Species Complex Research Articles

Ecological correlates of population genetics in Linum suffruticosum, an heterostylous polyploid and taxonomic complex endemic to the western Mediterranean Basin

Abstract Linum suffruticosum s.l. is a taxonomic complex widespread in the western Mediterranean basin. The complex is characterized by a high phenotypic and cytogenetic diversity, and by a unique three-dimensional heterostyly system that makes it an obligate outcrosser. We studied the patterns of genetic diversity and structure of populations throughout the entire distribution of L. suffruticosum s.l. with microsatellite markers. We analyzed their relationships with various biological and ecological variables, including the morph ratio and sex organ reciprocity of populations measured with a novel multi-dimensional method. Populations consistently showed an approximate 1:1 morph ratio with high sex organ reciprocity and high genetic diversity. We found high genetic differentiation of populations, showing a pattern of isolation by distance. The Rif mountains in NW Africa were the most important genetic barrier. The taxonomic treatment within the group was not related to the genetic differentiation of populations, but to their environmental differentiation. Genetic diversity was unrelated to latitude, elevation, population size, niche suitability or breeding system. However, there was a clear influence of ploidy level on the genetic diversity of populations, and a seeming center-periphery pattern in its distribution. Our results suggest that polyploidization events, high outcrossing rates, isolation by distance and important geographical barriers to gene flow have played major roles in the microevolutionary history of this species complex.

Apple Bitter Rot and Glomerella Leaf Spot: A Comprehensive Review of Causal Species and Their Biology, Fungicide Sensitivities, and Management Strategies.

Bitter rot and Glomerella leaf spot (GLS) are two distinct diseases of apple fruit and foliage caused by members of the ascomycete fungal genus Colletotrichum. While GLS is restricted to subtropical and in some areas to temperate climates, bitter rot is responsible for significant yield loss worldwide, particularly during the post-harvest period. Initially thought to be caused by just two species of Colletotrichum, C. acutatum and C. gloeosporioides, advances in molecular biology and sequencing techniques enabled the identification of 25 different species capable of causing bitter rot and/or GLS of apple belongs to the C. gloeosporioides species complex (CGSC), C. acutatum species complex (CASC) and C. boninense species complex (CBSC). Three species (C. gloeosporioides, C. fructicola, and C. chrysophilum) of CGSC cause both bitter rot and GLS, 18 species (6 of CGSC and 12 of CASC) only cause bitter rot, and four species (C. aenigma and C. asianum of CGSC, C. limetticola of CASC and C. karstii of CBSC) only cause GLS. These species were found to differ in their geographical distribution, environmental and host tissue preference, pathogenicity, and fungicide sensitivities. In this review, we summarize the distribution, life cycle, and pathogenicity mechanisms of all currently known Colletotrichum species responsible for bitter rot and GLS of apple. Furthermore, we describe known apple defense mechanisms and management strategies for the control of these economically significant pathogens and identify gaps in our present understanding for future research.

Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis.

Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer M. nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both M. decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid's predisposition to self-fertilize.

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae’s species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

Continuous Monoculture Alters the Fungal Community and Accumulates Potential Pathogenic Strains in the Rhizosphere of Codonopsis pilosula

Codonopsis pilosula (known as dangshen) is experiencing a serious replant disease caused by continuous monoculture in its main and endemic cultivation region in Dingxi, China. In this study, changes in physicochemical properties, fungal microbiomes, and isolated strains were investigated in the rhizosphere soil of 1-, 2-, 3-, and 5-year continuous monoculture natural fields. It was observed that wilted seedlings and a variety of root rot diseases occurred after the third year of continuous monoculture in the field. The soil-available potassium content and the pH value decreased significantly in the 3- and 5-year fields. Using Illumina sequencing, it was demonstrated that the 3- and 5-year fields had a higher diversity of fungal communities compared with the 1- and 2-year fields. At the genus level, abundance of some potentially pathogenic fungal taxa also increased. A total of 33 isolated strains belonging to the Fusarium species complexes Plectosphaerella cucumerina, Paraphoma ledniceana, Alternaria alstroemeriae, Mucor hiemalis, and Clonostachys rosea were obtained from the roots in 3- and 5-year fields. The correlation analysis revealed that the abundance of the fungal community at the genus level was positively correlated with the available phosphorus, total nitrogen, and soil organic matter. The results revealed that continuous monoculture has a negative impact on the fungal community and enriches potential pathogenic fungi in the rhizosphere of C. pilosula.

