Table of Contents

01 March 2023, Volume 61 Issue 2

Cover illustration: Upper left, Saxifraga longifolia migration routes from Pyrenees (Pyr) to another limestone Iberian Mountains and the High Atlas Mountains (HAM). Lower left, Saxifraga longifolia phylogenetic analysis and its relationships with other Saxifraga species of the Ligulatae section. Populations colors are the same as the above figure and correspond to the seven haplotypes found in the study. Upper right, Saxifraga longifolia flowers. Center right, the monocarpic Saxifraga longifolia can produce more than 1000 flowers. Lower right, Saxifraga longifolia basal rosette. Photographs taken by Pablo Vargas. See Pomeda-Gutiérrez et al., pp. 253–272 in this issue. Designed by Fernando Pomeda-Gutiérrez. [Detail] ...

  

Issue Information
• Issue Information

  J Syst Evol. 2023, 61(2): 0-4.
  https://doi.org/10.1111/jse.12870

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

  
Research Articles
• 

  The Pyrenees as a cradle of plant diversity: phylogeny, phylogeography and niche modeling of Saxifraga longifolia

  Fernando Pomeda‐Gutiérrez, María Begoña García, María Leo, Mario Fernández‐Mazuecos, Mostafa Lamrani Alaoui, Anass Terrab, and Pablo Vargas

  J Syst Evol. 2023, 61(2): 253-272.
  https://doi.org/10.1111/jse.12917

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

  The current distribution of most species results from ecological niche, past distribution, and migrations during glacial–interglacial periods and in situ evolution. Here, we disentangle the colonization history of Saxifraga longifolia Lapeyr., a limestone plant abundant in the Pyrenees and rare in other Iberian mountains and the African Atlas. Our working hypothesis is that the current distribution results from the shrinkage of a more extensive distribution in previous cold periods. We sampled 160 individuals of 32 populations across the whole distribution range and sequenced four DNA regions (rpl32-trnL, rps16-trnQ, trnS-trnG, and ITS). Ecological conditions were modeled to identify factors promoting high genetic diversity and long-term persistence areas for S. longifolia. In addition, we inferred phylogenetic relationships, phylogeographic divergence, genetic diversity, and migration routes. Seven plastid haplotypes were found, of which six occur in the Pyrenees and one in the High Atlas (Morocco). Discrete phylogeographic analysis (DPA) estimated migration routes predominantly from the Pyrenees to the other areas. Colonization events to those areas appear to have taken place recently given that the rest of the Iberian mountains do not harbor exclusive haplotypes. Iberian–Northern African distribution was inferred to be the result of long-distance dispersal because the split between Iberian and High Atlas haplotypes is estimated to have taken place in the last 4 million years ago when the Strait of Gibraltar was already open. Migrations from the Pyrenees to the south may have been favored by a corridor of predominant limestone rocks along Eastern Iberia, followed by successful overcoming the Strait of Gibraltar to reach northern Africa.

  The colonization history of Saxifraga longifolia begins in the Pyrenees, a cradle of plant diversity. Continues along the Eastern Iberian limestone corridor reaching the morrocan High Atlas by a long-distance dispersal event after the opening of the Strait of Gibraltar. However, this pattern appears to have been blurred during the Quaternary when S. longifolia colonized and recolonized the Iberian mountains.
• 

  Phylogenetic relationships, hybridization events, and drivers of diversification of East Asian wild grapes as revealed by phylogenomic analyses

  Zhi‐Yao Ma, Ze‐Long Nie, Xiu‐Qun Liu, Jing‐Pu Tian, Yong‐Feng Zhou, Elizabeth Zimmer, and Jun Wen

  J Syst Evol. 2023, 61(2): 273-283.
  https://doi.org/10.1111/jse.12918

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

  East Asian wild grapes show a high level of species diversity and have been widely recognized as important germplasm resources of wine, table grapes, and resistance to biotic and abiotic stresses for the grape industry. However, the deeper phylogenetic relationships and drivers of diversification of East Asian Vitis remain poorly understood. Hybridization and introgression events of East Asian Vitis are not well investigated, particularly at the genome-wide scale. The phylogenetic relationships of East Asian Vitis are herein explored using nuclear and plastid genome data based on target enrichment (Hyb-Seq). Seven major clades are recognized for East Asian Vitis based on the nuclear phylogenetic trees, but there is topological incongruence between concatenated and coalescent analyses. Furthermore, significant cytonuclear discordance is observed within East Asian Vitis. Species network analyses identified several hybridization events within East Asian Vitis. These interspecific hybridization events may have caused the topological discordances and relatively low support detected in our analyses. Ecological niche modeling shows that most of the diversification of East Asian Vitis species is driven by temperature and precipitation environmental variables. Sympatric parallel diversifications of major clades also may have facilitated the rich diversity in East Asian Vitis.

