Highly Cited Articles
The following is a list of the most cited articles published from 2018 to 2020, according to Web of Science.
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Collections-based science in the 21st Century
Vicki A. Funk
J Syst Evol 2018, 56 (3): 175–193  
doi: 10.1111/jse.12315
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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)
  
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
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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)
  
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
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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)
  
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)
  
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
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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)
  
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
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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)
  
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
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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)
  
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)
  
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)
  
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
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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)
  
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)
  
A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification
Santiago Martín‐Bravo, Pedro Jiménez‐Mejías, Tamara Villaverde, Marcial Escudero, Marlene Hahn, Daniel Spalink, Eric H. Roalson, Andrew L. Hipp, and the Global Carex Group (Carmen Benítez-Benítez, Leo P. Bruederle, Elisabeth Fitzek, Bruce A. Ford, Kerry A. Ford, Mira Garner, Sebastian Gebauer, Matthias H. Hoffmann, Xiao-Feng Jin, Isabel Larridon, Étienne Léveillé-Bourret, Yi-Fei Lu, Modesto Luceño, Enrique Maguilla, Jose Ignacio Márquez‐Corro, Mónica Míguez, Robert Naczi, Anton A. Reznicek, and Julian R. Starr)
J Syst Evol 2019, 57 (6): 695–718  
doi: 10.1111/jse.12549

The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a “museum” of extant species diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space.

Cited: Web of Science(12)
  
Chloroplast phylogenomic data support Eocene amphi‐Pacific early radiation for the Asian Palmate core Araliaceae
Virginia Valcárcel and Jun Wen
J Syst Evol 2019, 57 (6): 547–560  
doi: 10.1111/jse.12522
Traditional phylogenies based on analysis of multiple genes have failed to obtain a well‐resolved evolutionary history for the backbone of the Asian Palmate group of Araliaceae, the largest clade of the family. In this study, we applied the genome skimming approach of next‐generation sequencing to address whether the lack of resolution at the base of the Asian Palmate tree is due to molecular sampling error or the footprint of ancient radiation. Twenty‐nine complete plastid genomes of Araliaceae (17 newly sequenced) were analyzed (RAxML, Beast, Lagrange, and BioGeoBears) to provide the first phylogenomic reconstruction of the group (95% of genera included). As a result, the early divergences of the Asian Palmate group have been clarified but the backbone of its core is not totally resolved, with short internal branches pointing to an ancient radiation scenario. East Asia is inferred as the most likely ancestral area for the Asian Palmate group (from late Paleocene to Eocene) from which early colonization of the Neotropics is inferred during the Eocene. The radiation of the core Palmate group took place during the late Eocene, most likely in the context of the Boreotropical hypothesis. Recurrent episodes of southward migration (to the tropics) coupled with northern latitude local extinctions (promoting geographic isolation of lineages) followed by northward expansion (promoting contact of lineages that erased the trace of preceding geographic isolation) are hypothesized to have linked to the alternation of the cold and warm periods of the Eocene.
Cited: Web of Science(12)
  
Long distance dispersal in the assembly of floras: A review of progress and prospects in North America
AJ Harris, Stefanie Ickert-Bond, and Aarón Rodríguez
J Syst Evol 2018, 56 (5): 430–448  
doi: 10.1111/jse.12422
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Here, we review progress and prospects to explicitly test for long distance dispersal biogeographic events. Long distance dispersal represents a “jump” across some kind of barrier, such as a topographic feature or a zone of unsuitable climate and may include repeated jumps, or stepping‐stone dispersals. Long distance dispersals were considered integral for explaining the organization of biodiversity at large and small scales by early biogeographers, such as Darwin and Wallace. Darwin, Wallace, and others envisioned that long distance dispersals were predictable events because the vectors for dispersal, such as animals, winds, and currents, behaved in non‐random ways. However, these early biogeographers found that dispersal was hard to observe, and, later, with the advent of the theory of Continental Drift, vicariance became regarded as a better scientific explanation for the arrangement of biodiversity, because it represented a falsifiable hypothesis. Thus, long distance dispersal was reduced to a nuisance parameter in biogeography; a random possibility that could never fully be ruled out in a scenario in which evidence supported vicariance. Today, there is strong interest to more fully integrate long distance dispersal into understanding the assembly and organization of biodiversity on earth. In this review, we discuss progress and prospects for explicitly testing long distance dispersal hypotheses including through uses of molecular, morphological, paleontological, and informatics methods. We focus on hypothesis testing of long distance dispersals involved in the assembly of the flora of North America, which is a robust preliminary study system on account of its extant and extinct biodiversity being well‐catalogued.
Cited: Web of Science(12)
  
Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae)
Bin-Bin Liu, De-Yuan Hong, Shi-Liang Zhou, Chao Xu, Wen-Pan Dong, Gabriel Johnson, and Jun Wen
J Syst Evol 2019, 57 (6): 678–694  
doi: 10.1111/jse.12542

Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North and Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained uncertain. Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera, especially Photinia and Stranvaesia, and the hybrid origin hypothesis of Photinia bodinieri. This study employs complete plastomes and the entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach with a broad taxon sampling of 81 species in 30 genera of Rosaceae, especially Maleae. Based on three datasets, including the whole plastome, coding sequence, and nrDNA repeats, the results of maximum likelihood and Bayesian inference analyses showed that the previously circumscribed Stranvaesia and Photinia were each non‐monophyletic. Six clades have been recovered herein within Photinia and its allied genera: Aronia, Heteromeles, Photinia s.s., Pourthiaea, Stranvaesia, and a new genus Phippsiomeles consisting of the Central American species formerly placed in Photinia. The strong conflicts between the plastome and nrDNA phylogenies of Phippsiomeles and Stranvaesia tomentosa suggest the possibility that they may have each originated involving hybridization events, while no incongruence among datasets was detected to support the hybrid origin of Photinia bodinieri. We provide 12 new combinations, to transfer eight taxa of the New World Photinia into Phippsiomeles and clarify the generic placements of several species of Photinia and Stranvaesia.

Cited: Web of Science(11)
  
Exploring the generic delimitation of Phyllagathis and Bredia (Melastomataceae): A combined nuclear and chloroplast DNA analysis
Qiu-Jie Zhou, Che-Wei Lin, Jin-Hong Dai, Ren-Chao Zhou, and Ying Liu
J Syst Evol 2019, 57 (3): 256–267  
doi: 10.1111/jse.12451
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Phyllagathis Blume and Bredia Blume (Sonerileae?s.l., Melastomataceae) are two closely related Asian genera with similar morphology and overlapping geographical range. Their generic circumscription and phylogenetic relationships are far from fully understood. We present here a molecular phylogenetic investigation for the two genera using nuclear ribosomal internal transcribed spacer and chloroplast (trnV‐trnM) sequence data. Seventeen genera of Sonerileae s.l. were included in the analyses, with Phyllagathis and Bredia densely sampled to cover their geographical range and morphological diversity. We identified 14 well supported species clusters within Sonerileae s.l.–Medinilla. Phylogenetic analyses together with reconstruction of morphological characters clearly indicated the taxonomic mess in generic delimitation of Sonerileae s.l. Many of the characters traditionally used in generic delimitation were highly homoplasious. Bredia and Phyllagathis, as well as Allomorphia, Anerincleistus, Fordiophyton, and Oxyspora, were revealed to be non‐monophyletic. Bredia, as currently defined, contains two groups of species with different phylogenetic affiliations. Bredia should be recircumscribed to exclude the Bredia–Phyllagathis clade I and accommodate the Bredia–Phyllagathis clade II as the type of the genus is included in the latter clade. Most species sampled in Phyllagathis spread across eight well supported clades throughout the phylogenetic tree. The type of Phyllagathis showed no close affiliation with other members of Phyllagathis nor its putative relatives. Phyllagathis, as presently circumscribed, is heterogeneous, encompassing multiple evolutionary lineages. As sequence data of nuclear ribosomal internal transcribed spacer and chloroplast trnV‐trnM failed to resolve the phylogenetic relationships among these lineages, the formal taxonomic adjustment of Phyllagathis is postponed until further evidence can be gathered.
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Cited: Web of Science(11)
  
