Table of Contents

01 September 2023, Volume 61 Issue 5

Cover illustration: The middle image shows the global species diversity and diversification rate patterns of Smilacaceae on the left, and the ancestral area and trait evolution of the family on the right. See figure 1 and figure S9 of the article by Qi et al., pp.733-747 in this issue, for details. The top and bottom photos are Smilax species from the Old World and the New World, respectively. Photos by Pan Li, Cheng-Xin Fu, Zhe-Chen Qi, Bernard Dupont, Bruce Gray, Canek Ledesma, and Andrés Hernández. Designed by Zhe-Chen Qi, Pan Li, and Cheng-Xin Fu. [Detail] ...

  

Issue Information
• Issue Information

  J Syst Evol. 2023, 61(5): 0-4.
  https://doi.org/10.1111/jse.12888

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save
Research Articles
• 

  Climatic niche evolution in Smilacaceae (Liliales) drives patterns of species diversification and richness between the Old and New World

  Zhe-Chen Qi, Pan Li, Jun-Jie Wu, Alexander Gamisch, Tuo Yang, Yun-Peng Zhao, Wu-Qing Xu, Shi-Chao Chen, Kenneth M. Cameron, Ying-Xiong Qiu, and Cheng-Xin Fu

  J Syst Evol. 2023, 61(5): 733-747.
  https://doi.org/10.1111/jse.12998

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.

  ·By integrating the global phylogenetic and macroecological data on the diversification of Smilacaceae, the evolutionary histories and diversification patterns were reconstructed.
  ·The origin of the family Smilacaceae is estimated during the Late Cretaceous/Early Palaeocene, and began to diversify in the middle to low latitudes in Central America and Eurasia during the Late Eocene.
  ·The species diversification rate was positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene are proved to play important roles in species diversification dynamics within Smilacaceae.
• 

  Using phylogenomics to untangle the taxonomic incongruence of yellow-flowered Camellia species (Theaceae) in China

  Su-Juan Wei, Yong-Qing Liufu, He-Wen Zheng, Hai-Ling Chen, Yan-Chi Lai, Yan Liu, Quan-Qing Ye, and Shao-Qing Tang

  J Syst Evol. 2023, 61(5): 748-763.
  https://doi.org/10.1111/jse.12915

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  All yellow Camellia plants in China are threatened, but their classification is contentious. Here, we performed a phylogenetic reconstruction based on nuclear double-digest restriction site-associated DNA sequencing (ddRAD), transcriptomes, nuclear ribosomal internal transcribed spacer (nrITS), and the small single-copy region of the chloroplast genome, in combination with morphological evidence to help resolve taxonomic ambiguity of those rare and threatened species. Conflicting relationships were derived from nuclear and chloroplast sequences. The strong hybridization/introgression signal detected suggests reticulate evolution mainly caused this discordance pattern. The nuclear-ddRAD and RNA-seq phylogenies fit better to the yellow camellias' morphology, providing a clear resolution for inferring their relationships in China. Based on present phylogenetic analyses and morphological characters, we propose these taxonomic suggestions: (i) Camellia petelotii and Camellia nitidissima are distinct species; (ii) Camellia ptilosperma, Camellia longruiensis, Camellia longgangensis, and C. longgangensis var. grandis are conspecific with Camellia flavida; (iii) Camellia multipetala and C. longgangensis var. patens are synonyms of Camellia quinqueloculosa, and C. quinqueloculosa should be recognized as an independent species; (iv) Camellia wumingensis should be formally recognized as an independent species; (v) Camellia longzhouensis is a synonym of Camellia chrysanthoides; (vi) Camellia xiashiensis and Camellia parvipetala should be treated as synonyms of Camellia micrantha; (vii) Camellia achrysantha is a good species; (viii) Camellia tunghinensis is an independent species; (ix) species status of Camellia huana is well-supported; and (x) Camellia pingguoensis var. terminals should be correctly identified to species level as Camellia terminalis. These results provide the basis for the recognition 20 yellow Camellia species in China.

