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Fossil History of the Juglandaceae
... Pterocarya fraxinifolia occurs in northern Iran and the Caucasus Mountains, while the other species are distributed in East Asia with a center in central and southwest China (Lu, 1982;Lu et al., 1999). Based on the presence or absence of scales on the terminal buds, two sections have been recognized (e.g., Manning, 1978;Lu, 1982): Pterocarya section Pterocarya with naked buds (including P. fraxinifolia, P. hupehensis, P. stenoptera, and P. tonkinensis), and P. section Platyptera with scaled buds (including P. delavayi, P. insignis, P. macroptera, and Interestingly, the fossils of Pterocarya were widely distributed in the Northern Hemisphere during the Cenozoic (e.g., Lu, 1982;Manchester, 1987). The fruit fossil Pterocarya macginitii was considered the oldest record found in North America (Manchester, 1987), but it differs from extant Pterocarya in having the wings in the same plane as the long axis of the nut, and lacking persistent tepals at the nut apex. ...
... Based on the presence or absence of scales on the terminal buds, two sections have been recognized (e.g., Manning, 1978;Lu, 1982): Pterocarya section Pterocarya with naked buds (including P. fraxinifolia, P. hupehensis, P. stenoptera, and P. tonkinensis), and P. section Platyptera with scaled buds (including P. delavayi, P. insignis, P. macroptera, and Interestingly, the fossils of Pterocarya were widely distributed in the Northern Hemisphere during the Cenozoic (e.g., Lu, 1982;Manchester, 1987). The fruit fossil Pterocarya macginitii was considered the oldest record found in North America (Manchester, 1987), but it differs from extant Pterocarya in having the wings in the same plane as the long axis of the nut, and lacking persistent tepals at the nut apex. Therefore, Manchester (1991) suggested that P. macginitii might conform to the extinct platycaryoid genus Hooleya. ...
... Therefore, Manchester (1991) suggested that P. macginitii might conform to the extinct platycaryoid genus Hooleya. Until now, more than 83 fruit and foliage fossils representing four extant species and 19 extinct species of Pterocarya have been found in Asia, North America, and Europe since the Oligocene (e.g., Wolfe, 1977;Manchester & Dilcher, 1982;Manchester, 1987;Wilf, 2000;Xia et al., 2009;Yabe, 2009) (Fig. 1B). Of these, 46 fossil records have been recovered from the Miocene, which represent 14 extinct species and four extant species. ...
Pterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in the Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node‐dating (ND) based on plastomes of all eight extant species and tip‐dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD, respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% highest posterior density [HPD]: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant event without fossils, but as many as six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via the Bering Land Bridge during the early Oligocene and the early Miocene periods. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except for Pterocarya fraxinifolia and Pterocarya stenoptera , suitable habitats for this genus are predicted to contract by 2070 due to climate change.
... The earliest fossil record of the fruit of Engelhardia existed in South America and North America, and the oldest Alatonucula ignis fossil had been found in the early Eocene strata of Argentina [65]. At the same time, a fossil was found in the Miocene strata of Alaska, USA (Palaeocarya olsoni) [70]. This means that these taxonomic groups were widely present in parts of the Northern and Southern Hemispheres during the Eocene. ...
... We estimated the divergence time of Juglandaceae species based on 80 coding sequences (CDSs), combined with the calibration of four fossils (Table S9) [24,[70][71][72][73][93][94][95][96]. The nucleotide substitution model is the same as the MrBayes parameters mentioned above. ...
Background Engelhardia
(Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of 8 Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and 6 outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family.
Results
The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of 10 codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn’t support rapid radiation occurred in the evolution history of Engelhardia.
Conclusion
Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.
... Furthermore, as initially suggested by Manning and Hjelmqvist (1951) and Stone (1962), C. sinensis may be reinstated within the section Rhamphocarya of the Carya. According to Manchester (1987) and Zhang et al. (2013), the genus Carya probably originated in North America during the early Paleocene and subsequently migrated to Europe via the North Atlantic land bridge (NALB) during the Paleocene and Eocene. Then, Carya may have entered Asia either from Europe as the Turgai seaway receded or from North America via the Bering land bridge (BLB) during the late Miocene or early Pliocene. ...
