Article information
summary
The extremely diverse plant communities in the Neotropics are the result of diversification driven by multiple biotic (e.g., speciation, extinction, and dispersal) and abiotic (e.g., climatic and tectonic) processes. However, due to the lack of a well-preserved, thoroughly sampled, and rigorously evaluated fossil record, little is known about the processes associated with dispersal and extinction. We report an exceptional case study documenting extinction patterns in the Vitis viniferae family (Vitaceae Juss) based on fossil seeds found in four neotropical paleoflora found between 60 and 19 Ma. Among them is a new species that provides the earliest evidence of the Vitis vinifera family in the Western Hemisphere. Eight other species shed light on the previous existence of major clades of the family that currently do not exist in the neotropics, and shed light on previously unknown dispersal events. Our results suggest that regional extinctions and dispersal had a significant impact on the evolutionary history of the Neotropical grape family. They also argue that while the Neotropics have been the dynamic center of diversification throughout the Cenozoic, the extant Neotropical plant diversity has also been affected by widespread extinctions over the past 66 million years.
introduction
The Neotropics, which includes the tropics of the Americas and the Caribbean, have the largest population of vascular plants in the world, accounting for almost one-third of global biodiversity [1]. This outstanding diversity is the result of a long evolutionary history, which was greatly interrupted by extinction events at the end of the Cretaceous period [2], followed by biotic and abiotic processes, including geological tectonics and climate change, which led to large-scale diversification of neotropical taxa [3-6]. Advances in understanding the patterns and processes that lead to the aggregation of neotropical flora are based on multidisciplinary studies including paleobotany, systematics, biogeography, phylogeny, and population biology [7,8]. However, while phylogeny using time calibration has identified variations in the diversification rate and distribution of many plant groups in the Neotropical biome (e.g., Ref. 9-11), in the absence of a well-sampled and informative fossil record, it is more problematic to assess extinction and dispersal patterns in the Neotropics. Among the characteristic families of neotropical forests, the Vitis vinifera is unique in that its distinctive seeds are often preserved in the fossil record. These fossils provide critical phylogenetic resolution that can be used to study the deep history of this population, thanks to our further understanding of phylogenetic relationships through increasingly thorough molecular and genomic studies [12-30]. The Vitis family, which includes the subfamily Vitoideae (woody climbing plants, vines, shrubs, and trees) and the Leeoideae subfamily (perennial herbaceous plants, shrubs, and trees) [31-33], is a group of (major) tropical plants whose rich fossil record can be traced back to the Deccan Plateau (ca. 66 Ma) in central India during the Late Cretaceous period. This family is known for its isolated phylogenetic position in the rose branch [30,35,36] and also for its inclusion of an important economic species (common vine) [15]. Currently, there are five families within the subfamily Vitis vinifera [12,21], including 19-20 genera and about 950 major tropical species; Only a few genera (e.g., Vitis vinifera, Diogo) reach higher latitudes [33]. Today, there are about 100 species of grape plants in 6 genera in the Neotropics. They are found in the Caribbean and from Mexico to Patagonia, inhabiting low- to high-altitude forests [37-40]: Sour vine (neotropical plant), Snake vine (Mexico), Pepper vine (South America), Powdery Powder (Mexico, Central America, and South America), Bovine (Caribbean) [29], and Vitis (Mexico and Central America). The monogenus Leeoideae subfamily includes about 34 species in different habitats in the tropics of the Old World, ranging from dry deciduous forests and open grasslands, to lowland and montane rainforests [22,32]. This family has an extensive Cenozoic fossil record, but due to its predominance in North America and Eurasia (e.g., Ref. 41-43), it reflects historical biases in paleobotanical collections and does not fully explain the history of this major tropical family. Therefore, the hypothesis explaining the distribution of the extant Vitis vinifera is mainly inferred from its existing spatial distribution, molecular phylogeny, and biogeographic analysis, including the reconstruction of ancestral regions. These analyses suggest that the discontinuous intercontinental distribution of the Vitis viniferae may be the result of multiple relatively recent long-distance dispersal and/or migration events in and out of Central and South America (e.g., Ref. 13, 16, 18, 19). In this study, we propose new hypotheses about the origin and spread of the main lineages of Vitis vinifera, based on nine Vitis seed fossils found in four paleoflora in the Neotropics (Figures 1 and 2). These fossils record the presence of the Vitis vinifera in the region much longer than previously recognized, and the biogeographic history is more dynamic than previously recognized, characterized by multiple local/regional extinctions, including those of the two main lineages in the Neotropics (Figure 3). The Cenozoic fossil record of the grape family in South and Central America highlights the impact of extinction on shaping the composition of tropical forests of the Americas with high diversity.
