Highly Cited Articles
The following is a list of the most cited articles published since 2020, according to Web of Science.
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Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming
Yu-Bing Wang, Bin-Bin Liu, Ze-Long Nie, Hong-Feng Chen, Fa-Ju Chen, Richard B. Figlar, and Jun Wen
J Syst Evol 2020, 58 (5): 673-695.  
doi: 10.1111/jse.12588

With more than 300 species, the Magnoliaceae family represents a major Magnoliid lineage that is disjunctly distributed in Asia and the New World. The classification of Magnolia s.l. has been highly controversial among taxonomists, varying from one genus with several subgenera, sections, and subsections to several (up to 16) genera. We conducted a comprehensive phylogenetic study of Magnoliaceae on the basis of sequences of the complete chloroplast genomes with a broad taxon sampling of 86 species. The phylogenetic analyses strongly support 15 major clades within Magnolia s.l. due to the non‐monophyly of subgen. Magnolia, the previous subgeneric treatment that recognizes three subgenera, is not supported. Based on the phylogenetic, morphological, and geographic evidence, we recognize two subfamilies in Magnoliaceae: Liriodendroideae and Magnolioideae, each with one genus, Liriodendron and Magnolia, respectively. Magnolia is herein classified into 15 sections: sects. Magnolia, Manglietia, Michelia, Gwillimia, Gynopodium, Kmeria, Maingola, Oyama, Rytidospermum, Splendentes, Talauma, Tuliparia, Macrophylla, Tulipastrum, and Yulania.

Cited: Web of Science(46)
Collections-based science in the 21st Century
Vicki A. Funk
J Syst Evol 2018, 56 (3): 175-193.  
doi: 10.1111/jse.12315

Discoveries from collections‐based science change the way we perceive ourselves, our environment, and our place in the universe. The 18th Century saw the beginning of formal classification with Linnaeus proposing a system to classify all of life. The 19th Century ushered in the age of exploration as naturalists undertook large‐scale collecting expeditions leading to major scientific advances (the founding of Physical Geography, Meteorology, Ecology, Biogeography, and Evolution) and challenging long held beliefs about nature. In the 20th Century collections were central to paradigm shifts, including theories of Continental Drift and Phylogenetic Systematics; Molecular Phylogenetics added testable hypotheses, and computerized specimen records gave rise to the field of Biodiversity. In the first 15 years of the 21st Century we have seen tree‐thinking pervade the life sciences, leading to the emergence of Evolutionary Medicine, Evolutionary Ecology, and new Food Safety methods. More advances are on the way: (i) Open access to large amounts of specimen data & images, (ii) Linking of collections and climate data to phylogenies on a global scale, and (iii) Production of vast quantities of genomic data allowing us to address big evolutionary questions. As a result of collections‐based science people see themselves not as the center of all things but rather as part of a complex universe. It is essential that we integrate new discoveries with knowledge from the past (e.g., collections) in order to understand this planet we all inhabit. To ensure the health of collections‐based science we must come together and plan for the future.

Cited: Web of Science(36)
The role of land bridges, ancient environments, and migrations in the assembly of the North American flora
Alan Graham
J Syst Evol 2018, 56 (5): 405-429.  
doi: 10.1111/jse.12302
Continental‐scale assembly of floras results from past and present in situ diversification in association with several external processes. Among these processes are the making and breaking of connections among landmasses. Connections among landmasses are constantly in flux as are the climates and landscapes along the connection corridors, so that these corridors, or land bridges, may either facilitate or restrict migration at a given time. Across land bridges, changing landscape‐level and organismal factors include the dispersal potential and vectors of propagules, competition, predation, and distributions altered by pathogens. Assembly of a flora is, therefore, the outcome of complex, interacting, temporally‐varying factors that render simplistic explanations unlikely. In the case of North America, the continent experienced ephemeral connections with adjacent regions via five land bridges over the last 100 Ma at different times and under different climates and specific landscape morphologies, including edaphic characteristics. Here, I emphasize the earliest of these connections, Beringia, which probably comprised an initially‐incomplete land bridge during the Cretaceous and Paleocene resulting from compression, fragmentation, and rotation of Asian‐North American sub‐blocks as North America began moving westward from the northern portion of the Mid‐Atlantic Ridge. During the same time, additional land was added to Beringia with accretion of terranes and the subduction of the northern edge of the Pacific Plate beneath the North American‐Asian Plates in the Eocene to form the Aleutian Islands. Other connections between North America and adjacent landmasses were the North Atlantic, the Antilles, Central America, and the Magellan land bridge.
Cited: Web of Science(33)
Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae)
Jun Wen, AJ Harris, Yash Kalburgi, Ning Zhang, Yuan Xu, Wei Zheng, Stefanie M. Ickert-Bond, Gabriel Johnson, Elizabeth A. Zimmer
J Syst Evol 2018, 56 (4): 297-308.  
doi: 10.1111/jse.12447

Vitis L. (the grape genus) is the economically most important fruit crop, as the source of grapes and wine. Phylogenetic relationships within the genus have been highly controversial. Herein, we employ sequence data from whole plastomes to attempt to enhance Vitis phylogenetic resolution. The results support the New World Vitis subgenus Vitis as monophyletic. Within the clade, V. californica is sister to the remaining New World Vitis subgenus Vitis. Furthermore, within subgenus Vitis, a Eurasian clade is robustly supported and is sister to the New World clade. The clade of Vitis vinifera ssp. vinifera and V. vinifera ssp. sylvestris is sister to the core Asian clade of Vitis. Several widespread species in North America are found to be non‐monophyletic in the plastome tree, for example, the broadly defined Vitis cinerea and V. aestivalis each needs to be split into several species. The non‐monophyly of some species may also be due to common occurrences of hybridizations in North American Vitis. The classification of North American Vitis by Munson into nine series is discussed based on the phylogenetic results. Analyses of divergence times and lineage diversification support a rapid radiation of Vitis in North America beginning in the Neogene.

Cited: Web of Science(33)
A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles
Global Carex Group, Eric H. Roalson, Pedro Jiménez-Mejías, Andrew L. Hipp, Carmen Benítez-Benítez, Leo P. Bruederle, Kyong-Sook Chung, Marcial Escudero, Bruce A. Ford, Kerry Ford, Sebastian Gebauer, Berit Gehrke, Marlene Hahn, Muhammad Qasim Hayat, Mathias H. Hoffmann, Xiao-Feng Jin, Sangtae Kim, Isabel Larridon, Étienne Léveillé-Bourret, Yi- Fei Lu, Modesto Luceño, Enrique Maguilla, Jose Ignacio Márquez-Corro, Santiago Martín-Bravo, Tomomi Masaki, Mónica Míguez, Robert F. C. Naczi, Anton A. Reznicek, Daniel Spalink, Julian R. Starr, Uzma, Tamara Villaverde, Marcia J. Waterway, Karen L. Wilson, and Shu-Ren Zhang
J Syst Evol 2021, 59 (4): 726-762.  
doi: 10.1111/jse.12722
Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para- or polyphyletic. Yet, taxonomists continue to use subgenera and sections in Carex classification. Why? The Global Carex Group (GCG) here takes the position that the historical and continued use of subgenera and sections serves to (i) organize our understanding of lineages in Carex, (ii) create an identification mechanism to break the ~2000 species of Carex into manageable groups and stimulate its study, and (iii) provide a framework to recognize morphologically diagnosable lineages within Carex. Unfortunately, the current understanding of phylogenetic relationships in Carex is not yet sufficient for a global reclassification of the genus within a Linnean infrageneric (sectional) framework. Rather than leaving Carex classification in its current state, which is misleading and confusing, we here take the intermediate steps of implementing the recently revised subgeneric classification and using a combination of informally named clades and formally named sections to reflect the current state of our knowledge. This hybrid classification framework is presented in an order corresponding to a linear arrangement of the clades on a ladderized phylogeny, largely based on the recent phylogenies published by the GCG. It organizes Carex into six subgenera, which are, in turn, subdivided into 62 formally named Linnean sections plus 49 informal groups. This framework will serve as a roadmap for research on Carex phylogeny, enabling further development of a complete reclassification by presenting relevant morphological and geographical information on clades where possible and standardizing the use of formal sectional names.
Cited: Web of Science(32)
Plant adaptation to climate change—Where are we?
Jill T. Anderson and Bao-Hua Song
J Syst Evol 2020, 58 (5): 533-545.  
doi: 10.1111/jse.12649

