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
Biochemistry & Molecular Biology
Todd G. B. McLay, Rachael M. Fowler, Patrick S. Fahey, Daniel J. Murphy, Frank Udovicic, David J. Cantrill, Michael J. Bayly
Summary: This study conducted a phylogenetic analysis of 22 species of Eucalyptus subgenus Eudesmia in Australia using a targeted sequencing approach. The results showed that the evolution of eucalypts in Australia is complex and influenced by incomplete lineage sorting and hybridization. The custom bait kit developed in this study will serve as a powerful tool for investigating the evolutionary history of eucalypts more broadly.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Xinxin Tan, Jiwei Qi, Zhijin Liu, Pengfei Fan, Gaoming Liu, Liye Zhang, Ying Shen, Jing Li, Christian Roos, Xuming Zhou, Ming Li
Summary: In this study, a phylogenomic analysis was conducted on Macaca genus to investigate the intrageneric phylogenetic relationships among species. Strong evidence was found supporting the division of this genus into 7 species groups. Incomplete lineage sorting and hybridization events were identified as the main factors contributing to the discordance observed among gene trees. These findings provide insights into the rapid speciation occurring in nonhuman primates.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Liliya Doronina, Olga Reising, Hiram Clawson, Gennady Churakov, Juergen Schmitz
Summary: This study investigates the phylogenetics of Euarchontoglires using whole-genome analysis and a marker system with minimal homoplasy. By analyzing presence/absence patterns of transposed elements, diagnostic insertions were identified and provided support for current resolutions of Primatomorpha and Euarchonta, as well as alternative phylogenetic scenarios.
Article
Plant Sciences
Jianling You, Stephen C. Lougheed, Yao Zhao, Guojie Zhang, Wensheng Liu, Fan Lu, Yuguo Wang, Wenju Zhang, Ji Yang, La Qiong, Zhiping Song
Summary: Introgressive hybridization and incomplete lineage sorting play important roles in the phylogeography of plant species that experienced rapid diversification in the Qinghai-Tibetan Plateau and the Hengduan Mountains.
Article
Genetics & Heredity
Jennifer M. Korstian, Nicole S. Paulat, Roy N. Platt, Richard D. Stevens, David A. Ray
Summary: Using presence/absence data from over 10,000 Ves SINE insertions, the researchers reconstructed a phylogeny for 11 Myotis species. They found that phylogenetic conflict was rampant in this genus, with almost one-third of individual gene trees being discordant with the overall species tree. The study suggests that incomplete lineage sorting (ILS) is a major contributor to the discordance. The researchers also observed signs of introgression between Old and New World taxa, as well as within the New World Myotis species. The findings highlight the role of hybridization in the evolutionary history of Myotis.
Article
Fisheries
Zachary S. S. Randall, Gabriel A. A. Somarriba, Sampan Tongnunui, Lawrence M. M. Page
Summary: A review of the six recognized species of Pseudohomaloptera was conducted, and two species were re-described. Confusion in identifying populations of Pseudohomaloptera in mainland Southeast Asia was discovered, and an identification key was provided for accurate identification.
JOURNAL OF FISH BIOLOGY
(2023)
Article
Zoology
Arya Sidharthan, Rajeev Raghavan, V. K. Anoop, Ashwini Keskar, Neelesh Dahanukar
Summary: The Balitoridae family of teleostean fishes are adapted to swift-flowing mountain streams in South and Southeast Asia, with little known about their molecular phylogenetics and evolutionary biogeography. A study focusing on endemic balitorid lineages in the Western Ghats of India revealed a well-supported monophyletic clade forming endemic Western Ghats genera, with a sister-group relationship to Southeast Asian genus Pseudohomaloptera. Some endemic species show low genetic divergence and recent speciation, while misidentifications in available CO1 sequences suggest the need for accurate identification in the future.
Article
Biochemistry & Molecular Biology
Wenpan Dong, Yanlei Liu, Enze Li, Chao Xu, Jiahui Sun, Wenying Li, Shiliang Zhou, Zhixiang Zhang, Zhili Suo
Summary: This study reconstructed the phylogenetic relationships within Catalpa using a large genomic dataset, revealing that Catalpa is monophyletic with two main clades. Biogeographic analysis suggested three main dispersal events in the evolutionary history of Catalpa, highlighting the impact of incomplete lineage sorting.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Genetics & Heredity
Wei Li, Xiaggojiang Chen, Mengmeng Zheng, Yin Wang, Xingchen Zhou, Haiyang Li, Guolong Zhou, Bichun Li
Summary: The complete mitogenome sequence of Sinogastromyzon szechuanensis was obtained using next generation sequencing and confirmed via overlap-PCR method. The genome consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 23 transfer RNA genes, and 1 control region, with a slight A-T skew in the overall nucleotide composition of the heavy strand. Mitochondrial genome analyses based on ML analyses yielded identical phylogenetic trees.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Ivanna H. Tomasco, Facundo M. Giorello, Nicolas Boullosa, Matias Feijoo, Cecilia Lanzone, Enrique P. Lessa
Summary: Incomplete lineage sorting (ILS) and introgression have important roles in biological differentiation, particularly in rapid radiations. Assessment across genomic regions is essential to estimate the relative frequency of these processes. This study used transcriptomics to test for introgression and estimated the frequency of ILS in a set of closely related species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Devon A. DeRaad, Jenna M. McCullough, Lucas H. DeCicco, Paul M. Hime, Leo Joseph, Michael J. Andersen, Robert G. Moyle
Summary: Many organisms have multiple discrete genomes that are inherited separately and may have conflicting evolutionary histories. In Todiramphus kingfishers, mitonuclear discordance can be explained by extensive genome-wide incomplete lineage sorting, rather than gene flow. This suggests that similar demographic histories in other taxa across the Indo-Pacific may lead to high levels of incomplete lineage sorting and mitonuclear discordance.