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi.

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

Large‐scale integrative taxonomy of Swedish grass flies (Diptera, Chloropidae) reveals hitherto unknown complexity of a dark taxon

AbstractThe study of biodiversity is fundamental to preserving life on Earth but a challenging endeavour due to the taxonomic neglect associated with hyperdiverse lineages. To overcome this problem, we have implemented for the first time a Large‐scale integrative taxonomic (LIT) approach on the hyperdiverse insect family Chloropidae. This lineage of flies is a great fit for implementing emerging protocols such as LIT due to their ecological relevance, abundance and global distribution, poorly known genetic diversity and challenging taxonomy. In this study, we test cost‐effective barcoding workflows on nonoptimally preserved chloropid flies from Sweden and then apply targeted morphological validation to accelerate the species recognition process. Our dataset yielded DNA barcodes of 63 species that represent almost one‐third of the species diversity from Sweden and 15% of the European diversity. Applying LIT allowed us to uncover two new species and address for the first time three troublesome species complexes through a comprehensive framework. We also provide previously unknown DNA barcodes for 35% of the described species found and address distribution patterns with a focus on grassland environments. We have thus contributed significantly to overcoming the taxonomic neglect of this hyperdiverse lineage by tackling the diversity of chloropids using complementary sources of data, scalable techniques and quickly translating multiple sources of evidence into named species.

Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex.

Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.

Rapid detection of virulence-related genes by multiplex PCR in five pathogenic bacteria of mulberry bacterial wilt

Mulberry bacterial wilt is a devastating disease that is difficult to control and causes serious economic losses to the sericulture industry. This disease is mostly caused by a diverse group of pathogenic and opportunistic bacteria including, Ralstonia pseudosolanacearum, Pantoea ananatis, Enterobacter cloacae complex (ECC), Klebsiella pneumoniae species complex (KpSC), and K. oxytoca complex (KoC). Due to the lack of a rapid and reliable test to simultaneously detect these complex pathogens of mulberry wilt, we developed a multiplex PCR (mPCR) assay to detect five virulence-related genes carried by the pathogenic bacteria of mulberry bacterial wilt disease. The primers were designed for the virulence-related genes: pleD (GGDF structural domain-containing protein), yjfP (esterase), pelY (peripheral pectate lyase), ampD (N-acetyl-anhydromuranmyl-L-alanine amidase), and ripW (type III effector). Overall, the developed mPCR assay showed highly specific, sensitive and reproducible detection of target pathogens. Briefly, the results showed that the mPCR was highly specific in individual reactions, and the lowest detection concentration of the five pathogenic bacteria was 1.87 × 103 CFU/mL (DNA = 2.45 pg/μL). From 46 natural mulberry wilt samples, the mPCR detection rates of P. ananatis, ECC, KpSC, KoC and R. pseudosolanacearum were 8.69, 91.3, 34.7, 23.9 and 65.21%, respectively. The traditional culture media isolation methods showed comparable results. The pathogenicity test of 84 suspected pathogenic bacteria revealed that the morbidity (average morbidity level) caused by the pathogenic bacteria detected by mPCR was ≥ 65.5%, while the morbidity of the undetected pathogenic bacteria was ≤ 35.5%. Based on these results, we believe that the mPCR developed in the present study will be useful in rapid, reproducible, and sensitive detection of the pathogenic bacteria causing mulberry bacterial wilt including, R. pseudosolanacearum, P. ananatis, ECC, KpSC, and KoC.Graphical abstract

Alyxia Banks ex R.Br. in New Caledonia: a clarification of several species complexes, nomenclatural notes, and a description of three new species

The genus Alyxia Banks ex R.Br. is partially revised for New Caledonia, with 31 species recognised. The species complex Alyxia tisserantii Montrouz. is discussed and divided into seven species with existing names, and the synonymy is updated accordingly. Alyxia loeseneriana var. macrocarpa Boiteau is elevated to species status due to new flowering material with the name A. paniensis Lannuzel nom. nov., stat. nov. created to accommodate it, due to the preexisting Alyxia macrocarpa Koord. Detailed study of Alyxia caletioides (Baill.) Guillaumin ex Däniker revealed it was in fact made up of two distinct taxa; a new separate species, Alyxia urceolata Lannuzel, sp.nov. is therefore described. Two new species are also described following their recent collection: Alyxia humboldtensis Lannuzel & Gâteblé, sp.nov. is restricted to the summit of Mount Humboldt, and Alyxia minimiflora Lannuzel, sp.nov. is known from schistaceous cliffs around Nouméa. Finally, several nomenclatural issues are discussed, and an updated key to the genus in New Caledonia is provided.

