Journal of Systematics and Evolution

Neodon, genus of a short time evolutionary history, was reported to be diverged from its relatives in early stage of Pleistocene. Only 4 species were well documented in Neodon for a long period of time until last years when a systematic work described and added three new species, adjusted three species used to belong to Lasiopodomys, Phaiomys, Microtus to Neodon and removed one species (Neodon juldaschi) to genus Blanfordimys, leading to a total of eight species recorded in Neodon. To gain a better insight into the phylogeny and ecology of Neodon, we have systematically sampled Neodon species along the whole Hengduan and Himalayan Mountains in the last 20 years. In addition to morphological identification, we generated 1x - 15x whole genome sequencing (WGS) data and achieved the mitochondrial genomes and an average of 5,382 nuclear genes for each morpho-species. Both morphology and phylogeny results supported an extra six new species in Neodon (nominated Neodon shergylaensis sp. nov., N. namchabarwaensis sp. nov., N. liaoruii sp. nov., N. chayuensis sp. nov., N. bomiensis sp. nov., and N. bershulaensis sp. nov.). This is the first study that included Neodon samples covering its entire distribution area in China and this systematic sampling also revealed a long-time underestimation of Neodons diversity, and suggested its speciation events linked highly to founder event via dispersal (from Plateau to surrounding mountains). The results also revealed that the Qinghai-Tibetan Plateau is the center of origin of Neodon, and the impetus of speciation include climate change, isolation of rivers and mountains.

Standard barcodes and ultra-barcodes face challenges in delimitation and discrimination of closely related species with deep coalescence, hybrid speciation, gene flow or low sequence-variation. Single copy orthologs (SCOs) have been recommended as standardized nuclear markers in metazoan DNA taxonomy. Here, we assessed the performance of SCOs in identifying recently diverged species in subgenus Jensoa (Cymbidium) which has been poorly settled by ultra-barcode. More than 90% of target 9094 reference SCOs inferred from three genomes of Cymbidium were successfully retrieved for all 11 representative species in subg. Jensoa by ALiBaSeq from as low as 5x depth whole genome shotgun sequences. Species tree reconstructed from multiple refined SCO matrices under multispecies coalescent model successfully discriminated all species and discerned wrongly identified or labeled species. Plentiful and refined SCOs matrices obtained by implementing our pipeline facilitate not only phylogenetic study, but also high-resolution species diagnosing. Biparentally inherited SCOs as multi-locus marker not only advances the force of DNA barcoding, but also facilitates an eventual transition to species-tree-based barcoding strategies.

Theaceae, with three tribes and nine genera, is a family of great economic and ecological importance. Recent phylogenetic analyses based on plastid genome resolved the relationship among three tribes and the intergeneric relationships within Gordonieae and Stewartieae. However, generic level relationships within the largest tribe Theeae were not fully resolved and potential hybridization among genera within Theeae revealed previously also remains to be tested further. Here we conducted a comprehensive phylogenomic study of Theaceae based on transcriptomes and low-depth whole-genome sequencing of 57 species as well as additional plastome sequence data from previous work. Phylogenetic analyses suggested that Stewartieae was the first-diverging clade in Theaceae, consistent with previous study using plastomic data. Within Theeae, the highly supported Apterosperma-Laplacea clade grouped with Pyrenaria with maximum support based on the partitioned and unpartitioned concatenation analyses using the 610 low-copy nuclear genes, leaving Camellia and Polyspora as another sister genera in the tribe. PhyloNet analyses suggested one reticulation event within Camellia and Pyrenaria respectively, but no intergeneric reticulations were detected in Theeae. Another introgression was found between Gordonia lasianthus and the common ancestor of Gordonieae during the Late Oligocene. The existing land bridges (e.g. Bering land bridge) might have facilitated this ancient introgression. Further researches need to be conducted to uncover the interspecific introgression pattern within Camellia. Ks distribution analyses supported the tea family shared one whole-genome duplication (WGD) event Ad-{beta}, which was recently mapped to the clade containing core Ericales, Primuloids, Polemonioids and Lecythidaceae.

