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Single most parsimonious tree for Fagales based on 27-conglomerate-taxa matrix (data set 4) (length ¼ 2739 steps, CI ¼ 0:789, RI ¼ 0:758). A, Strict consensus tree of 1215 shortest trees based on data set 5, including 27 taxa with missing data. B, Bootstrap percentages are above branches, and the values below or near are Bayesian posterior probability. The two trees have the same topology as fig. 2 at family level, with only a few differences in intergeneric relationships within Fagaceae, Juglandaceae, and Betulaceae.
Source publication
Nucleotide sequences of six regions from three plant genomes—trnL-F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S rDNA (nuclear)—were used to analyze inter-and infrafamilial relationships of Fagales. All 31 extant genera representing eight families of the order were sampled. Congruence among data sets was assessed using the partition homogenei...
Context in source publication
Context 1
... 3; result not shown) data sets are one MPT of 2558 steps and one MPT of 2118 steps. All of the most parsimonious trees obtained based on analyses of these three combined data sets recognized three major clades in Fagales: (1) Notho- fagus, (2) Fagaceae, and (3) core higher hamamelids repre- sented by Casuarinaceae-Ticodendraceae-Betulaceae and fig. 3A) and data set 2 (all six sequences from a single species for each taxon; fig. 2) provided identical topologies at the family level. The results show sequences from different congeners do not have a major influence on phylogenetic accuracy, at least for this ...
Similar publications
Phylogenetic analyses of DNA sequences of the plastid rbcL gene were used to obtain a phylogenetic framework for the New Caledonian endemic genus Canacomyrica (monotypic). A further analysis of selected genera within Fagales combining DNA sequences of the rbcL gene, plastid trnL-F region and nuclear ITS region was also performed. In all analyses Ca...
Citations
... Fagales are well studied phylogenetically with numerous approaches to date, from ITS and small numbers of plastid loci (Li et al., 2004;Manos et al., 2007) to genomic data (Yang et al., 2021) and fossils (Larson-Johnson, 2016;Siniscalchi et al., 2023). Many of these studies focus primarily on higher-level relationships and are not densely sampled; for the purpose of spatial phylogenetics, maximising species presence is crucial . ...
Aim
Quantifying the phylogenetic diversity of temperate trees is essential for understanding the processes that have shaped the modern distribution of temperate broadleaf forest and other major forest biomes. Here, we focus on Fagales, an iconic member of forests worldwide, to uncover global diversity and endemism patterns and investigate the distribution of root nodule symbiosis (RNS), an important morphological specialisation in this clade, as a key factor behind these patterns.
Location
Global.
Taxon
Fagales.
Methods
We combined phylogenetic data covering 60.2% of living species, fine‐scale distribution models covering 90% of species, and nodulation data covering all species to investigate the distribution of species richness and phylogenetic diversity at fine spatial scales compared to the distribution of RNS. We identify abiotic environmental factors associated with RNS and with Fagales diversity in general.
Results
We find the highest species richness in temperate east Asia, eastern North America, and equatorial montane regions of Asia and Central America. By contrast, relative phylogenetic diversity (RPD) is highest at higher latitudes, where RNS also predominates. We found a strong spatial structuring of regionalisations of Fagales floras, reflecting distinct Northern and Southern Hemisphere floras (except a unique Afro‐Boreal region), each with distinct RNS‐environment relationships.
Main Conclusions
Although species richness and phylogenetic regionalisation for Fagales accord well with traditional biogeographic concepts for temperate forests, this is not the case for RPD. RNS is almost universal in the highest RPD regions, which may reflect ecological filtering promoting RNS in these regions. Our results highlight the utility of global‐scale, clade‐specific spatial phylogenetics and its utility for understanding drivers of diversity in species‐rich clades.
... Phylogenetic framework-Fagales are well-studied phylogenetically with numerous approaches to date, from Sanger sequencing (R. Li et al., 2004;Manos et al., 2007) to genomic data (Yang et al., 2021) and fossils (Larson-Johnson, 2016;Siniscalchi et al., 2023). For the purpose of spatial phylogenetics, maximizing species presence is most important (D. ...