  Diversity and phylogenetic relationships of East Asian Vitis. A. Vitis wilsoniae in Vitis davidii Clade. B. Vitis flexuosa in V. flexuosa Clade. C. Vitis hancockii in V. hancockii Clade. D. Vitis bryoniifolia in V. bryoniifolia Clade. E. Vitis chungii in V. chungii Clade. F. Vitis heyneana in V. heyneana Clade. G. Vitis amurensis in V. amurensis Clade. H. Concatenated tree of East Asian Vitis based on nuclear data.
• 

  Phylogenomic, morphological, and niche differentiation analyses unveil species delimitation and evolutionary history of endangered maples in Acer series Campestria (Sapindaceae)

  Xiao‐Kai Fan, Jing Wu, Hans Peter Comes, Yu Feng, Ting Wang, Shu‐Zhen Yang, Takaya Iwasaki, Hong Zhu, Yun Jiang, Joongku Lee, and Pan Li

  J Syst Evol. 2023, 61(2): 284-298.
  https://doi.org/10.1111/jse.12919

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

  Accurate species delimitation is crucial for biodiversity conservation. The Acer series Campestria comprises four species, A. campestre L., A. miyabei Maxim., A. miaotaiense P. C. Tsoong, and A. yangjuechi Fang & P. L. Chiu. To clarify controversies over the taxonomic status of the latter three endangered species, we undertook phylogenomic, morphological, and niche differentiation analyses in series Campestria. Our coalescent species tree of 544 and 77 single-copy nuclear genes supported series Campestria as monophyletic, with A. yangjuechi having the closest relationship with A. miaotaiense. However, in the plastome-derived tree based on 64 protein coding sequences, the four species did not cluster together, and each of them grouped with some other sympatric Acer species. Given this nuclear-cytoplasmic conflict, we hypothesize that A. yangjuechi have been subject to nuclear gene introgression and plastid (pt) capture involving another sympatric maple, that is, A. amplum Rehder. Principal component analysis and machine learning based on morphological data could not separate A. yangjuechi and A. miaotaiense, but they both could be clearly distinguished from A. miyabei. Moreover, the niche overlap tests of the two more widespread species, A. miyabei and A. miaotaiense, showed they clearly occupy distinct niches. Overall, we conclude that A. miyabei and A. miaotaiense are distinct species, while A. yangjuechi (endemic to Mt. Tianmu/East China) should be treated as a subspecies of A. miaotaiense. Our study points out that multiple lines of phylogenomic, morphological, and ecological evidence prove highly useful in species delimitation. Additionally, our results should help to inform conservation measures for endangered species of the genus Acer/series Campestria in East Asia.

  The Acer Series Campestria comprises four species, A. campestre, A. miyabei, A. miaotaiense, and A. yangjuechi. The nuclear-cytoplasmic conflict suggested that A. yangjuechi might have been subject to nuclear gene introgression and plastid (pt) capture involving another sympatric maple, that is, Acer amplum. Principal component analysis and machine learning based on morphological data could not separate A. yangjuechi and A. miaotaiense, but they both could be clearly distinguished from A. miyabei. Moreover, the niche overlap tests of the two more widespread species, A. miyabei and A. miaotaiense, showed that they clearly occupy distinct niches. Overall, we conclude that A. miyabei and A. miaotaiense are distinct species, while A. yangjuechi (endemic to Mt. Tianmu/East China) should be treated as a subspecies of A. miaotaiense.
• 

  Deep phylogeographic splits and limited mixing by sea surface currents govern genetic population structure in the mangrove genus Lumnitzera (Combretaceae) across the Indonesian Archipelago

