Article
Plant Sciences
Thais M. Teixeira, Alison G. Nazareno
Summary: Intraspecific genetic variation is crucial for wild populations, and evaluating genetic diversity patterns is essential for guiding conservation policies, especially for threatened species. A study on the critically endangered plant Mimosa catharinensis using SNP markers revealed moderate genetic diversity levels, high outcrossing rates, and an apparent lack of inbreeding, despite a recent bottleneck in population history. This population genomic research addresses key issues in evolution and conservation biology, providing valuable insights for safeguarding genetic diversity in this unique species.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Mathematics
Ruriko Yoshida
Summary: When applying comparative phylogenetic analyses to genome data, the problem of missing genes in given species/taxa poses a challenge. This paper proposes a novel method to infer the missing part of a gene tree using tropical geometry and a linear regression approach. By considering a tropical polytope, the method guarantees an estimated tree's RF distance of at most four from the ground truth, as demonstrated through computational experiments on simulated and empirical data.
Article
Biotechnology & Applied Microbiology
Balnd M. Albarzinji, Farhad M. Abdulkarim, Shaho A. Hussein, Dlshad Rashid, Hayder Lazim
Summary: This study investigates the population relationship of the Sorani Kurdish population in Sulaymaniyah province using DNA samples. The results show that the J2 subclade predominates in this population, and they cluster with Asian populations while being furthest from European and African populations.
Article
Plant Sciences
Samuel W. Flake, Eliane A. Honda, Natashi A. L. Pilon, William A. Hoffmann, Giselda Durigan
Summary: The encroachment of forests into savannas is a common phenomenon, with the rate depending on factors such as soil conditions, species composition, and changes in stand structure. Savanna specialist trees are being replaced by generalist species, causing faster rates of stand development. Generalists are able to persist in forests and have faster growth rates, enabling them to outcompete and suppress savanna specialists.
JOURNAL OF ECOLOGY
(2022)
Article
Biology
Theo Sanderson
Summary: The COVID-19 pandemic has generated an unprecedented amount of sequencing data for SARS-CoV-2, leading to the need for a scalable tool for exploring phylogenetic trees. Taxonium is a new tool that uses WebGL to enable the exploration of large trees with millions of nodes in the browser. This article describes the insights gained from analyzing a tree of five million sequences and provides a tool for exploring a public tree of over five million SARS-CoV-2 sequences.
Article
Multidisciplinary Sciences
Michael Kalyuzhny, Jeffrey K. Lake, S. Joseph Wright, Annette M. Ostling
Summary: For species to coexist, there must be a decline in performance as conspecific density increases. In this study, it is shown that adults of tropical forest tree species exhibit strong spatial repulsion, indicating substantial niche differences between species. The results demonstrate that conspecific negative density dependence can play a significant role in stabilizing species diversity.
Article
Biochemistry & Molecular Biology
Eric Wootton, Claude Robert, Jolle Taillon, Steeve Cote, Aaron B. A. Shafer
Summary: In this study, the relationships between measures of inbreeding, genomic constraint, and mutational load were investigated in white-tailed deer, caribou, and mountain goat. The results showed that mountain goats had higher inbreeding coefficients and more evolutionarily constrained regions compared to caribou and white-tailed deer. Additionally, white-tailed deer had the highest mutational load, followed by caribou, while mountain goats had the lowest.
Article
Biochemical Research Methods
Nika Abdollahi, Lucile Jeusset, Anne de Septenville, Frederic Davi, Juliana Silva Bernardes
Summary: B cell receptor (BCR) genes undergo somatic hypermutations and antigen selection, leading to B cell affinity maturation. This process increases antibody affinity and forms a specific B cell lineage. A new method called ClonalTree incorporates genotype abundances into minimum spanning tree algorithms, outperforming previous methods in terms of accuracy and running time. ClonalTree is particularly useful for building B-cell lineage trees from high-throughput BCR sequencing data in biomedical applications.
