Both geographic isolation and polyploidization are assumed to play an important role in driving species diversification. However, this is rarely illustrated through phylogenomic analyses. The genus Eutrema (Brassicaceae), which also includes the salt-resistant species, are distributed mainly in Asia with extensive species diversification in the Qinghai–Tibet Plateau (QTP) and adjacent regions. In this study, we revealed almost fully resolved backbone relationships of the genus with genome re-sequencing data for genomes of 168 individuals from 28 species. Phylogenetic analyses of both plastomes and single-copy nuclear genes from the whole genome recovered six well-supported clades with almost consistent relationships. The first two clades are mainly distributed in central China and central Asia, while the other four in the QTP and adjacent regions. All of them diversified within 12 million years. Within each clade, we recovered numerous conflicts in the interspecific relationships between nuclear and plastome phylogenies, likely suggesting hybridization and incomplete lineage sorting during species diversification. Our estimation of genome size and comparison of the number of the single-copy nuclear genes demonstrated frequent occurrences of polyploids in the genus. Except for an establishment of the backbone phylogeny, our phylogenomic analyses suggest that in addition to strong geographic isolation, polyploidization may have played an important role in species diversification of this genus.

The liquorice tribe Glycyrrhizeae is a leguminous herbaceous group of plants comprised of the genera Glycyrrhiza and Glycyrrhizopsis. Some Glycyrrhiza taxa contain glycyrrhizin, a pharmacologically significant sweet substance that also has applications in crafting industrial materials. Here, we utilized an expanded taxon sampling of Glycyrrhizeae to reconstruct the phylogenetic relationships in the tribe based on genome skimming data, including whole chloroplast genomes, nuclear ribosomal DNA, and low-copy nuclear DNA. We also launched machine learning analysis (MLA) for one species pair with controversial taxonomic boundary. The integrated results indicated Glycyrrhizopsis should be split from Glycyrrhiza, while the former genus Meristotropis should be treated as part of Glycyrrhiza. Glycyrrhizopsis includes two species, Glycyrrhizopsis asymmetrica and Glycyrrhizopsis flavescens, and we recognize 13 species in Glycyrrhiza: Glycyrrhiza acanthocarpa, Glycyrrhiza astragalina, Glycyrrhiza bucharica, Glycyrrhiza echinata, Glycyrrhiza foetida, Glycyrrhiza glabra, Glycyrrhiza gontscharovii, Glycyrrhiza lepidota, Glycyrrhiza macedonica, Glycyrrhiza pallidiflora, Glycyrrhiza squamulosa, Glycyrrhiza triphylla, and Glycyrrhiza yunnanensis. We propose a broader G. glabra that includes former Glycyrrhiza aspera, G. glabra s.s., Glycyrrhiza inflata, and Glycyrrhiza uralensis, and represents the glycyrrhizin-contained medicinal group. Our ancestral state inferences show the ancestor of Glycyrrhiza lacked glycyrrhizin, and the presence of glycyrrhizin evolved twice within Glycyrrhiza during the last one million years. Our integrative phylogenomics-MLA study not only provides new insights into long-standing taxonomic controversies of Glycyrrhizeae, but also represents a useful approach for future taxonomic studies on other plant taxa.

Oresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. The taxonomy of Mukdenia, especially of M. acanthifolia, has been controversial. To address this, we produced plastid and mitochondrial data using genome skimming for Mukdenia acanthifolia and Mukdenia rossii, including three individuals of each species. We assembled complete plastomes, mitochondrial CDS and nuclear ribosomal ETS/ITS sequences using these data. Comparative analysis shows that the plastomes of Mukdenia and Oresitrophe are relatively conservative in terms of genome size, structure, gene content, RNA editing sites and codon usage. Five plastid regions that represent hotspots of change (trnH-psbA, psbC-trnS, trnM-atpE, petA-psbJ and ccsA-ndhD) are identified within Mukdenia, and six regions (trnH-psbA, petN-psbM, trnM-atpE, rps16-trnQ, ycf1 and ndhF) contain a higher number of species-specific parsimony-informative sites that may serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between Mukdenia and Oresitrophe, we combined our data with published data based on three different datasets. The monophyly of each species (Oresitrophe rupifraga, M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M. acanthifolia), O. rupifraga) are well supported in trees reconstructed using the complete plastome sequences, but M. acanthifolia and M. rossii did not form a separate clade in the trees based on ETS + ITS data, while the mitochondrial CDS trees are not well-resolved. We found low recovery of genes in the Angiosperms353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordance between trees reconstructed from organellar and nuclear data. Considering its morphological distinctiveness and our molecular phylogenetic results, we strongly recommend that M. acanthifolia be treated as a distinct species.