Aim: Quantifying the phylogenetic diversity of temperate trees is essential for understanding what processes are implicated in shaping the modern distribution of temperate broadleaf forest and other major forest biomes. Here we focus on Fagales, an iconic member of forests worldwide, to uncover global diversity and endemism patterns and investigate potential drivers responsible for the spatial distribution of fagalean forest communities. Location: Global. Taxon: Fagales. Methods: We combined phylogenetic data covering 60.2% of living species, fine-scale
distribution models covering 90% of species, and nodulation data covering all species to investigate the distribution of species richness at fine spatial scales and compare this to relative phylogenetic diversity (RPD) and phylogenetic endemism. Further, we quantify phylogenetic betadiversity and bioregionalization of Fagales and determine hotspots of Fagales species engaging in root nodule symbiosis (RNS) with nitrogen-fixing actinomycetes. Results: We find the highest richness in temperate east Asia, eastern North America, and equatorial montane regions of Asia and Central America. By contrast, RPD is highest at higher latitudes, where RNS also predominates. We found a strong spatial structuring of regionalizations of Fagales floras as defined by phylogeny and traits related to RNS, reflecting distinct Northern and Southern Hemisphere floras (with the exception of a unique Afro-Boreal region) and highly distinct tropical montane communities. Main conclusions: Species richness and phylogenetic regionalization accord well with traditional biogeographic concepts for temperate forests, but RPD does not. This may reflect ecological filtering specific to Fagales, as RNS strategies are almost universal in the highest RPD regions. Our results highlight the importance of global-scale, clade-specific spatial phylogenetics and its utility for understanding the history behind temperate forest diversity.
... In addition to the conspicuously triaperturate, triangular, and oblate pollen grains, Slavicekia exhibits a number of floral characters that are widespread within this group: the flowers are epigynous; the perianth is reduced and simple, consisting only of small tepals; the stamens are positioned opposite the tepals; and the syncarpous gynoecium consists of three carpels, but the fruit contains only a single seed (Friis et al. 2006. Although there is still some uncertainty concerning the exact position of Myricaceae, the phylogenetic relationships among the major extant lineages within the order Fagales are fairly well understood and are mainly based on molecular data (Li et al. 2004;Yang et al. 2021). The order comprises seven families (APG 2016; eight if Rhoipteleaceae are recognized as a separate family and not as part of Juglandaceae) with Nothofagaceae and Fagaceae as subsequent sisters to the rest. ...
... It is now well established that Betulaceae is resolved into two subfamilies: Betuloideae (Betula L. and Alnus Mill.) and Coryloideae (Corylus L., Ostryopsis Decne., Ostrya Scop., and Carpinus L.). Nevertheless, different viewpoints on the phylogenetic relationships and morphological evolution among genera have been frequently proposed, with most controversies fastening on the divergence order among genera [9,13], paraphyletic or sister relationships between Alnus and Betula [2,14], phylogenetic status of Ostryopsis and Corylus [8,15], and whether Ostrya and Carpinus were reciprocal monophyly or mutually nested [2,16]. Throughout the above studies, the controversies can be attributed to morphologically parallel or convergent evolution, incomplete taxa sampling, and limited sequence variation (e.g., single or combined ITS, Nia, matK, and rbcL). ...
... Ancestral states for 14 morphological characters are summarized in Fig. 6 and Figs. S5, S6, S7, including five flower characters (1-5), three anatomical characters (6-8), three leaf characters (9)(10)(11), and three fruit characters (12)(13)(14). For flower characters, it is unambiguously that the ancestor of Betulaceae had bisexual inflorescence, raceme infructescence, staminate perianth or pistilloide in male floret present, separated thecae and partly divided filaments. ...
... Nevertheless, wide controversies still existed in terms of genera delimitation and their evolutionary relationships. Within Betuloideae, Betula and Alnus were either treated as sister monophyly [2,4,12] or assigned as paraphyly in which Alnus lay in the basal position [14,43]. ...