outcome
Detailed descriptions, systematic processing, and comparisons of these fossils are provided in the Supplemental Information on Phylogenetic Paleontology, illustrated by macrophotography and μCT data. Etymology of the genus Leea mcmillanae Herrera, Carvalho, Stull, Jaramillo & Manchester sp. nov. This species honors Jennifer McMillan for her continued support of paleontological research in the Neotropics. Holotype. UF201-56589 (Figures 1a and 2c, and supplemental Figures 1a, d, e). Ancient botanical collection at the Florida Museum of Natural History, University of Florida, Florida, USA. Place. Bucaro Beach, Asuro Peninsula, Panama (7°20′52.8"N, 80°21′12.1"W). Stratigraphy and age. The Tonosi Formation, late Eocene, is based on biostratigraphic correlation and radiometric data (~34 Ma) [44]. Specific diagnosis. Seeds are symmetrical on both sides, oval nearly spherical; The ventral and dorsal views are oval, and the lateral view is D-shaped. The apex is rounded and has no obvious grooves. The base is blunt, without a beak. The seed coat is thin. The seed surface is not faceted, but there are signs of ventral, lateral, and dorsal wrinkles. The ventral and dorsal surfaces are smooth, with wrinkles on the sides. The ventral surface folds inward, slit-like, narrow, parallel to each other. Folded inwards laterally, one on each side, marked by a C-shaped groove from which several secondary folds radiate outward. The narrow central groove in the bisymmetrical plane extends entirely around the dorsal surface. The junction knot is not obvious. There are central vascular bundles on the surface of the folds. Vitoideae Eaton, subfamily Viticulae, Seritis vitiforma-Vitis genus-Vitis genus Lithouva Herrera, Carvalho, Stull, Jaramillo & Manchester gen.nov.Lithouva susmanii Herrera, Carvalho, Stull, Jaramillo & Manchester sp.nov. etymology. Líthos (Greek): stone; uva (Latin): Grape. The moniker is in recognition of Arthur T. Susman's continued support for the study of paleobotany in South America. Holotype. UR-CP-0219 (Figures 1b and 2a, and supplemental Figures 2b-f). Collection of Paleontology, Universidad Rosario, Bogotá, Colombia. Place. Cundina, Macacogua, Colombia (5°7′25.10 N); Longitude 73°53′53.10"W). Stratigraphy and age. Bogotá group; Paleocene age (5860 Ma) based on biostratigraphic correlation [2]. General diagnosis. The seeds are symmetrical on both sides, obovate on the ventral dorsal view, D-shaped on the side, slightly M-shaped in cross-section, and not flattened on the sides. There is a shallow V-shaped notch at the apex. The base has a pronounced beak. The ventral side folds inward, parallel to each other, > >2/3 of the length of the ventral surface, and the outline is elliptical and deep, separated by a prominent straight middle rib (middle suture ridge) that does not extend to the dorsal side. The junction is rounded, located above the dorsal equator, and is not in contact with the notch. dorsal with 5-7 folds radiating from the junction; The ventral surface is smooth. The grooves at the base of the junction and at the apex of the junction are shallow. The thickness of the seed coat is kept constant by ventral infolding. Specific diagnosis. The results are the same as those of the genus. Etymology of Ampelocissuswenae Herrera, Carvalho, Stull, Jaramillo & Manchester sp.nov. This particular nickname is in honor of Jun Wen, an authority in the field of grape family who has contributed immensely to our understanding of the systematics, phylogeny, and evolution of the grape family. Holotype. UF60803 (Figures 1c and 2i, and supplementary Figure 3). Ancient botanical collection at the Florida Museum of Natural History, University of Florida, Florida, USA. Place. The Gaillard Cut of the Panama Canal (an outcropping rock formation east of Lirio; UF Location 19391; 9°3'20.00"N, 79°39'40.00"W). Stratigraphy and age. Lower Kukalacha Formation; Early Miocene age (19-18.5 Ma) based on geochronological and biostratigraphic data [45]. Specific diagnosis. The seeds are symmetrical on both sides, broadly elliptic on the ventral and dorsal surfaces, and D-shaped on the sides. The apex has a protruding apical V-notch. There is a short beak at the base. The ventral fold is two-fold, divergent (~50°), broad, elliptic in profile, deep, and separated by a prominent straight median rib (middle suture ridge) that does not extend to the dorsal side. The junction knot is concave, elliptic, broad, located in the dorsal center, touching the notch. dorsal with 12 broad, sharp ridges (folds) radiating outward from the central junction; The ventral surface is mostly smooth. The grooves at the base of the junction and at the apex of the junction are shallow. The thickness of the seed coat is kept constant by ventral infolding, as a single layer, consisting of anticlinally oriented columnar cells with a polygonal profile.
