Holarctic phylogeographic structure of Eurasian wigeon (Mareca penelope) by I. V. Kulikova, Y. N. Zhuravlev, I. G. Korobitsyn, G. A. Nemkova, K. G. McCracken, J. L. Peters

“…A reconstruction of haplotypes phylogeny revealed the absence of geographic structure in the data. …”
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Museomics of Carabus giant ground beetles shows an Oligocene origin and in situ alpine diversification by Pauli, Marie T., Gauthier, Jérémy, Labédan, Marjorie, Blanc, Mickael, Bilat, Julia, Toussaint, Emmanuel F. A.

“…Using this technique at both the intra- and interspecific levels, we infer the most robust phylogeny to date for Arcifera, an ecologically and morphologically diverse clade of Carabus giant ground beetles. …”
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Comparison of mucosal microbiota populations across the gastrointestinal tract of healthy dogs by Ching-Yen Lin, Tzu-Wen L. Cross, Kelly S. Swanson

“…Therefore, the objective of this study was to characterize the phylogeny and predicted functional capacity of microbiota residing on the gut mucosa across five GI regions of healthy young adult and geriatric dogs fed different diets. …”
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Endophytic strategies decoded by genome and transcriptome analysis of Fusarium nematophilum strain NQ8GII4 by Siyuan Yan, Qingchen Zhang, Shuxin Jia, Miaomiao Guo, Qiangqiang Zhang, Peiwen Gu, Peiwen Gu

“…However, the molecular mechanisms underlying the symbiotic relationship between NQ8GII4 and alfalfa roots remain poorly understood.MethodsIn this study, we conducted (1) a comparative genomic analysis of selected saprophytic, pathogenic, and endophytic fungi, including molecular phylogeny analysis, whole-genome alignment, and divergence date estimation positioning, and (2) transcriptomic profiling of alfalfa roots infected with NQ8GII4.ResultsOur findings reveal that NQ8GII4 is genetically closely related to F. solani, suggesting it diverged from Fusarium phytopathogens. …”
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Biogeographic Insights Into the Late Miocene Diversification of the Giant Deep‐Ocean Amphipod Eurythenes by Carolina E. González, Johanna N. J. Weston, Reinaldo Rivera, Marcelo Oliva, Rubén Escribano, Osvaldo Ulloa

“…We constructed a time‐calibrated phylogeny using two mitochondrial DNA genes by analyzing publicly available data on 14 species of Eurythenes across a global depth range from 839 to 8081 m. …”
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Probing the potential of InDel polymorphisms on the molecular identification of cetaceans by Dafne Adriana Abreu dos Anjos, Rodrigo Goldenberg Barbosa, Anna Luiza dos Santos Donato, Elizeu Fagundes de Carvalho, Cesar Rogerio Leal do Amaral

“…The regions selected in this study can be used for the construction of molecular identification assays for phylogeny and conservation studies, especially when degraded samples are included.…”
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Spatio-temporal diversity of dietary preferences and stress sensibilities of early and middle Miocene Rhinocerotidae from Eurasia: impact of climate changes by Hullot, Manon, Merceron, Gildas, Antoine, Pierre-Olivier

“…The very large hippo-like Brachypotherium brachypus was one of the most affected species at all concerned localities (but Sansan), whereas early-diverging elasmotheriines were very little affected, suggesting an influence of phylogeny and/or diet in stress susceptibility. …”
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Sequence Variation in Toxoplasma gondii rop17 Gene among Strains from Different Hosts and Geographical Locations by Nian-Zhang Zhang, Ying Xu, Si-Yang Huang, Dong-Hui Zhou, Rui-Ai Wang, Xing-Quan Zhu

“…Sequence analysis identified 33 variable nucleotide positions (2.1%), 16 of which were identified as transitions. Phylogeny reconstruction based on rop17 gene data revealed two major clusters which could readily distinguish Type I and Type II strains. …”
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Persistent cross-species transmission systems dominate Shiga toxin-producing Escherichia coli O157:H7 epidemiology in a high incidence region: A genomic epidemiology study by Gillian AM Tarr, Linda Chui, Kim Stanford, Emmanuel W Bumunang, Rahat Zaheer, Vincent Li, Stephen B Freedman, Chad R Laing, Tim A McAllister

“…We constructed a timed phylogeny using BEAST2 using a structured coalescent model. …”
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Characterization of tumor evolution by functional clonality and phylogenetics in hepatocellular carcinoma by Zeynep Kacar, Eric Slud, Doron Levy, Julián Candia, Anuradha Budhu, Marshonna Forgues, Xiaolin Wu, Arati Raziuddin, Bao Tran, Jyoti Shetty, Yotsawat Pomyen, Jittiporn Chaisaingmongkol, Siritida Rabibhadana, Benjarath Pupacdi, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Chirayu Auewarakul, Suleeporn Sangrajrang, Chulabhorn Mahidol, Mathuros Ruchirawat, Xin Wei Wang