A ribonucleopeptide world at the origin of life
Nizar Y. Saad
J Syst Evol 2018, 56 (1): 1–13  
doi: 10.1111/jse.12287
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The structural flexibility of RNA and its ability to store genetic information has led scientists to postulate that RNA could be the key molecule for the development of life on Earth, further leading to formulate the RNA world hypothesis that received a lot of success and acceptance after the discoveries of the last thirty-five years. Despite its highly structural and functional significance, the difficulty in synthesizing the four nucleobases that form the RNA polymer from the same primordial soup, its low stability, and limited catalytic repertoire, make the RNA world hypothesis less convincing even though it remains the best explanation for the origin of life. An increasing number of scientists are becoming more supportive of a more realistic approach explaining the appearance of life. In this review, I propose an enhanced explanation for the appearance of life supported by recent discoveries and theories. Accordingly, amino acids and peptides associated with RNA (e.g., ribonucleopeptides) might have existed at the onset of RNA and might have played an important role in the continuous development of self-sustaining biological systems. Therefore, in this review, I cover the most recent and relevant scientific investigations that propose a better understanding of the ribonucleopeptide world hypothesis and the appearance of life. Finally, I propose two hypotheses for a primitive translation machinery (PTM) that might have been formed of either a T box ribozyme or a ribopolymerase.
Cited: Web of Science(11)
  
Maple phylogeny and biogeography inferred from phylogenomic data
Jianhua Li, Mark Stukel, Parker Bussies, Kaleb Skinner, Alan R. Lemmon, Emily Moriarty Lemmon, Kenneth Brown, Airat Bekmetjev, and Nathan G. Swenson
J Syst Evol 2019, 57 (6): 594–606  
doi: 10.1111/jse.12535

Acer (the maple genus) is one of the diverse tree genera in the Northern Hemisphere with about 152 species, most of which are in eastern Asia. There are roughly a dozen species in Europe/western Asia and a dozen in North America. Several phylogenetic studies of Acer have been conducted since 1998, but none have provided a satisfactory resolution for basal relationships among sections of Acer. Here we report the first well‐resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography. Our phylogenetic results support the most recent taxonomic treatment of Acer by de Jong with some modifications; section Pentaphylla may be expanded to include section Trifoliata, and A. yangbiense may be included in section Lithocarpa. Sections Spicata, Negundo, Arguta, and Palmata form a clade sister to the rest of the genus where sections Glabra and Parviflora comprise the first clade followed by section Macrantha, sections Ginnala, Lithocarpa, Indivisa, sections Platanoidea and Macrophylla, section Rubra, section Acer, and section Pentaphylla. Monotypic sections Glabra and Macrophylla in North America are sister to the Japanese section Parviflora and Eurasian section Platanoidea, respectively. Ancestral area inferences using statistical dispersal and vicariance analysis (S‐DIVA) and dispersal and extinction cladogenesis (DEC) methods suggest that Asia might be the most likely ancestral area of Acer as proposed by Wolfe and Tanai and molecular dating using Bayesian evolutionary analysis by sampling trees (BEAST) indicate that section diversifications of Acer might have completed largely in the late Eocene and the intercontinental disjunctions of Acer between eastern Asia and eastern North America formed mostly in the Miocene.