  All yellow Camellia species in China are threatened. To avoid mistakes in species conservation, high-resolution phylogenetic analyses were performed by using genome-scale double-digest restriction site-associated (ddRAD) and transcriptomes sequencing, in combination with morphological evidences to resolve taxonomic incongruence of yellow-flowered Camellia species in China. These results provide the basis for the recognition at least 20 yellow Camellia species in China.
• 

  RAD sequencing, morphometry and synecology clarify the taxonomy of the Melica ciliata (Poaceae) complex in France and Poland

  Sergio Castro, Audrey Muratet, Magdalena Szczepaniak, Julie Nguefack, and Laurent Hardion

  J Syst Evol. 2023, 61(5): 764-775.
  https://doi.org/10.1111/jse.12940

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Melica (Poaceae) consist of about 92 species distributed across temperate regions of the world. Within section Dalycum, Melica ciliata sensu lato forms a taxonomic complex of several species and subspecies with clinal morphological variation causing conflicting identifications. To resolve taxonomic confusion, we used three complementary approaches, through molecular, morphological, and phytoecological analyses. The double-digest restriction-associated DNA markers significantly support the monophyly of three taxa: (i) the Mediterranean Melica magnolii, (ii) the Eurasian Melica transsilvanica subsp. transsilvanica, and (iii) the west-European M. ciliata subsp. glauca. This differentiation is corroborated by the analysis of 22 morphometric variables. Furthermore, phytoecological analysis of 221 floristic inventories revealed habitat distinctions among these taxa. Our approach of integrative taxonomy argues for a specific distinction for these three taxa, and we include a key to separate these forms. These new molecular data on the section Dalycum, subsection Ciliatae, call for further phylogenetic analyses including samples of M. ciliata subsp. ciliata and other East-Mediterranean and South African taxa.

  Three types of markers were used to clarify the taxonomic status of Melica magnolii, Melica ciliata subsp. glauca, and Melica transsilvanica subsp. transsilvanica. RAD sequencing-based phylogenetic analyses reveal the monophyletic nature of each taxon, which is congruent with morphometric clustering and habitat distinctions. Useful information for field recognition is presented. More work is needed to fully understand the evolution and diversification of this intricate taxonomic complex.
• 

  Biogeographic patterns of polyploid species for the angiosperm flora in China

  Kai-Lai Wang, Pu-Rong Deng, Zhi Yao, Jin-Yi Dong, Zhi He, Peng Yang, and Yong-Bo Liu

  J Syst Evol. 2023, 61(5): 776-789.
  https://doi.org/10.1111/jse.12909

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Exploring the frequency and distribution pattern of polyploid species in geographic parameters is of significance in understanding the mechanisms of polyploid speciation and evolutionary drivers of biodiversity. We here explored polyploid and paleopolyploid incidence frequency in a scale of 100×100 km grids in China. We found 33% of angiosperm species are polyploidy in China, and 23% of polyploid speciation. Western China and eastern China showed a significantly different polyploid and paleopolyploid frequency, with an evolutionary cradle of polyploid angiosperms in the Qinghai-Tibetan plateau. Herbaceous species exhibited higher polyploid frequency but lower paleopolyploid frequency than woody species, indicating the former experienced more rapid differentiation and speciation than the latter. Our results indicate that western China is an evolutionary cradle for polyploid angiosperms where harsh environment facilitates the establishment and survival of polyploids, while polyploid lineages tend to rediploidize to be diploids with sufficient time in suitable environment.