Didymodon Hedw., with approximately 140 species in the family Pottiaceae, is distributed nearly throughout the world, with the greatest diversity and important ecological functions in drought lands and alpine ecosystems. Several studies involving morphology, molecular systematics, and macro-systematic analysis have addressed the infrageneric classification of Didymodon, but controversy over the position of the infrageneric and species classification remains due to its high degree of morphological variation in micro-habitats and strong sensitivity to climate change at regional and global scale. To date, only a few phylogenetic studies have been conducted with an incomplete number of Didymodon species; further, there is no study published regarding the divergence time of Didymodon. Consequently, we conducted a comprehensive phylogenetic analysis of Didymodon species, sampling a total of 107 species, based on one nuclear (ITS) and five chloroplast DNA. Moreover, divergence time analysis was conducted to infer the age of origin and divergence of Didymodon species. Our results presented the largest scale phylogenetic relationship of Didymodon to date and resolved the phylogenetic status of some controversial taxa and the new species. The divergence time estimation showed that Didymodon species originated around the early Cretaceous, and the diversification was concentrated in the Cretaceous and Eocene. Paleoclimate and environmental change have a direct impact on the origin and divergence of Didymodon species by shaping their morphology, resource availability and ecological niche. Our study will help understand species origin and speciation of Didymodon as well as reflecting species adaptability and experience to historical events.

Volvocales forms a species-rich clade with wide morphological variety and is regarded as an ideal model for tracing the evolutionary transitions in multicellularity. The phylogenetic relationships among the colonial volvocine algae and its relatives are important for investigating the origin of multicellularity in the clade Reinhardtinia. Therefore, a robust phylogenetic framework of the unicellular and colonial volvocine algae with broad taxon and gene sampling is essential for illuminating the evolution of multicellularity. Recent chloroplast phylogenomic studies have uncovered five major orders in the Chlorophyceae, but the family-level relationships within Sphaeropleales and Volvocales remain elusive due to the uncertain positions of some incertae sedis taxa. In this study, we contributed six newly sequenced chloroplast genomes in the Volvocales and analyzed a dataset with 91 chlorophycean taxa and 58 protein-coding genes. Conflicting phylogenetic signals were detected among chloroplast genes that resulted in discordant tree topologies among different analyses. We compared the phylogenetic trees inferred from original nucleotide, RY-coding, codon-degenerate, and amino acid datasets, and improved the robustness of phylogenetic inference in the Chlorophyceae by reducing base compositional bias. Our analyses indicate that the unicellular Chlamydomonas and Vitreochlamys are close to or nested within the colonial taxa, and all the incertae sedis taxa are nested within the monophyletic Sphaeropleales s.l. We propose that the colonial taxa in the Reinhardtinia are paraphyletic and multicellularity evolved once in the volvocine green algae and might be lost in Chlamydomonas and Vitreochlamys.