O_LIInvestigating the mechanisms that underpin the diversity and distribution patterns of species is fundamental in ecology and evolution. However, the study of fungi, particularly the ectomycorrhizal group, has been relatively constrained in this field. C_LIO_LIWe conducted a high-resolution phylogenomic analysis of Boletales, an ecologically and economically significant group of fungi, covering 83 genera across 15 families. We subsequently investigated its evolutionary history using sequences at four genes obtained from 984 species across 121 genera within 15 families. C_LIO_LIThe findings unveiled that Boletales likely originated in Early Jurassic and underwent two remarkable episodes of rapid diversification, commencing in early Eocene ([~]54 Mya) and early Miocene ([~]17 Mya) epochs. The notable surges were predominantly driven by ectomycorrhizal clades, with a specific emphasis on East Asia and North America. These expansions were strongly correlated with the warm-humid paleoclimates during the Early Eocene Climatic Optimum and Mid-Miocene Climatic Optimum, as well as the rapid expansion of Fagales and Pinaceae hosts. C_LIO_LIThis study provides novel insights into the spatiotemporal evolution of fungi, highlighting the synergistic impact of abiotic factors, such as warm and humid paleoclimates, and the biotic factor of rapid diversification of host plants on the fungal diversification. C_LI

Although plant mitogenomes are small in size, their variations are no less than any other complex genomes. They are under rapid structure and size changes. These characters make the assembly a great challenge. This caused two intertwined problems, a slow growth of known mitogenomes and a poor knowledge of their evolution. In many species, mitogenome becomes the last genome that undeciphered. To have a better understanding of these two questions, we developed a strategy using short sequencing reads and combining current tools and manual steps to get high quality mitogenomes. This strategy allowed us to assembled 23 complete mitogenomes from 5 families in Fagales. Our large-scale comparative genomic analyses indicated the composition of mitogenomes is very mosaic that "horizontal transfers" can be from almost all taxa in seed plants. The largest mitogenome contains more homologous DNA with other Fagales, rather than unique sequences. Besides of real HGTs, sometimes mitovirus, nuclear insertions and other third-part DNA could also produce HGT-like sequences, accounting partially for the unusual evolutionary trajectories, including the cryptic size expansion in Carpinus. Mitochondrial plasmid was also found. Its lower GC content indicates that it may be only an interphase of a foreign DNA before accepting by the main chromosome. Our methods and results provide new insights into the assembly and mechanisms of mitogenome evolution.

As a cornerstone of biodiversity science, Linnaean taxonomy has been used for almost 300 years to catalogue and organize our knowledge of the living world. In this system, the names of species themselves take on additional functions, such as describing features of the organism or honoring individuals. Here, we analyze the connections between bird species descriptions and who they honor from 1950 to 2019 within a context of global structures of power and access to science to interrogate how authority over the natural world is designated through Western scientific naming practices. We find that 95% of bird species described during this period occur in the Global South, but these species are disproportionately described by and named in honor of individuals from the Global North. We also find an increase through time in authors from the Global South, but Global North authors continue to disproportionately hold first author positions. Our findings show how research and labor in the Global South continue to be disproportionately translated into power and authority in the Global North, upholding and re-enacting imperialistic structures of domination. Addressing these inequities as a scientific community will require reflection and collective dialogue on the social foundations and impacts of our science. For working definitions of key terms, see Table 1. For a Spanish language version of the manuscript, see Supplement (para la version en espanol, ver el Suplemento). O_TBL View this table: org.highwire.dtl.DTLVardef@361e94org.highwire.dtl.DTLVardef@111c641org.highwire.dtl.DTLVardef@1eef8d4org.highwire.dtl.DTLVardef@122f7eorg.highwire.dtl.DTLVardef@1ec2a78_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONDefinitions of terms, and how we use terms in the text. C_TABLECAPTION C_TBL

Phylogenetic networks, rather than purely bifurcating trees, more accurately depict the intricate evolutionary dynamics of most lineages, especially those characterized by extensive hybridization and allopolyploidization events. However, the challenges of achieving complete taxon sampling, and limited financial resources for studying non-model plant lineages, have hindered comprehensive and robust estimation of phylogenetic backbones with guidance from networks. The bellflower tribe, Campanuleae, characterized by a reticulate evolutionary history, serves as an ideal model to investigate how to diagnose nested ancient reticulation events. Here, by integrating multiple genomic data sources and a range of phylogenetic inference methods, we produced a robust phylogenetic backbone for the tribe Campanuleae. Our investigation of reticulate evolution indicates that hybridization and allopolyploidization were instrumental in shaping the diversity of the bellflower tribe, particularly during the initial diversification of the subtribe Phytematinae. Additionally, we ascertained that conflicting topologies resulting from distinct genomic datasets and inference methodologies significantly impact downstream estimates of divergence dating, ancestral area construction, and diversification rates. This study offers a universally relevant framework for deciphering how to use network-based phylogenetic structures using various genomic sources and inference methods. [Campanulaceae, Campanuleae, Cytonuclear discordance, paralog, phylogenomics, reticulate evolution]