  We analyzed the biogeographical patterns of polyploid and paleopolyploid frequency at a scale of 100×100km grids in China, and revealed the role of polyploidization and rediploidization of polyploids in understanding the mechanisms of speciation and evolutionary drivers of biodiversity. Our results indicate that western China is an evolutionary cradle for polyploid angiosperms where harsh environment facilitates the establishment and survival of polyploids, while polyploid lineages tend to rediploidize to be diploids with sufficient time in suitable environment.
• 

  Rapid structural evolution of Dendrobium mitogenomes and mito-nuclear phylogeny discordances in Dendrobium (Orchidaceae)

  Meng-Ting Wang, Zhen-Yu Hou, Chao Li, Jia-Peng Yang, Zhi-Tao Niu, Qing-Yun Xue, Wei Liu, and Xiao-Yu Ding

  J Syst Evol. 2023, 61(5): 790-805.
  https://doi.org/10.1111/jse.12912

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Reconstructing mitochondrial genomes of angiosperms is extremely intricate due to frequent recombinations which give rise to varied sized in Dendrobium mitogenomes and their structural variations, even in most orchid species. In this study, we first sequenced two complete and five draft mitochondrial genomes of Dendrobium using next-generation and third-generation sequencing technologies. The mitochondrial genomes were 420 538-689 048 bp long, showing multipartite (multichromosomal) structures that consisted of variably sized circular or linear-mapping isoforms (chromosomes). The comparison of mitochondrial genomes showed frequent gene losses in Dendrobium species. To explore structure variations of mitochondrial genomes in vivo, we quantified copy numbers of five mitochondrial genes and DNA contents per mitochondrion. The gene copy numbers and the DNA contents showed extreme differences during Dendrobium development, suggesting dynamic structures of mitochondrial genomes. Furthermore, phylogenetic relationships of 97 accessions from 39 Dendrobium species were constructed based on 12 nuclear single-copy genes and 15 mitochondrial genes. We discovered obvious discordance between the nuclear and mitochondrial trees. Reticulate evolution was inferred from the species network analysis in Dendrobium. Our findings revealed the rapid structural evolution of Dendrobium mitochondrial genomes and the existence of hybridization events in Dendrobium species, which provided new insights into in vivo structural variations of plant mitochondrial genomes and the strong potential of mitochondrial genes in deciphering plant evolution history.

  Mitochondrial genomes of Dendrobium showed multichromosomal structures with variably sized circular or linear isoforms. Mitochondrial protein-coding genes underwent frequent lost events in Dendrobium species. The structures of mitochondrial genomes were dynamic during Dendrobium development. The mitochondrial tree and the nuclear tree displayed obvious phylogenetic discordances in Dendrobium.
• 

  Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships

  Xiao-Gang Fu, Shui-Yin Liu, Robin van Velzen, Gregory W. Stull, Qin Tian, Yun-Xia Li, Ryan A. Folk, Robert P. Guralnick, Heather R. Kates, Jian-Jun Jin, Zhong-Hu Li, Douglas E. Soltis, Pamela S. Soltis, and Ting-Shuang Yi

  J Syst Evol. 2023, 61(5): 806-826.
  https://doi.org/10.1111/jse.12920

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies have clarified the most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 82 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto- nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances were most likely to stem from incomplete lineage sorting (ILS); nuclear gene-tree conflict might be caused by both ILS and gene flow between species. All genera of Cannabaceae were recovered as monophyletic, except for Celtis, which consisted of two distinct clades: Celtis I (including most Celtis species) and Celtis II (including Celtis gomphophylla and Celtis schippii). We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence. Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae, enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.

  Tanglegram showing the incongruence between the nuclear (left) and chloroplast (right) trees of Cannabaceae both inferred by partitioned RAxML analyses. Black lines connect the same taxa between the two trees. The colored branches indicate the major clades of Cannabaceae: black, outgroups; brown, Aphananthe; medium aquamarine, Gironniera; purple, Lozanella; red, Celtis II; light green, Chaetachme+Pteroceltis; green, Cannabis+Humulus; orange, Trema s.l.; and blue, Celtis I.
• 

  An integrative taxonomic study of Santolina (Asteraceae) from southern France and north-eastern Spain reveals new endemic taxa

  Antonio Giacò, Lucia Varaldo, Gabriele Casazza, Daniele De Luca, Paolo Caputo, Marco Sarigu, Gianluigi Bacchetta, Llorenç Sáez, and Lorenzo Peruzzi