Cited: Web of Science(10)
  
Plastome phylogenomic analysis of Torreya (Taxaceae)
Xu Zhang, Hua-Jie Zhang, Jacob B. Landis, Tao Deng, Ai-Ping Meng, Hang Sun, Yan-Song Peng, Heng-Chang Wang, and Yan-Xia Sun
J Syst Evol 2019, 57 (6): 607–615  
doi: 10.1111/jse.12482
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Torreya Arn., a small genus of Taxaceae, consists of six species occurring in North America and eastern Asia. Several phylogenetic studies have previously been undertaken to reveal relationships within this genus, although only a few DNA segments or species were used. In the present study, we sequenced five Torreya plastomes and combined these with two existing plastomes from the genus to investigate plastome evolution and phylogenetic relationships within Torreya. All sequenced Torreya plastomes shared the same complement of 82 protein‐coding genes, 4 ribosomal RNA genes, and 31 transfer RNA genes. Phylogenetic inference using a maximum likelihood framework consisted of an 82‐gene, 17‐taxon dataset, including all species of Torreya, resolved Torreya as a monophyletic clade. Strongly supported relationships within the genus include the position of the early diverging T. jackii Chun, the two sister pairs T. fargesii Franch.–T. nucifera (L.) Siebold & Zucc. and T. grandis Fortune ex Lindl.–T. californica Torr., and the monophyly of the clade including T. fargesii var. yunnanensis, T. fargesii, and T. nucifera. In addition to the inference of species relationships, divergence time estimation and biogeographical analysis were carried out. The diversification of Torreya was estimated to be approximately 8.9 Ma. Ancestral state reconstruction of the geographical area suggested China/eastern North America as the most likely ancestral region for the six extant Torreya species.