South China (SC) was a region with mixed rice–millet farming during the Middle Neolithic period and was also suggested to be the homeland of Tai-Kadai (TK)-speaking people. However, the formations of inland TK-speaking people and southwestern Hans are far from clear due to very few studies on this subject. Here, we reveal the spatiotemporally demographic history of SC by analyzing newly-generated genome-wide SNP data of 115 modern southwestern individuals and find that inland TK-speaking Dongs and Bouyeis have a close genomic affinity to coastal TK/Austronesian (AN)-speaking people and Neolithic Yangtze River basin (YZRB) farmers, while southwestern Hans and TK-speaking Gelaos possess a close genomic affinity to Neolithic Yellow River basin (YRB) farmers. Genetic differentiations are identified among TK people from SC and Southeast Asia, and between northern and southern inland Chinese TK people, in which the identified shared genetic ancestry between TK and AN people highlights a common origin of AN/TK groups. Conclusively, our findings indicate that millet farmers deriving from the YRB and rice farmers deriving from the YZRB substantially contribute to the present-day inland TK speakers and southwestern Hans via a two-way admixture scenario of bi-directional gene-flow events, which facilitates the formation of a modern two-way genetic admixture profile.

The population history of Southeast (SE) China remains poorly understood due to the sparse sampling of present-day populations and limited modeling with ancient genomic data. We report genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien (HM)-speaking She people from Fujian and Taiwan Island, SE China. We coanalyzed 66 Early Neolithic to Iron Age ancient Fujian and Taiwan Island individuals obtained from previously published works to explore the genetic continuity and admixture based on patterns of genetic variations of the high-resolution time transect. We found the genetic differentiation between northern and southern East Asians was defined by a north–south East Asian genetic cline and our studied southern East Asians were clustered in the southern end of this cline. The southeastern coastal modern East Asians are genetically similar to other southern indigenous groups as well as geographically close to Neolithic-to-Iron Age populations, but they also shared excess alleles with post-Neolithic Yellow River ancients, which suggested a southward gene flow on the modern southern coastal gene pool. In addition, we identified one new HM genetic cline in East Asia with the coastal Fujian HM-speaking She localizing at the intersection between HM and Han clines. She people show stronger genetic affinity with southern East Asian indigenous populations, with the main ancestry deriving from groups related to southeastern ancient indigenous rice farmers. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Our estimated north–south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze Age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in SE Asia.

The environment is a powerful selective pressure for sessile organisms, such as plants, and adaptation to the environment is particularly important for long-lived species, like trees. Despite the importance of adaptive trait variation to the survival and success of trees, the molecular basis of adaptation is still poorly understood. Gene expression patterns in three closely related, but phenotypically and ecologically divergent, pine species were analyzed to detect differentiation that may be associated with their adaptation to distinct environments. Total RNA of Pinus mugo, Pinus uncinata, and Pinus sylvestris samples grown under common garden conditions was used for de novo transcriptome assembly, providing a new reference dataset that includes species from the taxonomically challenging P. mugo complex. Gene expression profiles were found to be very similar with only 121 genes significantly diverged in any of the pairwise species comparisons. Functional annotation of these genes revealed major categories of distinctly expressed transcripts, including wood trait properties, oxidative stress response, and response to abiotic factors such as salinity, drought, and temperature. We discuss putative associations between gene expression profiles and adaptation to different environments, for example, the upregulation of genes involved in lignin biosynthesis in the species, which have adapted to mountainous regions characterized by strong winds and thick snow cover. Our study provides valid candidates for verification of the importance of the gene expression role, in addition to evidence for selection within genomic regions, in the process of ecological divergence and adaptation to higher altitudes in pine taxa.

The impact of climate change on biodiversity operates through a complex mixture of habitat loss and range shift through the emergence of newly suitable areas (Warren et al., 2013). The main question is therefore to determine whether species have the ability to balance the loss of suitable habitats by effectively shifting their ranges and track suitable areas under climate change (Nogués-Bravo et al., 2018). Zanatta et al. (2020) most recently simulated the dispersal of apparently extremely efficient dispersers, namely bryophytes, whose tiny spores (<20 µm on average) are wind-dispersed across large distances, under several climate change scenarios. They concluded that, despite their high dispersal capacities, bryophytes will lose suitable areas at a faster rate than they will colonize newly suitable areas. Paradoxically, mounting evidence points to striking range expansions in epiphytic floras in the context of the sharp decrease of SO₂ concentrations since the 1980s and climate warming (Tuba et al., 2011). Here, we addressed this apparent controversy by reassessing the results of Zanatta et al. (2020) in the light of the repartitioning of the data per habitat type.