  J Syst Evol. 2023, 61(5): 827-842.
  https://doi.org/10.1111/jse.12925

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Santolina is a clear example of a genus lying in an alpha-taxonomic status, with species accepted only based on qualitative morphological descriptions. In particular, taxonomic issues still need to be resolved for Santolina populations from southern France and north-eastern Spain, and so, we carried out an integrative taxonomic study involving morphometrics, cypsela morphometrics, niche overlap, and phylogenetic analysis based on six plastid markers (trnH-psbA, trnL-trnF, trnQ-rps16, rps15-ycf1, psbM-trnD, and trnS-trnG). Our results revealed that the current taxonomic circumscription is not adequate. In particular, the Santolina populations at the foothills of eastern Pyrenees, previously included in the variability of Santolina benthamiana, have to be considered as a distinct species, namely, Santolina intricata. In addition, despite their high phylogenetic relatedness, S. benthamiana s.str. and Santolina ericoides can still be considered as distinct species due to clear morphological and ecological differentiation. Finally, we demonstrated that three different subspecies can be recognized in Santolina decumbens, a species endemic to Provence. For one of these subspecies, due to its extremely restricted distribution range, conservation issues are pointed out.

  An integrative taxonomic approach involving morphometrics, niche analysis, and molecular systematics with plastid markers (trnH-psbA, trnL-trnF, trnQ-rps16, rps15-ycf1, psbM-trnD, and trnS-trnG) revealed new endemic taxa of Santolina in southern France and north-eastern Spain. In particular, Santolina intricata, previously considered as a synonym of Santolina benthamiana, has to be considered as a distinct species, endemic to eastern Pyrenees. Then, for Santolina decumbens, a species endemic to Provence, three subspecies can be recognized. Finally, despite a high phylogenetic relatedness, Santolina ericoides and S. benthamiana can still be considered as distinct species due to both morphological and ecological differentiation.
• 

  The evolutionary rate of leaf osmotic strength drives diversification of Primulina species in karst regions

  Gui-Lin Wu, Qing Ye, Hui Liu, De-Xiang Chen, Zhang Zhou, Ming Kang, Hang-Hui Kong, Zhi-Jing Qiu, and Hui Wang

  J Syst Evol. 2023, 61(5): 843-851.
  https://doi.org/10.1111/jse.12914

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Leaf water storage capacity and osmotic strength are important traits enabling species to adapt to environments that are often moisture limited. However, whether these drought tolerance traits are correlated with the species diversification rate (DR) of plant lineages is yet to be determined. In this study, we selected a species-rich genus (Primulina) of plants widely distributed in karst regions in which species frequently experience variable periods of drought. We measured water storage capacity-related traits (including leaf thickness and water content per mass) and saturated osmotic strength in the leaves of 58 Primulina species growing in a common garden. Subsequently, using phylogenetic methods, we examined the relationships between the rate of species diversification and the drought tolerance traits and between the species DR and evolutionary rates of these traits. We found that neither water storage capacity nor saturated osmotic strength showed significant relationships with the rate of species diversification. However, the evolutionary rate of saturated osmotic strength showed a significant correlation with the species DR, although no comparable significant relationship was detected regarding the evolutionary rate of water storage capacity. Our study indicates that the diversification among Primulina species has typically been accompanied by an extensive divergence of leaf osmotic strength but not a divergence in leaf water storage capacity. These findings will enhance our current understanding of how drought tolerance influences the diversification of plant species in karst regions.

  Leaf drought tolerance (including leaf water storage capacity and osmotic strength) was hypothesized drive diversification in Primulina which are widely distributed in karst regions. We found the evolutionary rate of saturated osmotic strength showed a significant correlation with the rate of diversification in Primulina. By contrast, leaf water storage capacity showed nonsignificant relationship with diversification rate in this genus. Our study indicate that the diversification among Primulina species has typically been accompanied by an extensive divergence of leaf osmotic strength, not a divergence in leaf water storage capacity.
• 

  Genomic analyses reveal natural selection on reproduction related genes between two closely related Populus (Salicaceae) species