Figure 1: Fossilized seeds of the Vitis vinifera. a, Orthotype specimen of the genus Torch (UF56589). November is from the late Eocene epoch in Panama and shows ventral, dorsal and lateral views. Note the parallel ventral medial fold and median suture groove (left); median dorsal sulcus (middle); C-shaped inward fold on the side (right) with branched secondary folds (arrows). b, Orthotype specimen of the new genus Lithouva susmanii (UR-CP-0219). Dorsal view of November from the Paleocene of Colombia, showing the junction knot (arrow) and the ridge radiating from it (left); Volumetric rendering (right) showing ventral (buried in sediment), note the inward fold and the pronounced median suture (arrow). c, Orthotype specimen of the genus Sorbeta (UF60803). November is from the Early Miocene of Panama and shows dorsal, ventral, and lateral views. Note the junction knot and the sharp ridge radiating outward from it (left); The second image from the left shows the ventral surface with a broad divergent inward fold; The third image from the left shows a volumetric rendering with junction knots (arrows) and pronounced ridges; Digital cross-section showing that the seed coat maintains thickness by ventral infold (right). d–g, a genus of Saxuva draculoidea, was produced in the late Eocene of Panama. d, dorsal and ventral views of the orthotype specimen (UF56166). e, depth map rendering of ventral, dorsal, lateral, and landscape/oblique views (UF85532); The left arrow shows a distinct spiny fold, note the ventral medial fold; The right arrow shows the tip of the linear lacing. F, G, cross-section of seeds (UF56168, UF56169) showing an M-shaped endosperm cavity towards the conjunctional region. h, orthotype specimen of the genus Whitewood (UF60884). November from the Early Miocene of Panama and shows ventral, dorsal, lateral and lateral views; Note the abrupt thinning of the linear perilabial lip (left arrow) and seed coat as it enters the ventral infold (right arrow). Scale bars, 500 μm (C right), 1 mm (B, C, H right), 2 mm (A, D–G, H). Cissus correae Herrera, Carvalho, Stull, Jaramillo & Manchester sp. nov. etymology. This special title is given in recognition of Mireya Correa (1940-2022) for her many contributions to botany and her work on the flora of Panama. Holotype. UF60884 (Figures 1H, G and Supplementary Figures 5A-D). Ancient botanical collection at the Florida Museum of Natural History, University of Florida, Florida, USA. Place. The Gaillard Cut of the Panama Canal (an outcropping rock formation east of Lirio; University of Florida Location: 19391; 9°3'20.00"N, 79°39'40.00"W") Stratigraphy and age. Lower Kukalacha Formation; Early Miocene age (19-18.5 Ma) based on geochronological and biostratigraphic data [45]. Specific diagnosis. The seeds are symmetrical on both sides, the ventral surface and the dorsal surface are oval, the side is D-shaped, the cross-section is M-shaped, and the sides are not flattened. The apex is rounded without obvious grooves. The base has a short to prominent beak. The ventral surface is folded inward, parallel (about 2/3 of the length of the ventral surface), and the outline is elliptical and deep, separated by a straight median rib (mid-suture ridge) that does not extend to the dorsal side. The linear perilabial lip is well-defined, passing through the full length of the vertices and dorsal surfaces. The groove at the base of the junction and at the top of the junction is absent. There are crests on the edges, and the surface of the seeds is smooth. The seed coat becomes abruptly thinned when it enters the ventral infold and is composed of thick-walled columnar cells in the anticline direction with a polygonal profile.