  Jeprianto Manurung, Blanca M. Rojas Andrés, Christopher D. Barratt, Jan Schnitzler, Bror F. Jönsson, Ruliyana Susanti, Walter Durka, and Alexandra N. Muellner‐Riehl

  J Syst Evol. 2023, 61(2): 299-314.
  https://doi.org/10.1111/jse.12923

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

  The Indonesian Archipelago accommodates the largest mangrove area in Southeast Asia and possesses the world's richest composition of mangrove species. The archipelago comprises areas of the biogeographic regions Sunda and Wallacea, separated by Wallace's line. Here, we used the true mangrove species Lumnitzera littorea and Lumnitzera racemosa as a study case for understanding the effects of phylogeographic history, sea surface currents, and geographical distance on genetic diversity and genetic structure. We sampled 14 populations of L. littorea (N = 106) and 21 populations of L. racemosa (N = 152) from Indonesia and used 3122 and 3048 SNP loci, respectively, genotyped using the ddRADseq approach. We assessed genetic diversity, genetic structure, and effective dispersal of the populations and related them to geographical distance and sea surface currents. Our study revealed low levels of genetic variation at the population level in Lumnitzera. Pronounced genetic differentiation between populations indicated two phylogroups in both species. While in L. littorea the two phylogroups were largely separated by Wallace's line, L. racemosa showed a northwest vs. southeast pattern with strong mixture in Wallacea. Our findings provide novel insights into the phylogeography of the mangrove genus Lumnitzera and the role of sea surface currents in the Indonesian Archipelago.

  Our population genomic data show pronounced genetic differentiation among populations, indicating two phylogroups in both species. While in Lumnitzera littorea the two phylogroups are largely separated by Wallace's line, Lumnitzera racemosa shows a northwest vs. southeast pattern with strong mixture in Wallacea.
• 

  Phylogeography of Scots pine in Europe and Asia based on mtDNA polymorphisms

  Witold Wachowiak, Weronika B. Żukowska, Annika Perry, Andrzej Lewandowski, Stephen Cavers, and Bartosz Łabiszak

  J Syst Evol. 2023, 61(2): 315-327.
  https://doi.org/10.1111/jse.12907

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

  We analyzed mitochondrial DNA polymorphisms to search for evidence of the genetic structure and patterns of admixture in 124 populations (N = 1407 trees) across the distribution of Scots pine in Europe and Asia. The markers revealed only a weak population structure in Central and Eastern Europe and suggested postglacial expansion to middle and northern latitudes from multiple sources. Major mitotype variants include the remnants of Scots pine at the north-western extreme of the distribution in the Scottish Highlands; two main variants (western and central European) that contributed to the contemporary populations in Norway and Sweden; the central-eastern European variant present in the Balkan region, Finland, and Russian Karelia; and a separate one common to most eastern European parts of Russia and western Siberia. We also observe signatures of a distinct refugium located in the northern parts of the Black Sea basin that contributed to the patterns of genetic variation observed in several populations in the Balkans, Ukraine, and western Russia. Some common haplotypes of putative ancient origin were shared among distant populations from Europe and Asia, including the most southern refugial stands that did not participate in postglacial recolonization of northern latitudes. The study indicates different genetic lineages of the species in Europe and provides a set of genetic markers for its finer-scale population history and divergence inference.

  The distribution of various mitochondrial DNA haplotypes (marked in different colors) of Scots pine in Europe and Asia has been studied. Major mitotype variants include the remnants of Scots pine at the most western distribution of the species that colonized the Scottish Highlands, the main variants (western and central European) that contributed to the contemporary populations in Norway and Sweden, the central-eastern European variant that colonized Baltic countries, Finland, and Russian Karelia, and a separate one common to most eastern European parts of Russia and western Siberia. The study highlights the complex population history of the species that influenced the distribution of genetic variations across the species range.
• 

  Mutational meltdown or controlled chain reaction: The dynamics of rapid plastome evolution in the hyperdiversity of Poaceae