  Yang Tian, Shu-Yu Liu, Pär K. Ingvarsson, Dan-Dan Zhao, Li Wang, Baoerjiang Abuduhamiti, Jin-Feng Cai, Zhi-Qiang Wu, Jian-Guo Zhang, and Zhao-Shan Wang

  J Syst Evol. 2023, 61(5): 852-867.
  https://doi.org/10.1111/jse.12911

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Identifying the factors that cause reproductive isolation and their relative importance in species divergence is crucial to our understanding of speciation processes. In most species, natural selection is commonly considered to play a large role in driving speciation. Based on whole genome re-sequencing data from 27 Populus alba and 28 Populus adenopoda individuals, we explored the factors related to reproductive isolation of these two closely related species. The results showed that the two species diverged ~5-10 million years ago (Ma), when the Qinghai-Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid. In highly differentiated genomic regions, the relative divergence (F_ST) and absolute divergence (d_xy) were significantly higher than the genomic background, θπ and shared polymorphisms decreased whereas fixed differences increased, which indicated that natural selection played a key role in the reproductive isolation of the two species. In addition, we found several genes that were related to reproduction that may be involved in explaining the reproductive isolation. Using phylogenetic trees resolved from haplotype data of Populus tomentosa and P. adenopoda, the maternal origin of P. tomentosa from P. adenopoda was likely to be located in Hubei and Chongqing Provinces.

  Using the re-sequencing data of 27 Populus alba and 28 Populus adenopoda, it was identified that the two species have obvious genetic structure. The uplift of the Qinghai-Tibet Plateau and climate change make the two populations differentiate and produce post-zygotic isolation. The hybrid offspring of Populus tomentosa are sterile. Natural selection plays an important role in this process.
• 

  Exploring morphological evolution in relation to habitat moisture in the moss genus Fissidens using molecular data generated from herbarium specimens

  Jessica M. Budke, Nikisha R. Patel, GoFlag Consortium, Mark D. Wienhold, and Maria A. Bruggeman-Nannenga

  J Syst Evol. 2023, 61(5): 868-889.
  https://doi.org/10.1111/jse.12926

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats, which can be tested using comparative phylogenetics. These lines of inquiry have been developed to include target capture sequencing, which can yield phylogenomic scale data from herbarium specimens. Here, we test the relationship between taxonomically important morphological characters in the moss genus Fissidens, using a 400- locus data set generated using a target-capture approach in tandem with a three-locus phylogeny generated using Sanger sequencing. Phylogenetic trees generated using ASTRAL and Bayesian inference were used to test the monophyly of subgenera/sections. These trees provide the basis for ancestral character state reconstructions and phylogenetic correlation analyses for five morphological characters and characters related to the moisture habitat, scored from the literature and by specimen inspection. Many of these characters exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border of the gametophyte) and habitat moisture niche breadth, which could be interpreted as the more extensive limbidium enabling species to survive across a wider variety of habitats. We also found correlations between costa anatomy, peristome morphology, and the limbidium, which could reflect the evolutionary recruitment of genetic networks from the gametophyte to the sporophyte phase. The correlation found between average habitat moisture and the sexual system indicates that dioicous and polyoicous species are more likely to be found in moist habitats and that these higher moisture levels could be particularly, reproductively advantageous to species with separate sexes.

  Phylogenetic trees were generated from both a 400-locus data set generated using a target-capture approach as well as a three-locus phylogeny generated using Sanger sequencing for mosses in the genus Fissidens. Taxonomically important morphological characters for the genus were found to exhibit statistically significant phylogenetic signals. Significant correlations were found between the limbidium and habitat moisture niche breadth, which could be interpreted as the more extensive limbidium enabling species to survive across a wider variety of habitats. We also found correlations between costa anatomy, peristome morphology, and the limbidium, which could reflect the evolutionary recruitment of genetic networks from the gametophyte to the sporophyte phase. The correlation found between average habitat moisture and the sexual system indicates that dioicous and polyoicous species are more likely to be found in moist habitats, and these higher moisture levels could be particularly reproductively advantageous to species with separate sexes.
• 

