Magnoliaceae, an assemblage of early diverged angiosperms, comprises two subfamilies, speciose Magnolioideae with approximately 300 species in varying numbers of genera and monogeneric Liriodendroideae with two species in Liriodendron L. This family occupies a pivotal phylogenetic position with important insights into the diversification of early angiosperms, and shows intercontinentally disjunct distribution patterns between eastern Asia and the Americas. Widespread morphological homogeneity and slow substitution rates in Magnolia L. s.l. resulted in poorly supported phylogenetic relationships based on morphology or molecular evidence, which hampers our understanding of the genus’ temporal and spacial evolution. Here, based on the newly generated genome skimming data for 48 Magnolia s.l. species, we produced robust Magnolia phylogenies using genome-wide markers from both plastid genomes and single nucleotide polymorphism data. Contrasting the plastid and nuclear phylogenies revealed extensive cytonuclear conflicts in both shallow and deep relationships. ABBA-BABA and PhyloNet analyses suggested hybridization occurred within sect. Yulania, and sect. Magnolia, which is in concordance with the ploidy level of the species in these two sections. Divergence time estimates and biogeographic reconstruction indicated that the timing of the three tropical Magnolia disjunctions coincided with the mid-Eocene cooling climate and/or late Eocene climate deterioration, and two temperate disjunctions occurred much later, possibly during the warm periods of the Miocene, hence supporting the boreotropical flora concept of Magnolia s.l.

Plant mitochondrial protein-coding genes are slow evolving, and therefore are less subject to substitution saturation, and therefore perhaps more suitable for resolving deep relationships of high taxonomic categories. Plant mitochondrial genes hold, however, hundreds of RNA editing sites, involving mostly non-synonymous substitutions in the first and second codon positions, which has been reported to affect phylogenetic reconstructions. We have previously identified ca. 4700 mitochondrial RNA editing sites within a group of liverworts representing the ordinal diversity of liverworts, allowing us to critically evaluate the impacts of RNA editing sites on phylogenetic reconstructions in liverworts. Our phylogenetic inferences are mostly congruent on topology inferred from the original mitochondrial gene dataset, dataset with RNA editing sites corrected, and dataset with RNA editing sites excluded. The RNA editing site excluded dataset recovered a topology identical to that of the RNA editing site corrected dataset, supporting the sister relationship of Ptilidium and Jungermanniales, whereas the original dataset supported the sister relationship of Ptilidium and Jungermanniidae. The controversial placements of Ptilidium could be explained by site-wise log-likelihood analysis, as the majority of liverwort RNA editing sites supported the sister relationship of Ptilidium and Jungermanniidae, hence the correction or exclusion of the RNA editing sites changed the tree topology and supported the sister relationship of Ptilidium and Jungermanniales. Our study shows that RNA editing sites potentially impact phylogenetic analyses, suggesting that both genome and transcriptome derived data should be used with caution for phylogenetic reconstruction with genes hosting vast numbers of RNA editing sites such as plant organellar genes.

Epifoliar fungi are a group of poorly studied fungal symbionts that coinhabit the surface of living plants. Meliolaceae is the largest group of epifoliar fungi and has been considered as obligate parasites. We investigated the taxonomy of Meliolaceae and the coevolutionary events with their host plants using time-calibrated cophylogeny based on large subunit, small subunit, and internal transcribed spacer (ITS) sequence data obtained from 17 different fungal taxa and rbcL, ITS, and trnH-psbA sequence data from their corresponding hosts. Nine new fungal species are introduced in this paper and Appendiculella is synonymized under Asteridiella. The dominant coevolutionary events during the Cretaceous and Cenozoic are cospeciation and host shift, respectively. We hypothesize that the evolutionary history of epifoliar fungi can be divided into three major periods: origins of families, formations of genera, and diversification of species. The rise of angiosperms prompted the evolution of modern epifoliar fungi and the diversification of orders of Angiospermae fostered the formation of epifoliar fungal genera. Phylogenetically, epifoliar fungal genera can be delimited according to their coevolutionary patterns and divergent periods.