First Pangenome of Corynebacterium rouxii, a Potentially Toxigenic Species of Corynebacterium diphtheriae Complex

First Pangenome of Corynebacterium rouxii, a Potentially Toxigenic Species of Corynebacterium diphtheriae Complex

Untangling the Defiant Taxonomy of Physaloptera (Nematoda: Chromadorea: Spirurida: Physalopteridae) Parasites in Reptiles: An Integrative Approach on the Enigmatic P. retusa Suggests Cryptic Speciation

(1) Background: Although Physaloptera retusa is one of the most widespread species infecting reptiles in the Americas, numerous taxonomic problems and little genetic data are associated with it. To clarify the taxonomy of this species, we used an integrative approach. (2) Methods: Physaloptera retusa-infecting Erythrolamprus typhlus (snake) from the Pantanal wetlands, Brazil, was morphologically and genetically characterised (18S and 28S rDNA; COI mtDNA) and compared with conspecific sequences available in GenBank, from parasites of Tupinambis teguixin (lizard), using species delimitation methods. Type specimens of P. liophis were re-evaluated given its morphological similarities with P. retusa. (3) Results: The morphology of the present specimens was equal to that of P. retusa, in which the only difference from P. liophis was the relative position of the vulva. Species delimitation methods were more accurate for the COI dataset; all of them (except ABGD) indicated interspecificity among P. retusa sequences. However, a lack of morphological data or voucher material, associated with the deposited sequences, prevented more assertive conclusions. (4) Conclusions: The present results highlight the importance of a clear association between genetic data and morphology of the isolation source, or at least its adequate vouchering. Moreover, P. retusa may represent a species complex in cryptic speciation, since it is widespread and has low hosts specificity.

Lopezia guerrerensis (Onagraceae, sect. Lopezia), a new species from the State de Guerrero, México

Lopezia guerrerensis (Onagraceae, sect. Lopezia), a new species from the State de Guerrero, México

Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex.

Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.

Notes on the distribution, food plants and morphology of Chlorophanus C. R. Sahlberg, 1823 species (Coleoptera: Curculionidae) in Turkey

Chlorophanus vittatus Schoenherr, 1832, known from the Caucasus and northern Iran, is here newly reported from eastern Turkey. Salix L., Populus L., Tamarix L. and Glycyrrhiza glabra L. are revealed as host plants of adults in Turkey. Feeding and mating behavior of adults were observed on leaves of G. glabra during the summer period in the Aras River valley. The lectotype of Ch. vittatus is designated, description and digital photographs of the genitalia are presented based on newly collected material. Distributional data for Ch. vittatus, Ch. excisus (Fabricius, 1801) and Ch. pollinosus (Fabricius, 1792) in Turkey are reported, the latter species is also recorded from Turkey for the first time. Chlorophanus flavescens (Fabricius, 1787) is deleted from the list of the Iranian fauna, and Ch. excisus, from the list of the Russian fauna. Characteristic ecological and distributional features of the genus Chlorophanus C. R. Sahlberg, 1823 are discussed, and notes on the riparian habitats in Turkey are given to attract attention to the necessity of their preservation. As a fragile member of the riparian insect species complex, a weevil, Corimalia aliena (Faust, 1890), formerly known only from Central Palaearctic, is reported for the first time from Turkey where it was found on Myricaria sp. in Erzurum Province. Chlorophanus excisus co-occurs with Ch. vittatus in eastern Turkey and western Iran, or at least their ranges overlap there. These two species contribute to the maximum local Chlorophanus diversity in Erzincan and Erzurum provinces. Chlorophanus micans is recorded in Crimean Mountains and Southern Bug River valley indicating a potential current contact between Ch. micans and Ch. pollinosus in Podolian Upland.