  The associated evolution among the extensive RNA editing, GC-biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae

  Jong-Soo Kang, Jigao Yu, Xian-Chun Zhang, and Qiao-Ping Xiang

  J Syst Evol. 2023, 61(5): 890-905.
  https://doi.org/10.1111/jse.12927

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Extensive C-to-U editing has been reported from plastid genomes (plastomes) and mitochondrial genomes (mitogenomes) of spikemoss. While “reverse” U-to-C editing was recorded in other seed-free plants such as hornworts, quillworts, and ferns, it was not observed in spikemosses. However, no comprehensive study on the association between RNA editing and other genomic features was conducted for the organelle genomes of spikemosses. Here, we report thousands of C-to-U editing sites from plastomes and mitogenomes of two species: 1767 and 2394 edits in Selaginella remotifolia, and 4091 and 2786 edits in Selaginella nipponica, respectively. Comparative analyses revealed two different editing frequencies among plastomes, but one similar frequency in mitogenomes. The different editing frequency in the Selaginella organelle genomes is related to the nonsynonymous substitution rate and the genome structural complexity. The high guanine and cytosine (GC) content caused by GC-biased mutations in organelle genomes might be related to the absence of U-to-C editing in Selaginellaceae. Using RNA-seq and whole-genome data, we screened the pentatricopeptide repeat (PPR) family and discovered that the number of aspartic acid-tyrosine-tryptophan (DYW) domain-containing PPR proteins corresponded roughly to the editing abundance in the Selaginella organelle genomes. Consequently, we hypothesize that associated evolution among RNA editing, GC-biased mutation in organelle genomes, and the PPR protein family encoded in the nuclear genome, is probably triggered by the aberrant DNA repair system in Selaginellaceae. Our study provides new insights into the association between organelle and nuclear genomes in Selaginellaceae, which would contribute to understanding the evolution of post-transcriptional modifications of organelle genomes in land plants.

  Organelle genomes in Selaginellaceae are notorious for genome architecture and extensive RNA editing. In order to understand the editing pattern in Selaginellaceae organelle genomes, thousands of RNA editing sites in the plastid and mitochondrial genomes of two Selaginella species were newly identified and compared with those from other previously reported Selaginella organelle genomes. Additionally, the analysis of pentatricopeptide repeat (PPR) genes using RNA-seq and whole-genome data demonstrated that the expansion of PPR proteins with the aspartic acid-tyrosine-tryptophan (DYW) domain corresponded to the editing abundance in their organelle genomes.
• 

  Excessive and asymmetrical removal of heterozygous sites by maxSH biases downstream population genetic inference: Implications for hybridization between two primroses

  Jie Zhang, Francisco Pina-Martins, Zu-Shi Jin, Yong-Peng Cha, Zu-Yao Liu, Jun-Chu Peng, Jian-Li Zhao, and Qing-Jun Li

  J Syst Evol. 2023, 61(5): 906-918.
  https://doi.org/10.1111/jse.12928

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Techniques of reduced-representation sequencing (RRS) have revolutionized ecological and evolutionary genomics studies. Precise establishment of orthologs is a critical challenge for RRS, especially when a reference genome is absent. The proportion of shared heterozygous sites across samples is an alternative criterion for filtering paralogs. In the prevailing pipeline for variant calling of RRS data - PYRAD/ IPYRAD, maxSH is an often overlooked parameter with implications to detecting and filtering paralogs according to shared heterozygosity. Using empirical genotyping by sequencing data of two primroses (Primula alpicola Stapf and Primula florindae Ward) and their putative hybrids, and extra data sets of Californian golden cup oaks, we explore the impact of maxSH on filtering paralogs and further downstream analyses. Our study sheds light on the simultaneous validity and risk of filtering paralogs using maxSH, and its significant effects on downstream analyses of outlier detection, population assignment, and demographic modeling, emphasizing the importance of attention to detail during bioinformatic processes. The mutual confirmation between results of population assignment and demographic modeling in this study suggested maxSH = 0.10 has a potentially excessive and asymmetrical effect on the removal of truly shared heterozygous sites as paralogs. These results indicate that hybridization origin hypotheses of putative hybrids represented by results with maxSH = 0.25 and 0.50 are more credible. In conclusion, we revealed the critical hazard of paralogs filtration according to sharing heterozygosity at first, so that we propose to use specific protocols, rather than maxSH, to filter potential paralogs for closely related lineages.

