and reproductive isolation were compared between two sympatric Lysimachia species: oil‐flowered L. congestiflora and nectar‐bearing L. stenosepala , which share the oil‐collecting bee Macropis omeiensis . Furthermore, we examined the mechanics of spatial partitioning by detecting the precise sites of pollen placement and stigma contact on the bee body for both species. In L. congestiflora , female M. omeiensis bees collected floral oil and pollen, and their pollen‐transfer efficiency (pollen deposition/pollen removal) was higher than that of other bees ( Halictus sp. and Lasioglossum occidens ). While in L. stenosepala , both female and male M. omeiensis foraged only for nectar, acting as efficient pollinators. Pollen placement sites on the female oil bee were ventral in L. congestiflora and on the head in L. stenosepala . Male M. omeiensis bees visited the nectar‐bearing flower, but not the oil flower. Female bees visited both oil‐offering and nectar‐bearing species; yet, differential pollen placement further reduced interspecific pollen transfer. These results suggest that mechanical isolation via spatial pollen placement on shared female bees is a key mechanism for reducing interspecific pollen transfer, while the specialized behavior of male bees provides a complementary barrier. This combination of floral reward divergence and sex‐specific foraging behavior facilitates the coexistence of sympatric congeners.
Abstract Triplophyllum is a fern genus of about 30 species, distributed across the moist tropical forests of Madagascar, Africa, and the Neotropics. The genus presents significant taxonomic challenges due to a combination of high morphological variability and subtle morphological differences among species. In this study, we use a molecular phylogenetic analysis to identify evolutionary lineages in the Neotropics and assess morphological characters useful for species delimitation. Our sampling encompasses most regions where the genus occurs and includes three‐quarters of the currently recognized species. Our results show that neotropical Triplophyllum species form a single clade, whereas paleotropical species form two clades, and that the circumscriptions of some neotropical species need to be revised. Optimization of morphological characters on the molecular tree reveals extensive homoplasy in indument traits, highlighting the limitations of morphology alone for phylogenetic inferences in the genus. Three new species are supported by both molecular and morphological analyses, and are described herein: Triplophyllum atlanticum, Triplophyllum ctenitoides , and Triplophyllum dalyi . We also designate a neotype for Triplophyllum funestum , one of the most widespread neotropical species, whose original type has been missing since its description. Because of the intricate evolutionary history of Amazonian biodiversity, traditional morphological taxonomy often fails to appreciate the true species richness of the Amazon and lumps superficially similar lineages into a single species. Our findings reinforce the importance of an integrative approach using molecular and morphological evidence for resolving species delimitation in these cryptic lineages.
Many bird species with broad geographic distributions show complex patterns of lineage divergence shaped by historical isolation, migration, and gene flow. The American robin, Turdus migratorius, is found throughout North America and includes seven described subspecies that differ in plumage and migratory behavior; yet, their evolutionary relationships remain uncertain. Here, we used genome-wide SNP data, population structure analyses, phylogenomic inference, divergence time estimation, and D-statistics to reconstruct relationships within the T. migratorius complex and evaluate patterns of lineage divergence and introgression. Our analyses consistently recovered four principal genomic lineages that do not correspond to currently recognized subspecies: (1) T. m. confinis from Baja California Sur, (2) a Mexican lineage, (3) western North America, and (4) boreal eastern North America. Time-calibrated analyses indicate a deep late-Miocene divergence (similar to 8 Ma) separating T. m. confinis from all other lineages, followed by Pleistocene diversification among the remaining groups. Genome-wide differentiation and long-term isolation support the recognition of T. m. confinis as an independently evolving lineage consistent with species-level status. In contrast, Turdus rufitorques, which is traditionally considered the sister species of T. migratorius, was nested within the Mexican lineage. Significant D-statistics revealed excess allele sharing between the Mexican lineage and T. rufitorques, supporting a history of introgression. This study refines species limits within the American robin complex and highlights the importance of genome-wide data for resolving evolutionary independence in widespread migratory birds.
With advances in transportation,information exchange,and technologies such as next-generation sequencing,a new era has dawned for investigating biodiversity and conservation in the Himalayan region.In this issue,we have gathered together leading researchers to deepen our understanding of the mechanisms and evolutionary processes shaping Himalayan biodiversity,as well as the implications of these for conservation.By considering the Himalayas within a broader geographic context,we seek to highlight their role in contributing to biodiversity both within the region and beyond.This is the second special issue devoted to this topic.Readers may also be interested in the first special issue published last year;further details can be found at the following link:.
