Review
Plant Sciences
Steven J. Fleck, Richard W. Jobson
Summary: Plastid molecular phylogenies reveal that carnivorous plants evolved independently at least 11 times. A nuclear gene-based phylogeny provides an overview of relationships within and between carnivorous families and genera.
Article
Biochemistry & Molecular Biology
Xiao-Mei Xia, Miao-Qin Yang, Cong-Li Li, Si-Xin Huang, Wei-Tao Jin, Ting-Ting Shen, Fei Wang, Xiao-Hua Li, Watanabe Yoichi, Le-Hua Zhang, Yuan-Run Zheng, Xiao-Quan Wang
Summary: By studying the Rhododendron genus, researchers discovered that most extant species originated from evolutionary radiations as the genus migrated southward from circumboreal areas to tropical/subtropical mountains during the Miocene. This geographical uneven diversification led to a higher species diversity in Asia, driven mainly by environmental variables such as elevation range and annual precipitation. The study showcases how the intensification of the Asian monsoon has facilitated evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Lei Zhao, Ying-Ying Yang, Xiao-Jian Qu, Hong Ma, Yi Hu, Hong-Tao Li, Ting-Shuang Yi, De-Zhu Li
Summary: This study improves our understanding of aroid phylogeny by using a large number of nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade's adaptation to aquatic environments, the results suggest that whole-genome duplication may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade.
Article
Plant Sciences
Jana Skopalikova, Jana Leong-Skornickova, Otakar Sida, Mark Newman, Zuzana Chumova, Vojtech Zeisek, Vlasta Jarolimova, Axel Dalberg Poulsen, Marcos V. Dantas-Queiroz, Tomas Fer, Eliska Zaveska
Summary: Hybridization is a common phenomenon in plant evolution and understanding its role is crucial for understanding the diversification processes of many taxonomic groups. Ancient hybridization has recently received more attention as it has been shown to be a trigger for evolutionary radiation, although it can also inhibit further diversification. The causes, frequency, and consequences of ancient hybridization are still to be explored.
Article
Plant Sciences
Fan Yang, Jiawei Luo, Wenmeng Guo, Yuxin Zhang, Yunxiao Liu, Ze Yu, Yaqiang Sun, Mingjun Li, Fengwang Ma, Tao Zhao
Summary: This study investigates the origin and evolutionary dynamics of SOT genes in the Rosaceae family by analyzing the synteny relationships among PLT genes in various plant lineages. The findings reveal the lineage-specific and synergistic duplications in Amygdaloideae that contribute to the expansion of SOTs in Rosaceae plants.
Article
Biochemistry & Molecular Biology
Tingru Mao, Yewei Liu, Mariana M. Vasconcellos, Marcio R. Pie, Gajaba Ellepola, Chenghai Fu, Jian Yang, Madhava Meegaskumbura
Summary: This study used RADseq to investigate the evolution of Sinocyclocheilus fishes in China. The results revealed the evolutionary relationships and mechanisms of troglomorphism in Sinocyclocheilus, showing that this species has evolved multiple derived cave-adapted traits. Six major clades were identified within Sinocyclocheilus, providing valuable insights for future research on the evolution and adaptation of cave life in this fish genus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Olena Meleshko, Michael D. Martin, Thorfinn Sand Korneliussen, Christian Schroeck, Paul Lamkowski, Jeremy Schmutz, Adam Healey, Bryan T. Piatkowski, A. Jonathan Shaw, David J. Weston, Kjell Ivar Flatberg, Peter Szovenyi, Kristian Hassel, Hans K. Stenoien
Summary: The study found significant phylogenetic discordance in the nuclear and organellar genomes of the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum), primarily attributed to extensive incomplete lineage sorting (ILS) following the rapid radiation of the genus rather than post-speciation introgression. Despite widespread interspecific hybridization in the group, recent gene flow among species was found to be highly restricted.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Tao Liang, Shai Meiri
Summary: This study explored the drivers of spatial patterns of lizard richness in China, using contemporary environmental, historical, and evolutionary factors. The results showed that lizard richness was positively correlated with current climatic and environmental factors, as well as short-term climatic stability. However, there was little correlation between lizard richness and diversification rates.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Biology
Xiu-Xiu Guo, Xiao-Jian Qu, Xue-Jie Zhang, Shou-Jin Fan
Summary: This study focuses on the plastomes of Aristidoideae, a subfamily in the family Poaceae. The plastomes of two species, Aristida adscensionis and Stipagrostis pennata, were newly sequenced and compared with a total of 16 Aristidoideae plastomes. The plastomes were found to be conservative in terms of genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common types. The study also analyzed codon usage and identified highly variable regions. The phylogenetic analysis supported the monophyly of Aristidoideae and the relationship between the three genera. The divergence between different species may be associated with factors such as carbon fixation patterns, geographical distributions, and ploidy. This study contributes to our understanding of the phylogeny and evolution of Aristidoideae.