Climate change poses critical challenges for population persistence in natural communities, for agriculture and environmental sustainability, and for food security. In this review, we discuss recent progress in climatic adaptation in plants. We evaluate whether climate change exerts novel selection and disrupts local adaptation, whether gene flow can facilitate adaptive responses to climate change, and whether adaptive phenotypic plasticity could sustain populations in the short term. Furthermore, we discuss how climate change influences species interactions. Through a more in‐depth understanding of these eco‐evolutionary dynamics, we will increase our capacity to predict the adaptive potential of plants under climate change. In addition, we review studies that dissect the genetic basis of plant adaptation to climate change. Finally, we highlight key research gaps, ranging from validating gene function to elucidating molecular mechanisms, expanding research systems from model species to other natural species, testing the fitness consequences of alleles in natural environments, and designing multifactorial studies that more closely reflect the complex and interactive effects of multiple climate change factors. By leveraging interdisciplinary tools (e.g., cutting‐edge omics toolkits, novel ecological strategies, newly developed genome editing technology), researchers can more accurately predict the probability that species can persist through this rapid and intense period of environmental change, as well as cultivate crops to withstand climate change, and conserve biodiversity in natural systems.

Cited: Web of Science(32)
Correlations among oligonucleotide repeats, nucleotide substitutions, and insertion–deletion mutations in chloroplast genomes of plant family Malvaceae
Abdullah, Furrukh Mehmood, Iram Shahzadi, Zain Ali, Madiha Islam, Muhammad Naeem, Bushra Mirza, Peter J. Lockhart, Ibrar Ahmed, and Mohammad Tahir Waheed
J Syst Evol 2021, 59 (2): 388-402.  
doi: 10.1111/jse.12585
The co‐occurrence of mutational events including substitutions and insertions–deletions (InDels) with oligonucleotide repeats has previously been reported for a limited number of prokaryotic, eukaryotic, and organelle genomes. In this study, the correlations among these mutational events in chloroplast genomes of species in the eudicot family Malvaceae were investigated. This study also reported chloroplast genome sequences of Hibiscus mutabilis, Malva parviflora, and Malvastrum coromandelianum. These three genomes and 16 other publicly available chloroplast genomes from 12 genera of Malvaceae were used to calculate the correlation coefficients among the mutational events at family, subfamily, and genus levels. In these comparisons, chloroplast genomes were pairwise aligned to record the substitutions and the InDels in mutually exclusive, 250 nucleotide long bins. Taking one among the two genomes as a reference, the coordinate positions of oligonucleotide repeats in the reference genome were recorded. The extent of correlations among repeats, substitutions, and InDels was calculated and categorized as follows: very weak (0.1–0.19), weak (0.20–0.29), moderate (0.30–0.39), and strong (0.4–0.69). The extent of correlations ranged 0.201–0.6 between “InDels and single‐nucleotide polymorphism (SNP)”, 0.182–0.513 between “InDels and repeat” and 0.055–0.403 between “SNPs and repeats”. At family‐ and subfamily‐level comparisons, 88%–96% of the repeats showed co‐occurrence with SNPs, whereas at the genus level, 23%–86% of the repeats co‐occurred with SNPs in same bins. Our findings support the previous hypothesis suggesting the use of oligonucleotide repeats as a proxy for finding the mutational hotspots.
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Cited: Web of Science(30)
Evolutionary history of the flora of Mexico: Dry forests cradles and museums of endemism
Victoria Sosa, J. Arturo De-Nova, Marilyn Vásquez-Cruz
J Syst Evol 2018, 56 (5): 523-536.  
doi: 10.1111/jse.12416
Mexico is considered an exceptional biogeographic area with a varied endemic flora, however spatial phylogenetic measures of biodiversity have not yet been estimated to understand how its flora assembled to form the current vegetation. Patterns of species richness, endemism, phylogenetic diversity, phylogenetic endemism and centers of neo‐ and paleo‐endemism were determined to examine differences and congruence among these measures, and their implications for conservation. Of 24 360 vascular plant species 10 235 (42%) are endemic. Areas of endemism and phylogenetic endemism were associated with dry forests in zones of topographic complexity in mountain systems, in deserts, and in isolated xeric vegetation. Every single locality where seasonally tropical dry forests have been reported in Mexico was identified as an area of endemism. Significant phylogenetic diversity was the most restricted and occurred in the Trans‐Mexican Volcanic Belt and in the Sierra de Chiapas. Notably, the highest degree of phylogenetic clustering comprising neo‐, paleo‐, and super‐endemism was identified in southernmost Mexico. Most vascular plant lineages diverged in the Miocene (5–20 mya) when arid environments expanded across the world. The location of Mexico between two very large landmasses and the fact that more than fifty percent of its surface is arid favored the establishment of tropical lineages adapted to extreme seasonality and aridity. These lineages were able to migrate from both North and South America across Central America presumably during the Miocene and to diversify, illustrating the signature of the flora of Mexico of areas of endemism with a mixture of neo‐ and paleo‐endemism.
Cited: Web of Science(28)
A new classification of Cyperaceae (Poales) supported by phylogenomic data
Isabel Larridon, Alexandre R. Zuntini, Étienne Léveillé-Bourret, Russell L. Barrett, Julian R. Starr, A. Muthama Muasya, Tamara Villaverde, Kenneth Bauters, Grace E. Brewer, Jeremy J. Bruhl, Suzana M. Costa, Tammy L. Elliott, Niroshini Epitawalage, Marcial Escudero, Isabel Fairlie, Paul Goetghebeur, Andrew L. Hipp, Pedro Jiménez-Mejías, Izai A.B. Sabino Kikuchi, Modesto Luceño, José Ignacio Márquez-Corro, Santiago Martín-Bravo, Olivier Maurin, Lisa Pokorny, Eric H. Roalson, Ilias Semmouri, David A. Simpson, Daniel Spalink, W. Wayt Thomas, Karen L. Wilson, Martin Xanthos, Félix Forest, and William J. Baker
J Syst Evol 2021, 59 (4): 852-895.  
doi: 10.1111/jse.12757
Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology due to their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C4 photosynthesis and holocentric chromosomes. Goetghebeur′s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower, and embryo characters, plus anatomical and other information. Since then, several family-level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family-wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal, and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time, we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes, and 10 subtribes, and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, and Oreobolinae.
Cited: Web of Science(24)
Passiflora plastome sequencing reveals widespread genomic rearrangements
Samar O. Rabah, Bikash Shrestha, Nahid H. Hajrah, Mumdooh J. Sabir, Hesham F. Alharby, Mernan J. Sabir, Alawiah M. Alhebshi, Jamal S. M. Sabir, Lawrence E. Gilbert, Tracey A. Ruhlman, and Robert K. Jansen
J Syst Evol 2019, 57 (1): 1-14.  
doi: 10.1111/jse.12425
Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.
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Cited: Web of Science(23)
Genomic architectural variation of plant mitochondria—A review of multichromosomal structuring
Zhi-Qiang Wu, Xue-Zhu Liao, Xiao-Ni Zhang, Luke R. Tembrock, and Amanda Broz
J Syst Evol 2022, 60 (1): 160-168.  
doi: 10.1111/jse.12655
Since the endosymbiont origin from α-Proteobacteria, mitochondrial genomes have undergone extremely divergent evolutionary trajectories among eukaryotic lineages. Compared with the relatively compact and conserved animal mitochondrial genomes, plant mitochondrial genomes have many unique features, especially their large and complex genomic arrangements. The sizes of fully sequenced plant mitochondrial genomes span over a 100-fold range from 66 kb in Viscum scurruloideum to 11 000 kb in Silene conica. In addition to the typical circular structure, some species of plants also possess linear, and even multichromosomal, architectures. In contrast with the thousands of fully sequenced animal mitochondrial genomes and plant plastid genomes, only around 200 fully sequenced land plant mitochondrial genomes have been published, with many being only draft assemblies. In this review, we summarize some of the known novel characteristics found in plant mitochondrial genomes, with special emphasis on multichromosomal structures described in recent publications. Finally, we discuss the future prospects for studying the inheritance patterns of multichromosomal plant mitochondria and examining architectural variation at different levels of taxonomic organization—including at the population level.
Cited: Web of Science(23)
Origins of the Hawaiian flora: Phylogenies and biogeography reveal patterns of long‐distance dispersal
Jonathan P. Price and Warren L. Wagner
J Syst Evol 2018, 56 (6): 600-620.  
doi: 10.1111/jse.12465
Botanists have long considered the origins of the Hawaiian flora in terms of long‐distance dispersal from particular source areas. We extensively reviewed phylogenetic studies of the Hawaiian angiosperm flora to determine the most likely region of origin for each lineage from a defined set of source areas. We also evaluated dispersal modes of each lineage to assess whether certain dispersal modes are associated with a given source area. The largest source category was Widespread (involving related taxa that extend across more than one region), although many of these comprised native non‐endemic species, and accounted for little of the total species diversity (after accounting for in situ speciation). The next largest source regions were Indo‐Malayan and Neotropical. Comparatively few lineages originated from the East Asian region, although these include the single largest lineage. Lineages originating in the Indo‐Malayan region predominantly arrived via Pacific Islands, whereas dispersal from all other regions appears to have been mostly direct. Compared with previous analyses, we found a higher proportion of lineages originating in the Neotropics and temperate North America. Widespread origins were positively associated with dispersal via flotation on water, whereas other origins were associated with dispersal by birds, either through internal transport or external adhesion. We identified thirty‐one potential cases of dispersal out of Hawaii to other islands. Our assessment is complicated by lineages with ancient origins, with further complications likely stemming from hybridization events. Overall, numerous lineages including some distinctive endemic genera have not had sufficient phylogenetic study to determine an origin.
Cited: Web of Science(22)
Evolutionary origin of species diversity on the Qinghai–Tibet Plateau
Kang-Shan Mao, Yi Wang, and Jian-Quan Liu
J Syst Evol 2021, 59 (6): 1142-1158.  
doi: 10.1111/jse.12809
The Qinghai–Tibet Plateau (QTP) sensu lato (sl) houses an exceptional species diversity in Asia. To develop a comprehensive understanding of species diversity in this fascinating region, we reviewed recent progress from biogeographic, paleogeographic, paleontological and genomic research of both plants and animals in the QTPsl. Numerous studies have been conducted to examine whether the QTPsl uplift triggered the production of rich species diversity there, whether a Quaternary “unified ice sheet” eliminated plants and animals on the central plateau and how high-altitude species developed the extreme environment adaptations. Major disputes arose about the first issue, mainly from different understanding of the QTP circumscriptions and related uplift, inaccurate dating of molecular phylogenetic trees, and non-causal correlations between uplift and species diversification. The QTPsl uplift is spatially and temporally heterogeneous, and abundant fossils reported recently similarly support such an asynchronous upheaval model across the entire region. Available phylogeographic studies of alpine plants and animals suggested their glacial refugia in the central QTPsl, rejecting a unified ice sheet during the Last Glacial Maximum. Genomic evidence from a limited number of alpine species has identified numerous candidate genes for high-altitude adaptation. In the future, more studies should be focused on speciation and adaptation mechanisms of the alpine species in the QTPsl based on the cutting-edge methods.
Cited: Web of Science(21)
A worldwide phylogenetic classification of the Poaceae (Gramineae) III: An update
Robert J. Soreng, Paul M. Peterson, Fernando O. Zuloaga, Konstantin Romaschenko, Lynn G. Clark, Jordan K. Teisher, Lynn J. Gillespie, Patricia Barberá, Cassiano A. D. Welker, Elizabeth A. Kellogg, De-Zhu Li, and Gerrit Davidse
J Syst Evol 2022, 60 (3): 476-521.  
doi: 10.1111/jse.12847