Fig. 2: Reconstruction of Neotropical Paleocene to Miocene forest grape seeds. a, Lithouva s usmanii from the Paleocene of Colombia. b, Leea olsonii from the early Oligocene in Peru. c, Leea mcmillanae from the Late Eocene in Panama. d, Saxuva draculoidea from the Late Eocene in Panama. e, f, Cissus lombardii and C. willardii from the early Oligocene of Peru. g, Cissus correae from the Early Miocene, Panama. h, Ampelocissus bravoi of the early Oligocene in Peru. i, from the early Miocene of Panama. Scale bar, 5 mm. The species was first described from the cross-sections and acetate skins of permeabilized specimens (Figures 1d-g and 2d, and supplementary Figures 4)44. New data based on volumetric rendering and virtual slicing of type materials indicate the presence of two spongy ventral infolds, a long and linear junction, and a mid-suture bundle embedded in the sclerotic layer of the seed coat. The positive model specimen (Figs. 1d and 2d) shows a decorated seed surface with distinct spiny folds on the sides, dorsal edges, and ventral view near the top. With these new details, the seeds of S. draculoidea are comparable to those of taxa in the Cayratieae family and are most similar to those endemic to China and Japan, the extant species of Pseudocayratia Wen, Lu, and Chen [28,46]. In particular, the prickly ornamentation is relatively rare in grape seeds, but it is also seen and even more pronounced in the modern (but probably now extinct) genus Acareosperma spireanum Gagnep. [28,46]。
Figure 3: Historical biogeography of the four branches of the Vitis vinifera. Viteae, Leea, Cayratieae, and Cisseae based on molecular phylogeny and extant distribution. Reconstruction of ancestor regions using the DEC model in RASP and a stochastic mapping of time-calibrated phylogeny (supplementary information). All ancestral regional analyses concluded that these clades originated in the Old World, while fossil evidence strongly supports Neotropical origin. Neotropical fossils are represented by †. For more information, see Supplemental Information; Ancient map obtained from Ref. 100. Phylogenetic and biogeographic analysis of the Vitis familyIn order to compare with the neotropical fossil record of the Vitis family, we have made new phylogenetic and biogeographic reconstructions of the family based on extant species only (Figure 3 and supplementary information). The results of two independent biogeographic analyses using the diffusion-extinction-branching (DEC) model and the stochastic mapping under the simple maximum likelihood (ML) model are consistent with the assumption that the oldest fossil evidence (available here) of the clade from the Neotropics is of Old World origin (Figure 3). Specifically, the tropical Pacific Ocean (Asia) was inferred as the ancestral region of Cisseae (pp=0.96), Cayratieae (pp=0.84), and Viteae (pp=0.54) (pp is a posterior probability, calculated as relative frequencies on a random map), consistent with previous biogeographic studies [18,19]. DEC analysis shows greater ambiguity about the deeper nodes of the ancestral region, but speculates that the ancestors of the Sisaiaceae and Cajaratyacone were found in the Old World tropics (tropical Pacific or Africa). Viteae's ancestors had an unclear ancestry reconstruction, but it was inferred in DEC and random mapping analyses that Vitis Vitis originated in Mesoamerica (pp=92), which is consistent with previous studies (e.g., Ref. 18). The history of the loss of grape plants in the NeotropicsAs far as we know, the only Neotropical fossil record belonging to the Vitis family comes from the "Cissites" patagonica leaves of the Paleocene in Argentina [47]. However, recent reviews of the species and new collections do not support kinship with the grape family [48]. The findings presented here are the only evidence of Neotropical Vitis fossils, adding depth and new perspective to the interpretation of the group's historical biogeography. Considering the current distribution of the main branches of the Vitis vinifera and their biogeographical reconstructions, they reveal a noteworthy history of the family in the Neotropics, which is unexpected (Figure 3). Today, only about one-tenth of the extant species of the Vitis family are naturally distributed in South America, Central America and the West Indies, and considering the distribution of these extant taxa alone, it is impossible to discern the complex history of the Vitis vinifera in our biogeographic reconstruction (Figure 3). The discovery of Lithouva susmanii (Fig. 1b and 2a) in the Paleocene sediments of Colombia (ca. 60 Ma) coincided with the initial development of closed canopy and multi-layered rainforest structures after the Terminal Cretaceous event [2,49,50] (Fig. 3) and laid the foundation