Article
Biochemical Research Methods
Baqiao Liu, Tandy Warnow
Summary: This study introduces two new methods, NJst-J and FASTRAL-J, for estimating the species tree based on partial knowledge. The results show that both NJst-J and FASTRAL-J are faster than ASTRAL-J, and all three methods are statistically consistent under the given constraint.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Forestry
Bartosz Labiszak, Witold Wachowiak
Summary: This study investigates the role of hybridization and introgression in the evolutionary history of closely related pine taxa. The results indicate the significant impact of interspecific gene flow in the divergence of species and reveal asymmetrical migration patterns between different pine species. The study provides insights into the role of reticulation evolution in maintaining species integrity in forest trees.
Article
Mycology
Sandra Hilario, Liliana Santos, Artur Alves
Summary: The study focused on the delineation of species boundaries within the Diaporthe genus, specifically the D. amygdali complex. Results indicated that the species within this complex do not show clear boundaries, supporting the idea that they constitute a single species.
Article
Biology
Andrew Richards, Laura Kubatko
Summary: This paper introduces two new methods for species tree inference, Lily-T and Lily-Q, and compares them with two frequently used methods, SVDQuartets and ASTRAL. The results show that Lily-Q generally outperforms the other methods in most simulation settings.
BULLETIN OF MATHEMATICAL BIOLOGY
(2021)
Article
Biodiversity Conservation
Hae-Jun Baek, Soyeon Cho, Minjeong Seok, Joo-Won Shin, Dae-In Kim
Summary: This study aimed to assess the reutilization, distribution, and import status of invasive alien turtles in South Korea. It found that nine invasive alien turtle species, including the ecosystem disturbing species (EDS) Trachemys scripta, were traded in traditional markets. Additionally, 84 out of 169 registered turtles were reintroduced to new breeders, and the distribution of invasive alien turtles was confirmed in 341 locations across 109 cities. The study also revealed that an average of 7 tons of non-indigenous turtles are imported annually from over 20 countries to South Korea.
Article
Biochemistry & Molecular Biology
Henry L. North, Angela McGaughran, Chris D. Jiggins
Summary: The use of genomic data in invasion biology can provide valuable insights into processes such as invasion routes reconstruction and the importance of balancing selection and hybridization. While currently only a few invasive systems have utilized whole-genome resequencing, these studies have confirmed the significance of leveraging new technologies and approaches for a more comprehensive understanding of invasive species.
Review
Forestry
Paul S. Manos, Andrew L. Hipp
Summary: The oak flora of North America is diverse and species-rich, with recent research utilizing advanced techniques and detailed data to conduct systematic classification and phylogenetic studies, revealing the radiation history and biogeographical information of North American oaks.
Article
Multidisciplinary Sciences
Daemin Kim, Andrew T. Taylor, Thomas J. Near
Summary: Informed management and conservation efforts are crucial for sustainable recreational fishing and biodiversity conservation. This study successfully delimits 19 species of the Black Basses (Micropterus) using phylogenomic analyses, providing an important basis for their management and conservation.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Yichao Liu, Yongtan Li, Shuxiang Feng, Shufang Yan, Jinmao Wang, Yinran Huang, Minsheng Yang
Summary: This study aimed to investigate the chloroplast genomes of five Ulmus species and compare them with other Ulmus and Ulmaceae species. The results showed that the five species had typical tetrad structure with similar GC contents. Additionally, a number of potential markers and hotspots were identified for species identification and phylogeny reconstruction within Ulmus.
SCIENTIFIC REPORTS
(2022)
Article
Evolutionary Biology
Zhi Yan, Megan L. Smith, Peng Du, Matthew W. Hahn, Luay Nakhleh
Summary: Recent phylogenetic methods have focused on accurately inferring species trees in the presence of gene tree discordance due to incomplete lineage sorting (ILS). Most of these methods assume that data for each locus consist of orthologous, single-copy sequences, excluding loci with more than one copy in any of the studied genomes. This study examines the consequences of running such methods on data with paralogs, with or without ILS. Through simulations and analysis of biological data sets, the researchers demonstrate that these methods can still provide accurate results when paralogs are present. The findings have significant implications for expanding the data available for phylogenetic inference.