We present an updated worldwide phylogenetic classification of Poaceae with 11 783 species in 12 subfamilies, 7 supertribes, 54 tribes, 5 super subtribes, 109 subtribes, and 789 accepted genera. The subfamilies (in descending order based on the number of species) are Pooideae with 4126 species in 219 genera, 15 tribes, and 34 subtribes; Panicoideae with 3325 species in 242 genera, 14 tribes, and 24 subtribes; Bambusoideae with 1698 species in 136 genera, 3 tribes, and 19 subtribes; Chloridoideae with 1603 species in 121 genera, 5 tribes, and 30 subtribes; Aristidoideae with 367 species in three genera and one tribe; Danthonioideae with 292 species in 19 genera and 1 tribe; Micrairoideae with 192 species in nine genera and three tribes; Oryzoideae with 117 species in 19 genera, 4 tribes, and 2 subtribes; Arundinoideae with 36 species in 14 genera and 3 tribes; Pharoideae with 12 species in three genera and one tribe; Puelioideae with 11 species in two genera and two tribes; and the Anomochlooideae with four species in two genera and two tribes. Two new tribes and 22 new or resurrected subtribes are recognized. Forty-five new (28) and resurrected (17) genera are accepted, and 24 previously accepted genera are placed in synonymy. We also provide an updated list of all accepted genera including common synonyms, genus authors, number of species in each accepted genus, and subfamily affiliation. We propose Locajonoa, a new name and rank with a new combination, L. coerulescens. The following seven new combinations are made in Lorenzochloa: L. bomanii, L. henrardiana, L. mucronata, L. obtusa, L. orurensis, L. rigidiseta, and L. venusta.

Cited: Web of Science(20)
An updated Chinese vascular plant tree of life: Phylogenetic diversity hotspots revisited
Hai-Hua Hu, Bing Liu, Yi-Shuo Liang, Jian-Fei Ye, Saddam Saqib, Zhen Meng, Li-Min Lu, and Zhi-Duan Chen
J Syst Evol 2020, 58 (5): 663-672.  
doi: 10.1111/jse.12642

Large‐scale phylogenies provide a framework for interdisciplinary investigations in taxonomy, evolutionary biology, biogeography, ecology, and conservation. Integration of regional tree of life and species distribution data has greatly promoted spatial phylogenetic studies on biodiversity, floristic assembly, and biogeographic regionalization. In this study, we updated the phylogenetic tree of Chinese vascular plants by integrating data from public databases and sequences newly generated by our laboratory, to facilitate the exploration of floristic and ecological questions at a country scale. A phylogenetic tree with 15 092 tips and 14 878 species was obtained, including 13 663 species (44.0%) and 2953 genera (95.7%) native to China. Only two families (Corsiaceae and Mitrastemonaceae) and 133 genera native to China are not sampled in this study. Low proportion of sampling is detected in orders with high species diversity and those with low species diversity. The Hengduan Mountains, plus the western Qinghai–Tibet Plateau and western Xinjiang, show the greatest gap of target molecular data for angiosperms. Our phylogeny of Chinese vascular plants recovers relationships among and within major lineages that are highly congruent with published phylogenies at a broader scale. Most families (98.7%) are supported as monophyletic, and 573 genera (17.9%) are recognized as non‐monophyletic. Finally, hotspots of phylogenetic diversity for the Chinese angiosperms at both the genus and species levels are identified based on our phylogram, implicating conservation priorities for phylogenetic diversity. The updated phylogeny of Chinese vascular plants is publically available to generate subtrees through our automated phylogeny assembly tool SoTree in the DarwinTree platform (http://www.darwintree.cn/flora-sotree-v2/index.shtml).