Emerging threat to Indian agriculture: Fusarium incarnatum-equiseti species complex as a novel pathogen imperiling bajra, cowpea, finger millet, green gram, moth bean, and soybean crops

India, renowned for its diverse agro-climatic regions and agricultural legacy, relies on staple crops for sustenance. Cereals and Legumes, crucial to Indian agriculture and diet, contribute significantly to food security, economic prosperity, and environmental sustainability. Between August and October 2023, symptoms of grain/pod rot were observed in bajra, finger millet, cowpea, moth bean, green gram, and soybean crops in Uttarakhand. Based on morphological traits and the sequencing of the ITS (Internal Transcribed Spacer), rpb2 (RNA Polymerase II Second Largest Subunit), tef1 (Translation Elongation Factor 1-alpha) genes, the identified pathogens fall within the Fusarium incarnatum-equiseti species complex (FIESC). Pathogenicity tests confirmed the fulfillment of Koch's postulates, establishing the responsibility of the FIESC in grain/pod rot. This study unveils the first incidence of the FIESC causing grain/pod rot in bajra, cowpea, finger millet, soybean, green gram, and moth bean in India. Considering the economic importance of these crops, it is imperative to implement robust disease management strategies to alleviate the adverse effects of these pathogens on agricultural production. The findings underscore the necessity for continued research on emerging diseases to safeguard global crop production and food security.

A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species

BackgroundMosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.MethodsSampling was carried out in three biogeographical regions of Croatia over six years (2017–2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.ResultsA total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.ConclusionWe present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.Graphical

Spatio‐temporal shift in body size and plumage coloration is associated with the magnitude of climate change in a cosmopolitan owl

AbstractAimClimatic gradients shape geographic variation in phenotypic traits that are involved in animal thermoregulation. Therefore, increasing temperatures under global warming are expected to cause change over time in traits that show predictable spatial patterns according to environmental clines (body and appendage size, tegument coloration), as well exemplified by biogeographic rules and shown by increasing literature at a local scale. However, whether temporal shifts in phenotypic traits vary spatially according to the magnitude of the change in local climatic conditions is still unknown.LocationWorld.TaxonBarn owl species complex (Tyto alba group).MethodsBy using thousands of museum specimens collected across the globe from 1901 to 2018, we calculated within‐population change over time in wing length, bill length and melanin‐based plumage coloration and examined whether these trends differed across geographic regions, latitudes and gradients of climate changes.ResultsWe showed that populations exposed to an increasing warmer climate were subjected to a more marked decrease in body size, as gauged by wing length, and also absolute bill length that displayed a similar, although less steep, pattern of shrinking over time. In addition, phaeomelanin‐based ventral plumage colour has become paler in regions where the climate changed into warmer and drier, and darker where both temperature and precipitation increased.Main ConclusionsThese trends are generally coherent with the predictions based on Bergmann's and Gloger's rules, but not Allen's rule, and suggest that temporal shifts in body size and tegument colour depend on the magnitude of the alteration in climatic conditions, with populations living in regions where the climate has changed the most that are subjected to more marked phenotypic changes. Spatio‐temporal variation in climate has driven within‐species phenotypic clines, and it is expected to increase differences among populations according to the predicted further climate change.

A synoptic review of plant disease epidemics and outbreaks published in 2022

This scientometric study reviews the scientific literature and CABI distribution records published in 2022 to find evidence of major disease outbreaks and first reports of pathogens in new locations or on new hosts. This is the second time we have done this, and this study builds on our work documenting and analysing reports from 2021. Pathogens with three or more articles identified in 2022 literature were: Xylella fastidiosa, Bursaphelenchus xylophilus, Meloidogyne species complexes, Candidatus Liberibacter asiaticus, Raffaelea lauricola, Fusarium oxysporum formae specialis and Puccinia graminis f. sp. tritici. Our review of CABI distribution records found 29 pathogens with confirmed first reports in 2022. Pathogens with four or more first reports were: Meloidogyne species complexes, Pantoea ananatis, grapevine red globe virus and Thekopsora minima. Analysis of the proportion of new distribution records from 2022 indicated that grapevine red globe virus, sweet potato chlorotic stunt virus and Ca. Phytoplasma vitis may have been actively spreading. As we saw last year, there was little overlap between the pathogens identified by reviewing scientific literature versus distribution records. Strikingly, too, there was also no overlap between species assessed to be actively spreading in this year’s study and those identified last year. In general, introduction of new pathogens and outbreaks of extant pathogens threaten food security and ecosystem services. Continued monitoring of these threats is essential to support phytosanitary measures intended to prevent pathogen introductions and management of threats within a country.

A Diverging Species within the Stewartia gemmata (Theaceae) Complex Revealed by RAD-Seq Data

Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the S. gemmata complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an Fst of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an Fst value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex.