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Manchester SR, Judd WS, Handley B.. Foliage and fruits of early poplars (Salicaceae: Populus from the eocene of Utah, Colorado, and Wyoming. Int J Plant Sci 167: 897-908
Abstract and Figures
A new species of poplar is recognized based on abundant specimens from the early Middle Eocene Parachute Creek Member of the Green River Formation in eastern Utah and western Colorado and compared with two other contemporary species. A rare twig bearing both leaves and fruits serves as a Rosetta stone, linking the vegetative and reproductive structures that formerly were only known from dispersed organs. Fruit and foliage characters distinguish Populus tidwellii sp. n. from Populus cinnamomoides (Lesquereux) MacGinitie (typified on specimens from Green River Station, WY), to which the isolated leaves had formerly been attributed. In addition, new data from fruits and foliage confirm that there were two distinct sympatric species of Populus in the Parachute Creek flora (P. tidwellii and Populus wilmattae). These species, together with Pseudosalix and Salix, provide our earliest record of diverse Salicaceae. An interesting feature of P. tidwellii is that the inflorescence is terminal in contrast to extant species of Populus, in which the catkins are axillary and borne on wood of the previous season. In addition, the infructescence shows lateral branching near its base, distin-guishing it from the simple racemes of extant species of the genus.
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... The best-preserved fossils of Populus with a rare twig that bore both leaves and fruits originate from the Eocene Green River Formation in Utah, Colorado, and Wyoming in the United States, and these fossils occurred in the early Middle Eocene (∼48 Ma) (Boucher et al., 2003;Manchester et al., 2006). All of them were similar to P. mexicana (Manchester et al., 1986) and attributed to sect. ...
... All of them were similar to P. mexicana (Manchester et al., 1986) and attributed to sect. Abaso (Eckenwalder, 1977;Manchester et al., 2006). At the same formation, another famous fossil is Pseudosalix handleyi, which also has leaves and fruits attached and represents a lineage separate from Populus and indicates that Populus (and likely Salix) represented a unique lineage(s) at this time (Boucher et al., 2003). ...
... Ancestral area reconstruction with DEC + J model based on nuclear SNPs phylogeny indicated that Populus originated in the New World (Figure 5). Both morphological and fossil evidence also support the hypothesis of North American origin (Manchester et al., 1986(Manchester et al., , 2006Collinson, 1992;Eckenwalder, 1996). The first confirmed fossil of Populus in the early Middle Eocene, were attributed to sect. ...
Populus not only has significant economic and ecological values, but also serves as a model tree that is widely used in the basic research of tree growth, physiology, and genetics. However, high levels of morphological variation and extensive interspecific hybridization of Populus pose an obstacle for taxonomy, and also to the understanding of phylogenetic interspecific relationships and biogeographical history. In this study, a total of 103 accessions representing almost all the wild species of Populus were collected and whole-genome re-sequenced to examine the phylogenetic relationships and biogeography history. On the basis of 12,916,788 nuclear single nucleotide polymorphisms (SNPs), we reconstructed backbone phylogenies using concatenate and coalescent methods, we highly disentangled the species relationships of Populus , and several problematic taxa were treated as species complexes. Furthermore, the phylogeny of the chloroplast genome showed extensive discordance with the trees from the nuclear genome data, and due to extensive chloroplast capture and hybridization of Populus species, plastomes could not accurately evaluate interspecies relationships. Ancient gene flow between clades and some hybridization events were also identified by ABBA–BABA analysis. The reconstruction of chronogram and ancestral distributions suggested that North America was the original region of this genus, and subsequent long dispersal and migration across land bridges were contributed to the modern range of Populus . The diversification of Populus mainly occurred in East Asia in recent 15 Ma, possibly promoted by the uplift of the Tibetan Plateau. This study provided comprehensive evidence on the phylogeny of Populus and proposed a four-subgeneric classification and a new status, subgenus Abaso . Meanwhile, ancestral distribution reconstruction with nuclear data advanced the understanding of the biogeographic history of Populus .