“…Furthermore, we observe significant B cell enrichment in linear trees compared to non-linear trees suggesting the need for further research to uncover potential variations in immune cell types within genomically determined phylogeny types. These results hint at the possibility that tumor cells and their microenvironment may collectively influence the tumor evolution process.…”
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Virulence-associated variants in Cryptococcus neoformans sequence type 93 are less likely to be associated with population structure compared to independent rare mutations by Katrina M. Jackson, Kisakye Diana Kabbale, Marissa Macchietto, David Meya, Peter Tiffin, Kirsten Nielsen

“…We additionally found that recurrent SNPs associated with virulence were less frequently evolutionarily linked and were two times more likely to be independent, congruent mutations rather than tied to phylogeny.IMPORTANCECryptococcus neoformans is an important pathogen that is widely distributed and ubiquitous in the environment. …”
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Squamanitaceae and three new species of Squamanita parasitic on Amanita basidiomes by Jian-Wei Liu, Zai-Wei Ge, Egon Horak, Alfredo Vizzini, Roy E. Halling, Chun-Lei Pan, Zhu L. Yang

“…In this study, with newly generated sequences of the type of the genus Squamanita, S. schreieri, and several additional species of the family, the phylogeny is reinvestigated with a concatenated (18S-5.8S-nrLSU-RPB2-TEF1-α) dataset. …”
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The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales by Qiang Li, Wenqi Xiao, Peng Wu, Ting Zhang, Peng Xiang, Qian Wu, Liang Zou, Mingying Gui

“…This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.…”
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The complete chloroplast genome sequences of monotypic genus Pseudogalium, and comparative analyses with its relative genera by Wei Yu, Xiao-Juan Li, Zhen Lv, Li-E Yang, De-Li Peng

“…Conclusions The complete chloroplast genomes of P. paradoxum were first reported in this study, which provided a new insight into phylogeny and taxonomy of this genus. Phylogenetic analyses strongly supported the following proposals: (1) P. paradoxum can be isolated as a genus closely related to Galium; (2) P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei form distinct clades, both of which can be considered as subspecies of P. paradoxum.…”
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III International Scientific and Practical Conference “Eagles of the Palearctic: Study and Conservation”, September 24–29, 2023, Almaty Resort Sanatorium, Almaty, Kazakhstan by Igor V. Karyakin, Elvira G. Nikolenko

“…The Key topics of the Conference: - populations of eagles – current status and trends, - threats – human persecution, poisoning, electrocution, and collisions, - conservation – approaches and techniques, international collaboration and cooperation, - methods and techniques for studying eagles,  - breeding biology, ecology, - movements – dispersal, habitat use and migration studies, including by means of ringing and transmitters, - genetics, evolution, phylogeny, and phylogeography of eagles, taxonomy, - climate change – potential influences and impacts, - breeding in captivity and sustainable use, - eagles as ecological indicators.…”
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Project ChemicalBlooms: Collaborating with citizen scientists to survey the chemical diversity and phylogenetic distribution of plant epicuticular wax blooms by Le Thanh Dien Nguyen, Nicole Groth, Kylie Mondloch, Edgar B. Cahoon, Keith Jones, Lucas Busta

“…By mapping the 78 wax bloom chemical profiles onto a phylogeny and using phylogenetic comparative analyses, we found that secondary alcohol and triterpenoid‐rich wax blooms were present in lineage‐specific patterns that would not be expected to arise by chance. …”
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Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae by Xinbi Jia, Jiaqi Wei, Yuewen Chen, Chenghong Zeng, Chan Deng, Pengchen Zeng, Yufei Tang, Qinghong Zhou, Yingjin Huang, Qianglong Zhu

“…The chloroplast genome (CPG) is useful for studying on plant taxonomy and phylogeny, and the analysis of codon usage bias (CUB) in CPGs provides further insights into the intricate phylogenetic relationships among Aroideae. …”
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Invasive mealybug Pseudococcus jackbeardsleyi Gimpel and Miller on Curcuma aeruginosa Roxb. on the seed rhizome in storage: a record of a new host by Rohimatun, Nida Nur Rahmah, Dewi Sartiami, Mahindra Dewi Nur Aisyah, Miftakhurohmah Miftakhurohmah, Melati, Devi Rusmin, Tri Lestari Madiningsih

“…Amplification of the COI gene yielded DNA bands measuring 490 base pairs (bp), while homology and phylogeny analysis confirmed the morphological identification. …”
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How Marine Megabenthos Fauna Responds to River Discharge and Artificial Flood in Large River Estuary by Debin Sun, Qinglu Fu, Jiao Wang, Linlin Chen, Jing Chen, Yilin Wang, Baoquan Li

“…The comprehensive indices of biodiversity (C‐diversity), phylogeny (C‐phyl), and stability (C‐stability) were synthesized from 24 basic indices to characterize the overall traits of megabenthos faunas. …”
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Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods by A. Yu. Pronozin, A. A. Paulish, E. A. Zavarzin, A. Yu. Prikhodko, N. M. Prokhoshin, Yu. V. Kruchinina, N. P. Goncharov, E. G. Komyshev, M. A. Genaev

“…Intraspecific classification of cultivated plants is necessary for the conservation of biological diversity, study of their origin and their phylogeny. The modern cultivated wheat species originated from three wild diploid ancestors as a result of several rounds of genome doubling and are represented by di-, tetra- and hexaploid species. …”
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