for the long history of the South American grape family. Other fossils from North America that are related to this group [51] suggest that Vitis vinifera was widespread in the Late Paleocene, emphasizing the uncertainty reflected by vague ancestral reconstructions of the imaginary ancestors of this group (Figure 3). Differentiation time estimates also suggest that most genera of the Vitis vinifera diverged during the Oligocene (Figure 3), which is consistent with new findings in paleobotany. The genus Sorrium (19–18.5 Ma) found in Miocene sediments in Panama (Figs. 1c and 2i) is very similar to extant Mesoamerican and Caribbean species (e.g., Erdwinberg's snake grape) as well as Robinson's snake grape. Within the Vitis vipe-Vitis vinifera clade [46] (Supplementary Figure 6). Whereas, in molecular phylogenetic studies, Erdwenberg's snake grape and several Neotropical grape genera (Vitis vinifera roundleaf Vitis spp.) have been found as successive sisters to other grape genera, this has been interpreted as evidence that this economically important genus originated in the Neotropics [18]. The presence of this branch in Mesoamerica in the Miocene is documented by the Vista vibrae, and is consistent with the proposed neotropical origin of the vine. Late Eocene Saxuva draculoidea (Cayratieae) (Figures 1d-h and 2d) and Leea mcmillanae (Leeoideae) (Figures 1a and 2c) from Panama are the earliest fossil evidence of Cayratieae and Leeoideae, respectively, and also provide the oldest fossil evidence of the Protomesoamerican Vitis family (Fig. 1a, d-g). However, since both Cayratieae and Leeoideae are currently confined to the Old World, ancestral regional reconstructions based on modern distributions (Figure 3) conflict with these records, suggesting that the hypothetical ancestors in these clades may have been limited to Asia (Figure 3). This conclusion is further complicated by Saxuva draculoidea and Leea mcmillanae. Their first appearance coincides with the earliest evidence of terrestrial landscapes on the Mesoamerican isthmus [52], and the fossil assemblage in which they appear also contains species from the sumacaceae, areca nut family, and other major Old World taxa, such as McDonnellon [44], further emphasizing these plants. Leea olssonii [53,54] (Fig. 2b) seeds from younger, Early Oligocene sediments in Peru demonstrate that Leea was previously present on the west coast of South America as well as in Proto-Central America. However, in a thorough sampling of the Paleocene and Eocene flora of North America, no Leea or Cayratieae-related species were found (e.g., Ref. 55, 56), suggesting that the spread through North America is unlikely to explain the presence of these fossils in the Neotropics. Sackova and Leea appear to have disappeared after the Oligocene, as they are no longer seen in relatively good samples of pear wood from Panama, the Andean region, or the Amazon basin (e.g., Ref. 45, 57-59). The co-occurrence of the genus Acanthocarpus (Evodiaceae) with Leea in the Peruvian Oligocene Belém flora exhibits a similar pattern. Similar to Lea, its presence in the Neotropics is also surprising, since today it is limited to the tropics of the Old World [60] . Habitat transitions associated with the Andean uplift and the aridifying effects of the Humboldt Current on forests along the Pacific coast may have led to the loss of past community assemblages and locally restricted taxa [8,53]. In addition to two species from the Peruvian Oligocene Belém flora, Powdery Vine and C. lombardii [54] (Fig. 2e, f), C. correae from the Miocene of Panama (Fig. 1c and 2g) is the third fossil species of this genus. Can be described from the Neotropics. These two Belém species are the earliest known species of the genus Powdery Vine. Most extant powdery vine species occur in Africa, and only extant biogeographic reconstructions suggest that the genus powdery millet arrived in the Neotropics from Africa in the middle of the Eocene, and that its pattern also occurs in certain mammalian clades (e.g., rodent guinea pigs [61]), while in the Neotropics it is in Africa. Australian extractions in the genus Powdery Vine are estimated to date back to the Miocene [16,19]. Cissus correae and C. willardii are very similar, and their occurrence on both sides of the Mesoamerican seaway suggests a continuous spread from South America to the Panama Peninsula before the Miocene, as well as in the early Miocene pollen records of Panama [62,63]. Other plant taxa have also hypothesized similar patterns of dispersal across seaways (e.g., Ref. 64,65). The extinction and spread of neotropical forestsThe impact of the late Cretaceous extinction event profoundly changed the evolutionary trajectory of low-latitude forests in northern South America, promoted