... However, there are no phylogenetically based estimations of divergence times, and the biogeography of Populus is poorly understood. Currently, most research on the origin and evolution of Populus has been based exclusively on the fossil record (Manchester et al., 1986;Boucher et al., 2003;Manchester et al., 2006). Lineages and their biogeographic distributions have been mapped with the use of molecular phylogenies, and significant geological and ecological events have been more precisely dated using molecular clock, with fossil records serving as a calibrator for gene phylogenies (Berbee and Taylor, 2010). ...
... The only remaining genetic traces of ancient species are from chloroplast capture (the chloroplast genome of one species was completely swapped out for that of another) by male plants of the ancestral species of P. mexicana, which also became extinct, such as P. cinnamomoides (Lesquereux) MacGinitie (MacGinitie, 1969;Eckenwalder, 1980), P. wilmattae Cockrell (Manchester et al., 1986), and P. tidwellii sp. n. (Manchester et al., 2006). Chloroplast capture is a common phenomenon in biological organisms (Petit et al., 2004). ...
Introduction
Populus (Salicaceae) species harbour rich biodiversity and are widely distributed throughout the Northern Hemisphere. However, the origin and biogeography of Populus remain poorly understood.
Methods
We infer the divergence times and the historical biogeography of the genus Populus through phylogenetic analysis of 34 chloroplast fragments based on a large sample.
Results and Discussion
Eurasia is the likely location of the early divergences of Salicaceae after the Cretaceous-Paleogene (K-Pg) mass extinction, followed by recurrent spread to the remainder of the Old World and the New World beginning in the Eocene; the extant Populus species began to diversity during the early Oligocene (approximately 27.24 Ma), climate changes during the Oligocene may have facilitated the diversification of modern poplar species; three separate lineages of Populus from Eurasia colonized North America in the Cenozoic via the Bering Land Bridges (BLB); We hypothesize that the present day disjunction in Populus can be explained by two scenarios: (i) Populus likely originated in Eurasia and subsequently colonized other regions, including North America; and (ii) the fact that the ancestor of the genus Populus that was once widely distributed in the Northern Hemisphere and eventually wiped out due to the higher extinction rates in North America, similar to the African Rand flora. We hypothesize that disparities in extinction across the evolutionary history of Populus in different regions shape the modern biogeography of Populus . Further studies with dense sampling and more evidence are required to test these hypotheses. Our research underscores the significance of combining phylogenetic analyses with biogeographic interpretations to enhance our knowledge of the origin, divergence, and distribution of biodiversity in temperate plant floras.
... The rst calibration point was set at 48 Ma (normal distribution, SD = 0.3) for the root node of Salicaceae sensu strict. This was based on an approximately 48-million-year-old fossil from the early Eocene in North America ("Populus tidwellii"), which most likely represents the stem lineage leading to Populus and Salix (Manchester et al. 2006). The second calibration was set at 23 Ma (normal distribution, SD = 0.3) for the root node of the Vetrix/Chamaetia clade, based on the earliest reliable Salix fossils from Late Oligocene deposits (23 Ma) in Alaska, which were found to be a liated with subg. ...
Here we examine the evolutionary history of Salix in Japan, and in particular the subg. Vetrix/Chamaetia complex. To do so, we performed molecular phylogenetic analyses covering all available native species, using multilocus datasets of low-copy nuclear genes and chloroplast sequences. Using phylogenetic network analysis and divergence time estimation, we identified three major lineages within Japanese subg. Vetrix , confirmed the polyphyly of subg. Chamaetia , and further resolved the taxonomic status of various taxa at the section to species levels. Moreover, this study also highlighted the speciation processes for many endemic species. These include S. hukaoana , a novel monotypic section of Hukaoana that distinctly shows ancient divergence and not hybrid speciation, and S. miyabeana (sect. Helix ), which shows evidence of genomic and morphological differentiation from subsp. miyabeana via intersectional hybridization and introgression with the sympatric species S. schwerinii (sect. Viminella ). Finally, we also identified local endemics classified into sect. Hastatae (i.e., S. rupifraga , S. shiraii , and S. japonica ) which show evidence of radiative speciation from a single lineage descended from S. vulpina (sect. Cinerella ).