Plants have evolved a remarkable capacity for regeneration,allowing them to recover from wounding and severe environmental stress(Ikeuchi et al.,2019;Chen et al.,2024).In seed plants,two key regenerative processes,somatic embryogenesis and de novo organ regeneration(i.e.,de novo root and shoot regeneration),enable the formation of new plants(Ikeuchi et al.,2019;Zona & Howard,2022;Chen et al.,2024).Specifically,somatic embryogenesis exemplifies the cell totipotency theory proposed by Haberlandt in 1902(Haberlandt,1902).In some plants,such as Kalanchoë daigremontiana and Malaxis paludosa,somatic embryogenesis occurs spontaneously and enables vegetative propagation(Garcês et al.,2007,2014;Fambrini et al.,2022).De novo organ regeneration demonstrates cellular pluripotency,a capability that enables plants to survive by forming adventitious roots and shoots from wounds.The regeneration abilities of plants have been widely adopted for agricultural biotechnology,including cuttings,tissue culture,transgenesis,and gene editing.
Singing is a key innovation that drives the diversification of crickets. However, acoustic-related traits have not been investigated in a broad phylogenetic context, making the evolution of acoustic communication enigmatic. To explore the evolution and regression of singing and hearing, we examined over 100 species of tree crickets (Oecanthidae), a family with diverse acoustic-related traits that has never been considered in an evolutionary context. We investigated homologous traits related to sound production (stridulatory file, harp, and mirror) and reception (tympana, inner, and outer). Using a robust, time-calibrated molecular phylogeny, we estimated ancestral states and evolutionary rates and tested for correlated evolution. We quantified the phylogenetic signal for each trait to assess how evolutionary relatedness predicted acoustic trait similarity. Our analyses revealed multiple independent losses of sound-producing structures in the forewings and hearing organs, providing evidence for the convergent evolution of the silent phenotype. Our results also suggest a high level of integration among wing veins, particularly those related to acoustic communication. We discuss the potential ecological drivers of these patterns, such as predator avoidance and habitat shifts, and substantiate how alternative phenotypes, like "silent listeners" and "deaf singers", facilitate evolutionary transitions between acoustic and vibratory signaling (biotremology). Our findings provide a model for understanding the macroevolutionary dynamics of sensory regression, a pattern shared across diverse animal systems. The evolutionary trends in the acoustic signaling of Oecanthidae provide a powerful system for studying the macroevolutionary dynamics of communication.
Selligueoid ferns are arguably one of the only relatively large groups of ferns with uncertain phylogeny, biogeography, and systematics. Previous studies identified some well-supported or moderately supported clades but their relationships were largely unresolved, and thus, it remains controversial whether these ferns originated from tropical Asia or the Himalaya and how many genera should be recognized. Here, we reconstructed phylogenies based on Sanger sequencing data of five plastid markers of 261 accessions representing ca. 103 species and 67 (49 ingroup) plastomes representing 41 species of selligueoids and 18 species of outgroups. Our data resolved selligueoids into six major clades and recovered the monophyly of Arthromeris, Pichisermollodes, and Phymatopteris (excl. type) + Gymnogrammitis, whereas Selliguea will become monophyletic if two isolated species are excluded. Contrasting lumping all genera into one genus, here, we propose to recognize six genera: Arthromeris, Phymatopteris, Pichisermollodes, Selliguea, Coumariphylla (four spp.), and Vietiglossa (one sp.), in addition to the hybrid genus, & times; Phymatomeris. We support the proposal to conserve Phymatopteris with a new type. Phymatopteris and Selliguea are found not to co-occur in any locality. Our results suggested that selligueoids originated in the late Eocene (ca. 36.4 Mya) in the Malesia-Pacific area, consistent with the tropical Asian origin hypothesis. Quite surprisingly, only two long-distance dispersals and local range expansions/diversifications contributed to the current distribution pattern of selligueoid ferns. In support of our classification, we provide a key to the six genera, their morphological and geographical synopses, and lists of their constituent species and important synonyms.
Islands are natural laboratories for studying speciation, where geographic isolation can promote rapid diversification. This study investigates the divergence of an insular population of the orchid Epidendrum fulgens on Alcatrazes Island, a land-bridge island off the Brazilian coast. Using an integrative approach, we combined genomic (nuclear and plastid microsatellites), phenotypic (leaf functional traits and floral morphometrics), and ecological (plant community structure and diversity) analyses to test for differentiation from mainland populations. Our results revealed significant genetic divergence, with the island population exhibiting exclusive plastid haplotypes and a distinct genetic cluster, indicating prolonged reproductive isolation despite historical land connections. Phenotypically, insular plants consistently displayed succulent leaves and smaller flowers, traits suggestive of local adaptation to drier conditions and a distinct pollinator regime. Although community-level analyses revealed similar species and phylogenetic diversity, the insular community differed compositionally and exhibited a distinct phylogenetic structure. The confluence of genetic distinctness, adaptive phenotypic traits, and ecological isolation satisfies multiple species criteria, leading us to describe the Alcatrazes population as a new cryptic species. This finding underscores the role of land-bridge islands as engines of speciation, even for species with high dispersal potential, and highlights the critical importance of integrative taxonomy for identifying evolutionarily significant units and informing conservation efforts for insular endemics.