DNA barcode databases are increasingly available for a range of organisms facilitating the wide application of DNA barcode-based pursuits. Here we announce the development of a comprehensive DNA barcode database of the Japanese woody flora representing 43 orders, 99 families, 303 genera and 834 species and comprising 77.3% of genera and 72.2% of species of woody plants in Japan. A total of 6,216 plant specimens were collected from 223 sites (municipalities, i.e. city, town, village) across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This database utilised three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,404 barcode sequences. Individual regions varied in their identification rates with species-level and genus-level rates for rbcL, trnH-psbA and matK being 57.4%/ 96.2%, 78.5%/ 99.1 % and 67.8%/ 98%, respectively. Identification rates were higher using region combinations with total species level rates for two region combinations (rbcL & trnH, rbcL & matK, and trnH-psbA & matK) ranging between 90.6-95.8%, and for all three regions equal to 98.6%. Genus level identification rates were even higher ranging between 99.7-100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode database is an effective resource for investigations of woody plants in Japan using DNA barcodes and provides a useful template for development of libraries for other components of the Japanese flora.

Compared to the plants with C3 photosynthesis, the plants with C4 photosynthesis have higher light, water, and nitrogen use efficiencies. Though only 3% of higher plants have C4 photosynthesis, C4 photosynthesis contribute about 23% of terrestrial gross primary productivity. Currently, it remains elusive how the procedure of the evolution from C3 towards C4 photosynthesis is driven. Here, Flaveria genus, the chief model for C4 evolutionary researches, was used to study this driving through a combined analysis of ecological, physiological and biochemical data. From proto-Kranz to C4-like, results showed that precipitation was negatively associated with the activity of C4 metabolic core enzyme and C4 flux, respectively. With increased vein density, an increased temperature and precipitation were observed during the earlier evolutionary stage. Our study indicated that decreasing precipitation and increasing temperature accompanied the transition from C3 to C2 photosynthesis and further transition from C2 to developing C4 photosynthesis. There was a positive relationship between CO2 compensation point, stomatal density and precipitation, supporting the notion that decreasing precipitation enhances photorespiration through reducing stomatal conductance during the evolution. As the driving force from proto-Kranz to C4-like, our study highlights that drought dominated rather than heat during C4 evolution. This study suggests that the driving force between certain stages during the evolution towards C4 photosynthesis are different and increased water availability should be needed in the initial phase.

O_LIThe expansive Himalayan-Hengduan Mountains (HM) and Qinghai-Tibet Plateau (QTP) form a biodiversity hotspot imperiled by global change. The species diversity, resulting from myriad factors led to plant diversification from 10 million years ago till now. However, despite understanding speciation timing better, a lack of in-depth population-level studies and a dearth of organismal sampling among closely related species and populations leaves an incomplete view of diversification trends and biotic influences. C_LIO_LIWe delve into the complex factors influencing diversification through genomic and eco-morphological analysis within the Stellera chamaejasme L. complex, known for its significant floral diversity. C_LIO_LIOur results uncover four cryptic species, indicating a more recent and younger diversification period ([~]2.67-0.9 Mya), driven by Pleistocene glaciation and a complex set of interacting biotic factors. These factors prompted allopatric speciation and advocated cyclical warming-cooling episodes along latitudinal and altitudinal gradients throughout the Pleistocene. C_LIO_LIThe study emphasizes the existence of cryptic species within these mountains, broadening our understanding of species diversification to more recent than previously recognized. This novel perspective may reshape evolutionary paradigms in plant science. Additionally, it also brings to light concerns over future warmings possible impacts on alpine species distribution and speciation, underlining the urgency for increased conservation efforts. C_LI