... The sex-determining locus is on different chromosome in different Populus species (reviewed in Renner and Müller 2021), and both XY and ZW systems exist in both genera (He et al. 2021a) (Table 1). These observations suggest the possibility of sex chromosome turnovers, and that at least four turnover events have been suggested in the Salicaceae (Manchester et al. 2006;Mank et al. 2014;Yang et al. 2021). More recent studies detected at least four turnovers in Populus alone; two translocation events may have occurred in P. alba Müller et al. 2020). ...
Dioecious Salix evolved more than 45 million years ago, but have homomorphic sex chromosomes, suggesting that turnover event(s) prevented major differentiation. Sex chromosome turnover events have been inferred in the sister genus Populus. The genus Salix includes two main clades, Salix and Vetrix, with several previously studied Vetrix clade species having female-heterogametic (ZW) or male-heterogametic (XY) sex-determining systems (SDSs) on chromosome 15, while three Salix clade species have XY SDSs on chromosome 7. We here studied two basal taxa of the Vetrix clade, S. arbutifolia and S. triandra using S. purpurea as the reference genome. Analyses of whole genome resequencing data for genome-wide associations (GWAS) with the sexes and genetic differentiation between the sexes (F ST values) showed that both species have male heterogamety with a sex-determining locus on chromosome 15, suggesting an early turnover event within the Vetrix clade, perhaps promoted by sexually antagonistic or (and) sex-ratio selection. Changepoint analysis based on F ST values identified small sex-linked regions of~3.33 Mb and~2.80 Mb in S. arbutifolia and S. triandra, respectively. The SDS of S. arbutifolia was consistent with recent results that used its own genome as reference. Ancestral state reconstruction of SDS suggests that at least two turnover events occurred in Salix. Heredity; https://doi.
... The Wagon Bed occurrence extends the North American range of the genus to the Rocky Mountains. In the Green River Formation, Salicaceae are represented by compressed fruit capsules as well as leaves of Populus (Manchester et al. 2006) and Pseudosalix L.Boucher, MancheSter et Judd (Boucher et al. 2003). Although it is difficult to make a detailed comparison because of the different modes of preservation, there is a noteworthy similarity between Saxifragispermum and the capsules of Populus tidwellii MancheSter et Judd from Utah and P. cinnamomoides (leSq.) ...
The early middle Eocene Wagon Bed fruit and seed flora of central Wyoming encompasses nine morphotypes that are assignable to extant genera (Alangium, Aphanathe, Canarium, Carya, Celtis, Iodes, Mastixia, Nyssa, Pleiogynium), four that are assignable to extinct genera in extant families (Chandlera, Menispermaceae; Coryloides, Betulaceae; Pentoperculum, Anacardiaceae; Saxifragispermum, Salicaceae) and one morphotype potentially assignable to an extant family (Pandanaceae). At least 11 morphotypes remain unidentified due to incomplete characters, although some exhibit features suggestive, but not definitive, of extant families (e.g., Euphorbiaceae, Lauraceae, Nymphaeaceae, Rosaceae). Individual taxa exhibit paleobiogeographic links with the Eocene floras of the west coast of North America, as well as with those of the Eocene of Europe. Together with previously described pollen and woods, these fruits and seeds indicate a mixed evergreen and deciduous forest, existing under moist circumstances, possessing primary taxonomic affinities with extant paratropical taxa of the Old World.
Dioecious Salix evolved more than 45 million years ago, but have homomorphic sex chromosomes, suggesting that turnover event(s) prevented major differentiation. Sex chromosome turnover events have been inferred in the sister genus, Populus . The genus Salix includes two main clades, Salix and Vetrix , with several previously studied Vetrix clade species having female-heterogametic (ZW) sex-determining systems (SDSs) on chromosome 15, while two Salix clade species have male-heterogametic (XY) SDSs on chromosome 7. We here studied two basal taxa of the Vetrix clade , S. arbutifolia and S. triandra . Analyses of whole genome resequencing data for genome-wide associations (GWAS) with the sexes and genetic differentiation between the sexes (F ST values) showed that both species have male heterogamety with a sex-determining locus on chromosome 15, suggesting an early turnover event within the Vetrix clade, perhaps promoted by sexually antagonistic or (and) sex-ratio selection. Changepoint analysis based on F ST values identified small sex-linked regions of ~3.33 Mb and ~2.80 Mb in S. arbutifolia and S. triandra , respectively. The molecular mechanism of sex-determination remains unknown. Ancestral state reconstruction of SDS and stamen numbers suggests that at least two turnover events occurred in Salix . Willows with XY SDS usually have multiple stamens, while ZW species have two stamens.