Orchidantha, the sole genus in the family Lowiaceae (Zingiberales), shows distinctive, orchid-like flowers that emit a carrion-like scent, attracting dung beetles for pollination. Despite their ecological and ornamental value, many Orchidantha species are endangered and face an elevated risk of extinction. Here, we present the first chromosome-scale genome assembly of the endangered Orchidantha insularis from Hainan Island. The 2.24 Gb genome was assembled into nine pseudochromosomes, and 31 541 protein-coding genes were annotated. Phylogenomic analysis places O. insularis within the "banana group" of Zingiberales and indicates divergence from Musaceae approximately 65 Ma, following a shared recent whole-genome duplication (WGD). We identify significant expansions in gene families related to photosynthesis and carbon fixation, consistent with adaptation to low-light tropical understory habitats. Our analysis uncovers the genetic basis of the carrion-like floral scent in O. insularis by revealing complete biosynthetic pathways for dimethyl disulfide (DMDS) and indole. In parallel, the expansions of flavin-containing monooxygenase (FMO) genes and signatures of positive selection reinforce indole metabolism, which links floral scent production to both adaptation and defense. Whole-genome resequencing of population samples revealed high genetic differentiation and low nucleotide diversity. Demographic inference indicates severe Pleistocene bottlenecks, followed by continued population decline. Together, these results provide a genomic foundation for understanding genome evolution in early-diverging Zingiberales and inform conservation and horticultural use.
The Eurasian and North African Asparagaceae subtribe Hyacinthinae Parl. comprises 15-21 genera of mostly spring-flowering bulbs with great diversity in the Mediterranean. Many genera are horticulturally important, notably hyacinths, grape hyacinths, and squills. Understanding of relationships among these genera remains limited, with widely differing classifications in use and scattered phylogenetic sampling. A comprehensive morphological investigation of the Hyacinthinae increased the number of recognized genera from nine to 21, based largely on bulb characteristics. However, this treatment has not been widely adopted despite some support from later molecular analyses. This case study on the generic limits of a horticulturally important plant group raises key issues of gaining user acceptance of a nomenclatural system where some familiar genera are substantially redefined. To date, there has not been a detailed combined molecular and morphological study of the subtribe. We reconstructed the most comprehensively sampled phylogeny of Hyacinthinae to date, using 246 low-copy nuclear genes from Angiosperms353 and plastome sequences. Morphological data were compiled from published literature and direct observations. Our nuclear and plastid phylogenies of Hyacinthinae recover 18 of 21 possible genera, while the remaining three are para- or polyphyletic. However, relationships among the genera vary between data sets. Quartet scores indicate incomplete lineage sorting or hybridization/introgression, especially where there is cytonuclear discordance. Our data provide strong support for the transfer of two species of Hyacinthus to Fessia, illustrating the problems arising from convergent floral traits. This paper offers a major step forward in the delimitation of Hyacinthinae genera.
Nymphaeales, an early-diverging angiosperm order, is pivotal for understanding floral evolution; yet, the processes of floral organogenesis and the evolutionary transitions between Cabombaceae and Nymphaeaceae remain incompletely resolved. Here, we integrate scanning electron microscopy, phylogeny-based ancestral state reconstruction, and comparative genomics to investigate floral organogenesis and MADS-box gene families in Brasenia schreberi (Cabombaceae) and Euryale ferox (Nymphaeaceae). Brasenia schreberi shows a stable trimerous, whorled initiation pattern; its floral apex remains dome-shaped and produces a superior gynoecium with free (apocarpous) carpels. In contrast, E. ferox displays a tetramerous pattern with unidirectional (abaxial-to-adaxial) initiation, followed by spiral centripetal organ formation; its apex becomes concave early, forming a complex receptacle that develops into an inferior gynoecium with syncarpous carpels. Ancestral state reconstructions indicate that Cabombaceae retains more plesiomorphic traits of the Nymphaeales ancestor, whereas Nymphaeaceae shows multiple derived innovations. Using a domain- validated, de-redundant data set, we further compare MADS-box phylogeny and motif architectures, revealing relatively conserved motifs in ABCDE-related MIKC clades but more heterogeneous patterns in certain non-ABCDE lineages, partly influenced by annotation quality. Together, these results support independent evolutionary trajectories for Cabombaceae and Nymphaeaceae and shed light on the evolution of floral organization in basal angiosperms.