North China and South Siberia, populated by Altaic- and Sino-Tibetan-speaking populations, possess extensive ethnolinguistic diversity and serve as the crossroads for the initial peopling of America and western–eastern transcontinental communication. However, the population genetic structure and admixture history of northern East Asians remain poorly understood due to a lack of genome-wide data, especially for Mongolic-speaking people in China. We genotyped genome-wide single nucleotide polymorphisms for 510 individuals from 38 Mongolic, Tungusic, and Sinitic-speaking populations. We first explored the shared alleles and haplotypes within the studied groups. We then merged with 3508 published modern and ancient Eurasian individuals to reconstruct the deep evolutionary and natural selection history of northern East Asians. We identified genetic substructures within Altaic-speaking populations: Western Turkic people harbored more western Eurasian-related ancestry; Northern Mongolic people in Siberia and eastern Tungusic people in Amur River Basin (ARB) possessed a majority of Neolithic ARB related ancestry; Southern Mongolic people in China possessed apparent genetic influence from Neolithic Yellow River Basin (YRB) farmers. Additionally, we found the differentiated admixture history between western and eastern Mongolians and geographically close Northeast Hans: the former received a genetic impact from western Eurasians, and the latter retained the primary Neolithic YRB and ARB ancestry. Moreover, we demonstrated that Kalmyk people from the northern Caucasus Mountains possessed a strong genetic affinity with Neolithic Mongolian Plateau (MP) people, supporting the hypothesis of their eastern Eurasian origin and long-distance migration history. We also illuminated that historical pastoral empires in the MP contributed considerably to the gene pool of northern Mongolic people but rarely to the southern ones. We finally found natural selection signatures in Mongolians associated with alcohol metabolism. Our results demonstrated that the Neolithic ancestral sources from the MP or ARB played an important role in spreading Altaic populations and languages. The observed multisources of genetic diversity contributed significantly to the extensive ethnolinguistic diversity in northern East Asia.

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 2022:

Akita, Shingo

Allen, Geraldine

An, Xin-Min

Appelhans, Marc

Bacci, Lucas

Bhardwaj, Pankaj

Brothers, Denis

Cai, Wan-Zhi

Cameron, Kenneth

Cardoso, Pedro

Cellinese, Nico

Chao, Zhi

Chen, Jin-Ming

Chen, Shi-Chao

Chen, Xiao-Yong

Chen, Zhi-Duan

Cheng, Feng

Chesters, Douglas

Cilli, Elisabetta

Corlett, Richard

Del Rio, Cédric

Denk, Thomas

Dering, Monika

Dillenberger, Markus

Domina, Gianniantonio

Draper, David

Du, Fang

Duckett, Jeffrey

Ebersbach, Jana

Edera, Alejandro

Edwards, Christine

Escudero, Marcial

Fan, Xing

Franco, Fernando

Fujiwara, Tao

Gao, Lian-Ming

Garnatje, Teresa

Ge, Song

Gibernau, Marc

Gillespie, Lynn

Gong, Yan-Bing

Guo, Xian-Guang

Guo, Ya-Long

He, Bin

Heřmanová, Zuzana

Herrera, Fabiany

Hetterscheid, Wilbert

Holstein, Norbert

Howard, Cody

Huang, Bin-Quan

Huang, Shuang-Quan

Huang, Ji-Hong

Huang, Xiao-Lei

Huang, Zheng-Zhong

Ickert-Bond, Stefanie

Ikeda, Hajime

Jia, Hui

Jiang, Ting-Lei

Jiang, Xiao-Long

Jiao, Heng-Wu

Jiao, Yuan-Nian

Jin, Xiao-Hua

Jin, Jian-Hua

Johnson, Steven D.