Article
Biochemistry & Molecular Biology
Ze-Long Nie, Richard Hodel, Zhi-Yao Ma, Gabriel Johnson, Chen Ren, Ying Meng, Stefanie M. Ickert-Bond, Xiu-Qun Liu, Elizabeth Zimmer, Jun Wen
Summary: The north temperate region had a warm climate and a rich thermophilic flora before the Eocene, but the early diversifications of the temperate biome under global climate change and biome shift are not well understood. Hybridization/introgression is an important driving force of speciation in plant diversity. In this study, we analyzed genomic data from the New World Vitis, a temperate North American flora, and found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Plant Sciences
Lu-Shui Zhang, Chun-Lin Chen, Xing-Xing Mao, Jian-Quan Liu
Summary: In this study, the phylogenetic relationships and diversification patterns of economically important species in the subfamily Polygonoideae were investigated. The results revealed well-defined clades and provided insights into the origins and evolutionary patterns of these species. The findings also shed light on the effects of climatic oscillations on the diversification of this subfamily.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Chenyang Cai, Erik Tihelka, Mattia Giacomelli, John F. Lawrence, Robin Kundrata, Shuhei Yamamoto, Margaret K. Thayer, Alfred F. Newton, Richard A. B. Leschen, Matthew L. Gimmel, Liang Lu, Michael S. Engel, Patrice Bouchard, Diying Huang, Davide Pisani, Philip C. J. Donoghue
Summary: Beetles are the most biodiverse animal order, and this study uses phylogenomic techniques to propose new classification changes and analyze the origin and divergence time of beetles, finding differences from previous hypotheses.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Plant Sciences
Fei Qin, Tiantian Xue, Xiaoxia Zhang, Xudong Yang, Jianghong Yu, Sudhindra R. Gadagkar, Shengxiang Yu
Summary: This study reconstructed the phylogenetic relationships and evolutionary history of Impatiens sect. Impatiens using plastome data and a comprehensive sampling. The results revealed that the section originated in the Hengduan Mountains and Southeast China, and subsequently dispersed to other regions during the Pliocene and Pleistocene. The diversification rate was high in the early history, especially in the Hengduan Mountains, but decreased over time. Species richness was strongly associated with elevation range, elevation, and mean annual temperature.
Article
Microbiology
Matthew P. Nelsen, Steven D. Leavitt, Kathleen Heller, Lucia Muggia, H. Thorsten Lumbsch
Summary: This study investigates the evolution of climatic niches in Trebouxia, the most common genus of lichen-forming algae. The analysis reveals different evolutionary models for the climatic niche divergence and predicts that the current pace of climate change will exceed the previous evolution of Trebouxia climatic niches.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Chao Zhang, Yiming Zhao, Edward L. Braun, Siavash Mirarab
Summary: The text discusses the issue of erroneous data in sequence datasets and the need for automatic error detection methods as datasets grow larger. It introduces the TAPER method, which detects errors in species-specific stretches of sequence alignments to improve accuracy in downstream analyses.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Samuel Lopez-Nieves, Jorge El-Azaz, Yusen Men, Cynthia K. Holland, Tao Feng, Samuel F. Brockington, Joseph M. Jez, Hiroshi A. Maeda
Summary: l-Tyrosine plays a crucial role in protein synthesis and is synthesized by plants through TyrA arogenate dehydrogenase. Some plant lineages, like Fabaceae and Caryophyllales, have TyrA enzymes that are less sensitive to tyrosine inhibition, leading to elevated production of tyrosine-derived compounds. Specific amino acid substitutions, such as E208D in Caryophyllales, play key roles in deregulating TyrAs, presenting a potential for boosting essential plant natural products.
Article
Biochemistry & Molecular Biology
Emmanuel Paradis, Santiago Claramunt, Joseph Brown, Klaus Schliep
Summary: This paper introduces three bootstrap methods to infer confidence intervals for branch lengths in molecular phylogenies. The methods perform well under a strict clock model, but are less successful when an uncorrelated or correlated relaxed clock model is used. Factors such as the number of calibration points, sequence length, and number of sequences can impact the performance of the confidence intervals.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Evolutionary Biology
Ben Bettisworth, Stephen A. Smith, Alexandros Stamatakis
Summary: Computing ancestral ranges using the DEC model of biogeography is time-consuming due to the large matrix exponential computation. This study introduces Lagrange-NG, a faster version of the Lagrange tool, which achieves significant speedups and allows analysis of datasets with a large number of regions. Lagrange-NG also improves coding quality standards compared to its predecessor.