Ghost introgression, or the transfer of genetic material from extinct or unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost introgression, especially in plant species, remains scarce. Here, we newly assembled chromosome‐level genomes for both Carya sinensis and Carya cathayensis , and additionally re‐sequenced the whole genomes of 43 C. sinensis individuals as well as 11 individuals representing 11 diploid hickory species. These genomic datasets were used to investigate the reticulation and bifurcation patterns within the genus Carya (Juglandaceae), with a particular focus on the beaked hickory C. sinensis . By combining the D ‐statistic and BPP methods, we obtained compelling evidence that supports the occurrence of ghost introgression in C. sinensis from an extinct ancestral hickory lineage. This conclusion was reinforced through the phylogenetic network analysis and a genome scan method VolcanoFinder, the latter of which can detect signatures of adaptive introgression from unknown donors. Our results not only dispel certain misconceptions about the phylogenetic history of C. sinensis but also further refine our understanding of Carya 's biogeography via divergence estimates. Moreover, the successful integration of the D ‐statistic and BPP methods demonstrates their efficacy in facilitating a more precise identification of introgression types.
... The flora of the Parachute Creek Member of the Green River Formation in Utah and Colorado, which included the Palibinia species treated here, was composed of a diversity of angiosperms, some with clear affinities to extant families such as Hernandiaceae (Illigera; Manchester & O′Leary, 2010), Menispermaceae (Han et al., 2018), Arecaceae (Allen, 2015), Araceae (Kvaček, 1995), Platanaceae (MacGinitie, 1969;Manchester, 1986), Juglandaceae (Manchester, 1987a), Ulmaceae (Manchester, 1987b), Fabaceae (MacGinitie, 1969;Call & Dilcher, 1994), Anacardiaceae (Manchester & Judd, 2022), Simaroubaceae (Corbett & Manchester, 2004), Myrtaceae , Vitaceae (Chen & Manchester, 2007), Salicaceae (Boucher et al., 2003;Manchester et al., 2006), Eucommiaceae (Call & Dilcher, 1997), Polemoniaceae (Lott et al., 1998), and Tetramelaceae (Correa-Narvaez et al., 2023). However, many of the taxa reported in prior monographs of the flora (e.g., Knowlton, 1923;Cockerell, 1925;Brown, 1934;MacGinitie, 1969) are in need of revision. ...
Newly investigated leafy twigs bearing axillary fruits from the Eocene Parachute Creek Member of the Green River Formation in eastern Utah, USA, have provided more information on the species previously attributed to the Proteaceae as Banksia comptonifolia R.W.Br. The leaves are simple, estipulate with short petioles, and elongate laminae with prominent angular nonglandular teeth. The laminae have a thick midvein and pinnate craspedodromous secondaries, and are distinctive in the presence of a thick, often coalified, marginal rim. Vegetative and reproductive buds occur in the axils of the leaves. These features indicate that the species belongs to Palibinia Korovin-an extinct Eudicot genus previously known only from the Paleogene of Asia and Europe. Small pedicellate ovoid fruits 1.5-2.2 mm wide are borne in fascicles of three and are seen to be capsules with four apical valves. Despite the specific epithet referring to similarity of the foliage to that of Comptonia (Myricaceae), the fasciculate inflorescence organization with axillary flowers is quite distinct from the catkins characteristic of that family. Assignment to Banksia or other Proteaceae with complex inflorescences and follicular fruits is also problematic. Additionally, MacGinitie′s transfer of the species to Vauquelinia of the Rosaceae is contradicted by the lack of stipule scars on the twig and by differences in leaf venation and floral morphology. We transfer the species to Palibinia comptonifolia (R.W.Br.) comb. nov., but its familial affinity within the Pentapetalae remains uncertain. This new occurrence augments records from the Paleogene of Turkmenistan,
... The flora of the Parachute Creek Member of the Green River Formation in Utah and Colorado, which included the Palibinia species treated here, was composed of a diversity of angiosperms, some with clear affinities to extant families such as Hernandiaceae (Illigera; Manchester & O′Leary, 2010), Menispermaceae (Han et al., 2018), Arecaceae (Allen, 2015), Araceae (Kvaček, 1995), Platanaceae (MacGinitie, 1969;Manchester, 1986), Juglandaceae (Manchester, 1987a), Ulmaceae (Manchester, 1987b), Fabaceae (MacGinitie, 1969;Call & Dilcher, 1994), Anacardiaceae (Manchester & Judd, 2022), Simaroubaceae (Corbett & Manchester, 2004), Myrtaceae , Vitaceae (Chen & Manchester, 2007), Salicaceae (Boucher et al., 2003;Manchester et al., 2006), Eucommiaceae (Call & Dilcher, 1997), Polemoniaceae (Lott et al., 1998), and Tetramelaceae (Correa-Narvaez et al., 2023). However, many of the taxa reported in prior monographs of the flora (e.g., Knowlton, 1923;Cockerell, 1925;Brown, 1934;MacGinitie, 1969) are in need of revision. ...