Premise of the study:
Angiosperm leaves present a classic identification problem due to their morphological complexity. Computer-vision algorithms can identify diagnostic regions in images, and heat map outputs illustrate those regions for identification, providing novel insights through visual feedback. We investigate the potential of analyzing leaf heat maps to reveal novel, human-friendly botanical information with applications for extant- and fossil-leaf identification.
Methods:
We developed a manual scoring system for hotspot locations on published computer-vision heat maps of cleared leaves that showed diagnostic regions for family identification. Heat maps of 3114 cleared leaves of 930 genera in 14 angiosperm families were analyzed. The top-5 and top-1 hotspot regions of highest diagnostic value were scored for 21 leaf locations. The resulting data were viewed using box plots and analyzed using cluster and principal component analyses. We manually identified similar features in fossil leaves to informally demonstrate potential fossil applications.
Key results:
The method successfully mapped machine strategy using standard botanical language, and distinctive patterns emerged for each family. Hotspots were concentrated on secondary veins (Salicaceae, Myrtaceae, Anacardiaceae), tooth apices (Betulaceae, Rosaceae), and on the little-studied leaf margins of untoothed leaves (Rubiaceae, Annonaceae, Ericaceae). Similar features drove the results from multivariate analyses. The results echo many traditional observations, while also showing that most diagnostic leaf features remain undescribed.
Conclusions:
Machine-derived heat maps that initially appear to be dominated by noise can be translated into human-interpretable knowledge, highlighting paths forward for botanists and paleobotanists to discover new diagnostic botanical characters. This article is protected by copyright. All rights reserved.
Leaves are the most abundant and visible plant organ, both in the modern world and the fossil record. Identifying foliage to the correct plant family based on leaf architecture is a fundamental botanical skill that is also critical for isolated fossil leaves, which often, especially in the Cenozoic, represent extinct genera and species from extant families. Resources focused on leaf identification are remarkably scarce; however, the situation has improved due to the recent proliferation of digitized herbarium material, live-plant identification applications, and online collections of cleared and fossil leaf images. Nevertheless, the need remains for a specialized image dataset for comparative leaf architecture. We address this gap by assembling an open-access database of 30,252 images of vouchered leaf specimens vetted to family level, primarily of angiosperms, including 26,176 images of cleared and x-rayed leaves representing 354 families and 4,076 of fossil leaves from 48 families. The images maintain original resolution, have user-friendly filenames, and are vetted using APG and modern paleobotanical standards. The cleared and x-rayed leaves include the Jack A. Wolfe and Leo J. Hickey contributions to the National Cleared Leaf Collection and a collection of high-resolution scanned x-ray negatives, housed in the Division of Paleobotany, Department of Paleobiology, Smithsonian National Museum of Natural History, Washington D.C.; and the Daniel I. Axelrod Cleared Leaf Collection, housed at the University of California Museum of Paleontology, Berkeley. The fossil images include a sampling of Late Cretaceous to Eocene paleobotanical sites from the Western Hemisphere held at numerous institutions, especially from Florissant Fossil Beds National Monument (late Eocene, Colorado), as well as several other localities from the Late Cretaceous to Eocene of the Western USA and the early Paleogene of Colombia and southern Argentina. The dataset facilitates new research and education opportunities in paleobotany, comparative leaf architecture, systematics, and machine learning.