  Jie Wang, Gao‐Fei Fu, Luke R. Tembrock, Xue‐Zhu Liao, Song Ge, and Zhi‐Qiang Wu

  J Syst Evol. 2023, 61(2): 328-344.
  https://doi.org/10.1111/jse.12854

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

  The study of genomic structural evolution associated with accelerated evolutionary rates that result in avoidance of meltdown and increase biodiversity is becoming ever more possible as the number of available plastomes increases. To more comprehensively analyze rate heterogeneity among monocots and within Poaceae, we sequenced plastomes from four Poaceae species, combined them with publicly available data from ~200 plastomes, and conducted comparative analyses to quantify the pattern of rate heterogeneity between different lineages, functional groups, and periods of evolutionary time. We compared structural differences across the Poaceae to quantify how changes in plastome size correspond to different genomic subunits and the evolution of IR–SC junction boundaries. The substitution rates among ancestral Poaceae were inferred to be exceptionally rapid compared to other monocots but slowed after divergence into extant lineages, which could not be sufficiently explained by positive selection. As such, rapid rates in the ancestral lineage leading to Poaceae might be more closely linked to large-scale structural changes like the loss of ycf1 and ycf2. The total increase in plastome size across Poaceae was positively correlated with the total length of intergenic spacers, tandem repeats, and dispersed repeats as well as large single copy, and inverted repeats (IRs). The continuous evolution of IR–SC junction boundaries was asynchronous with sizes of total genome and subunits across Poaceae. Future work is needed to better understand what factors in ancestral Poaceae evolved to harness such rapid rates of plastome evolution, avoid a mutational meltdown, and escape the stagnation of strong purifying selection as well as if these factors could be utilized to synthetically control rates.

  Comprehensive sampling of plastomes across monocots and Poaceae further elucidates the meltdown of rapid nucleotide substitution rates and genome size dynamics influenced by different factors.
• 

  Patterns and impacting factors of gene evolutionary rate between wild and cultivated emmer wheat (Triticum turgidum)

  Peng-Zheng Lei, Qi Ai, Zhu-Pei Xiong, Jia‐Nan Lu, Xiu-Lan Wei, Weining Song, Xiao-Qin Liu, and Xiao-Jun Nie

  J Syst Evol. 2023, 61(2): 345-355.
  https://doi.org/10.1111/jse.12852

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

  Tetraploid emmer wheat (Triticum turgidum L., BBAA) is the founder progenitor of bread wheat, providing the valuable genetic resource and gene pool for wheat improvement. However, the evolutionary trajectory of tetraploid wheat, especially the evolutionary fate of different types of genes has not been well studied. In this study, the rate of non-synonymous substitution (d_N) and synonymous substitution (d_S) was calculated by comparing the orthologs between the wild emmer and cultivated durum wheat at the whole genome and subgenome levels to obtain the positively selected genes (PSGs) and negatively selected genes (NSGs). Then, mutation rate, gene length, exon number, GC content, codon bias, and expression level were comprehensively investigated and compared between the PSGs and NSGs. Within both wild emmer and cultivated durum wheat, PSGs between A and B subgenome displayed shorter gene and exon lengths as well as fewer exon numbers compared with NSGs, whereas from wild emmer to cultivated durum wheat, PSGs showed longer gene length and more exon numbers. Furthermore, PSGs displayed much higher expression levels and stronger codon usage bias, but lower genetic diversity compared with NSGs. Finally, two PSGs TdER1-6B, and TdLC7-2A, were found to play the crucial roles in regulating grain width and plant height of tetraploid wheat, respectively. This study systematically investigated the evolutionary, structural, and functional difference between PSGs and NSGs in tetraploid wheat, which will contribute to a better understanding of the selective mode and evolutionary trajectory during wheat domestication and evolution.

  Frequency distributions of dN (a), dS (b), gene length (c), exon length (d), exon number (e), GC content (f), expression level (g) and tissue specificity (h) between positively selected genes (PSGs) and negatively selected genes (NSGs) in tetraploid wheat. Red and blue lines represent PSGs and NSGs, respectively.
• 

  Phylogenetics of global Camellia (Theaceae) based on three nuclear regions and its implications for systematics and evolutionary history