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Comparative genomics of figworts (Scrophularia, Scrophulariaceae), with implications for the evolution of Scrophularia and Lamiales
Wu-Qin Xu, Jocelyn Losh, Chuan Chen, Pan Li, Rui-Hong Wang, Yun-Peng Zhao, Ying-Xiong Qiu, Cheng-Xin Fu
J Syst Evol 2019, 57 (1): 55–65  
doi: 10.1111/jse.12421
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The figwort genus Scrophularia L. (Scrophulariaceae) comprises 200–300 species and is widespread throughout the temperate Northern Hemisphere. Due to reticulate evolution resulting from hybridization and polyploidization, the taxonomy and phylogeny of Scrophularia is notoriously challenging. Here we report the complete chloroplast (cp) genome sequences of S. henryi Hemsl. and S. dentata Royle ex Benth. and compare them with those of S. takesimensis Nakai and S. buergeriana Miq. The Scrophularia cp genomes ranged from 152 425 to 153 631 bp in length. Each cp genome contained 113 unigenes, consisting of 78 protein‐coding genes, 31 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, gene content, AT content and IR/SC boundary structure were nearly identical among them. Nine cpDNA markers (trnH‐psbA, rps15, rps18‐rpl20, rpl32‐trnL, trnS‐trnG, ycf15‐trnL, rps4‐trnT, ndhF‐rpl32, and rps16‐trnQ) with more than 2% variable sites were identified. Our phylogenetic analyses including 55 genera from Lamiales strongly supported a sister relationship between ((Bignoniaceae + Verbenaceae) + Pedaliaceae) and (Acanthaceae + Lentibulariaceae). Within Scrophulariaceae, a topology of (S. dentata + (S. takesimensis + (S. buergeriana S. henryi))) was strongly supported. The crown age of Lamiales was estimated to be 85.1 Ma (95% highest posterior density, 70.6–99.8 Ma). The higher core Lamiales originated at 65.6 Ma (95% highest posterior density, 51.4–79.4 Ma), with a subsequent radiation that occurred in the Paleocene (between 55.4 and 62.3 Ma) and gave birth to the diversified families. Our study provides a robust phylogeny and a temporal framework for further investigation of the evolution of Lamiales.
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Reinerantha foliicola, a new genus and species of Lejeuneaceae subtribe Cololejeuneinae (Marchantiophyta) from Ecuador
S. Robbert Gradstein, Rui-Liang Zhu, Lei Shu, Álvaro J. Pérez
J Syst Evol 2018, 56 (1): 67–75  
doi: 10.1111/jse.12293
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Cololejeuneinae is the largest subtribe of the liverwort family Lejeuneaceae and the crown group of the family. The species often grow on the surfaces of living leaves and twigs or in swiftly running waters and many of them possess neotenic gametophytes, considered an adaptation to these extreme habitats. We describe a new, epiphyllous genus and species in Cololejeuneinae from the Western Cordillera of Ecuador, Reinerantha foliicola Gradst. & R.L.Zhu. Analysis of combined molecular datasets with parsimony, maximum likelihood and Bayesian methods revealed Reinerantha in a sister relationship to the large pantropical genus Diplasiolejeunea. Reinerantha differs from Diplasiolejeunea in leaf segmentation, epidermal wall thickening, stylus, male bracts and perianth keels, and is morphologically more similar to the genus Tuyamaella. In the molecular analysis, however, Reinerantha and Tuyamaella were resolved in different clades and not closely related. Tuyamaella is shown to be restricted to Asia; the report of Tuyamaella from South America (Peru) was erroneous and a case of mislabeling.
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Occurrence of Christella (Thelypteridaceae) in Southwest China and its indications of the paleoenvironment of the Qinghai–Tibetan Plateau and adjacent areas
Cong-Li Xu, Tao Su, Jian Huang, Yong-Jiang Huang, Shu-Feng Li, Yi-Shan Zhao, and Zhe-Kun Zhou
J Syst Evol 2019, 57 (2): 169–179  
doi: 10.1111/jse.12452
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The uplift of the Qinghai–Tibetan Plateau dramatically changed the regional topography and climate, profoundly impacting the distribution of many plant lineages. Plant responses to environmental changes are particularly prominent in lineages that require ecological factors differentiated from those present before the uplift of the QTP. Two fossil occurrences of Christella H. Lév., Fl. Kouy–Tchéou (Thelypteridaceae), a fern genus now distributed mainly at low elevations of the pantropics with warm and moist habitats, are described based on fossilized Cenozoic leaf fronds recovered from SW China: late Paleocene Christella nervosa (J. R. Tao) C. L. Xu, T. Su & Z. K. Zhou comb. nov. found in Liuqu, southern Tibet and middle Miocene Christella sp. recovered from the Jinggu Basin in western Yunnan. The frond fossils from both sites share key morphological characteristics that diagnose these fossils as Christella. After detailed comparisons, we further clarified Christella papilio (C. Hope) Holttum, a species distributed in warm, humid habitats at altitudes no more than 1300?m, as the nearest living relative of C. nervosa. This finding suggested that southern Tibet had not reached its present elevation during the late Paleocene (ca. 56 Ma). We propose that the uplift, accompanied by severe cooling and aridification after the late Paleocene, caused the disappearance of Christella in southern Tibet, whereas paleoenvironmental conditions enabled the genus to survive in Yunnan. Our study provides the first example of distributional constraints of ferns in SW China in response to paleoenvironmental changes in the Qinghai–Tibetan Plateau and nearby areas.
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Phylogenetic diversity is a better measure of biodiversity than taxon counting
Joseph T. Miler, Garry Jolley-Rogers, Brent D. Mishler, and Andrew H. Thornhill
J Syst Evol 2018, 56 (6): 663–667  
doi: 10.1111/jse.12436

Biodiversity is most commonly measured in taxonomic richness. For example, it is common to describe how diverse a genus or a geographic area is by counting the number of species within them. Phylogenetic diversity (PD), a measurement of the branch lengths in a phylogenetic tree, is a better measure of biodiversity that provides a comparable, evolutionary measure of biodiversity not possible with species counts. Despite its advantages, PD is rarely used as the primary measure of biodiversity. We developed a genus-level phylogeny for nearly 90% of taxonomically described Australian land plants and compared PD to genus richness in multiple clades. The proportion of PD per genera was skewed among clades. Non-angiosperm clades had more PD than expected given the number of genera while angiosperm clades had less PD than expected. For example, ferns comprised only 4.7% of the genera yet 13.0% of the PD, while the angiosperms as a whole comprised 78.9% of the genera but only 62.7% of the PD. It is likely that cultural reasons, such as taxonomic biases, are more important than methodological and biological phenomena in explaining these discrepancies. Regardless of reasons for the observed results, we conclude that a shift towards the use of PD as the primary descriptor of biodiversity will promote an important conceptual shift in biodiversity studies as a quantitative science.