Newly investigated leafy twigs bearing axillary fruits from the Eocene Parachute Creek Member of the Green River Formation in eastern Utah, USA, have provided more information on the species previously attributed to the Proteaceae as Banksia comptonifolia R.W.Br. The leaves are simple, estipulate with short petioles, and elongate laminae with prominent angular nonglandular teeth. The laminae have a thick midvein and pinnate craspedodromous secondaries, and are distinctive in the presence of a thick, often coalified, marginal rim. Vegetative and reproductive buds occur in the axils of the leaves. These features indicate that the species belongs to Palibinia Korovin-an extinct Eudicot genus previously known only from the Paleogene of Asia and Europe. Small pedicellate ovoid fruits 1.5-2.2 mm wide are borne in fascicles of three and are seen to be capsules with four apical valves. Despite the specific epithet referring to similarity of the foliage to that of Comptonia (Myricaceae), the fasciculate inflorescence organization with axillary flowers is quite distinct from the catkins characteristic of that family. Assignment to Banksia or other Proteaceae with complex inflorescences and follicular fruits is also problematic. Additionally, MacGinitie′s transfer of the species to Vauquelinia of the Rosaceae is contradicted by the lack of stipule scars on the twig and by differences in leaf venation and floral morphology. We transfer the species to Palibinia comptonifolia (R.W.Br.) comb. nov., but its familial affinity within the Pentapetalae remains uncertain. This new occurrence augments records from the Paleogene of Turkmenistan,
... Remarks: the set of anatomical features allows us to assign the fossil to the species Engelhardia orsbergensis, showing similar shape, margin and venation to specimens figured in Jähnichen et al. (1977, Pl. 38 . This species was a thermophilic element of Eocene to Pliocene floras in Europe (Manchester, 1987;Kvaček, 2002;Hably, 2020). Iberian specimens related to this species have been recorded in the late Oligocene La Val site (Moreno-Domínguez et al., 2021), in the early Miocene site of Cristo Rey (Antunes et al., 1999) and in the middle Miocene of the Madrid Basin (Fernández-Marrón et al., 2002). ...
... The flora of the Parachute Creek Member of the Green River Formation in Utah and Colorado, which included the Palibinia species treated here, was composed of a diversity of angiosperms, some with clear affinities to extant families such as Hernandiaceae (Illigera; Manchester & O′Leary, 2010), Menispermaceae (Han et al., 2018), Arecaceae (Allen, 2015), Araceae (Kvaček, 1995), Platanaceae (MacGinitie, 1969;Manchester, 1986), Juglandaceae (Manchester, 1987a), Ulmaceae (Manchester, 1987b), Fabaceae (MacGinitie, 1969;Call & Dilcher, 1994), Anacardiaceae (Manchester & Judd, 2022), Simaroubaceae (Corbett & Manchester, 2004), Myrtaceae , Vitaceae (Chen & Manchester, 2007), Salicaceae (Boucher et al., 2003;Manchester et al., 2006), Eucommiaceae (Call & Dilcher, 1997), Polemoniaceae (Lott et al., 1998), and Tetramelaceae (Correa-Narvaez et al., 2023). However, many of the taxa reported in prior monographs of the flora (e.g., Knowlton, 1923;Cockerell, 1925;Brown, 1934;MacGinitie, 1969) are in need of revision. ...