Cited: Web of Science(20)
Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)
Verônica A. Thode, Lúcia G. Lohmann, and Isabel Sanmartín
J Syst Evol 2020, 58 (6): 1071-1089.  
doi: 10.1111/jse.12579

The accurate analyses of massive amounts of data obtained through next‐generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate “supergene” approach. The effects of molecular evolutionary models and character partition strategies on plastome‐based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well‐supported conflicting topologies). We compared different datasets (e.g., non‐coding regions, exons, and codon‐aligned and translated amino acids) using concatenated approaches under site‐heterogeneous and site‐homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.

Cited: Web of Science(20)
Phylogeny and biogeography of the hollies (Ilex L., Aquifoliaceae)
Xin Yao, Yu Song, Jun-Bo Yang, Yun-Hong Tan, and Richard T. Corlett
J Syst Evol 2021, 59 (1): 73-82.  
doi: 10.1111/jse.12567
The holly genus, Ilex L., in the monogeneric Aquifoliaceae, is the largest woody dioecious genus (>664 spp.), with a near‐cosmopolitan distribution in mesic environments. We constructed a phylogeny based on two nuclear genes, representing 177 species spread across the geographical range, and dated using macrofossil records. The five main clades had a common ancestor in the early Eocene, much earlier than previously suggested. Ilex originated in subtropical Asia and extant clades colonized South America by 30 Ma, North America by 23 Ma, Australia by 8 Ma, Europe by 6 Ma, and Africa by 4 Ma. South and North America were colonized multiple times. Ilex also reached Hawaii (10 Ma) and other oceanic islands. Macrofossil and pollen records show the genus has tracked mesic climates through time and space, and had a wider distribution before late Miocene global cooling. Our phylogeny provides a framework for studies in comparative ecology and evolution.
Cited: Web of Science(20)
Conflicting phylogenetic signals in genomic data of the coffee family (Rubiaceae)
Niklas Wikström, Birgitta Bremer, and Catarina Rydin
J Syst Evol 2020, 58 (4): 440-460.  
doi: 10.1111/jse.12566

Reconstructions of phylogenetic relationships in the flowering plant family Rubiaceae have up until now relied heavily on single‐ or multi‐gene data, primarily from the plastid compartment. With the availability of cost‐ and time‐efficient techniques for generating complete genome sequences, the opportunity arises to resolve some of the relationships that, up until now, have proven problematic. Here, we contribute new data from complete 58 plastid genome sequences, representing 55 of the currently 65 recognized tribes of the Rubiaceae. Also contributed are new data from the nuclear rDNA cistrons for corresponding taxa. Phylogenetic analyses are conducted on two plastid data sets, one including data from the protein coding genes only, and a second where protein coding data are combined with non‐coding regions, and on a nuclear rDNA data set. Our results clearly show that simply adopting a “more characters” approach does not resolve the relationships in the Rubiaceae. More importantly, we identify conflicting phylogenetic signals in the data. Analyses of the same plastid data, treated as nucleotides or as codon‐degenerated data, resolve and support conflicting topologies in the subfamily Cinchonoideae. As these analyses use the same data, we interpret the conflict to result from erroneous assumptions in the models used to reconstruct our phylogenies. Conflicting signals are also identified in the analyses of the plastid versus the nuclear rDNA data sets. These analyses use data from different genomic compartments, with different inheritance patterns, and we interpret the conflicts as representing “real” conflicts, reflecting biological processes of the past.

Cited: Web of Science(19)
Spatial phylogenetics of the North American flora
Brent D. Mishler, Robert Guralnick, Pamela S. Soltis, Stephen A. Smith, Douglas E. Soltis, Narayani Barve, Julie M. Allen, and Shawn W. Laffan
J Syst Evol 2020, 58 (4): 393-405.  
doi: 10.1111/jse.12590

North America is a large continent with extensive climatic, geological, soil, and biological diversity. As biota faces threat from habitat destruction and climate change, making a quantitative assessment of biodiversity becomes critically important. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much‐needed broad synthesis of species occurrences with phylogenetic data. In this study, the first such synthesis of a flora from such a large and diverse part of the world is attempted, all seed plants from the North American continent (here defined to include Canada, United States, and Mexico), with a focus on examining phylogenetic diversity and endemism. We collected digitized plant specimen records and chose a coarse grain for analysis, recognizing that this grain is currently necessary for reasonable completeness per sampling unit. We found that raw richness and endemism patterns largely support previous hypotheses of biodiversity hotspots. The application of phylogenetic metrics and a randomization test revealed novel results, including a significant phylogenetic clustering across the continent, a striking east–west geographical difference in the distribution of branch lengths, and the discovery of centers of neo‐ and paleoendemism in Mexico, the southwestern USA, and the southeastern USA. Finally, our examination of phylogenetic beta diversity provides a new approach to compare centers of endemism. We discuss the empirical challenges of working at the continental scale and the need for more sampling across large parts of the continent, for both DNA data for terminal taxa and spatial data for poorly understood regions, to confirm and extend these results.

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Fine‐scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing
Guang-Lin He, Ying-Xiang Li, Meng-Ge Wang, Xing Zou, Hui-Yuan Yeh, Xiao-Min Yang, Zheng Wang, Ren-Kuan Tang, Su-Min Zhu, Jian-Xin Guo, Ting Luo, Jing Zhao, Jin Sun, Zi- Yang Xia, Hao-Liang Fan, Rong Hu, Lan-Hai Wei, Gang Chen, Yi- Ping Hou, and Chuan-Chao Wang
J Syst Evol 2021, 59 (1): 1-20.  
doi: 10.1111/jse.12670
Archaeological, genetic, and linguistic evidence has supported the idea that northern China is the original center of modern Sino‐Tibetan‐speaking populations. However, the demographic history of subsequent southward migration and genetic admixture of Han Chinese with surrounding indigenous populations remain uncharacterized, and the language shifts and assimilations accompanied by movement of people, or just an adaptation of cultural ideas among populations in central China is still unclear, especially for Tibeto‐Burman‐speaking Tujia and central Han Chinese populations. To resolve this, we genotyped over 60K genome‐wide markers in 505 unrelated individuals from 63 indigenous populations. Our results showed both studied Han and Tujia were at the intermediate position in the modern East Asian North–South genetic cline and there was a correlation between the genetic composition and the latitude. We observed the strong genetic assimilation between Tujia people and central Han Chinese, which suggested massive population movements and genetic admixture under language borrowing. Tujia and central Han Chinese could be modeled as a two‐way admixture deriving primary ancestry from a northern ancestral population closely related to the ancient DevilsCave and present‐day Tibetans and a southern ancestral population closely related to the present‐day Tai‐Kadai and Austronesian‐speaking groups. The ancestral northern population we suspect to be related to the Neolithic millet farming groups in the Yellow River Basin or central China. We showed that the newly genotyped populations in Hubei Province had a higher proportion of DevilsCave or modern Tungusic/Mongolic‐related northern ancestries, while the Hunan populations harbored a higher proportion of Austronesian/Tai‐Kadai‐related southern ancestries.
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Origins of cultivars of Chrysanthemum—Evidence from the chloroplast genome and nuclear LFY gene
Yue-Ping Ma, Liang Zhao, Wen-Jie Zhang, Ying-Hua Zhang, Xia Xing, Xia-Xia Duan, Jing Hu, AJ Harris, Pei-Liang Liu, Si-Lan Dai, and Jun Wen
J Syst Evol 2020, 58 (6): 925-944.  
doi: 10.1111/jse.12682

The origins of cultivated chrysanthemums have attracted considerable attention, but they remain poorly known. Here, we reconstructed the phylogeny of representative well‐known cultivars and wild species of the genus Chrysanthemum using chloroplast genomes and the nuclear LEAFY gene. Our results suggest that geographic and ecological factors may determine the opportunities for wild species to be involved in the origin of the cultivars. The wild species C. indicum, C. zawadskii, C. dichrum, C. nankingense, C. argyrophyllum, and C. vestitum were likely directly or indirectly involved as paternal species of most of the chrysanthemum cultivars examined in this study. Yet, the maternal species is supported to be a lineage of an extinct wild Chrysanthemum species and its subsequent cultivars, as all accessions of chrysanthemum cultivars sampled formed a strongly supported clade, distinct from all other species of Chrysanthemum in the plastome tree. Thus, the cultivated chrysanthemums originated from multiple hybridizations involving several paternal species rather than only two or a few wild species, with an extinct species and its subsequent cultivars serving as the maternal parents. This finding is consistent with Chrysanthemum having high rates of hybridization and gene flow, which has been demonstrated within previous studies; nevertheless, it is important to unravel the role of an extinct wild Chrysanthemum species as the ultimate maternal parent species for all the chrysanthemum cultivars. Our results also suggest that C. vestitum from Tianzhu and Funiu Mountains in Anhui and Henan Provinces of China represent two distinct cryptic species.