  Tuning an overlooked parameter (maxSH) in PYRAD/IPYRAD, a prevalent pipeline for reduced-representation sequencing assembly and analysis, can strongly influence our biological inferences of the origin of putative hybrids.
• 

  Landscape and evolutionary dynamics of Helitron transposons in plant genomes as well as construction of online database HelDB

  Shu-Fen Li, Xin-Yu Zhang, Long-Long Yang, Ke-Li Jia, Jia-Rong Li, Li-Na Lan, Yu-Lan Zhang, Ning Li, Chuan-Liang Deng, and Wu-Jun Gao

  J Syst Evol. 2023, 61(5): 919-931.
  https://doi.org/10.1111/jse.12929

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Helitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high-quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user-friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20-30 Ma and peaking at approximately 24 Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.

  Helitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high-quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user-friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20-30 Ma and peaking at approximately 24Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.
• 

  Integrative taxonomy of the stalk-eyed bug genus Chauliops (Heteroptera: Malcidae: Chauliopinae) reveals orogeny-driven speciation

  Yan-Fei Li, Shu-Jing Wang, Jia-Yue Zhou, Cui-Qing Gao, Chen-Guang Zheng, Huai-Jun Xue, and Wen-Jun Bu

  J Syst Evol. 2023, 61(5): 932-947.
  https://doi.org/10.1111/jse.12931

  Abstract  |  References  |  Full Text HTML  |  Full Text PDF  |  Save

  Economically significant bean pests of the genus Chauliops are species rich in the areas surrounding the Qinghai-Tibet Plateau and provide an excellent system for speciation studies. Here, an integrative taxonomic approach, employing morphological analyses, population genetic methods, and multiple molecular species delimitation methods, was used to clarify the taxonomy of Chauliops in East and Southeast Asia. Four new species (Chauliops parahorizontalis Li & Bu, sp. nov., Chauliops albida Li & Bu, sp. nov., Chauliops bicoloripes Li & Bu, sp. nov., and Chauliops paraconica Li & Bu, sp. nov.) were described, which increases the number of Chauliops species in this area from six to 10; a key for Chauliops species is also provided. Phylogenetic analysis and divergence time estimation revealed that Chauliops was divided into four clades: Clade A (Chauliops bisontula + [Chauliops horizontalis + C. parahorizontalis sp. nov.]), Clade B (C. albida sp. nov. and C. bicoloripes sp. nov.), Clade C (Chauliops quaternaria and Chauliops zhengi), and Clade D (Chauliops fallax + [Chauliops conica + C. paraconica sp. nov.]). Two species diversification events of Chauliops estimated to have occurred 7-1 million years ago (Ma) and 25-13 Ma were detected. These speciation events were consistent with the two historical uplift events of the Qinghai-Tibet Plateau, suggesting that orogeny might have provided opportunities for the diversification of Chauliops species on the southeastern margin of the Qinghai-Tibet Plateau. Our findings show that population genetic analyses can be used to delimit related species and that orogeny is a key driver of species diversification on the southeastern margin of the Qinghai-Tibet Plateau.

  An integrative taxonomic approach employing morphology, population genetic methods based, was used to clarify the taxonomy of Chauliops in East and Southeast Asia, four new species were described. Two species diversification events of Chauliops suggested that orogeny might have provided opportunities for the diversification of Chauliops species in the southeast margin of the Qinghai-Tibet Plateau. Population genetic analyses can be used to delimit related species and orogeny is a key driver of species diversification in the southeast margin of the Qinghai-Tibet Plateau.