Germplasm resource is the source of herbal medicine production. Cultivation of superior germplasm resources helps to resolve the serious conflict between long-term population persistence and growing market demand by producing materials with high quality consistently. Cibotium barometz is the original plant of cibotii rhizoma ("Gouji"), a traditional Chinese medicine used in the therapy of pain, weakness, and numbness of lower extremity. Long-history use of Cibotium has rendered wild populations of this species declined seriously in China. Without sufficient understanding of species and lineage diversity of Cibotium, it is difficult to propose a targeted conservation scheme at present, let alone selecting high-quality germplasm resources. In order to fill such a knowledge gap, this study sampled C. barometz and relative species throughout their distribution in China, performed genome skimming to obtain plastome data, and conducted phylogenomic analyses. We constructed a well-supported plastome phylogeny of Chinese Cibotium, which showed that three species with significant genetic difference distributed in China, namely C. barometz, C. cumingii, and C. sino-burmaense, a cryptic species endemic to NW Yunnan and adjacent region of NE Myanmar. Moreover, our results revealed two differentiated lineages of C. barometz distributed in the east and west side of a classic phylogeographic boundary that probably shaped by monsoons and landforms in China. We also evaluated the resolution of nine traditional barcode loci, and designed five new DNA barcodes based on the plastome data which can discriminate all these species and lineages of Chinese Cibotium accurately. These novel findings integrated genetic basis will guide conservation planners and medicinal plant breeders to build systematic conservation plans and exploit germplasm resources of Cibotium in China.

Background--Major northern temperate tree genera emerged in the Eocene and now have vast ranges across the Northern Hemisphere. Here we undertake a multi-discipline study to provide novel insights into the formation and biogeographic history of a dominant, yet understudied temperate tree genus, Fagus L. Data and methodology--A whole chloroplast genome phylogeny (eighty-two chloroplast genomes) with multi-accessions of most species was determined and contrasted with the timing of lineage diversification inferred from three different nuclear and chloroplast gene time-calibrated phylogenies using 101 fossils as age priors. Main results--Five deeply diverged chloroplast lineages were revealed that, with the exception of a Eurasian lineage, underwent divergence decoupled from speciation predating modern species lineages by up to 28 million years (Ma). The geographic distribution of chloroplast lineages reflects a complex history of genetic admixture during past contact between extinct and modern species including between different subgenera in East Asia and long-term persistence particularly in Japan which is the hotspot of plastome diversity. Conclusion--Modern Fagus forests are the consequence of 62 million years of evolution, migration, genetic exchange and species extinction with most modern species harbouring a mosaic of genetic material, a legacy of multiple admixture events in deep time.

Only twenty-two net-winged beetle species (Elateroidea: Lycidae) are known from the Western Palearctic region (WPR), i.e., less than 0.5% of the global lycid diversity and much fewer than from the similar latitudes of East Asia or Northern America. We use the comprehensive distribution data and the molecular phylogeny of [~]400 world lycids, including fourteen European species, to provide a new perspective for understanding the structure and evolution of this group in the WPR. All Mediterranean species represent deeply rooted lineages with relatives in Eastern Asia. These species occur in relictual ranges close to the familys Pleistocene refugial edge. The phylogeny points to the loss of biological connection with East Asia since the Mid Miocene. A third of WPR species is widespread in Central and Northern Europe, reaching Eastern Asia, some of them possibly younger elements of the European fauna. Unlike relatively high diversity in the Eocene amber, the extant net-winged beetles represent a small fraction of elateroid diversity in the WPR and are generally rare. Therefore, we assume that most WPR species are relics trapped in Mediterranean refugia since the onset of the Plio-Pleistocene cooling and are critically endangered by the ongoing loss of suitable habitats.

The Japanese subalpine zone is dominated by a distinct and ecologically important conifer rich forest biome, subalpine coniferous forests, that are an outlier of the extensive boreal forests of Eurasia. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small populations size effects. However, there is a severe lack of genetic resources available for the study of this biomes major constituent plant species. This study aims to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species via genome skimming of whole genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4-10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 to 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterized by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. This data will be useful for genetic studies of the taxonomic relationship of populations within Japan and to other parts of northeast Asia, investigating phylogeographic patterns within species, conservation genetics and has potential application for studies of environmental and ancient DNA.