Cited: Web of Science(19)
A new phylogenetic tribal classification of the grape family (Vitaceae)
Jun Wen, Li-Min Lu, Ze-Long Nie, Xiu-Qun Liu, Ning Zhang, Stefanie Ickert-Bond, Jean Gerrath, Steven R. Manchester, John Boggan, Zhi-Duan Chen
J Syst Evol 2018, 56 (4): 262-272.  
doi: 10.1111/jse.12427

Vitaceae (the grape family) consist of 16 genera and ca. 950 species primarily distributed in tropical regions. The family is well‐known for the economic importance of grapes, and is also ecologically significant with many species as dominant climbers in tropical and temperate forests. Recent phylogenetic and phylogenomic analyses of sequence data from all three genomes have supported five major clades within Vitaceae: (i) the clade of Ampelopsis, Nekemias, Rhoicissus, and Clematicissus; (ii) the Cissus clade; (iii) the clade of Cayratia, Causonis, Cyphostemma, Pseudocayratia, Tetrastigma, and an undescribed genus “Afrocayratia”; (iv) the clade of Parthenocissus and Yua; and (v) the grape genus Vitis and its close tropical relatives Ampelocissus, Pterisanthes and Nothocissus, with Nothocissus and Pterisanthes nested within Ampelocissus. Based on the phylogenetic and morphological (mostly inflorescence, floral and seed characters) evidence, the new classification places the 950 species and 16 genera into five tribes: (i) tribe Ampelopsideae J.Wen & Z.L.Nie, trib. nov. (47 species in four genera; Ampelopsis, Nekemias, Rhoicissus and Clematicissus); (ii) tribe Cisseae Rchb. (300 species in one genus; Cissus); (iii) tribe Cayratieae J.Wen & L.M.Lu, trib. nov. (370 species in seven genera; Cayratia, Causonis, “Afrocayratia”, Pseudocayratia, Acareosperma, Cyphostemma and Tetrastigma); (iv) tribe Parthenocisseae J.Wen & Z.D.Chen, trib. nov. (ca. 16 spp. in two genera; Parthenocissus and Yua); and (v) tribe Viteae Dumort. (ca. 190 species in two genera; Ampelocissus and Vitis).

Cited: Web of Science(19)
Phylogenomics enables biogeographic analysis and a new subtribal classification of Andropogoneae (Poaceae—Panicoideae)
Cassiano A. D. Welker, Michael R. McKain, Matt C. Estep, Rémy S. Pasquet, Gilson Chipabika, Beatrice Pallangyo, and Elizabeth A. Kellogg
J Syst Evol 2020, 58 (6): 1003-1030.  
doi: 10.1111/jse.12691

The grass tribe Andropogoneae (Poaceae—Panicoideae) includes several important crops such as maize, sugarcane, and sorghum, and dominates the tropical grasslands of the world. We present here a plastome phylogeny of the tribe with the largest sample of genera to date (about 73%), including 65 newly assembled plastomes, together with a broad biogeographic analysis of Andropogoneae. Major relationships found in previous phylogenetic studies were confirmed here, with most nodes having higher resolution and support, including those of the backbone of the tree, which had been a major problem in previous phylogenies of the tribe. Our dated tree suggests that Andropogoneae diverged from Arundinelleae in the Early Miocene, while the “core Andropogoneae” clade originated in the Late Miocene. The tribe originated in East Asia, but intercontinental dispersal has been common, with many independent dispersal events to Africa and the New World. Based on the plastome phylogeny, we propose here a new classification of Andropogoneae as most of its previously accepted subtribes are not monophyletic. Our classification comprises 14 subtribes, 92 genera, and ∼1224 species. About 90% of the Andropogoneae species could be assigned to a subtribe, which represents a major step toward clarification of the taxonomy of the tribe. The remaining taxa were placed incertae sedis pending additional molecular data. The new subtribes Chrysopogoninae and Rhytachninae are described herein. Our plastome trees also indicate that several Andropogoneae genera are para‐ or polyphyletic and require additional studies to define their circumscriptions.

Cited: Web of Science(19)
Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)
Wen-Pan Dong, Jia-Hui Sun, Yan-Lei Liu, Chao Xu, Yi-Heng Wang, Zhi-Li Suo, Shi-Liang Zhou, Zhi-Xiang Zhang, and Jun Wen
J Syst Evol 2022, 60 (6): 1263-1280.  
doi: 10.1111/jse.12802

The olive genus Olea includes c. 30–40 taxa in three subgenera (Olea, Tetrapilus, and Paniculatae) within the family Oleaceae. Historically, the Olea genus was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus Tetrapilus and poor resolution within clades. These analyses also showed that the genus was not monophyletic. Reliable identification of Olea species is important for both their conservation and utilization of this economically important genus. In this study, we used phylogenomic data from genome skimming to resolve relationships within Olea and to identify molecular markers for species identification. We assembled the complete plastomes, and nrDNA of 26 individuals representing 13 species using next-generation sequencing and added 18 publicly available accessions of Olea. We also developed nuclear SNPs using the genome skimming data to infer the phylogenetic relationships of Olea. Large-scale phylogenomic analyses of 138 samples of tribe Oleeae supported the polyphyly of Olea, with Olea caudatilimba and Olea subgenus Tetrapilus not sharing their most recent common ancestor with the main Olea clade (subgenus Paniculatae and subgenus Olea). The interspecific phylogenetic resolution was poor owing to a possible rapid radiation. By comparing with the plastome data, we identified the markers ycf1b and psbE-petL as the best Olea-specific chloroplast DNA barcodes. Compared with universal barcodes, specific DNA barcodes and super-barcode exhibited higher discriminatory power. Our results demonstrated the power of phylogenomics to improve phylogenetic relationships of intricate groups and provided new insights into barcodes that allow for accurate identification of Olea species.

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Dynamism and context‐dependency in diversification of the megadiverse plant genus Solanum (Solanaceae)
Susy Echeverría-Londoño, Tiina Särkinen, Isabel S. Fenton, Andy Purvis, and Sandra Knapp
J Syst Evol 2020, 58 (6): 767-782.  
doi: 10.1111/jse.12638

Explosive radiations—substantial increases in net species diversification—have been considered one of the most intriguing diversification patterns across the Tree of Life, but the subsequent change, movement, and extinction of the constituent lineages make radiations hard to discern or understand as geological time passes. We used the megadiverse angiosperm genus Solanum L. (Solanaceae), with ca. 1200 currently accepted species distributed worldwide in a wide array of habitats, to explore these patterns on a global scale. We synthesized phylogenetic and distributional data for this ongoing radiation to show how dispersal events and past climatic changes have interacted to shape diversification. We find that, despite the vast diversity of Solanum lineages in the Neotropics, lineages in the Old World are diversifying more rapidly. This recent increase in diversification coincides with a long‐distance dispersal event from the Neotropics to regions where major climatic changes were taking place. Two separate groups of Solanum have migrated and established in Australia, but only the arid‐adapted lineages underwent significant increases in diversification rate, as they were able to adapt to the continent's long‐term climatic trend towards seasonally dry and arid biomes (a pattern observed in the diversification of other arid‐adapted groups). Our findings provide a clear example of how successful colonization of new areas and niches can—but does not always—drive explosive diversifications.