Newly investigated leafy twigs bearing axillary fruits from the Eocene Parachute Creek Member of the Green River Formation in eastern Utah, USA, have provided more information on the species previously attributed to the Proteaceae as Banksia comptonifolia R.W.Br. The leaves are simple, estipulate with short petioles, and elongate laminae with prominent angular nonglandular teeth. The laminae have a thick midvein and pinnate craspedodromous secondaries, and are distinctive in the presence of a thick, often coalified, marginal rim. Vegetative and reproductive buds occur in the axils of the leaves. These features indicate that the species belongs to Palibinia Korovin-an extinct Eudicot genus previously known only from the Paleogene of Asia and Europe. Small pedicellate ovoid fruits 1.5-2.2 mm wide are borne in fascicles of three and are seen to be capsules with four apical valves. Despite the specific epithet referring to similarity of the foliage to that of Comptonia (Myricaceae), the fasciculate inflorescence organization with axillary flowers is quite distinct from the catkins characteristic of that family. Assignment to Banksia or other Proteaceae with complex inflorescences and follicular fruits is also problematic. Additionally, MacGinitie′s transfer of the species to Vauquelinia of the Rosaceae is contradicted by the lack of stipule scars on the twig and by differences in leaf venation and floral morphology. We transfer the species to Palibinia comptonifolia (R.W.Br.) comb. nov., but its familial affinity within the Pentapetalae remains uncertain. This new occurrence augments records from the Paleogene of Turkmenistan,
... The species contains a wealth of medicinal compounds, such as polysaccharides, flavones, and triterpenoids, as well as several trace elements [13][14][15][16][17], and has long been used as a traditional Chinese medicine to control human blood glucose and lipid concentrations [14,18]. The species was reported to have an abnormal number of chromosomes (x = 28) [19], whereas all other Juglandaceae species are diploids with 32 chromosomes (2n = 2x = 32) [19,20]. The unique chromosome number was considered to be the distinctness of Cyclocarya from its sister genus Pterocarya [19]. ...
Background
Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid–autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual.
Results
Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture.
Conclusions
Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.
... At least four modern morphological data matrices 9,14,19,24 have been unable to unambiguously place Platycarya, even when fossil taxa were included (Discussion). The first such analysis 20 , however, inferred a Platycarya/Engelhardia clade (also see Manchester 25 ; our Fig. 1a). ...
In lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that differ in gene content and syntenic structure. Presence or absence of genes and microsynteny along chromosomal blocks can serve to differentiate subgenomes and to infer phylogenies. We here apply genome-structural data to infer relationships in an ancient allopolyploid lineage, the walnut family (Juglandaceae), by using seven chromosome-level genomes, two of them newly assembled. Microsynteny and gene-content analyses yield identical topologies that place Platycarya with Engelhardia as did a 1980s morphological-cladistic study. DNA-alignment-based topologies here and in numerous earlier studies instead group Platycarya with Carya and Juglans, perhaps misled by past hybridization. All available data support a hybrid origin of Juglandaceae from extinct or unsampled progenitors nested within, or sister to, Myricaceae. Rhoiptelea chiliantha, sister to all other Juglandaceae, contains proportionally more DNA repair genes and appears to evolve at a rate 2.6- to 3.5-times slower than the remaining species.
Middle Eocene interbasaltic deposits of Hareø, West Greenland, have yielded a rich leaf and fruit record, which was described in the second half of the nineteenth century. In this study, we describe dispersed spores and pollen from the Aumarûtigssâ Member of the Hareøen Formation in order to obtain a more comprehensive picture of the late middle Eocene vegetation of West Greenland. The spore/pollen assemblage, derived from a resinite-rich coal bed, comprises 123 taxa, of which 14 belong to mosses, ferns and fern-allies, 14 to gymnosperms, and 95 to angiosperms. The most diverse groups of angiosperms are Fagales, comprising 27 taxa, and Rosales, represented by nine taxa. Along with conifers belonging to Pinaceae, these groups reflect the temperate character of the Hareø flora. In addition, a few ‘exotic’ elements include cycads probably belonging to an extinct temperate lineage that was widespread across the Northern Hemisphere during the Paleogene, palm trees, members of Mastixioideae and Santalaceae, both of which were characteristic elements of more southern warm temperate floras of Europe. A detailed comparison with macrofossil and spore/pollen assemblages of roughly coeval sites from Axel Heiberg Island (Canada), Spitsbergen (Arctic Ocean), and ODP site 151-913B in the Norwegian-Greenland Sea, show a highly consistent picture of the vegetation during this time.
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