Journal of Systematics and Evolution最新文献

Banksia L.f., an iconic genus of the Proteaceae, is endemic to Australia, with its highest species richness and phylogenetic diversity (PD) in southwestern Western Australia. Analysis of the phylogenetic component of richness and endemism uncovered important patterns of Banksia evolutionary history that are not seen at the species level. We found that Banksia is significantly phylogenetically clustered in this region, likely due to recent evolutionary radiations. We also found significant concentrations of phylogenetic endemism in this region, both neoendemism (short, range-restricted evolutionary branches) and paleoendemism (long, range-restricted evolutionary branches). There is a striking northwest to southeast divide in phyloturnover in southwestern Western Australia. The majority of the variation in turnover patterns can be explained by environmental factors, with climate representing the largest covariate. This study adds to the growing body of evidence that indicates the importance of integrating phylogenetic and biodiversity data to inform conservation planning.

The sclerophyllous syndrome is characterized by well-defined traits (evergreen coriaceous leaves, inconspicuous flowers, and fleshy fruits). It has been hypothesized that lineages displaying the sclerophyllous syndrome show lower speciation rates than non-sclerophyllous lineages after the establishment of the mediterranean climate. Daphne gnidium displays sclerophyllous traits and some differentiation into three subspecies (gnidium, mauritanica, maritima), but the spatio-temporal origin of this taxonomic group is unknown due to the lack of a time-calibrated phylogeny of the whole genus. Here, we inferred phylogenetic relationships and divergence times of Daphne (32 species, 238 samples) and other genera of Thymelaeaceae (16 genera, 38 species, 34 samples) using the internal transcribed spacer (ITS), which revealed that the current circumscription of Daphne is profoundly polyphyletic because some species are nested within the genera Wikstroemia and Edgeworthia. In contrast, D. gnidium formed a well-supported clade as recognized in taxonomic accounts (subgenus Spachia). We found morphological and phylogenetic support for Daphne mauritanica as a monophyletic lineage sister to D. gnidium. Divergence between D. gnidium and D. mauritanica appears to have predated the establishment of seasonally dry conditions, which supports a pre-mediterranean temporal origin of the lineage. A phylogeographical analysis within D. gnidium based on 66 nrDNA (ITS) and 84 cpDNA (rps16, trnV) sequences agreed with the low differentiation of the species in the Pleistocene despite its large distribution range. Altogether, D. gnidium illustrates one more example of the sclerophyllous syndrome with no speciation after the onset of the mediterranean climate.

Newly investigated leafy twigs bearing axillary fruits from the Eocene Parachute Creek Member of the Green River Formation in eastern Utah, USA, have provided more information on the species previously attributed to the Proteaceae as Banksia comptonifolia R.W.Br. The leaves are simple, estipulate with short petioles, and elongate laminae with prominent angular nonglandular teeth. The laminae have a thick midvein and pinnate craspedodromous secondaries, and are distinctive in the presence of a thick, often coalified, marginal rim. Vegetative and reproductive buds occur in the axils of the leaves. These features indicate that the species belongs to Palibinia Korovin—an extinct Eudicot genus previously known only from the Paleogene of Asia and Europe. Small pedicellate ovoid fruits 1.5–2.2 mm wide are borne in fascicles of three and are seen to be capsules with four apical valves. Despite the specific epithet referring to similarity of the foliage to that of Comptonia (Myricaceae), the fasciculate inflorescence organization with axillary flowers is quite distinct from the catkins characteristic of that family. Assignment to Banksia or other Proteaceae with complex inflorescences and follicular fruits is also problematic. Additionally, MacGinitie′s transfer of the species to Vauquelinia of the Rosaceae is contradicted by the lack of stipule scars on the twig and by differences in leaf venation and floral morphology. We transfer the species to Palibinia comptonifolia (R.W.Br.) comb. nov., but its familial affinity within the Pentapetalae remains uncertain. This new occurrence augments records from the Paleogene of Turkmenistan, Kazakhstan, China, England, and Germany.