Background
Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae.
Results
All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions ( P i > 0.02) and five noncoding regions ( P i > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus , Ostryopsis , and Carpinus - Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus . Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution.
Conclusions
Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.
... Five plastid (including trnL intron, trnL-F spacer, atpB-rbcL spacer, rbcL, and matK) and four nuclear (including ITS, phyA, phyC, and CRC) DNA regions were used. A total of 559 new sequences were generated in this study; the other sequences used were mainly generated in our previous studies (Li et al., 2004;Xiang et al., 2014), and taken from GenBank. The nine-locus data set comprised 10,698 aligned nucleotides: trnL, 684 bp; trnL-F, 569 bp; atpB-rbcL, 933 bp; rbcL, 1,365 bp; matK, 1,116 bp; ITS, 813 bp; phyA, 1,050 bp; phyC, 1,014 bp; and CRC, 3,154 bp. ...
The dominant species of a biome can be regarded as its genuine indicator. Evergreen broadleaved forests (EBLFs) in subtropical East Asia harbor high levels of species biodiversity and endemism and are vital to regional carbon storage and cycling. However, the historical assembly of this unique biome is still controversial. Fagaceae is the most essential family in East Asian subtropical EBLFs and its dominant species are vital for the existence of this biome. Here, we used the dominant Fagaceae species to shed light on the dynamic process of East Asian subtropical EBLFs over time. Our results indicate high precipitation in summer and low temperature in winter are the most influential climatic factors for the distribution of East Asian subtropical EBLFs. Modern East Asian subtropical EBLFs did not begin to appear until 23 Ma, subsequently experienced a long‐lasting development in the Miocene and markedly deteriorated at about 4 Ma, driven jointly by orogenesis and paleoclimate. We also document that there is a lag time between when one clade invaded the region and when its members become dominant species within the region. This study may improve our ability to predict and mitigate the threats to biodiversity of East Asian subtropical EBLFs and points to a new path for future studies involving multidisciplinary methods to explore the assembly of regional biomes.
... All the character states were unordered, unpolarized, and unweighted, and missing values were scored as "?". The character states were thus scored and mapped onto the simplified phylogenetic trees of the Fagales and the Fagaceae obtained by Li et al. (2004) and Oh and Manos (2008) to reconstruct their evolutionary patterns. ...
Main conclusion
Extensive histology of pistillate flowers revealed two pollen tube arresting sites (the style-joining and micropyle) within the pistil of Quercus acutissima during the postpollination–prezygotic stage, which reflects a unique female and male gametophyte recognition/selection mechanism.
Abstract
Sexual reproduction is among the most delicate and essential stages in plant life cycles and involves a series of precise interactions between pistils and male gametophytes. Quercus is a woody genus that dominates Northern Hemisphere forests and is notorious for interspecific hybridization, but its sexual reproduction is poorly understood, especially its pollen tube (PT) growth dynamics within pistils. This study used microtome techniques and scanning electron microscopy to observe the postpollination–prezygotic process in the biennially fruiting oak Quercus acutissima. Many pollen grains germinated at anthesis instantly, and PTs penetrated stigmatic surfaces and elongated through the stylar transmitting tissue, then arrested at style-joining for about 12–13 months. Few PTs resumed growth along the compitum in the upper ovarian locule wall in the subsequent April, concurrent with the rapid growth of rudimentary ovules. PTs arrived in the micropyle, and upper septum during megaspore mother cell meiosis, then arrested again for 7–10 days waiting for the embryo sac maturation. Fertilization occurred one week later. Our study shows a clear female dominant crosstalk growth pattern between PT and the ovule. The intermittent PT growth might reflect a unique male gametophyte recognition/selection mechanism to avoid self-pollination and enhance PT competition while increasing interspecific hybridization.