SYSTEMATIC BIOLOGY
(2023)
Article
Plant Sciences
Emily M. Lewis, Jeremie B. Fant, Michael J. Moore, Krissa A. Skogen
Summary: This study demonstrated the importance of animal pollinators in pollen and seed dispersal and showed that different pollinator functional groups can have differential impacts on genetic diversity. The research focused on two closely related taxa, Oenothera gayleana and O. hartwegii subsp. filifolia, and found that genetic structure is primarily driven by pollen dispersal.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
M. Alejandra Guerrero-Rubio, Nathanael Walker-Hale, Rui Guo, Hester Sheehan, Alfonso Timoneda, Fernando Gandia-Herrero, Samuel F. Brockington
Summary: This study revisited a publication by Bean et al. (2018) on the evolution of l-DOPA 4,5-dioxygenase (DODA) activity in Caryophyllales. The authors replicated the analyses conducted by Bean et al. (2018) and found additional residues that were implicated in the activity of BvDODAa1. Their in vivo and in vitro assays showed that the original seven residue substitutions identified by Bean et al. (2018) had minimal effect on the catalytic activity of BvDODAa2. The authors concluded that the evolutionary pathway to high DODA activity is more complex than previously thought.
Article
Evolutionary Biology
Ryan A. Folk, Michelle L. Gaynor, Nicholas J. Engle-Wrye, Brian C. O'Meara, Pamela S. Soltis, Douglas E. Soltis, Robert P. Guralnick, Stephen A. Smith, Charles J. Grady, Yudai Okuyama
Summary: Applications of molecular phylogenetic approaches have revealed evidence of hybridization across various clades of life. This study focuses on the Heuchereae clade in Saxifragaceae and uses a combination of nuclear and chloroplast data to confirm previous hybridization events and identify a new one. The results suggest that past climate change and species' ecological strategies play important roles in shaping patterns of range contact and opportunities for hybridization.
SYSTEMATIC BIOLOGY
(2023)
Article
Biodiversity Conservation
Juan Pablo Ortiz-Brunel, Helga Ochoterena, Michael J. Moore, Juvenal Aragon-Parada, Joel Flores, Guadalupe Munguia-Lino, Aaron Rodriguez, Maria Magdalena Salinas-Rodriguez, Hilda Flores-Olvera
Summary: Gypsum soils are widely distributed in arid regions around the world and support unique flora with high levels of endemism. However, the flora of gypsum outcrops in Mexico has been poorly studied. This study aimed to assess the sampling coverage, species richness, endemism centers, and protected areas of Mexican gypsum flora.
Article
Plant Sciences
Stephen A. A. Smith, Nathanael Walker-Hale, Charles Tomomi Parins-Fukuchi
Summary: Heterogeneity in composition has been observed in both nucleotide and amino acid datasets of plants. Shifts in composition occur more frequently in nucleotides and are associated with certain plant clades. Although genes in these clades do not share the same composition, they tend to shift in the same direction. Further investigation is needed to understand the underlying biological processes.
Article
Plant Sciences
Boas Pucker, Nathanael Walker-Hale, Jasmina Dzurlic, Won C. Yim, John C. Cushman, Alexandra Crum, Ya Yang, Samuel F. Brockington
Summary: In this study, the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales were investigated. The analysis of transcriptomic and genomic datasets revealed that most flavonoid synthesis genes remain conserved in betalain-pigmented lineages, but TT19 orthologs, crucial for the final step in anthocyanidin synthesis, were repeatedly lost. Furthermore, there were observed losses and alterations in the MBW transcription complex essential for canonical anthocyanin synthesis. These findings suggest that the loss and exclusion of anthocyanins in betalain-pigmented species are orchestrated through multiple mechanisms.
Article
Plant Sciences
Melanie Tietje, Alexandre Antonelli, Felix Forest, Rafael Govaerts, Stephen A. Smith, Miao Sun, William J. Baker, Wolf L. Eiserhardt
Summary: Regions with high unique phylogenetic diversity (PD) are important for conservation. The global distribution of plant PD remains poorly understood, but our analysis using a comprehensive global checklist of vascular plants identifies hotspots of unique plant PD. Our results support three hypotheses: PD is more evenly distributed than species diversity, areas of highest PD do not maximize cumulative PD, and multiple biomes are needed to maximize cumulative PD.
Article
Plant Sciences
William N. Weaver, Stephen A. Smith
Summary: LeafMachine2 is a machine learning and computer vision tool that can automatically extract leaf traits from digital plant data sets. It has been trained on a large number of annotated images and can efficiently extract trait data from various types of plant images, overcoming some of the limitations of traditional methods.
APPLICATIONS IN PLANT SCIENCES
(2023)
Article
Biology
Tao Feng, Boas Pucker, Tianhui Kuang, Bo Song, Ya Yang, Nan Lin, Huajie Zhang, Michael J. Moore, Samuel F. Brockington, Qingfeng Wang, Tao Deng, Hengchang Wang, Hang Sun
Summary: Glasshouse plants have evolved specialized morphology to adapt to intensive UV radiation and low temperature. The glasshouse structure of specialized cauline leaves effectively absorbs UV light and creates an optimal microclimate for reproductive organ development. The genome sequence of Rheum nobile, a flagship glasshouse plant, reveals key genetic network modules related to the morphological transition to specialized glasshouse leaves.
COMMUNICATIONS BIOLOGY
(2023)
Article
Plant Sciences
William N. Weaver, Brad R. Ruhfel, Kyle J. Lough, Stephen A. Smith
AMERICAN JOURNAL OF BOTANY
(2023)