Keywords
Angiosperms, cleared leaves, data science, fossil leaves, leaf architecture, paleobotany
Circumscription of Flacourtiaceae was investigated with a phylogenetic analysis of plastid rbcL DNA sequences, and the family was found to be composed of two clades that are more closely related to other families in Malpighiales than to each other. In one of these, that containing the type genus Flacourtia, Salicaceae are embedded, whereas the other clade includes the members of the peculiar and poorly known South African Achariaceae. The latter family name is conserved against all listed synonyms. Thus we propose the recognition of two families: i) Salicaceae sensu lato, including tribes Banareae, Bembicieae, Scolopieae, Samydeae (syn. Casearieae), Homalieae, Flacourtieae, Prockieae and Saliceae, as well as Abatieae (by some authors of Passifloraceae) and Scyphostegieae (Scyphostegia of the monogeneric Scyphostegiaceae); and ii) Achariaceae sensu lato, including tribes Pangieae, Lindackerieae, Erythrospermeae and Acharieae (Acharia, Ceratiosicyos and Guthriea of Achariaceae). Several genera considered by many previous authors to be members of Flacourtiaceae are excluded from Malpighiales: Berberidopsis and Aphloia fall near the base of the higher eudicots. Several tribes require different names from those used in previous systems, and we include an appendix indicating a tentative revised tribal taxonomy for both Salicaceae and Achariaceae sensu lato.
The Eocene and Oligocene epochs were times of major evolutionary, biogeographic, and vegetational changes in terrestrial plants. From a floristic perspective three major trends characterize this period in the Rocky Mountain region: 1) development of more distinct phytogeographic provinces from a relatively homogeneous Paleocene holarctic flora, 2) the early diversification in Eocene upland areas of presently important temperate families, and 3) the first appearances of many extant angiosperm genera and disappearance of many typically Cretaceous and Paleocene forms. From a vegetational perspective there are two strong trends. Initially there was an early Eocene spread of broad-leaved, evergreen forest to high northern latitudes (60⚬N), possibly the greatest geographic coverage such vegetation ever achieved. This was followed by the subsequent fragmentation of these forests to produce more open vegetation of lower stature in many areas. These floristic and vegetational trends were of great consequence for angiosperm evolution and biogeography. They were also significant in creating the ecological milieu for the evolution of early and mid Tertiary animals.
The taxonomy of Salix in the southeastern United States was studied in the field and herbarium. Twelve species and one variety of native willows are recognized and seven species and one subspecies are shown to be introduced and naturalized. A quantitative study of variation in S. caroliniana and S. nigra supported species rank for these entities and showed that infraspecific variation was too diffuse to warrant taxonomic recognition. Salix humilis has been shown to consist of two varieties: var. humilis and var. microphylla. Salix floridana is an endemic species that belongs in sect. Humboldtiana. It may be a Tertiary relict that survived the Pleistocene glaciation in northern Florida. The phytogeographical patterns displayed by this and other species of Salix are related to Pleistocene events. During the Full-Glacial some northern willows presumably extended far south of their present ranges and some northern species had their ranges fragmented. Some northern species occur here now as peripheral species (S. amygdaloides, S. bebbiana, S. discolor, and S. lucida); others, such as S. eriocephala, left major disjunct populations behind following deglaciation. The disjunct Ozark population of S. caroliniana may also be related to these events, or it may have had its origin in Tertiary times. The recognition of these taxa of Salix is aided by keys to staminate, pistillate, and vegetative specimens, detailed descriptions, and comparison with related and similar species. Taxonomy, nomenclature, variation, and hybridization of each native species are discussed. Each species is illustrated; range maps are also provided.
Heteroblastic leaf development and seasonal heterophylly in some extant species of Populus result in diverse mature leaf forms during ontogeny of a single individual. Juvenile leaves of heteroblastic poplars, such as P. mexicana Wesmael and P. monticola T. Brandegee, are narrower than adult leaves of the same species and share corresponding differences in foliar venation. In species with seasonal heterophylly, early leaves of adult individuals are formed in the season preceding leaf expansion and overwinter in buds, while late leaves expand in the same season in which they are initiated. In P. monticola, late leaves have finer, more regular serrations than early leaves of the same shoots, but other species show other differences between the two leaf forms. Although their fossilized leaves are found as single detached organs, several Tertiary species of Populus that are related to extant heterophyllous species, exemplified by P. cinnamomoides (Lesquereux) MacGinitie, P. adamantea H. Becker, and P. cedrusensis J. Wolfe, probably possessed heteromorphic leaf types as well. Diverse leaf types of each of these species have been divided among two or three species apiece by paleobotanists. Some have been considered representatives of different genera. Foliar heteromorphism of the kinds found in Tertiary and Recent Populus may be a more prevalent source of taxonomic confusion in fossil floras than has heretofore been recognized.