  Dong‐Wei Zhao, Trevor R. Hodkinson, and John A. N. Parnell

  J Syst Evol. 2023, 61(2): 356-368.
  https://doi.org/10.1111/jse.12837

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

  Camellia contains tea, oil camellia, and camellias which benefit people globally. Its infrageneric classification is, however, controversial and unstable, and former phylogenetic analyses failed to yield robust and consistent trees. Here, we aimed to reconstruct a robust phylogenetic tree, date all clades and discuss the evolutionary history of Camellia. Emphasizing the taxonomically comprehensive sampling rather than more DNA data, orthologous nuclear RPB2 introns 11–15 and 23, and waxy were sequenced for 99 taxa of Camellia to reconstruct its phylogenetic history. Ten clades are identified in Camellia: Camellia II, Camelliopsis, Corallina, Furfuracea, Heterogenea, Paracamellia, Piquetia, Stereocarpus, Thea and Yellow camellias II. Camellia grijsii and C. shensiensis are not closely related with other oil camellias that form the clade Paracamellia. Sections Camelliopsis and Theopsis together form the clade Camelliopsis, while clade Furfuracea consists of sect. Furfuracea and C. hongkongensis. Camellia connata is separated from C. lanceolata but nested in the clade Heterogenea, and C. longissima is nested in the clade Thea, suggesting a new germplasm for tea breeding. Molecular dating using four fossil calibration points suggests that the crown age of Camellia is 39.5 Ma with clade Corallina probably the earliest infrageneric clade to diversify and the most widespread clade, Paracamellia, the latest. Our findings provide new insights into the phylogenetic relationships, systematics and evolutionary history of Camellia.

  The maximum clade credibility tree reconstructed using the concatenated RPB2 (introns 11–15 and 23) and waxy data with four fossil points (marked by squares, A: Camellia japonoxyla; B: C. nanningensis; C: C. kueishanensis; D: Gordonia warmanensis) for Camellia. Blue bars indicate the 95% highest posterior density intervals of the node ages. The geological epochs are shown above the time axis (Pli.Ple.H.: Pliocene, Pleistocene and Holocene).
• 

  Diversification and phylogenetic correlation of functional traits for co-occurring understory species in the Chinese boreal forest

  Bo Liu, Jin‐Long Zhang, Matthew K. Lau, Xu‐Gao Wang, Yu Liang, and Tian‐Xiao Ma

  J Syst Evol. 2023, 61(2): 369-382.
  https://doi.org/10.1111/jse.12840

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

  Functional traits impact species interactions, community composition, and ecosystem functioning. However, few studies have focused on the diversification and phylogenetic correlation of multiple functional traits over geological time. We conducted phylogenetic comparative analysis for boreal forest understory species in northeast China to examine the diversification and phylogenetic correlation in several functional traits: leaf area (LA), leaf carbon content (LCC), leaf dry matter content (LDMC), leaf nitrogen content (LNC), plant height (PH), and specific leaf area (SLA). Phylogenetic signals showed that there were very low levels of phylogenetic niche conservatism (PNC) in understory leaf-related traits and plant height, suggesting divergence of functional traits for the co-occurring understory species. The disparity through time analyses (DTT) indicated that trait disparities mainly originated during recent divergence events and there were no differences in the observed trait disparities compared with that expected under Brownian motion. Furthermore, we found both positive and negative phylogenetic correlations among the measured functional traits. The very low levels of PNC suggest that these functional traits diverged among co-occurring understory species, and that those species are distantly phylogenetically related. The phylogenetic correlations among traits may be caused by both positively and negatively correlated adaptions that correspond to resource acquisition strategies. This study provides evidence that divergence in functional traits may reflect understory adaptions to boreal conditions.

  We observed and measured functional traits for 37 understory plant species, belonging to 20 families. We mapped leaf area (LA) on the phylogenetic tree and found that LA exhibited large differences among phylogenetically related species, which ranged from 16.52 to 6891.35 mm² with the ancestral trait being 979.23 mm². There was no significant disparity of LA compared with the Brownian motion model throughout the geological time, as the morphological disparity index (MDI) value was not significantly different from the null. In addition, the positive MDI value for LA indicated an accelerating rate of morphological diversification through time.
• 

  Drivers of intraspecific differentiation of an alpine cold-tolerant herb, Notopterygium oviforme: Roles of isolation by distance and ecological factors

  Mi‐Li Liu, Qian‐Han Shang, Yan‐Jun Cheng, Na Wang, Wei Sa, Bao‐Guo Li, and Zhong‐Hu Li