the emergence of closed canopy and multi-layered biomes dominated by angiosperms, and also brought about great changes in floristic composition. New plant lineages and diversity of plant-insect interactions in the region [2]. The initial consequence of this extinction event in the Neotropics was a long period of low plant diversity in the Paleocene, which lasted about 6 million years. Ultimately, however, this extinction event paved the way for the diversification and origin/arrival of key tropical taxa, such as the Vitis viniferae lineage, Fabaceae [66], Annonaceae, Araceae [67], Areca [68], Malvaceae [69], Phyllaceae [70,71], and Passifloraceae [72], which contribute to the family-level composition and species diversity patterns of tropical rainforests [73,74] and present-day tropical dry forests [75]. Over the past 66 million years, changing climate and tectonic processes have shaped the evolution of neotropical vegetation. Most events that are thought to trigger diversification in the Neotropics, such as the Andean uplift (e.g., Ref. 63) and climate change (e.g., areas where Paleogene high temperatures, Miocene climate optimum, and intertropical climate change intensity) converge) may also contribute to habitat transitions (e.g., the emergence of dry and xerophytic forests and savannahs at low latitudes) and the extinction of locally limiting taxa and/or entire community assemblages [5,8,76,77]. The history of Cenozoic extinction in northern South America is slowly coming into focus, and the few well-documented examples of the Cenozoic include a potential bottleneck observed in warm-acclimatized cacti, which was a pollen record of the Eocene-Oligocene transition caused by the onset of the last glacial maximum [78] and the observed high level of extinction [77]. However, to more accurately identify which plant lineages in the region have experienced significant extinction over the past 66 million years, well-preserved plant fossils are needed to provide a more detailed systematic interpretation. For example, according to the Cenozoic pollen record of the Mauritius palm, widespread extinction of the palm in the wider tropics has been identified in Africa and India [79]. An important example in the high latitudes of South America is the disappearance of the Early Eocene diverse forests of Lake Hongco in Patagonia [80] and many of its "Australian" (e.g., eucalyptus, cone [81,82]) and Old World taxa (e.g., Asterium [83]). Extinction rates cannot be reliably estimated based solely on extant phylogeny (e.g., Ref. 84-87) and may be of particular interest for older lineages such as Vitis vinifera. Further development of methods to include the fossil record in biogeographic analysis would be helpful, as would the development of more realistic models to explain origins, extinctions, and environmental changes simultaneously (e.g., Ref. 4, 88-91). The extinctions of the neotropical Cayratieae and Leeoideae are examples of regional extinctions that coincided with the clustering of modern neotropical plant communities. Whether their disappearance is the result of the accidental action of narrowly ranged species or reflects the disappearance of diverse communities remains to be determined.
discuss
For the foreseeable future, for many taxa, attempts to reconstruct historical biogeographic patterns can only be made based on the distribution of existing representatives. However, as in the case of the Vitis vinifera, greater progress will be made through multidisciplinary studies including paleobotany, biogeography, species distribution models, phylogeny, and population biology. The growing interest in the generation and use of new fossil data offers the potential for a deeper understanding of local and regional extinctions. Paleobotany in the Neotropics remains underexplored compared to paleobotany in the high and mid-latitudes of the Northern and Southern Hemispheres, and regional extinctions of plant lineage are well documented in the high and mid-latitudes of the Northern and Southern Hemispheres. Each new fossil whose relationship can be reliably determined may provide new information about the past distribution and evolution of the clade to which it belongs. Vitis Vitis presents a prominent case study in which information from the fossil record necessitates the re-evaluation of only extant hypotheses. The fossil record not only shows the family's long history in the Neotropical forest, dating back to the Late Paleocene, but also shows the regional extinction of the two main clades (Leeoideae and Cayratieae) after the Oligocene, which are now confined to the Old World. It also sheds light on the spread of the Miocene in the Mesoamerican seaways and supports the neotropical origin of vines in the Neotropics [18].