SYSTEMATIC BIOLOGY
(2022)
Article
Agronomy
Ewout Van Oost, Leen Leus, Bert De Rybel, Katrijn Van Laere
Summary: This study investigated genetic relationships, genome sizes and chromosome numbers in a collection of 82 lavender genotypes, including hybrids. AFLP marker analysis identified 5 clusters and revealed variations in genome sizes and chromosome numbers. The results can be utilized to predict cross compatibility among different species and guide targeted breeding for new improved Lavandula cultivars.
Article
Green & Sustainable Science & Technology
Georgios A. Gkafas, Joanne Sarantopoulou, Chrysoula Apostologamvrou, Chryssanthi Antoniadou, Athanasios Exadactylos, Georgios Fleris, Dimitris Vafidis
Summary: By analyzing RAD sequencing data, this study found strong evidence of admixture between two congeneric holothurians, Holothuria (Holothuria) tubulosa and Holothuria (Roweothuria) poli, living in sympatry in the Hellenic Seas. The populations of the two species diverged around 13.5 thousand years ago, just after the Last Glacial Maximum, indicating a role for admixture upon secondary contact and supporting the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.
Review
Geosciences, Multidisciplinary
Jean-Jacques Cornee, Philippe Munch, Melody Philippon, Marcelle BouDagher-Fadel, Frederic Quillevere, Mihaela Melinte-Dobrinescu, Jean-Frederic Lebrun, Aurelien Gay, Solene Meyer, Leny Montheil, Serge Lallemand, Boris Marcaillou, Muriel Laurencin, Lucie Legendre, Clement Garrocq, Milton Boucard, Marie-Odile Beslier, Mireille Laigle, Laure Schenini, Pierre-Henri Fabre, Pierre-Olivier Antoine, Laurent Marivaux
Summary: Our study reconstructs the palaeogeography of the northern part of the Lesser Antilles to analyze potential emerged areas during the Cenozoic era, allowing for terrestrial faunal dispersals between South America and the Greater Antilles. It reveals sequences of uplift and emergence during specific periods, indicating the existence of episodic mega-islands and transient terrestrial connections between different regions.
EARTH-SCIENCE REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Arthur Weyna, Lucille Bourouina, Nicolas Galtier, Jonathan Romiguier
Summary: Hybridization plays a central role in evolutionary processes such as speciation or adaptation, but its prevalence and distribution across different species remains largely unknown. In this study, a new statistical method is developed and implemented to detect F1 hybrids from single-individual genome sequencing data. The method is applied to sequencing data from over 1,500 species of arthropods, revealing the highest number of candidate F1 hybrids in Hymenoptera, particularly ants, suggesting a higher rate of recent hybridization in these groups. The prevalence of F1 hybrids is found to be heterogeneously distributed across ant taxa, with specific ecological and life-history traits being associated with many candidates. This study demonstrates the potential of large-scale genomic comparative studies in uncovering the determinants of first-generation hybridization across different taxa.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Sofiia Kolchanova, Alexey Komissarov, Sergei Kliver, Anyi Mazo-Vargas, Yashira Afanador, Jafet Velez-Valentin, Ricardo Valentin de la Rosa, Stephanie Castro-Marquez, Israel Rivera-Colon, Audrey J. Majeske, Walter W. Wolfsberger, Taylor Hans, Andre Corvelo, Juan-Carlos Martinez-Cruzado, Travis C. Glenn, Orlando Robinson, Klaus-Peter Koepfli, Taras K. Oleksyk
Summary: This study sequenced and annotated full mitochondrial genomes of Amazon parrots from the Greater Antilles, revealing the lowest sequence diversity in the population of A. vittata in Puerto Rico. The results support a stepping-stone dispersal and speciation hypothesis, contributing to the understanding of evolutionary history and guiding future conservation efforts in the Caribbean.
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)