Incomplete taxonomic knowledge may seriously hamper biodiversity conservation efforts that are crucial in a context of global change. Gastridium P.Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, inhabiting ephemeral grass habitats, whose species number and diversity are still imperfectly known. In order to progress towards a comprehensive taxonomic treatment of this genus, we examined patterns of DNA diversity in the four taxa (Gastridium lainzii, G. phleoides, G. scabrum, and G. ventricosum) that have been recently advanced by different authors, based on new morpho-ecological descriptors. We explored nucleotide sequence variation at two plastid (trnH-psbA, trnL-F) and one nuclear (ITS) DNA markers in 44 total individuals. Diversity data were treated with multiple statistical and phylogenetic tools, and integrated with available GenBank sequences of Gastridium and other closely related genera. Despite the limited variability detected, evidence of within-taxon genetic cohesion and estimates of molecular divergence comparable with those of species in the same subtribal lineage (Agrostidinae) were recovered. The identified plastid genealogies appeared congruent with a subdivision of the genus into (at least) three distinct entities, and coherent with collected morphological descriptors. Phylogenetic reconstructions with ITS were less corresponding to taxa identities, likely due to reticulation and polyploidization. Once placed in a broader taxonomic context, the investigated dataset produced plastid and nuclear tree topologies consistent with previous assessments, highlighting the overall little resolution of species and genera within Agrostidinae. In the plastid tree, a sister relationship between Gastridium and Triplachne was weakly supported. In the ITS tree, relationships among these genera were unresolved. The hypothesis of closely related but separately evolving lineages within Gastridium is discussed, suggesting a re-evaluation of its current assessment in taxonomic authorities to enhance our knowledge of the grass family, and assist future biodiversity surveys of key Mediterranean grassland ecosystems.

AimTropical rainforests harbour the richest biodiversity among terrestrial ecosystems, but few studies have addressed underlying processes of species diversification in these ecosystems. We use the pantropical and early divergent flowering plant family Annonaceae as a model system to investigate how abiotic factors such as climate and biogeographic events contribute to the diversification process and lead to its high diversity across a long evolutionary history. LocationTropics and subtropics TaxonAnnonaceae MethodsA super-matrix was constructed for 835 taxa (34% of Annonaceae species), based on eight chloroplast regions. To understand the patterns of diversification, we reconstructed climatic niche evolution and historical biogeographical events, and tested their association with diversification rates. ResultsThe analysis of temperature-dependent models in Annonaceae lineages provides strong support for the significant influence of global temperature on net diversification and accumulation of species diversity. The pattern of lineage accumulation in the initial radiation is better aligned with the "museum model," followed by later accumulation consistent with the "recent cradle model" from the late Oligocene to the present. The increase in the diversification rate of the family (around 25 Ma) lags behind the accumulation of niche divergences (around 15 Ma). Biogeographic events are related to only two of the five diversification rate shifts detected. While no direct relationship to shifts in the diversification rate was uncovered, shifts in niche evolution appear to be associated with increasingly seasonal environments. Main ConclusionsGlobal temperature plays a crucial role in driving recent rapid diversification in the Annonaceae. Our study challenges the prevailing assumption of the "museum model" alone and proposes instead a transition from the "museum model" to the "recent cradle model" during the diversification history of the family. However, our findings do not support the direct correlation of any particular climatic niche shifts or historical biogeographical events with shifts in diversification rate. Instead, Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. The evolutionary direction of niche shifts furthermore provides insight into the future expansion of Annonaceae into temperate regions. Our results highlight the complexity of the diversification process in taxa with long evolutionary histories, indicating that identifying isolated driving factors is simplistic and inadequate for explaining the observed patterns. Further comprehensive analyses of range evolution are necessary to delve deeper into the interplay among key opportunities, key innovation, and species diversification.

Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to dry-hot valleys of the Yalong River in western Sichuan, China, requires urgent conservation efforts due to its extremely rarity and restricted distribution. In this study, we present a high-quality chromosome-level reference genome of A. pentaphyllum (626 Mb, 2n = 26), comprising 70.64% repetitive sequences and 38,540 protein-coding genes. Phylogenetic analysis shows that A. pentaphyllum diverged from a clade consisting of A. yangbiense and A. saccharum in the late Eocene ([~]37.83 Ma). In the genome of A. pentaphyllum, genes involved in responding to external environmental change have undergone expansion and positive selection, potentially reflecting its adaptive strategies. While no recent independent whole-genome duplication events were detected, a recent rapid amplification of transposable elements was observed. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 {+/-} 0.97 x 10-3) compared to other woody species. Phylogeographic patterns suggest an upstream colonization along the Yalong River, with two severe population bottlenecks correlating with major Pleistocene climatic transitions. In addition, most populations exhibit high inbreeding and genetic load, particularly those at range edges (TKX, CDG, TES). Based on these genomic insights, we propose targeted conservation strategies, including genetic rescue measures, to safeguard this unique maple species. These findings not only contribute to the preservation of A. pentaphyllum but also enhance our understanding of plant adaptation to extreme environments and the impacts of climate change on species with restricted distributions.