way
Fossil sites and comparison materials are detailed in the supporting information. Fossil preparation, tomography and imaging of seeds of S. draculoidea, L. mcmillanae, A. wenae and C. correae were preserved in calcareous sediments. We used a GE Phoenix V|tome|xm240 CT scanner from the University of Florida College of Engineering's Nanoresearch Facility to scan type specimens for all species described here; GE dual-tube X-ray computed tomography scanner in the Department of Organic Biology and Anatomy at the University of Chicago; and synchrotron radiation X-ray tomography on the beamline of the Advanced Photon Source 2BM at Argonne National Laboratory (Lemont, IL). Voltage, current, and timing vary depending on the required resolution. The micro CT dataset was analyzed using Avizo Lite 2023.1 (FEI Visualization Science Group, Bordeaux, France) and MeshLab [92] to provide horizontal and vertical volumetric rendering, isosurface rendering, and virtual cross-section (depth mapping and X-ray rendering options). The original CT scan dataset was archived at https://www.morphosource.org/projects/000515707/temporary_link/qNRRT59boFcNbfWqpXGXV2K6?locale=en. Macro photographs of reflected light fossils with a 100mm macro lens were taken using a Canon Rebel (Japan) camera connected to a StackShot system (Cognisys) and sequential digital images were merged using Helicon Focus software (Helicon Soft). Phylogenetic and biogeographic analysis: We used GenBank's data to generate phylogenetic trees of Vitales (195 species). To this end, we generated a dataset that included 10 loci from 195 species (atpB-rbcL, atpF-atpH, matK, rbcL, rpl16, rpoC1, rps16, trnC-petN, trnH-psbA, trnL-F), selecting phylogenetic diversity and geographic breadth representing the Vitis vinifera (see Supplementary Information, Dataset 1 for species list and NCBI germplasm, and 2 to understand the distribution (synonyms related to new genus combinations are provided in these documents). The loci were aligned individually using MAFFT (v.7.220) [93], cleaned up using the function "pxclsq" (-p0.1) from the program Phyx (v.1.3.1) [94], and then joined using the Phyx function "pxcat" to form a matrix of 8,665 sites. We used RAxML-ng (v.1.2.0) [95] to generate phylogenetic trees using ML, employing the GTR+G model and 200 guided replications and searching for ML trees (–all). Due to the poor resolution of some branches, we used constraint trees (as indicated in the supplementary information) to determine the primary relationship based on the latest phylogenetic hypotheses based on phylogenetic analysis [14,21,30]. We then constrained the Vitis viniferae roots using the ML tree and five fossil calibrations as well as a secondary calibration using treePL [96] (supplementary information); Prior to analysis, we use "prime" for parameter optimization and cross-validation to determine the optimal smoothing value. We then used the tree for several biogeographic reconstructions and modern distribution scores for the following regions: Africa, Eurasia, Central America, North America, South America, Tropical Pacific. We performed two types of biogeographic reconstruction (see supplementary information). First, we implemented the DEC model in RASP (v.4) [97], discarding the parameter "J" (which stands for "jump dispersion"), as this has proven to be conceptually and statistically flawed [98]. We also performed a simple reconstruction of the ancestral region using the stochastic mapping in PhyTools (v.1.5) as well as the "isorate" model and 100 simulations [99].
期刊：nature plants
文章标题：Cenozoic seeds of Vitaceae reveal a deep history of extinction and dispersal in the Neotropics
作者信息：Fabiany Herrera，Mónica R. Carvalho，Gregory W. Stull，Carlos Jaramillo，Steven R. Manchester
Original link: https://doi.org/10.1038/s41477-024-01717-9
The pictures in the article and the cover picture are from the original article