Dalbergia (Leguminosae) is a pantropical genus that serves as an ideal system for studying pantropical biogeography and diversification. However, limited taxon sampling and molecular data have hindered the resolution of intrageneric relationships and understanding of its evolutionary history. Here, we reconstruct a densely sampled phylogeny of Dalbergia based on hybrid capture of 89 low-copy nuclear loci, including 98 species spanning all major biogeographic regions and most previously recognized taxonomic clades. Phylogenetic analyses using concatenated and coalescent approaches support the monophyly of Dalbergia and consistently identify six major clades, including a distinct and newly identified Africa-Madagascar lineage (clade E) with potential taxonomic significance. Our results propose merging two of its sections, sect. Dalbergia and sect. Selenolobium, and expanding sect. Ecastaphyllum to include some African species. Topological incongruences observed between concatenated and coalescent trees, together with the high gene tree conflict at certain nodes, are consistent with localized effects of hybridization and/or incomplete lineage sorting. Divergence dating and model-based biogeographic analyses support a Neotropical origin of Dalbergia in the middle Eocene (similar to 39 Ma), followed by repeated long-distance dispersal events from Africa to Asia, Neotropics, and Madagascar, and back into the Neotropics. An early diversification burst in Africa during the late Oligocene-early Miocene (similar to 27-18 Ma) preceded the genus ' s intercontinental expansion. Diversification rates were high across all four regions, with Madagascar showing the highest speciation rate. These macroevolutionary dynamics coincided with Eocene-Miocene climatic changes and habit shifts. This study provides a robust phylogenetic framework for Dalbergia, refines its temporal and biogeographic history, and illustrates how dispersal, climatic change, and lineage-specific diversification have interacted to generate pantropical biodiversity.
Sex chromosomes frequently undergo turnover through the recruitment of new sex-determining genes or translocation of ancestral genes. This phenomenon is particularly evident in Salix (Salicaceae). In Populus, the sister genus of Salix, a partial-ARR17-based sex-determination mechanism has been reported, and is also found in several Salix species. In Vetrix 15ZW clade I of Salix, species share a female heterogamety system on chromosome 15. A partial-PI (PISTILLATA)-based mechanism has been proposed for several species in this clade, except for Salix purpurea, which appears to use a two-gene model involving ARR17 and GATA15. To further investigate the evolution of sex-determining factors in this clade, we assembled a high-quality, haplotype-resolved genome of Salix integra, a close relative of S. purpurea. Based on resequencing data from males and females, we identified W and Z-linked regions located in pericentromeric regions on chromosome 15, consistent with those reported in other Salix species. Comparative analyses showed that S. integra possesses a partial-PI-based mechanism, supporting the hypothesis that PI sequences were recruited in the ancestor of 15ZW clade I, whereas the ancestor of S. purpurea recruited a two-gene model later. Together, these results advance our understanding of the relationship between sex-determining plasticity and sex chromosome evolution in plants.
DNA methylation is an essential epigenetic mark that is involved in a range of biological activities in all domains of life. Molecular mechanisms underlying how the DNA methyltransferases (DNMTs) catalyze cytosine methylation have been well documented in model species. However, it still remains underinvestigated as to how the functional divergence of different DNMT duplicates has evolved among closely related species. Here, our study addressed evolutionary dynamic, transcriptional regulation and enzyme activities of all three DNMTs (DNMT1, DNMT2, and DNMT3) in extant Poaceae species. Our results show that, although all Poaceae species are derived from the most recent common ancestor, biased genetic fractionation acting on different DNMT duplicates has resulted in high copy number variations among extant species. In addition, expression-level subfunctionalization (i.e., differential expression genes) is a common mechanism that regulates the transcriptional pattern of different DNMT duplicates in extant Poaceae species. Neo-functionalization and positive selection further promote functional divergence (i.e., different catalytic efficiency) among different DNMT duplicates. In particular, estimates of enzyme activities demonstrate that highly expressed gene copies of the DNMT1 (i.e., MET1a and MET1b) tend to show high catalytic efficiency. Furthermore, functional analyses of seven DNMT mutants also reveal that loss of function of three DNMT genes (OsCMT3a, OsCMT2, and OsDRM2) exerts complementary impacts on the transcriptional landscape. Our study provides evidence that, while DNA methylation of all three cytosine contexts (CG, CHG, and CHH) is catalyzed by the three DNMTs, different mechanisms have together promoted high evolutionary dynamic and functional divergence in extant Poaceae species.