  J Syst Evol. 2023, 61(2): 383-398.
  https://doi.org/10.1111/jse.12844

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

  Determining the mechanisms that drive phenotypic and genetic divergence by species has been a central topic in evolutionary biology for many years. However, the relative contributions of isolation by distance (IBD) and environment factors to species divergence are largely unknown in perennial herbs in East Asia. In this study, we collected population genetic samples of the cold-tolerant perennial herb Notopterygium oviforme R. H. Shan in central China. We integrated the population transcriptomes, whole chloroplast genomes, genotyping-by-sequencing, microsatellite markers, and ecological factors to determine the relative contributions of geography, climate, and soil factors to genetic, chemical, and phenotypic divergence. A clear genetic distinction was identified between the West Qinling and East Qinling Mountains geographical groups of N. oviforme based on various molecular datasets. Interestingly, obvious niche conservation might have been responsible for the similarity of most of the leaf functional traits in the two groups. Multiple matrix regression with randomization analysis showed that the spatial intraspecific divergence pattern was mainly due to IBD rather than isolation by environment. In addition, transcriptomic expression divergence and some ecological factors have played key roles in intraspecific lineage differentiation. Approximate Bayesian Computation showed that both lineages have experienced historical population expansion and recent range contraction. Molecular dating suggested that intraspecific divergence was closely associated with dramatic uplifts of the Qinling Mountains in East Asia. These results demonstrate that geographical, geological, and environmental factors together shaped cryptic intraspecific diversification and shifts in the population dynamics of the perennial cold-tolerant herb N. oviforme.

  A clear genetic distinction was identified in the cold-tolerant herb Notopterygium oviforme between the west and east Qinling Mountains geographical groups. Niche conservatism might be responsible. Multiple matrix regression with randomization analysis showed that the spatial pattern of intraspecific genetic divergence mainly resulted from the effects of isolation by distance (IBD), not isolation by environment. Transcriptomic expression divergence and some ecological factors have played key roles in differentiation of intraspecific lineages. The intraspecific allopatric divergence was closely associated with the dramatic uplift of the Qinling Mountains in East Asia during the Early Pleistocene period. Our results indicated that geographical, geological, and environmental factors together shaped the cryptic intraspecific diversification and population dynamics shifts of this perennial cold-tolerant herb.
• 

  Extremely high diversity and endemism of chlorotypes in Wikstroemia monnula Hance (Thymelaeaceae) shed light on the effects of habitat heterogeneity on intraspecific differentiation in southeast China

  Chao‐Qiang Zhang, Yi‐Wei Tang, De‐Feng Tian, Yan‐Yan Huang, Guang‐Hui Yang, Peng Nan, Yu‐Guo Wang, Ling‐Feng Li, Zhi‐Ping Song, Ji Yang, Yang Zhong, and Wen‐Ju Zhang

  J Syst Evol. 2023, 61(2): 399-413.
  https://doi.org/10.1111/jse.12848

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

  Southeast China is one of the core areas of the Sino-Japanese floristic region and a hotspot of biodiversity in East Asia. This region has been considered as both a museum and a cradle of woody genera in China. Why a region with highly stable topography and climate could be a cradle of species diversity remains unclear. In this study, the phylogeographic pattern and genetic structure of Wikstroemia monnula, an endemic species to southeast China, were analyzed by sequencing four chloroplast DNA fragments (4679 bp in total) of 836 individuals from 39 populations. Extremely high diversity and endemism of chlorotypes were found. Out of 54 chlorotypes, 51 (94.44%) were private, with genetic diversity index (H_T) near 1 (H_T = 0.992), and 96.51% of the genetic variation occurring among populations, indicating that this species has undergone strong intraspecific differentiation and very limited migration. The correlational analysis showed that the population differentiation of W. monnula was driven not only via isolation by distance (IBD), but more importantly via isolation by environment (IBE). A significant phylogeographic structure was not found (N_ST = 0.979, G_ST = 0.833, P > 0.05); however, the spatial pattern of the sublineages of chlorotypes was largely consistent with the biogeographic boundaries on a smaller scale in the region. These results suggest that habitat heterogeneity in southeast China not only promoted speciation on a long time-scale, but still continues to impact population differentiation in recent times.