Jud, Nathan

Kandasamy, Dineshkumar

Kikuchi, Satoshi

Kim, Sang-Tae

Kociolek, John

Koenemann, Daniel

Köhler, Matias

Kong, Xiang-Bo

Kunzmann, Lutz

Laffan, Shawn

Leslie, Andrew

Li, Hong-Tao

Li, Jianhua

Li, Jia-Tang

Li, Lang

Li, Lin-Feng

Li, Lu-Lu

Li, Ming-He

Li, Pan

Li, Xin-Xin

Liao, Wan-Jin

Lin, Ai-Qing

Liu, Dong

Liu, Hong-Mei

Liu, Shih-Hui

Liu, Tong-Yi

Liu, Zhi-Yong

Loizeau, Pierre-André

Long, Chun-Lin

Lu, Li-Min

Luo, A-Rong

Luo, Yi-Bo

Lyskov, Dmitry

Ma, Tao

Mandel, Jennifer

Manen, Jean-François

Mao, Jian-Feng

Mao, Kang-Shan

Mao, Ling-Feng

Marques, Isabel

McAdam, Scott

Mi, Xiang-Cheng

Michelangeli, Fabian

Mishler, Brent

Mishra, Geetanjali

Morgan, John

Múlgura, Maria Ema

Nickrent, Daniel

Nicolas, Antoine

Nie, Ze-Long

Olofsson, Jill

Olsson, Sanna

Park, Seonjoo

Patrizia, Serventi

Piwczyński, Marcin

Qiu, Ying-Xiong

Raguso, Robert

Ramos, Sergio

Ran, Jin-Hua

Rebollo, Roberto

Ren, Zong-Xin

Rojas-Andrés, Blanca

Rose, Jeffrey

Saavedra, Serguei

Salazar, Gerardo

Sanchez Reyes, Luna Luisa

Sawicki, Jakub

Schlueter, Philipp

Schneider, Harald

Shi, Gong-Le

Shi, Su-Hua

Shi, Wei

Stökl, Johannes

Stuessy, Tod

Su, Tao

Suda, Shoichiro

Sun, Hong-Zheng

Sun, Miao

Sundue, Michael

Tan, Yun-Hong

Tang, Liang

Tang, Long

Tang, Qing

Tembrock, Luke

Tomasello, Salvatore

Tribble, Carrie

Tu, Tie-Yao

Valcarcel, Virginia

Varga, Sandra

Vatanparast, Mohammad

Wan, Justin S. H.

Wang, Ai-Ying

Wang, Bao-Sheng

Wang, Gang

Wang, Geoff

Wang, Heng-Chang

Wang, Hong-Wei

Wang, Jing

Wang, Mao-Jun

Wang, Nian

Wang, Wei

Wang, Yin-Zheng

Wang, Ze-Fu

Watanabe, Shin

Weng, Mao-Lun

Wu, Yun-Ke

Wu, Zeng-Yuan

Wu, Zhi-Qiang

Xiang, Chun-Lei

Xiang, Qiao-Ping

Xiang, Qiu-Yun (Jenny)

Xiang, Xiao-Guo

Xie, San-Ping

Xie, Shu-Lian

Xing, Yao-Wu

Xu, Jian-Hong

Xu, Xiao-Ting

Xue, Huai-Jun

Yan, Yu-Jing

Yan, Yue-Hong

Yang, Melinda

Yang, Shi-Xiong

Ye, Hang

Ye, Jian-Fei

Yi, Xueling

Yoon, Hwan Su

Yu, Xiang-Qin

Yu, Yan

Yu, Yi-Lun

Zander, Richard

Zhang, Zhi-Qiang

Zhang, Chi

Zhang, Hai-Qing

Zhang, Ling

Zhang, Qun-Jie

Zhang, Xian-Chun

Zhang, Xiao-Ming

Zhang, Xiao-Xia

Zhang, Xu

Zhao, Liang

Zhao, Yi-Yong

Zhou, Ren-Chao

Zhou, Zhi-Jun

Zhu, An-Dan

Zou, Zheng-Ting

Zu, Pengjuan