BMC BIOINFORMATICS
(2023)
Article
Biodiversity Conservation
Hannes Gaisberger, Tobias Fremout, Chris J. Kettle, Barbara Vinceti, Della Kemalasari, Tania Kanchanarak, Evert Thomas, Josep M. Serra-Diaz, Jens-Christian Svenning, Ferry Slik, Wichan Eiadthong, Kandasamy Palanisamy, Gudasalamani Ravikanth, Vilma Bodos, Julia Sang, Rekha R. Warrier, Alison K. S. Wee, Christian Elloran, Lawrence Tolentino Ramos, Matieu Henry, Md Akhter Hossain, Ida Theilade, Simon Laegaard, K. M. A. Bandara, Dimantha Panduka Weerasinghe, Suchitra Changtragoon, Vivi Yuskianti, Peter Wilkie, Nguyen Hoang Nghia, Stephen Elliott, Greuk Pakkad, Pimonrat Tiansawat, Colin Maycock, Chaloun Bounithiphonh, Rozi Mohamed, M. Nazre, Baktiar Nur Siddiqui, Soon-Leong Lee, Chai-Ting Lee, Nurul Farhanah Zakaria, Ida Hartvig, Lutz Lehmann, Dzaeman B. Dzulkifli David, Jens-Peter Barnekow Lilleso, Chhang Phourin, Zheng Yongqi, Huang Ping, Hugo A. Volkaert, Lars Graudal, Arief Hamidi, So Thea, Sineath Sreng, David Boshier, Enrique Tolentino Jr, Wickneswari Ratnam, Mu Mu Aung, Michael Galante, Siti Fatimah Md Isa, Nguyen Quoc Dung, Tran Thi Hoa, Tran Chan Le, Md Danesh Miah, Abdul Lateef Mohd Zuhry, Deepani Alawathugoda, Amelia Azman, Gamini Pushpakumara, Nur Sumedi, Iskandar Z. Siregar, Hong Kyung Nak, Jean Linsky, Megan Barstow, Lian Pin Koh, Riina Jalonen
Summary: This study assessed the vulnerability of 63 socioeconomically important tree species in Asia's tropical and subtropical forests to various threats. The findings revealed that the majority of priority areas for conserving these trees are located outside protected areas, and all species are severely threatened across an average of 47% of their native ranges. The study also identified specific areas for conservation and restoration efforts, as well as potential options for agroforestry.
CONSERVATION BIOLOGY
(2022)
Article
Forestry
Richard Condit
Summary: This study used matrix demography to analyze the expected adult lifespan and maturation time of tropical trees. The results showed that fast-growing pioneer species had shorter expected adult lifespans compared to slow-growing shade-tolerant species. However, there was also high variation in expected adult lifespan within the slow-growth category.
Article
Biology
Lena Collienne, Kieran Elmes, Mareike Fischer, David Bryant, Alex Gavryushkin
Summary: This study introduces and investigates a space of discrete coalescent trees, focusing on time trees inference methods, clock-like tree models, and the geometrical properties of coalescent tree spaces. The results provide insights into how these properties impact various algorithms used in phylogenetic analyses, offering a discretization of previously introduced time tree space for approximating solutions to open problems.
JOURNAL OF MATHEMATICAL BIOLOGY
(2021)
Article
Biodiversity Conservation
Israel Flor Silva de Araujo, Elaine Cristina Fernandes, Felipe Neves da Silva, Patricia Sanae Sujii
Summary: This study assessed the impact of changes in seed and pollen dispersal on the genetic variability of an isolated population of Caryocar brasiliense. The results showed that populations with well preserved pollinators had lower rates of inbreeding and maintained greater genetic diversity over time, while reductions in pollen dispersal distance or pollination efficiency led to increased inbreeding and decreased genetic diversity. Conservation strategies should consider both tree and pollinator protection.
CONSERVATION GENETICS
(2022)
Article
Forestry
Olga Cholewinska, Andrzej Keczynski, Barbara Kusinska, Bogdan Jaroszewicz
Summary: The study found that the species of large trees have a significant impact on the diversity, distance, and frequency of adjacent trees, and as the diameter of the large tree increases, the distance between neighboring trees and the large tree also increases.
Article
History & Philosophy Of Science
Celso Neto
Summary: This paper explores the role of idealizations in social activities within science, such as the recruitment of experts and the organization of laboratories, emphasizing the importance of understanding the relationship between idealizations and these social practices.
Article
Ecology
Sean Tsz Sum Law, Wenyan Nong, Ho Yin Yip, Eric Ka Yip Liu, Terence Pun Tung Ng, Ryan Ho Leung Tsang, Nianhe Xia, Pang-Chui Shaw, Hon Ming Lam, David Tai Wai Lau, Jerome Ho Lam Hui
Summary: This study sequenced 346 individuals of the incense tree from Hong Kong and southern mainland China, revealing a genetically distinct subpopulation in Hong Kong that requires special conservation measures and establishing a foundation for future conservation efforts.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Ezgi Ogutcen, Camille Christe, Kanae Nishii, Nicolas Salamin, Michael Moller, Mathieu Perret
Summary: Gesneriaceae, a pantropical plant family with diverse growth forms and floral morphology, has had its systematics improved with the development of a specific gene capture kit targeting 830 single-copy loci. This allowed for the resolution of phylogenetic relationships within the family, providing high support for major lineages and high resolution within recent radiations. This molecular resource opens new perspectives for studying Gesneriaceae phylogeny at different taxonomical levels and understanding the factors underlying the diversification of this plant group.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Carlos G. Boluda, Victor J. Rico, Yamama Naciri, David L. Hawksworth, Christoph Scheidegger
Summary: This study investigated the phylogeography and genetic diversity of the lichen species Bryoria fuscescens in Europe and western North Africa, revealing Scandinavia as the region with the highest genetic diversity. Three gene pools were identified, with two linked to phenotypic characteristics and the third related to an American sister species. Migration routes were estimated to be from north to south, contradicting glacial refugia distributions. The presence of ancestral shared alleles in distant populations may bias phylogeographic reconstructions.