The South China mainland and nearby islands are biodiversity hotspots. Section Nintooa, widely distributed across mainland China, Vietnam, and Hainan Island, exhibits a typical disjunct distribution pattern. However, the origins of the flora of Hainan Island and the phylogenetic relationships within Section Nintooa remain contentious. In this study, we collected 81 samples encompassing all recognized species of Section Nintooa, along with samples from other sections of Lonicera. We reconstructed the phylogenetic relationships using 491 orthologous nuclear genes and complete plastomes generated by target enrichment and genome skimming sequencing. Our nuclear gene-based species and concatenated trees support the monophyly of Section Nintooa. The species tree indicates that the Vietnamese and Hainan populations form sister clades. However, the plastome results indicate that Section Nintooa is polyphyletic, with subsection Volubilis forming a monophyletic group and subsection Calcaratae forming a sister clade with other members of subgenus Chamaecerasus. Our hybridization network analysis reveals extensive gene flow within Section Nintooa, whereas subsection Calcaratae shows no gene flow with subsection Volubilis, leaving the origin of Calcaratae unclear. Lonicera species from Hainan Island exhibit unstable phylogenetic positions and underwent a rapid radiation during the Miocene. Biogeographical results indicate that populations from Vietnam and Hainan both originated from mainland China. Overall, our findings enhance the understanding of the evolutionary diversification history of Lonicera.

Lanthanomelissa is a controversial taxonomic group of bees that was treated as subgenus of Chalepogenus or an independent genus. All of its species are endemic to the south-eastern grasslands of South America, an endangered and still poorly known environment. We aimed to understand the origin of this group of bees in time and space as well as the influence of Quaternary climatic fluctuations on its current distribution and possible link to the history of the Southern Grasslands. We inferred phylogenetic relationships of Lanthanomelissa species using 37 terminals and 3430 nucleotides of three mitochondrial and two nuclear markers and estimated divergence times and ancestral geographic range. We performed an ensemble with the algorithms SVM, Maxent, and Random Forest in a dataset of 192 georeferenced occurrence points using 19 WorldClim bioclimatic variables to analyse species distribution during the current and two past climatic scenarios (LIG, ∼120 kya and LGM, ∼21 kya). The results support the monophyly of the genus and taxonomic changes including the species Lanthanomelissa parva n. comb. on Lanthanomelissa, and the treatment of the goeldianus group of Chalepogenus as the genus Lanthanella. The genus originated at the Oligocene-Miocene border in the Chacoan-Pampean region, and the glacial-interglacial models indicated expansion in Last Glacial Maximum and retraction in Last Interglacial. Expansion and retraction of Lanthanomelissa distribution in the last glacial-interglacial indicated grasslands distributional shifts during periods of climate cooling and warming. The diversification of Lanthanomelissa supported the estimated expansion of southern grasslands in South America concurrently with the origin of Cerrado during the late Miocene. Their origin was approximately synchronized with their exclusive floral host, Sisyrinchium (Iridaceae).View Full Text

O_LIDiversification rates vary through time, with bursts of rapid diversification underscoring species richness across the Tree of Life. Yet the abiotic and biotic factors that correlate with periods of rapid diversification are not well known. C_LIO_LIWe explored the diversification dynamics of Gypsophila (Caryophylleae: Caryophyllaceae), a large and diverse genus with a high degree of endemism in the Irano-Anatolian and Caucasus biodiversity hotspots. We tested the hypothesis of young and recent diversification of biodiversity in these two hotspots and investigated the biotic and abiotic, and paleoenvironmental cofactors of diversification within the Caryophylleae tribe, with a special focus on Gypsophila. C_LIO_LIOur analysis identified multiple shifts in the diversification rate within Caryophylleae, including a newly identified shift in Gypsophila, which began approximately 3 million years ago and was triggered by both paleoenvironmental factors and morphological novelties. These novelties were enabled by explosive diversification of woodiness and perenniality and were facilitated through the high adaptability of Gypsophila to gypsum soil and the harsh environments of alpine habitats. C_LIO_LIThese findings reveal the highly dynamic evolutionary history of both the Caryophylleae clade and Gypsophila, consistent with the extensive historical fluctuations in the geology and climate of the Irano-Anatolian and Caucasus biodiversity hotspots. This study significantly improves our understanding of the dynamics of evolution in the Irano-Anatolian and Caucasus biodiversity hotspots and highlights the impact of environmental changes and morphological innovations on diversification rates. C_LI