Cited: Web of Science(17)
Historical biogeography of Melicope (Rutaceae) and its close relatives with a special emphasis on Pacific dispersals
Marc S. Appelhans, Jun Wen, Marco Duretto, Darren Crayn, Warren L. Wagner
J Syst Evol 2018, 56 (6): 576-599.  
doi: 10.1111/jse.12299
The genus Melicope (Rutaceae) occurs on most Pacific archipelagos and is perfectly suited to study Pacific biogeography. The main goal was to infer the age, geographic origin and colonization patterns of Melicope and its relatives. We sequenced three nuclear and two plastid markers for 332 specimens that represent 164 species in 16 genera of Rutaceae. Phylogenetic reconstruction, molecular dating, ancestral area reconstruction and diversification analyses were carried out. The two main clades (Acronychia‐Melicope and Euodia) originated in Australasia and their crown ages are dated to the Miocene. Diversification rates differed among the subclades and were lowest in the Euodia lineage and highest in the Hawaiian Melicope lineage. The Malagasy and Mascarene species form a clade, which split from its SE Asian relatives in the Pliocene/Pleistocene. At least eight colonizations to the Pacific islands occurred. The timing of all colonizations except for the Hawaiian group is congruent with age of the island ages. Australia, New Guinea and New Caledonia have been the source of colonizations into the Pacific islands in the Melicope clade. Melicope shows high dispersability and has colonized remote archipelagos such as the Austral and Marquesas Islands each twice. Colonization of islands of the Hawaiian‐Emperor seamount chain likely predates the ages of the current main islands, and the initial colonization to Kaua'i occurred after the splitting of the Hawaiian lineage into two subclades. Wider ecological niches and adaptations to bird‐dispersal likely account for the much higher species richness in the Acronychia‐Melicope clade compared to the Euodia clade.
Cited: Web of Science(16)
Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma
Rafael Medina, Matthew G. Johnson, Yang Liu, Norman J. Wickett, A. Jonathan Shaw, and Bernard Goffinet
J Syst Evol 2019, 57 (4): 404-417.  
doi: 10.1111/jse.12516

Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with reduced architectures. The Funariaceae are a cosmopolitan and diverse lineage of mostly annual mosses, and exhibit variable sporophyte complexities, spanning from long, exerted, operculate capsules with two rings of well‐developed teeth, to capsules immersed among maternal leaves, lacking a differentiated line of dehiscence (i.e., inoperculate) and without peristomes. The family underwent a rapid diversification, and the relationships of taxa with reduced sporophytes remain ambiguous. Here, we infer the relationships of five taxa with highly reduced sporophytes based on 648 nuclear loci (exons complemented by their flanking regions), based on inferences from concatenated data and concordance analysis of single gene trees. Physcomitrellopsis is resolved as nested within one clade of Entosthodon. Physcomitrella s. l., is resolved as a polyphyletic assemblage and, along with its putative relative Aphanorrhegma, nested within Physcomitrium. We propose a new monophyletic delineation of Physcomitrium, which accommodates species of Physcomitrella and Aphanorrhegma. The monophyly of Physcomitrium s. l. is supported by a small plurality of exons, but a majority of trees inferred from exons and their adjacent non‐coding regions.

Cited: Web of Science(16)
Phylogenomics of the hyperdiverse daisy tribes: Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae
Linda E. Watson, Carolina M. Siniscalchi, and Jennifer Mandel
J Syst Evol 2020, 58 (6): 841-852.  
doi: 10.1111/jse.12698

Asteraceae account for 10% of all flowering plant species, and 35%–40% of these are in five closely related tribes that total over 10 000 species. These tribes include Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae, which form one of two enormous clades within Subfamily Asteroideae. We took a phylogenomics approach to resolve evolutionary relationships among these five tribes. We sampled the nuclear and plastid genomes via HybSeq target enrichment and genome skimming, and recovered 74 plastid genes and nearly 1000 nuclear loci, known as Conserved Orthologous Sequences. We tested for conflicting support in both data sets and used network analyses to assess patterns of reticulation to explain the early evolutionary history of this lineage, which has experienced whole‐genome duplications and rapid radiations. We found concordance and conflicting support in both data sets and documented four ancient hybridization events. Due to the timing of the early radiation of this five‐tribe lineage, shortly before the Eocene–Oligocene extinction event (34 MYA), early lineages were likely lost, obscuring some details of their early evolutionary history.

Cited: Web of Science(16)
A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily
Hong-Xin Wang, Diego F. Morales-Briones, Michael J. Moore, Jun Wen, and Hua-Feng Wang
J Syst Evol 2021, 59 (5): 897-914.  
doi: 10.1111/jse.12745
The use of diverse data sets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we used target enrichment data, species tree, and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we here recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and plastid genomes to reconstruct deep and shallow phylogenies of plants.
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Fine-scale north-to-south genetic admixture profile in Shaanxi Han Chinese revealed by genome-wide demographic history reconstruction
Guang-Lin He, Meng-Ge Wang, Ying-Xiang Li, Xing Zou, Hui-Yuan Yeh, Ren-Kuan Tang, Xiao-Min Yang, Zheng Wang, Jian-Xin Guo, Ting Luo, Jing Zhao, Jin Sun, Rong Hu, Lan-Hai Wei, Gang Chen, Yi-Ping Hou, and Chuan-Chao Wang
J Syst Evol 2022, 60 (4): 955-972.  
doi: 10.1111/jse.12715

The Han Chinese are the world's largest ethnic group residing across China. Shaanxi province in northern China was a pastoral–agricultural interlacing region sensitive to climate change since Neolithic times, which makes it a vital place for studying population dynamics. However, genetic studies of Shaanxi Han are underrepresented due to the lack of high-density sampling and genome-wide data. Here, we genotyped 700 000 single nucleotide polymorphisms (SNPs) in 200 Han individuals from nine populations in Shaanxi and compared with available modern and ancient Eurasian individuals. We revealed a north–south genetic cline in Han Chinese with Shaanxi Han locating at the northern side of the cline. We detected the western Eurasian-related admixture in Shaanxi populations, especially in Guanzhong and Shanbei Han Chinese in proportions of 2%–4.6%. Shaanxi Han were suggested to derive a large part of ancestry (39%–69%) from a lineage that also contributed largely to ancient and present-day Tibetans (85%) as well as southern Han, supporting the common northern China origin of modern Sino-Tibetan-speaking populations and southwestward expansion of millet farmers from the middle-upper Yellow River Basin to the Tibetan Plateau and to southern China. The rest of the ancestry of Shaanxi Han was from a lineage closely related to ancient and present-day Austronesian and Tai-Kadai speaking populations in southern China and Southeast Asia. We also observed a genetic substructure in Shaanxi Han in terms of north–south-related ancestry corresponding well to the latitudes. Maternal mitochondrial DNA and paternal Y-chromosome lineages further demonstrated the aforementioned admixture pattern of Han Chinese in Shaanxi province.