To understand the process and mechanism of speciation, a detailed analysis of origin and demographic history of recently diverged species pairs is necessary. Here, we investigate the evolutionary history of Actaea purpurea (P.K. Hsiao) J. Compton and its closest relatives, A. japonica Thunb. and A. biternata (Siebold and Zuccarini) Prantl. We aim to estimate important parameters of the divergence event, and to lay the foundation for further investigation of the speciation mechanism of this system. Floral and vegetative traits were measured and analyzed. Genetic structure, divergence history, and historical gene flow were also inferred from the plastid and single nucleotide polymorphism data. Floral traits were divergent, and a strong match between pollinator and floral traits was revealed. Genetically the two species were also well diverged, and the time of divergence was dated to the Pleistocene. The demographic modelling results suggest that A. purpurea had continuous limited gene flow with A. japonica and A. biternata since divergence. More work is now needed to confirm that floral trait divergence was selected by pollinators, as well as to understand how pollinator isolation acts in conjunction with other reproductive barriers to reduce gene flow between the two species.

Bakerantha is one of the three genera of subfamily Hechtioideae (Bromeliaceae). This genus was re-established recently, and it currently contains four species (B. caerulea, B. lundelliorum, B. purpusii, and B. tillandsioides), which are distributed throughout the central region of Mexico. Bakerantha tillandsioides has the widest geographical distribution of the four species, and some populations currently referred to it do not match the species description. In this study, we used extensive sampling (81 accessions) of four plastid regions (matK, rpl32-trnL, rps16-trnK, and ycf1) and the nuclear PRK gene to reconstruct the phylogenetic relationships and delimit the species boundaries in Bakerantha. Our results confirm the monophyly of Bakerantha, and the species delimitation analysis supports five evolutionary lineages within Bakerantha, showing that B. tillandsioides is nonmonophyletic as currently circumscribed. Diagnostic characters and coherent geographical distributions support the five lineages. On the basis of our results, we describe and illustrate B. hidalguense as a new species and provide evidence that B. caerulea is morphologically and ecologically different from B. tillandsioides, with which it has been confused in the past. Additionally, we provide a morphological key to the Bakerantha species.

Pea (Pisum sativum L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (Pisum sp.) remain controversial. To characterize patterns of genetic and morphological variation and investigate the classification of Pisum, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea, representing three species of Pisum and utilizing 34 morphological traits and 87 polymorphic simple sequence repeat markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of Pisum fulvum, Pisum abyssinicum, and some wild P. sativum accessions, whereas Groups II and III consisted of the two genetic groups under P. sativum that represented different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of Pisum, P. fulvum and P. abyssinicum possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of P. sativum described by some authors were not supported in this study, with the exception of several genotypes of P. sativum subsp. elatius that clustered with P. fulvum and P. abyssinicum. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.

Udoteaceae is a morphologically diverse family of the order Bryopsidales. Despite being very widespread geographically, this family is little known as compared with the closely related Halimedaceae or Caulerpaceae. Using the most extensive Udoteaceae collection to date and a multilocus genetic data set (tufA, rbcL, and 18S rDNA), we reassessed the species diversity of the family, as well as the phylogenetic relationships, the diagnostic morphoanatomical characters, and evolutionary history of its genera, toward a proposed taxonomic revision. Our approach included a combination of molecular and morphological criteria, including species delimitation methods, phylogenetic reconstruction, and mapping of trait evolution. We successfully delimited 62 species hypotheses, of which 29 were assigned (existing) species names and 13 represent putative new species. Our results also led us to revise the genera Udotea s.s., Rhipidosiphon s.s., and Chlorodesmis s.s., to validate the genus Rhipidodesmis, and to propose three new genera: Glaukea gen. nov., Ventalia gen. nov., and Udoteopsis gen. nov. We also identified two large species complexes, which we refer to as the “Penicillus–Rhipidosiphon–Rhipocephalus–Udotea complex” and the “Poropsis–Penicillus–Rhipidodesmis complex”. Using a time-calibrated phylogeny, we estimated the origin of the family Udoteaceae at Late Triassic (ca. 216 Ma), whereas most of the genera originated during Paleogene. Our morphological inference results indicated that the thallus of the Udoteaceae ancestor was likely entirely corticated and calcified, composed of a creeping axis with a multisiphonous stipe and a pluristromatic flabellate frond. The frond shape, cortication, and calcification are still symplesiomorphies for most extant Udoteaceae genera and represent useful diagnostic characters.