  Map showing the 39 sampled populations of Wikstroemia monnula and the distribution of 54 chloroplast DNA haplotypes (C1–C54) screened in the species (pie charts showing the proportion of haplotypes within each population).
• 

  Characterization of genome-wide long terminal repeat retrotransposons provide insights into trait evolution of four grapevine species

  Guang‐Qi He, Hui‐Ying Jin, Yi‐Zhe Cheng, Yi‐He Yu, and Da‐Long Guo

  J Syst Evol. 2023, 61(2): 414-427.
  https://doi.org/10.1111/jse.12850

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

  Grapevine is one of the most economically important crops in the world. Although long terminal repeat (LTR) retrotransposons are thought to have played an important role in plants, its distribution in grapevine is not clear. Here, we identified genome-wide intact LTR retrotransposons in a total of six high-quality grapevine genomes from Vitis vinifera L., Vitis sylvestris C.C. Gmel., Vitis riparia Michx. and Vitis amurensis Rupr. with an average of 2938 per genome. Among them, the Copia superfamily (particularly for Ale) is a major component of the LTR retrotransposon in grapevine. Insertion time and copy number analysis revealed that the expansion of 70% LTR retrotransposons concentrating on approximately 2.5 Ma was able to drive genome size variation. Phylogenetic tree and syntenic analyses showed that most LTR retrotransposons in these genomes formed and evolved after species divergence. Furthermore, the function and expression of genes inserted by LTR retrotransposons in V. vinifera (Pinot noir) and V. riparia were explored. The length and expression of genes related to starch metabolism and quinone synthesis pathway in Pinot noir and environmental adaptation pathway in V. riparia were significantly affected by LTR retrotransposon insertion. The results improve the understanding of LTR retrotransposons in grapevine genomes and provide insights for its potential contribution to grapevine trait evolution.

  We identified genome-wide intact long terminal repeat (LTR) retrotransposons in a total of six high-quality grapevine genomes from Vitis vinifera, Vitis sylvestris, Vitis riparia, and Vitis amurensis and showed that most LTR retrotransposons of these genomes formed and evolved after species divergence. Genes related to starch metabolism and the quinone synthesis pathway in Pinot noir and environmental adaptation pathway in V. riparia were significantly affected by LTR retrotransposon insertion.
• 

  Experimental sympatry suggests geographic isolation as an essential reproductive barrier between two sister species of Pedicularis

  Ju Tang, Shi‐Guo Sun, and Shuang‐Quan Huang

  J Syst Evol. 2023, 61(2): 428-439.
  https://doi.org/10.1111/jse.12835

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

  Although mechanical isolation mediated by shared pollinators has been considered as a classic model of pollinator-mediated floral isolation in Pedicularis, a superdiverse genus in Hengduan Mountains, southwest China, there has been no empirical study of interspecific pollen flow between closely related species. We examined reproductive barriers at six different stages between Pedicularis cranolopha and Pedicularis tricolor, two sister species. The two sister species were geographically isolated from each other based on our field survey and the records of herbarium specimens. Translocation experiments showed that flowering phenology partly overlapped and bumblebee pollinators did not discriminate between flowers of the two species. Bumblebee interspecific moves could mediate interspecific pollination as traced using fluorescent powder, in which pollen analogs placed on one species were transferred to the stigmas of the other species in experimental plots containing both species. Heterospecific pollen tubes grew in the style as well as conspecific pollen in hand-pollination experiments. Reciprocal hybridization between the two species could produce (partially) viable seeds, suggesting weak post-pollination barriers. Our results showed that geographic isolation was an important barrier of two species, and the total reproductive isolation between two species was incomplete when without geographical isolation. The formation of Big Snow Mountains could introduce an important pre-zygotic reproductive barrier between the two sister species of Pedicularis; such geographical isolation could be responsible for allopatric speciation, giving a clue to understanding the rapid radiation on mountain areas.

  The relative contributions of reproductive barriers at six stages to total isolation including all barriers (A), and in sympatry (B) without geographic isolation between Pedicularis cranolopha (white bars) and Pedicularis tricolor (gray bars), illustrating that except the geographic isolation alone could contribute complete reproductive isolation between the two species, the other five barriers could not. Flowering phenology partly overlapped and bumblebee pollinators did not discriminate between flowers of the two species. Bumblebee interspecific moves could mediate interspecific pollination and reciprocal hybridization between the two species could produce (partially) viable seeds, suggesting that post-pollination barriers were weak.