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First fossil record of Cedrelospermum (Ulmaceae) from the Qinghai–Tibetan Plateau: Implications for morphological evolution and biogeography
Lin-Bo Jia, Tao Su, Yong-Jiang Huang, Fei-Xiang Wu, Tao Deng, and Zhe-Kun Zhou
J Syst Evol 2019, 57 (2): 94-104.  
doi: 10.1111/jse.12435
Cedrelospermum Saporta is an extinct genus in the Ulmaceae with abundant fossil records in North America and Europe. However, so far, fossil records of this genus from Asia are sparse, which limits the interpretations of the morphological evolution and biogeographical history of the genus. Here we report well‐preserved fruits (Cedrelospermum tibeticum sp. nov.) and a leaf (Cedrelospermum sp.) of Cedrelospermum from the upper Oligocene Lunpola and Nyima basins in the Qinghai–Tibetan Plateau (QTP). This is the first fossil record of Cedrelospermum in the QTP, showing that this genus grew in this region during the late Oligocene. Cedrelospermum tibeticum fruits are double‐winged, morphologically similar to the Eocene and Oligocene double‐winged Cedrelospermum species from North America. This supports the hypothesis that Cedrelospermum migrated to Asia from North America by way of the Bering Land Bridge. Given that Cedrelospermum was a typical element of Northern Hemispheric flora in the Paleogene and Neogene, the presence of this genus indicates that the central region of the QTP was phytogeographically linked with other parts of the Northern Hemisphere during the late Oligocene. The morphological observations of C. tibeticum fruits and other double‐winged Cedrelospermum fruits suggest an evolutionary trend from obtuse to acute apex for the primary wing. Cedrelospermum tibeticum likely had warm and wet climatic requirements. This type of an environment possibly existed in the central QTP in the late Oligocene, thereby supporting the survival of C. tibeticum.
Cited: Web of Science(15)
Restriction‐site associated DNA sequencing data reveal a radiation of willow species (Salix L., Salicaceae) in the Hengduan Mountains and adjacent areas
Li He, Natascha Dorothea Wagner, and Elvira Hörandl
J Syst Evol 2021, 59 (1): 44-57.  
doi: 10.1111/jse.12593
The Hengduan Mountains (HDM) in China are an important hotspot of plant diversity and endemism, and are considered to be a secondary diversification center for the woody plant genus Salix L. (Salicaceae). Here we aimed to reconstruct the spatiotemporal evolution of the Salix ChamaetiaVetrix clade in the HDM and to test for the occurrence of a local radiation. We inferred phylogenetic relationships based on more than 34 000 restriction‐site associated DNA loci from 27 species. Phylogenetic analyses recovered a well‐resolved tree topology with two major clades, the Eurasian clade and the HDM clade, with a divergence time of ca. 23.9 Ma. Species in the HDM clade originated in the northern part of the range and adjacent areas, and then dispersed into the southern HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses reveal that range contractions occurred in the northern areas during the last glacial maximum, while southward expansions resulted in range overlaps. Reconstructions of character evolution related to plant height, inflorescence, and flower morphology suggest that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data support the occurrence of a radiation in the HDM within the Salix ChamaetiaVetrix clade. Dispersal within the mountain system, and to adjacent regions, in addition to survival in glacial refugia shaped the biogeographical history of the clade, while adaptations of the HDM willows along an altitudinal gradient could be important ecological factors explaining the high species diversity of Salix in this area.
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Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae)
Wenbin Zhou, Qiu-Yun (Jenny) Xiang, and Jun Wen
J Syst Evol 2020, 58 (5): 571-603.  
doi: 10.1111/jse.12599

Nyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM) Nyssa talamancana was sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested that Nyssa had an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central American N. talamancana represents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals of Nyssa and the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution of Nyssa coincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution of Nyssa in EA and ENA.

Cited: Web of Science(15)
Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima
Jie Gao, Zhi-Long Liu, Wei Zhao, Kyle W. Tomlinson, Shang-Wen Xia, Qing-Yin Zeng, Xiao-Ru Wang, and Jin Chen
J Syst Evol 2021, 59 (3): 541-556.  
doi: 10.1111/jse.12568
Understanding the effects of the demographic dynamics and environmental heterogeneity on the genomic variation of forest species is important, not only for uncovering the evolutionary history of the species, but also for predicting their ability to adapt to climate change. In this study, we combined a common garden experiment with range-wide population genomics analyses to infer the demographic history and characterize patterns of local adaptation in a subtropical oak species, Quercus acutissima (Carruthers). We scanned approximately 8% of the oak genome using a balanced representation of both genic and non-genic regions and identified a total of 55 361 single nucleotide polymorphisms (SNPs) in 167 trees. Genomic diversity analyses revealed an east–west split in the species distribution range. Coalescent-based model simulations inferred a late Pleistocene divergence in Q. acutissima between the east and west groups as well as subsequent preglaciation population expansion events. Consistent with observed genetic differentiation, morphological traits also showed east–west differentiation and the biomass allocation in seedlings was significantly associated with precipitation. Environment was found to have a significant and stronger impact on the non-neutral than the neutral SNPs, and also significantly associated with the phenotypic differentiation, suggesting that, apart from the geography, environment had played a role in determining non-neutral and phenotypic variation. Our approach, which combined a common garden experiment with landscape genomics data, validated the hypothesis of local adaptation of this long-lived oak tree of subtropical China. Our study joins the small number of studies that have combined genotypic and phenotypic data to detect patterns of local adaptation.
Cited: Web of Science(14)
The spatial structure of phylogenetic and functional diversity in the United States and Canada: An example using the sedge family (Cyperaceae)
Daniel Spalink, Jocelyn Pender, Marcial Escudero, Andrew L. Hipp, Eric H. Roalson, Julian R. Starr, Marcia J. Waterway, Lynn Bohs, and Kenneth J. Sytsma
J Syst Evol 2018, 56 (5): 449-465.  
doi: 10.1111/jse.12423
Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this diversity based on the historical biogeography of the family. Incorporating a phylogeny, over 400 000 herbarium records, and a database of functional traits mined from online floras, we find that species richness and functional trait diversity peak in the Northeastern USA, while phylogenetic diversity peaks along the Gulf of Mexico. Floristic turnover among assemblages increases significantly with distance, but phylogenetic turnover is twice as rapid along latitudinal gradients as along longitudinal gradients. These patterns reflect the expected distribution of Cyperaceae, which originated in the tropics but radiated in temperate regions. We identify assemblages with an abundance of rare, range‐restricted lineages, and assemblages composed of species generally lacking from diverse regions. We argue that both of these metrics are useful for developing targeted conservation strategies. We use the data generated here to establish future research priorities, including the testing of a series of hypotheses regarding the distribution of chromosome numbers, photosynthetic pathways, and resource partitioning in sedges.
Cited: Web of Science(13)
Genomic insights into speciation history and local adaptation of an alpine aspen in the Qinghai–Tibet Plateau and adjacent highlands
Jia-Liang Li, Lin-Ling Zhong, Jing Wang, Tao Ma, Kang-Shan Mao, and Lei Zhang
J Syst Evol 2021, 59 (6): 1220-1231.  
doi: 10.1111/jse.12665
Natural selection serves as an important agent to drive and maintain interspecific divergence. Populus rotundifolia Griff. is an alpine aspen species that mainly occurs in the Qinghai–Tibet Plateau (QTP) and adjacent highlands, whereas its sister species, P. davidiana Dode, is distributed across southwest and central to northeast China in much lower altitude regions. In this study, we collected genome resequencing data of 53 P. rotundifolia and 42 P. davidiana individuals across their natural distribution regions. Our population genomic data suggest that the two species are well delimitated in the allopatric regions, but with hybrid zones in their adjacent region in the eastern QTP. Coalescent simulations suggest that P. rotundifolia diverged from P. davidiana in the middle Pleistocene with following continuous gene flow since divergence. In addition, we found numerous highly diverged genes with outlier signatures that are likely associated with high-altitude adaptation of these alpine aspens. Our finding indicate that Quaternary climatic changes and natural selection have greatly contributed to the origin and distinction maintenance of P. rotundifolia in the QTP.
Cited: Web of Science(13)
Better together: Joint consideration of anatomy and morphology illuminates the architecture and life history of the Carboniferous arborescent lycopsid Paralycopodites
William A. DiMichele and Richard M. Bateman
J Syst Evol 2020, 58 (6): 783-804.  
doi: 10.1111/jse.12662

Paralycopodites Morey & Morey, a Carboniferous‐age arboreous lycopsid that grew in the tropical wetlands of Pangea, is the phylogenetically basalmost member of the Carboniferous stigmarian lycopsids to be conceptually reconstructed. We update its description through reciprocal illumination between anatomy (coal‐balls) and gross morphology (adpressions). Revised assessment of its architecture and development shows that the determinate, columnar main trunk eventually underwent several isotomous divisions to form a crown. Two opposite rows of closely‐spaced, compact lateral branches were initiated anisotomously throughout the trunk and crown, each branch further undergoing multiple anisotomous divisions to form an apparently planar scaffold for numerous bisporangiate cones. We infer that branches were initially emitted near‐vertically, but rapidly moved to a more horizontal position; they were abscised after the cones had matured but before the continuous phellogen had produced a centripetal periderm. Leaves were not abscised, though anatomy and morphology both suggest a photosynthetic economy that was localized within the plant body. Character content and clarity of interpretation make Paralycopodites the preferred name for the reconstructed plant rather than Anabathra, Ulodendron, or Bergeria. Phylogenetic analysis of rhizomorphic lycopsids based on a reduced spectrum of features observable in adpression returns the same topology as that based on a full matrix combining both anatomical and externally visible traits, permitting adpression fossils to be assigned to anatomically‐circumscribed genera rather than perpetuating an unnecessary parallel taxonomy.

Cited: Web of Science(12)
Ancestral gene duplications in mosses characterized by integrated phylogenomic analyses
Bei Gao, Mo-Xian Chen, Xiao-Shuang Li, Yu-Qing Liang, Dao-Yuan Zhang, Andrew J. Wood, Melvin J. Oliver, and Jian-Hua Zhang
J Syst Evol 2022, 60 (1): 144-159.  
doi: 10.1111/jse.12683

Mosses (Bryophyta) are a key group occupying an important phylogenetic position in land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage, containing more than 95% of modern mosses, whereas other classes are species‐poor. Two branches with large numbers of gene duplications were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida, and Tetraphidopsida. The analysis of the phylogenetic progression of duplicated paralogs retained on genomic syntenic regions in the Physcomitrella patens genome confirmed that the whole‐genome duplication events WGD1 and WGD2 were re‐recognized as the ψ event and the Funarioideae duplication event, respectively. The ψ polyploidy event was tightly associated with the early diversification of Bryopsida, in the ancestor of Bryidae, Dicranidae, Timmiidae, and Funariidae. Together, four branches with large numbers of gene duplications were unveiled in the evolutionary past of P. patens. Gene retention patterns following the four large‐scale duplications in different moss lineages were analyzed and discussed. Recurrent significant retention of stress‐related genes may have contributed to their adaption to distinct ecological environments and the evolutionary success of this early‐diverging land plant lineage.

Cited: Web of Science(12)
Phylogenomics, biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation
Kira Lindelof, Julieta A. Lindo, Wenbin Zhou, Xiang Ji, Qiu-Yun (Jenny) Xiang
J Syst Evol 2020, 58 (5): 604-645.  
doi: 10.1111/jse.12676

The eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography of the Northern Hemisphere. Despite 20 years of studies dedicated to identification of taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. The blue‐ or white‐fruited dogwoods (BW) are the most species‐rich among the four major clades of Cornus L., consisting of ~35 species divided into three subgenera (subg. Yinquania, subg. Mesomora, and subg. Kraniopsis). The BW group provides an excellent example of the EA–ENA floristic disjunction for biogeographic study due to its diversity distribution centered in eastern Asia and eastern North America, yet its species relationships and delineation have remained poorly understood. In this study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, and climate data to understand species relationships, biogeographic history, and ecological niche and morphological evolution. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well‐resolved phylogeny of the BW group with three intercontinental disjunct clades in EA and ENA or Eurasia and North America, of which two are newly identified within subg. Kraniopsis. These analyses also recovered a potential new species but failed to resolve relationships within the C. hemsleyiC. schindleri complex. In an effort to develop an approach to reduce computation time, analysis of different nodal age settings in treePL suggests setting a node's minimum age constraint to the lower bound of a fossil's age range to obtain similar ages to that of BEAST. Divergence time analyses with BEAST and treePL dated the BW stem back to the very Late Cretaceous and the divergence of the three subgenera in the Paleogene. By integrating fossil ages and morphology, a total evidence‐based dating approach was used in conjunction with time‐slice probabilities of dispersal under a DEC model to resolve ancestral ranges of each disjunct in the Miocene: Eurasia and ENA (disjunct 1), EA and western North America (disjunct 2), and EA (disjunct 3). The dated biogeographic history supports dispersal via the North Atlantic Land Bridge in the late Paleogene in disjunct 1 and dispersal via the Bering Land Bridge in the Miocene for disjuncts 2 and 3. Character mapping with a stochastic model in phytools and comparison of ecological niche, morphospace, and rate of evolution indicated differential divergence patterns in morphology, ecological niche, and molecules between disjunct sisters. Although morphological stasis was observed in most of the characters, evolutionary changes in growth habit and some features of leaf, flower, and fruit morphology occurred in one or both sister clades. A significant differentiation of ecological habitats in temperature, precipitation, and elevation between disjunct sisters was observed, suggesting a role of niche divergence in morphological evolution post‐isolation. The patterns of evolutionary rate between morphology and molecules varied among disjunct clades and were not always congruent between morphology and molecules, suggesting cases of non‐neutral morphological evolution driven by ecological selection. Our phylogenetic evidence and comparisons of evolutionary rate among disjunct lineages lend new insights into the formation of the diversity anomaly between EA and ENA, with particular support of an early diversification in EA. These findings, in conjunction with previous studies, again suggest that the EA–ENA disjunct floras are an assembly of lineages descended from the Mesophytic Forests that evolved from the early Paleogene “boreotropical flora” through varied evolutionary pathways across lineages.

Cited: Web of Science(12)
Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis
Michelle L. Gaynor, Chao-Nan Fu, Lian-Ming Gao, Li-Min Lu, Douglas E. Soltis, and Pamela S. Soltis
J Syst Evol 2020, 58 (5): 646-662.  
doi: 10.1111/jse.12646

Diapensiaceae (Ericales) are a small family of about 15 species. Within this clade, two species are broadly distributed throughout the Northern Hemisphere, whereas the remaining species have a disjunct distribution between eastern North America and eastern Asia. To address patterns and processes of diversification in Diapensiaceae, we conducted biogeographic analyses and inferred shifts in the ecological niche across the phylogeny of the clade. Although Diapensiaceae have been the focus of multiple phylogenetic and biogeographic studies, previous studies have been taxonomically limited. This study has greatly improved the phylogenetic underpinning for Diapensiaceae with the most inclusive taxonomic sampling thus far, employing both nuclear and plastid gene sequence data for at least one sample per species in the family. Our estimates indicate that genera of Diapensiaceae variously diverged in the Eocene, Oligocene, and early to mid‐Miocene. The biogeographic analysis suggests that the probable ancestor of the Diapensiaceae crown clade originated in the Nearctic, with vicariance events contributing to the current distribution of the disjunct taxa. Ecological niche, when considered in a phylogenetic context, was observed to be clustered on the basis of biogeographic realm. In general, a greater ecological overlap was found at younger nodes and a greater niche divergence was found among distantly related species. Diversification in Diapensiaceae appears to have been shaped by both large‐scale biogeographic factors, such as vicariance, and divergence in an ecological niche among closely related species.

Cited: Web of Science(12)
Song Ge
Jun Wen
Impact Factor
JCR 2021 IF ranking: 63/238 (Plant Sciences, top 26.26%, Q2 quartile)
Journal Abbreviation: J Syst Evol
ISSN: 1674-4918 (Print)
1759-6831 (Online)
CN: 11-5779/Q
Frequency: Bi-monthly




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