Article
Plant Sciences
Carlos G. Boluda, Camille Christe, Aina Randriarisoa, Laurent Gautier, Yamama Naciri
Summary: The study focused on the taxonomy and conservation of two species complexes within Capurodendron, with the Western Complex containing three well-delimited species and the Arid Complex containing three morphologically well-defined but genetically intermixed species. Hybridization patterns were observed between some species, providing insight into the complex evolutionary history of these plant species in Madagascar.
Article
Plant Sciences
Daniel Jeanmonod, Yamama Naciri
Summary: A study on the species of Ranunculus sect. Batrachium DC. in Corsica was conducted based on biometric analysis and field observations. Several species were excluded from the section, while certain groups were retained and statistically discriminated based on fruiting pedicel length and multifidous leaf length. The study identified three species present on the island and provided an identification key as well as information on their ecology and distribution.
Article
Plant Sciences
Carlos G. Boluda, Camille Christe, Yamama Naciri, Laurent Gautier
Summary: The genus Capurodendron in Madagascar is the largest genus of the family Sapotaceae, but the species-level identification and conservation assessment of its valued hardwood trees are challenging. This study used morphology and molecular analysis to identify two deeply divergent lineages within Capurodendron, potentially suggesting the presence of new species.
Article
Ecology
Angela Cano, Fred W. Stauffer, Tobias Andermann, Isabel M. Liberal, Alexander Zizka, Christine D. Bacon, Harri Lorenzi, Camille Christe, Mats Topel, Mathieu Perret, Alexandre Antonelli
Summary: This study explores the historical assembly of understorey palms in Central American rainforests. The results suggest that most understorey palm species in Central America evolved locally after repeated dispersal events, mainly from South America. The diversification of understorey palms in Central American rainforests primarily occurred after closure of the Central American Seaway, indicating the importance of the Great American Biotic Interchange.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Biodiversity Conservation
Antoine Jousson, Camille Christe, Fred Stauffer, Brigitte Marazzi, Frederique Aberlenc, Guido Maspoli, Yamama Naciri
Summary: This study investigates the invasion of Trachycarpus fortunei in Switzerland and Italy and compares the results obtained from two genetic markers. Genetic analysis reveals that the palm's expansion in the invaded areas is active and the genetic pattern is related to the colonization process.
BIOLOGICAL INVASIONS
(2022)
Article
Plant Sciences
Laurent Gautier, Carlos G. Boluda, Richard Randrianaivo, Yamama Naciri
Summary: During the revision of Malagasy species of Sapotaceae, two new species belonging to Capurodendron Aubrey were discovered. One of them was earlier assumed to be a hybrid but was later confirmed as a valid species through genetic and morphological analyses. The second species is distinct both morphologically and geographically. Both species are considered threatened based on preliminary conservation assessments.
Article
Plant Sciences
Yamama Naciri, Zeynep Toprak, Honor C. Prentice, Laetitia Hugot, Angelo Troia, Concetta Burgarella, Josep Lluis Gradaille, Daniel Jeanmonod
Summary: The study focused on Silene section Italicae and used 500 specimens sequenced for one nuclear and two plastid markers to investigate species delimitation within the section. While confident delimitation of 50% of the species was achieved, the delimitation of other species, such as Silene nemoralis, S. nodulosa, and S. andryalifolia, proved to be more challenging. The study also confirmed that adaptation to chasmophytic habitats occurred independently among chasmophyte species and showed that species from the Western Mediterranean Basin exhibited more conflicting species boundaries than those from the Eastern Mediterranean Basin.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Aina Randriarisoa, Yamama Naciri, Kate Armstrong, Carlos Galan Boluda, Stephanie Dafreville, Charles Pouchon, Laurent Gautier
Summary: Phylogenetic studies have shown that Manilkarinae is a monophyletic subtribe excluding Northia, with four genera: Faucherea, Labourdonnaisia, Labramia, and Manilkara. However, taxonomic issues about unclear generic delimitations and unresolved relationships have been raised. This study aims to resolve these issues using molecular phylogeny, morphological characters, divergence time estimation, and ancestral state reconstruction. The phylogeny reveals four main lineages, with Manilkara being sister to Labramia, and Labourdonnaisia-Faucherea clade being sister to the three Pacific Manilkara species. Faucherea is synonymized with Labourdonnaisia, and the three Pacific Manilkara species are considered a separate genus called Abebaia. The ancestral state reconstruction shows that ancestral Manilkarinae had a hexamerous corolla, well-developed dorsal appendages and staminodes, and a pubescent ovary.
Article
Plant Sciences
Philippe Clerc, Yamama Naciri
Summary: The use of molecular data in species delimitation and evolutionary history reconstruction is prevalent across all organisms, but caution is needed to avoid incorrect conclusions due to misidentification of specimens. Research findings support distinct morphological and anatomical differences between Usnea barbata and U. dasopoga, with separate clusters in the molecular phylogeny, and refute the previous synonymization of U. substerilis with U. lapponica. The study highlights the importance of correct identification of voucher specimens in DNA databases and offers general suggestions to prevent false specimen identifications in phylogenetic studies.
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)