Article
Biochemistry & Molecular Biology
Yi Wang, Markus Ruhsam, Richard Milne, Sean W. Graham, Jialiang Li, Tongzhou Tao, Yujiao Zhang, Kangshan Mao
Summary: This study used a large number of homologous nuclear and plastid genes to reconstruct the phylogenetic relationships within the genus Chamaecyparis, revealing strong cytonuclear discordance and conflicting topologies between nuclear gene trees.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Evolutionary Biology
Bo He, Youjie Zhao, Chengyong Su, Gonghua Lin, Yunliang Wang, Luyan Li, Junye Ma, Qun Yang, Jiasheng Hao
Summary: This study resolves the phylogenetic relationships among subgenera in the alpine butterfly Parnassius using nuclear and mitochondrial genome datasets. It identifies gene-tree/species-tree conflicts and considerable phylogenetic discordance due to incomplete lineage sorting (ILS). The study also compares different approaches and explores sources of phylogenomic conflict, providing insights for future evolutionary studies of the genus.
SYSTEMATIC ENTOMOLOGY
(2023)
Article
Genetics & Heredity
Shantanu Kundu, Manokaran Kamalakannan, Ah Ran Kim, Vishwanath D. Hegde, Dhriti Banerjee, Won-Kyo Jung, Young-Mog Kim, Hyun-Woo Kim
Summary: The current study reevaluates the systematic status of Suncus niger from its original distribution in Southern India using morphology and mitochondrial genetic data. It confirms S. niger as a distinct species and adds new range extension and elevation records in the Western Ghats biodiversity hotspot. The study highlights the importance of further genomic studies to understand the evolutionary trend of Soricomorphs.
Article
Ecology
J. W. Ray, M. Husemann, D. J. Lutz-Carrillo, R. S. King, P. D. Danley
ENVIRONMENTAL BIOLOGY OF FISHES
(2015)
Article
Biochemistry & Molecular Biology
Martin Husemann, Rachel Nguyen, Baoqing Ding, Patrick D. Danley
Article
Evolutionary Biology
Martin Husemann, Jesse W. Ray, Ryan S. King, Emily A. Hooser, Patrick D. Danley
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2012)
Review
Biology
Jan C. Habel, Martin Husemann, Aline Finger, Patrick D. Danley, Frank E. Zachos
BIOLOGICAL REVIEWS
(2014)
Article
Ecology
Patrick D. Danley, Martin Husemann, Justin Chetta
ENVIRONMENTAL BIOLOGY OF FISHES
(2012)
Article
Fisheries
Chunchi Liu, Xin Gao, Huanshan Wang, Huanzhang Liu, Wenxuan Cao, Patrick D. Danley
Article
Marine & Freshwater Biology
Baoqing Ding, Jason Curole, Martin Husemann, Patrick D. Danley
Article
Ecology
Martin Husemann, Noelia Veronica Guzman, Patrick D. Danley, Maria Marta Cigliano, Viviana Andrea Confalonieri
JOURNAL OF BIOGEOGRAPHY
(2013)
Review
Ecology
M. Husemann, M. Tobler, C. Mccauley, B. Ding, P. D. Danley
JOURNAL OF EVOLUTIONARY BIOLOGY
(2014)
Article
Multidisciplinary Sciences
Baoqing Ding, Daniel W. Daugherty, Martin Husemann, Ming Chen, Aimee E. Howe, Patrick D. Danley
Article
Multidisciplinary Sciences
Martin Husemann, Jan Christian Habel, Suk Namkung, Axel Hochkirch, Daniel Otte, Patrick D. Danley
Article
Fisheries
Jesse W. Ray, Martin Husemann, Ryan S. King, Patrick D. Danley
TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY
(2012)
Article
Evolutionary Biology
Martin Husemann, Suk Namkung, Jan C. Habel, Patrick D. Danley, Axel Hochkirch
Article
Biochemistry & Molecular Biology
Saisai Wang, Mohamed Diaby, Mikhail Puzakov, Numan Ullah, Yali Wang, Patrick Danley, Cai Chen, Xiaoyan Wang, Bo Gao, Chengyi Song
Summary: This study focused on the structure and diversity of the DD37D/maT and DD39D/GT families within the Tc1/mariner transposons, shedding light on their role in the evolution of eukaryotic genomes. The findings revealed different distributions of maTs and GTs, with potential horizontal transfer events between kingdoms and phyla of eukaryotes. The intact transposases and target site duplications suggest that these families may still be active in influencing genome evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)