Streptocarpus ionanthus (Gesneriaceae) is endemic to Tanzania and Kenya, distributed in Tanga, Morogoro, and Kilifi regions. The species houses nine subspecies characterized by complex morphotypes and poorly understood evolutionary relationships, and thus is an ideal model for investigating evolutionary dynamics over time. Using multiple methods, we sought to test our hypothesis that the infraspecific taxa in Str. ionanthus are slightly variable and evolving populations. We first examined the genetic diversity, population differentiation, and phylogeographic structure among the populations of Str. ionanthus using both chloroplast and nuclear markers. We then estimated the divergence time of Str. ionanthus lineages and modeled past and future distribution. Despite Str. ionanthus exhibiting bottleneck events across its range, the populations maintain relatively high genetic diversity attributed to historical population admixture or local adaptation arising from habitat heterogeneity. The phylogeographic and genetic structure revealed a high connection among the Usambara mountains populations, while molecular dating suggested most diversification of haplotypes began ~1.32–0.18 million years ago and intensified toward the present, a conclusion of recent diversification. Phylogenetic relationship of Str. ionanthus cpDNA haplotypes revealed five main lineages with unique haplotypes that could be suggestive of past isolated refugia during the Pleistocene climate shifts. According to niche modeling, the stability of suitable areas during the Last Glacial Maximum (LGM) offered protective micro-habitats that have preserved the genetic diversity of Str. ionanthus to date. In conclusion, our findings suggest a complex Str. ionanthus with slightly variable lineages or populations attributed to multiple refugia and on the verge of divergence.

Whole genome duplication (WGD) provides new genetic material for genome evolution. After a WGD event, some duplicates are lost, while other duplicates still persist and evolve diverse functions. A particular challenge is to understand how this diversity arises. This study identified two WGD-derived duplicates, MYB158 and MYB189, from Populus tomentosa. Populus MYB158 and MYB189 had expression divergence. Populus tomentosa overexpressing MYB158 or MYB189 had similar phenotypes: creep growth, decreased width of xylem and secondary cell wall thickness. Compared to wild-type, neither myb158 mutant nor myb158 myb189 double mutant showed obvious phenotypic variation in P. tomentosa. Although MYB158 and MYB189 proteins could repress the same structural genes involved in lignin, cellulose, and xylan biosynthesis, the two proteins had their own specific regulatory targets. Populus MYB158 could act as the upstream regulator of secondary cell wall NAC master switch and directly represses the expression of the SND1-B2 gene. Taken together, Populus MYB158 and MYB189 have retained similar functions in negatively regulating secondary cell wall biosynthesis, but have evolved partially distinct functions in direct regulation of NAC master switch, with MYB158 playing a more crucial role. Our findings provide new insights into the evolutionary and functional divergence of WGD-derived duplicate genes.

Pollinator shift and its influence on floral traits have been well documented to explain the diversity of angiosperms, but such effects are still less known at the intraspecific level, especially the responses of different morphs of distylous plants. We hypothesized that the pollen transfer efficiency would decrease if the pollinator shifted from a long-tongued to short-tongued insect across populations, and plants would evolve towards selfing in response to the stressed pollination environment. Given the gender specialization between flower morphs, the long styled (L-morph) plants would increase female reproduction. Our study showed that the short-tongued Bombus tianshanicus, the most-visit pollinator in high elevation populations of distylous Primula nivalis, was less efficient in pollen transfer than long-tongued Bombylius major. The plants evolved to promote selfing through reducing the anther–stigma separation and increasing intramorph self-compatibility. The hand pollination experiment showed that after intramorph selfing, the fruit set and seed set increased with increasing elevation. Moreover, anther and stigma were closer in the L-morph than in the short styled (S-morph) plants, and the L-morphs showed higher pollen transfer efficiency than the S-morphs. Along with increased self-compatibility, the fruit set and seed set of L-morph plants were significantly higher than those of S-morph plants. We described the pollinator shifts along an elevation gradient in a distylous plant and the response of plants by promoting selfing, which confirmed our hypothesis and supported the pollinator-shift model. Our study also highlighted the different response in self-compatibility between flower morphs.