Phylogenetics is crucial in the study of evolutionary processes and events transpiring in the course of species diversification. Phylogenetic studies within kingdom Plantae often reveal hybridization and introgression. Here, we study a subsection rife with historic hybridization and discuss the impacts of such processes on evolutionary trajectories. Aliciella subsection Subnuda comprises seven species of herbaceous plants occurring in Utah, the Navajo Nation, and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of nuclear ITS and chloroplast DNA regions and genome-wide RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from chloroplast and nuclear ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny and multispecies coalescent species tree robustly resolve relationships between six species-level clades. We use STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest that hybridization has occurred among all species in the subsection at some point in their history. Cytonuclear discordance reveals historic chloroplast capture, and we discuss potential causes of the observed discordance. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.

In 2015, Journal of Systematics and Evolution (JSE) established the Awards of JSE Outstanding Papers to recognize the papers published in JSE with important impact in systematics and evolution (Ge & Wen, 2015). Two Outstanding Papers and two Outstanding Papers by Young Investigators have been awarded each year since 2018. The selection of the awards was based on votes and assessments from all 17 editors of the journal with the consideration of the citations (data from Clarivate Web of Science) and the perceived impact on systematics and evolution. The winners of the Awards will receive a certificate and a prize of $800 (JSE Outstanding Papers) or $500 (JSE Outstanding Papers by Young Investigators) (Ge & Wen, 2021, 2022). Here we are delighted to announce the recipients of the awards for the 2021 papers and highlight the significance of the four awarded papers.

Roalson et al. A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles

The genus Carex L. (Cyperaceae) is widely distributed across continents and represents one of the largest genera in angiosperms, including about 2000 species. Although taxonomists continue to use subgenera and sections in Carex classification, the current understanding of phylogenetic relationships in this genus is not yet sufficient for a global reclassification of the genus within a Linnean infrageneric framework because numerous phylogenetic studies have demonstrated that most subgenera and sections in the genus are polyphyletic. In this study, Roalson et al. (2021) presented a hybrid classification framework of Carex to reflect the current state of our knowledge using a combination of informally named clades and formally named infrageneric groups. Based on an order corresponding to a linear arrangement of the clades on a ladderized phylogeny, the authors organized Carex into six subgenera, which were further subdivided into 62 formally named sections plus 49 informal groups. As the authors remarked, as many as 113 species were not placed in a clade with any confidence in this study and difficulties remained for untangling intricate nomenclature and identifying types for the many available sectional names. Despite these challenges, the proposed infrageneric classification of Carex will serve as a roadmap for better organizing our understanding of phylogeny, identifying species groups and stimulating further studies of this important genus.

Larridon et al. A new classification of Cyperaceae (Poales) supported by phylogenomic data

As the third largest monocot family with great economic and ecological importance, Cyperaceae (sedges) represent an ideal model family to study various questions in evolutionary biology. Despite considerable advances in molecular phylogenetic studies at the family level, evolutionary relationships at the tribal and g

Crassulaceae is a mid-sized family of angiosperms, most species of which are herbaceous succulents, usually with 5-merous flowers and one or two whorls of stamens. Although previous phylogenetic studies revealed seven major “clades” in Crassulaceae and greatly improved our understanding of the evolutionary history of the family, relationships among major clades are still contentious. In addition, the biogeographic origin and evolution of important morphological characters delimiting infrafamilial taxa have not been subject to formal biogeographic and character evolution analyses based on a well-supported phylogeny backbone. In this study, we used plastomic data of 52 species, representing all major clades revealed in previous studies to reconstruct a robust phylogeny of Crassulaceae, based on which we unraveled the spatiotemporal framework of diversification of the family. We found that the family may originate in southern Africa and then dispersed to the Mediterranean, from there to eastern Asia, Macaronesia, and North America. The crown age of Crassulaceae was dated at ca. 63.93 million years ago, shortly after the Cretaceous–Paleogene (K-Pg) boundary. We also traced the evolution of six important morphological characters previously used to delimit infrafamilial taxa and demonstrated widespread parallel and convergent evolution of both vegetative (life form and phyllotaxis) and floral characters (number of stamen whorls, petals free or fused, and flower merism). Our results provide a robust backbone phylogeny as a foundation for further investigations, and also some important new insights into biogeography and evolution of the family Crassulaceae.

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.