... The tree topology was consistent with the traditional tribal-level classi cation and nuclear RAD-Seq data of Juglandaceae 24,69 . Furthermore, the ML and BI tree showed that Juglandaceae was more closely related to Betulaceae than to Fagaceae, this is consistent with the ndings in prior studies 70 . ...
Platycarya longipes of the Juglandaceae family is an important woody species in maintaining the stability of community structure of karst forests. However, its phylogenetic relationship within Juglandaceae is still unclear. In this study we assembled the complete cp genome of P. longipes . The genome comprises a 158,592 bp quadripartite circular that includes a large single copy (LSC) region of 88,066 bp and a small single copy (SSC) region of 18,524 bp separated by a pair of inverted repeats (IRA and IRB) with 26,001 bp. The genome contains 113 unique genes, including 80 protein-coding genes, 29 tRNAs and 4 rRNAs. Additionally, we detected 49 long repeat sequences and 66 simple sequence repeats (SSRs). Analysis of the Ka/Ks substitution rate values in the comparison of P. longipes VS. Platycarya strobilacea , supported that P. longipes and P. strobilacea are two species. Compared with other species of Juglandaceae, the cp genome of P. longipes has a conserved gene order and structure. Phylogenetic analysis based on ML and BI methods using genomes of the Fagales order showed that P. longipes is most closely related to Platycarya strobilacea . Our research provides a critical genetic resource for P. longipes supporting future phylogenetic and population genetics studies.
... Their results suggest that A. sinensis is closely related to the Carya genus. In contrast, Li et al. (2004) [8] separated A. sinensis and Carya on different branches of infrafamilial relationships of the order Fagales based on six genes (atpB, matK, matR, rbcL, trnL-F and 18S rDNA). Manos et al. (2007) [9] investigated the evolution of Juglandaceae by integrating fossils and nucleic sequence evidence. ...
... Their results suggest that A. sinensis is closely related to the Carya genus. In contrast, Li et al. (2004) [8] separated A. sinensis and Carya on different branches of infrafamilial relationships of the order Fagales based on six genes (atpB, matK, matR, rbcL, trnL-F and 18S rDNA). Manos et al. (2007) [9] investigated the evolution of Juglandaceae by integrating fossils and nucleic sequence evidence. ...
Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species’ chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.
... The accepted phylogeny for the Fagales shows the Juglandaceae is monophyletic and most closely related to the Myricaceae [28][29][30]. The Juglandaceae are lumped with five other families (Betulacea, Casuarinaceae, Fagaceae, Nothofagaceae, and Ticodendraceae) to constitute the order Fagales [28,31,[33][34][35][36][37][38]. ...
Background
The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes.
Results
We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea , J. hopeiensis , and Platycarya strobilacea . Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae.
Conclusions
A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).
... Subsequently, cladistic analyses of existing morphological data and newly acquired molecular characters resulted in the concept of a more inclusive monophyletic Fagales, requiring the addition of some families that once had been placed in their own orders, for example, Juglandaceae, Myricaceae, and Casuarinaceae (Stevens 2001-;APG IV 2016). Li et al. (2004) supported this broader concept of the order and also included the recently recognized family Ticodendraceae. They used nucleotide sequences of six regions from three plant genomes-trnL-F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S rDNA (nuclear)-with a sampling of 31 extant genera. ...
... The position of Myricaceae is inconsistent in molecular phylogenetic analyses. According to Li et al. (2004) and Larson-Johnson (2016), Myricaceae are sister to Juglandaceae, but, in the work of Sauquet et al. (2012) and Xing et al. (2014), the Myricaceae are the direct sister to the clade that includes Betulaceae, Casuarinaceae, and Ticodendraceae, which collectively form a clade that is sister to Juglandaceae. ...
... We have chosen to use the phylogenetic analysis of Li et al. (2004) as a reference point for discussing the relationships among families ( fig. 1). More recent analyses of the order have included fossil taxa (mainly reproductive structures) in addressing questions of the rates and timing of diversification (e.g., Xing et al. 2014;Larson-Johnson 2016). ...