Because many plants ensure their reproductive success using some level of self-fertilization, it is predicted that the balance between pollinator-mediated pollen transfer and autonomous selfing will be correlated with habitat harshness and pollinator activity. To study these correlations, we used three annual species that differ in their self-incompatibility and compared their reproductive success in the form of fruit production and seed viability, with and without pollinators, along a rainfall gradient and in relation to pollinator activity. We found that pollinator activity decreased with increasing aridity. Although the reproductive success in the absence of pollinators fitted the species’ level of self-incompatibility, no clear trend was detected between pollinator visits or site harshness and relative reproductive success. Only one of the species, Sinapis alba, showed a consistent increase in autonomous selfing with both increased aridity and decreased pollinator visits, a finding that was supported by an increase in the viability of seeds produced in the absence of pollinators. Nevertheless, unlike our prediction, the absolute number of seeds produced per S. alba flower increased with aridity. Our overall findings suggest that despite decreasing pollinator abundance and diversity with increasing aridity, the reproductive success of annual species, even of those with high self-incompatibility, remains relatively high. Although there may be several mechanisms governing these results, the overall constant seed production despite environmental uncertainties may be part of the mechanism by which plants in arid ecosystems buffer environmental variations.

Insects produce pheromones to serve a range of ecological functions throughout their lifetime. The chemical composition, production pattern, and interspecies specificity provide information for carrying out their function and biological significance. Several species of Drosophila produce a class of volatile esters considered as “fruity smells”; however, the production pattern and ecological functions of these “fruity smell” volatiles in genus Drosophila are poorly understood. Here, using the headspace solid-phase microextraction (SPME) method, we tested the production pattern of volatile pheromones in Drosophila immigrans and factors that possibly affected pheromone production, including mating, feeding conditions, age of adult flies, and geographical distribution. We also explored the evolution and production pattern of volatile pheromones in 14 species of genus Drosophila. Our result showed that male D. immigrans adult flies produce three male-specific volatile ester pheromones, which are also considered as “fruity smell” chemicals, in a relatively stable pattern. In addition, a series of “fruity smell” ester pheromones with similar structure and chemical properties were found to appear in the species of D. virilis and D. immigrans species group, but not in the species of D. melanogaster species group. The ester volatile pheromone production of male flies has a correspondence with the female's demand for host plants. Integrating the production and evolution pattern of these volatile chemicals, we inferred the interaction between insects and host plants reflected in the Drosophila “fruity smell” pheromones.

The genus Osmunda L. contains approximately 10 extant species widely distributed in tropical and temperate regions, with the greatest concentration of species in East and Southeast Asia. Osmunda is characterized by dimorphic or commonly hemidimorphic fronds with dimorphic pinnae. Its geological history has been traced back to the Triassic. Most records of the genus are based on rhizomes and rarely on pinnae bearing sporangia and spores. Here, we describe fossil pinnae, sporangia, and spores of Osmunda lignitum (Giebel) Stur recovered from the middle Eocene of the Changchang Formation in the Changchang Basin, Hainan Island and the Youganwo Formation in the Maoming Basin, Guangdong, South China. The fossils closely resemble the extant Osmunda banksiifolia (C. Presl) Kuhn of the subgenus Plenasium on the basis of their morphological and anatomical structures. The present occurrence of O. lignitum indicates subg. Plenasium flourished and extended from the high latitude regions such as Northeast China to the low latitude areas of South China during the middle Eocene. Large numbers of specimens described here also indicate that Osmunda was the dominant understory fern element beneath mixed evergreen broad-leaf angiosperm and gymnosperm forests living in a warm and humid environment.

The Journal of Systematics and Evolution would like to acknowledge and thank the following reviewers for their contributions in the period January 1–December 31 in 2021:

Allen, Geraldine

Appelhans, Marc

Areces-Berazain, Fabiola

Averianov, Alexander O.

Bai, Wei-Ning

Bard, Nicholas

Bell, Charles

Besnard, Guillaume

Bisang, Irene

Bitencourt, Cássia

Bouckaert, Remco

Brandrud, Marie Kristine

Buellesbach, Jan

Câmara, Paulo

Cameron, Kenneth

Cannon, Chuck

Carta, Angelino

Chen, Jun

Chen, Xiao-Yong

Chen, Zhi-Duan

Christie, Kyle

Corlett, Richard

Dering, Monika

Ding, Wen-Na

Durka, Walter

Ebersbach, Jana

Edwards, Christine

Engle-Wrye, Nick

Eriksson, Torsten

Escudero, Marcial

Fady, Bruno

Favre, Adrien

Fazekas, Aron

Ford, Kerry

Franco, Fernando

Gao, Jiang-Yun

Gao, Lian-Ming

Gauquelin, Thierry

Ge, De-Yan

Ge, Xue-Jun

Gerrath, Jean

Goertzen, Leslie

Gong, Yan-Bing

Gradstein, Robbert

Harris, AJ

Hoffmann, Matthias H.