Chinese Tajiks are an Indo-Iranian-speaking population in Xinjiang, northwest China. Although the complex demographic history has been characterized, the ancestral sources and genetic admixture of Indo-Iranian-speaking groups in this region remain poorly understood. We here provide the genome-wide genotyping data for over 700 000 single-nucleotide polymorphisms (SNPs) and mtDNA multiplex sequencing data in 64 Chinese male Tajik individuals from two dialect groups, Wakhi and Selekur. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, treemix, qpWave/qpAdm, Admixture-induced Linkage Disequilibrium for Evolutionary Relationships (ALDER), and Fst analyses to infer a fine-scale population genetic structure and admixture history. Our results reveal that Chinese Tajiks showed the closest affinity and similar genetic admixture pattern with ancient Xinjiang populations, especially Xinjiang samples in the historical era. Chinese Tajiks also have gene flow from European and Neolithic Iran farmers-related populations. We observed a genetic substructure in the two Tajik dialect groups. The Selekur-speaking group who lived in the county had more gene flow from East Asians than Wakhi-speaking people who inhabited the village. These results document the population movements contributed to the influx of diverse ancestries in the Xinjiang region.

The chemical communication between plants and insects plays a pivotal role in shaping plant–insect interactions and ecological networks, making it a vital component in both natural and agricultural ecosystems. Despite the considerable advancements in the field of chemical ecology (Meinwald & Eisner, 2008), numerous challenges remain due to its interdisciplinary nature (encompassing evolutionary biology, neurobiology, chemistry, animal behavior, and network ecology), as well as the complexity of chemical communication (including mediating mutualistic and antagonistic relationships, and multifunctional roles at the community level). In this special issue of the Journal of Systematics and Evolution, we present a collection of 10 papers addressing these challenges through original research and comprehensive reviews of relevant subfields. The contributions can be organized into four primary themes: (i) community-level communication theory (Zu et al., 2022) and its application to plant–pollinator communities (Yang et al., 2022); (ii) the evolutionary history of communication from a phylogenetic and macroevolutionary perspective (Martel et al., 2021; Schwery et al., 2022); (iii) various communication types, including plant–pollinator (Martel et al., 2021), plant–pest (Fang et al., 2023), and plant–fungi–insect interactions (Xu et al., 2023); and (iv) an exploration of different communication factors such as distyly (Zeng et al., 2022), odor dynamics (Feng et al., 2022), chemical structures (Zhang et al., 2022), and the impact of herbicides (Ramos et al., 2022).

Ecological communities are characterized by complex interaction networks involving numerous interdependent species. However, traditional studies of plant–insect chemical communication have primarily focused on specific species, with only a few links between plant–insect interactions. With the rapid development of chemical collection instruments, there has been a growing interest in community-level studies on plant–insect chemical communication (reviewed by Zu et al., 2022). This development highlights the need for a conceptual framework and practical methodologies to expand our mechanistic understanding of plant–insect chemical communication from pairwise species interactions to ecological network levels.

Zu et al. (2020) proposed an innovative approach by incorporating Shannon information theory (Shannon, 1948), originally developed for telecommunication, into the study of plant–insect communication. In this special issue, Zu et al. (2022) contribute a perspective paper outlining the fundamentals of information theory and its application in studying the patterns and processes of cross-species chemical communication from both top-down and bottom-up perspectives. Shan

Plants, insects, and fungi have successfully colonized almost all terrestrial ecosystems, and their interactions have been the subject of numerous studies in recent decades. Plant-associated fungi include endophytic, arbuscular mycorrhizal, ambrosia, saprotrophic, pathogenic, and floral fungi. These fungi interact with insects through various mechanisms, including the modification of plant nutritional quality and degradation of plant defensive allelochemicals that are toxic to insects. Additionally, certain fungi assist plants in defending against insect attacks. Correspondingly, insects have evolved sophisticated nervous, digestive, and muscular systems that assist them in recognizing, preying on, and dispersing plant-associated fungi; these organ systems allow insects to detect and respond to various chemical signatures in the environment. Insects can be nourished, attracted, repelled, poisoned, and killed by chemical molecules produced by plant-associated fungi, which could be beneficial or detrimental to plants. This review summarizes the functions of different chemicals from the perspective of plant–fungus–insect interactions and discusses the challenges and future perspectives in this chemical ecology research field.