Cited: Web of Science(9)
  
Dispersal is associated with morphological innovation, but not increased diversification, in Cyphostemma (Vitaceae)
David J. Hearn, Margaret Evans, Ben Wolf, Michael McGinty, Jun Wen
J Syst Evol 2018, 56 (4): 340–359  
doi: 10.1111/jse.12417

Multiple processes − including dispersal, morphological innovation, and habitat change − are frequently cited as catalysts for increased diversification. We investigate these processes and the causal linkages among them in the genus Cyphostemma (Vitaceae), a clade comprising ∼200 species that is unique in the Vitaceae for its diversity of growth habits. We reconstruct time‐calibrated evolutionary relationships among 64 species in the genus using five nuclear and chloroplast markers and infer the group's morphological and biogeographic history. We test for changes in speciation rate and evaluate the temporal association and sequencing of events with respect to dispersal, habitat change, and morphological evolution using a Monte Carlo simulation approach. In Cyphostemma, neither dispersal nor morphological evolution is associated with shifts in speciation rate, but dispersal is associated with evolutionary shifts in growth form. Evolution of stem succulence, in particular, is associated with adaptation to local, pre‐existing conditions following long‐distance dispersal, not habitat change in situ. We suggest that the pattern of association between dispersal, morphological innovation, and diversification may depend on the particular characters under study. Lineages with evolutionarily labile characters, such as stem succulence, do not necessarily conform to the notion of niche conservatism and instead demonstrate remarkable morphological adaptation to local climate and edaphic conditions following dispersal.

Cited: Web of Science(9)
  
Phylogeny and spatio‐temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum (Rosaceae) in the Malesian region
Liang Zhao, Daniel Potter, Yuan Xu, Pei-Liang Liu, Gabriel Johnson, Zhao-Yang Chang, Jun Wen
J Syst Evol 2018, 56 (6): 637–651  
doi: 10.1111/jse.12467
The goals of this study were to reconstruct the phylogeny of Prunus subgenus Laurocerasus section Mesopygeum and to provide a preliminary assessment of its spatio‐temporal diversification in the Malesian region. We inferred the phylogeny using nuclear ITS and ETS and plastid psbA‐trnH, rps16, rpl16, and trnC‐petN sequences. Our analyses support the monophyly of sect. Mesopygeum. Within sect. Mesopygeum, we identified four main subclades: (i) Prunus lancilimba from continental Asia; (ii) Prunus ruthii from Malay Peninsula; (iii) a subclade comprising species from areas centered on the Sunda shelf and also a few species from continental Asia and Wallacea; and (iv) a subclade composed of species from areas of the Sahul shelf, with a small number of taxa also from areas of the Sunda shelf, continental Asia, and the Philippines. We estimated that sect. Mesopygeum originated in continental Asia at c. 44.71 Mya (95% HPD: 31.66–46.90). Nine dispersals between major geographic areas were inferred. From continental Asia, three and two dispersals were inferred to the Sunda shelf and the Sahul shelf in the mid‐Oligocene, respectively. Two dispersals were inferred from the Sahul shelf region to the Sunda shelf in late Oligecene and early Miocene, respectively. There were also two dispersals inferred from the Sunda shelf region, one to the Philippines and one to Wallacea, in the middle and late Miocene, respectively. The diversification in sect. Mesopygeum was likely driven by active geologic events and orogenies in the Neogene in the Malesian region.
Cited: Web of Science(8)
Editors-in-Chief
Song Ge
Jun Wen
Impact Factor
2.779
JCR 2019 IF ranking: 56/234 (Plant Sciences, top 23.72%, Q1 quartile)
Journal Abbreviation: J Syst Evol
ISSN: 1674-4918 (Print)
1759-6831 (Online)
CN: 11-5779/Q
Frequency: Bi-monthly

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