Howard, Cody

Huang, Ji-Hong

Huang, Jia-Xing

Huang, Shuang-Quan

Huarte, Roberto

Hultine, Kevin R.

Ickert-Bond, Stefanie

Ignatov, Michael

Ikeda, Hajime

Jiang, Hong-En

Jiménez-Mejías, Pedro

Jin, Xiao-Hua

Johnson, Steven D.

Kainulainen, Kent

Kandasamy, Dineshkumar

Kang, Long-Li

Kang, Ming

Klahs, Phillip

Klopper, Ronell

Kooyman, Robert

Ksepka, Daniel

Kutanan, Wibhu

Landrein, Sven

Lepais, Olivier

Li, Bo

Li, Jianhua

Li, Lin-Feng

Li, Xin-Xin

Li, Zhong-Hu

Liang, Er-Yuan

Liao, Wan-Jin

Liu, Bo-Ling

Liu, Xiao-Yan

Liu, Zhi-Jin

Liu, Zhi-Yong

Lou, Hai-Yi

Luo, A-Rong

Luo, Yi-Bo

Ma, Liang

Ma, Yong-Peng

Mao, Jian-Feng

Mao, Kang-Shan

Márquez-Corro, José Ignacio

Martín-Bravo, Santiago

McFarlane, Terry

McNeal, Joel

Michelangeli, Fabian A.

Miller, Joseph

Mondal, Mayukh

Morgan, John

Musser, Grace

Nawal, Shrestha

Oh, Sang-Hun

Olofsson, Jill

Ortiz, Edgardo

Passalacqua, Nicodemo

Pennell, Matthew

Phillips, Matthew

Pipes, Leonore

Pócs, Tamás

Qian, Hong

Qiu, Ying-Xiong

Ranker, Tom

Razafimandimbison, Sylvain G.

Rebollo, Roberto

Ree, Richard

Ren, Guang-Peng

Ren, Zong-Xin

Roalson, Eric

Roeser, Martin

Ruiz-Sanchez, Eduardo

Saarela, Jeffery

Salazar-Mendias, Carlos

Sánchez-Vilas, Julia

Sanmartin, Isabel

Santos-Gally, Rocio

Schlueter, Philipp

Schneider, Harald

Schwery, Orlando

Shrestha, Nawal

Shi, Tao

Šmarda, Petr

Sniderman, Kale

Snow, Neil

Song, Gang

Song, Yi-Gang

Soreng, Robert

Sosa, Pedro A.

Stark, Lloyd

Stedje, Brita

Su, Tao

Su, Xu

Sun, Hang

Sun, Kun

Sun, Miao

Sun, Yan-Xia

Sun, Yong-Shuai

Sundue, Michael

Thiv, Mike

Thomas, Daniel

Tian, Bao-Liang

Tribble, Carrie

Triplett, Jimmy

Vaillancourt, Rene

Vallès, Joan

van der Merwe, Marlien

Vanderpoorten, Alain

Villar, Jose

von Balthazar, Maria

Vorontsova, Maria S.

Walker, Joseph F.

Wang, Bao-Sheng

Wang, Heng-Chang

Wang, Hongru

Wang, Jing

Wilson, Paul

Wu, Yong-Jie

Wu, Zhi-Qiang

Xiang, Chun-Lei

Xiang, Qiao-Ping

Xie, Shu-Lian

Xing, Yao-Wu

Xu, Qing

Xu, Xiao-Ting

Yan, Yujing

Yang, Shi-Xiong

Yang, Ying-Bo

Yu, Yan

Zander, Richard

Zhang, De-Zhi

Zhang, Xiao-Ming

Zhang, Zhi-Yong

Zhao, Shi-Lei

Zhou, Ren-Chao

Zu, Pengjuan