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
Zheng Bin Randolph Quek, Jia Jin Marc Chang, Yin Cheong Aden Ip, Yong Kit Samuel Chan, Danwei Huang
Summary: The mitochondrial genetic code in invertebrates is more diverse than the standard genetic code, with the identification of new initiation codons in sea stars. Gene order among asteroids, echinoids, and holothuroids is remarkably conserved, with few changes over 500 million years of echinoderm evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Entomology
Shu-Yi Li, Yan-Min Zhao, Bing-Xin Guo, Chen-Hong Li, Bing-Jiao Sun, Xiao-Long Lin
Summary: This study reports the complete mitochondrial genome sequences of 12 Chironomus species and one Microchironomus species for the first time. The analysis of these mitogenomes, combined with previously reported ones, provides insights into the nucleotide composition, codon usage, selection pressure, and heterogeneity of Chironomus species. The phylogenetic relationships of Chironomus based on these mitogenomes were also reconstructed. The findings demonstrate the conservative nature of Chironomus mitogenomes in terms of nucleotide composition and gene order, enriching the existing knowledge of chironomid mitochondrial genomes and contributing to a better understanding of the evolutionary history of Chironomus.
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
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
Plant Sciences
Mengting Wang, Wenhui Yu, Jiapeng Yang, Zhenyu Hou, Chao Li, Zhitao Niu, Benhou Zhang, Qingyun Xue, Wei Liu, Xiaoyu Ding
Summary: Our study focuses on the Dendrobium orchids, which have large morphological divergence and difficulties in species taxonomy. We assembled the complete mitogenomes of two Dendrobium species and compared them with other orchids. The results reveal extensive variations in repetitive and chloroplast-derived sequences in Dendrobium mitogenomes, and the intergenic content has undergone expansion during evolution. We also sequenced the mitogenomes of 26 Dendrobium species and reconstructed their phylogenetic relationships based on mitochondrial and plastid data. The mitochondrial phylogeny shows partial characteristics of the plastid phylogeny and provides new insights into the phylogenetic relationships of Dendrobium species.
Article
Entomology
Mujie Qi, Huifeng Zhao, Fang Yu, Aibing Zhang, Houhun Li
Summary: The Odontiinae is a small group in the Pyraloidea with diverse moths, and the mitochondrial genome data helps in resolving the phylogenetic relationships of Pyraloidea.
Article
Genetics & Heredity
Wenqian Wang, Huan Zhang, Jerome Constant, Charles R. Bartlett, Daozheng Qin
Summary: The complete mitogenomes of nine Fulgoridae species were sequenced and annotated to explore their mitogenome diversity. Phylogenetic analysis revealed that Fulgoridae is divided into two groups, with Aphaenini and Pyropsini being part of the monophyletic group.
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
Entomology
Huicong Du, Jiaxing Fang, Xia Shi, Sufang Zhang, Fu Liu, Chunmei Yu, Zhen Zhang, Xiangbo Kong
Summary: Comparative studies of the structural characteristics and phylogenetic relationships of bark beetles' mitogenomes can enhance our understanding of mitogenome evolution. The analysis revealed conservation of start and stop codon usage, amino acid abundance, and relative frequency of codon use among the eight bark beetle species studied. Additionally, different regions of tRNA exhibited varying degrees of conservatism.
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.
Review
Immunology
Rocio Fernandez-Fernandez, Rocio Lopez-Igual, Josep Casadesus, Maria Antonia Sanchez-Romero
Summary: Microbial cell individuality has attracted increasing interest in the scientific community due to the noticeable phenotypic heterogeneity observed within clonal populations. Advances in fluorescent protein technology and single-cell analysis have allowed for the identification of phenotypic cell variants in bacterial populations, which exhibit differences in gene expression, survival under selective conditions and stresses, and host interactions. Cell sorting approaches have been utilized to study bacterial subpopulations and analyze their evolutionary traits, gene expression patterns, response to cellular stresses, and phenotypic variants.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Fisheries
Erik R. Schoen, Kristen W. Sellmer, Mark S. Wipfli, Juan A. Lopez, Renae Ivanoff, Benjamin E. Meyer
Summary: Research in Alaska indicates that predation on juvenile salmon varies across seasons, habitats, and streamflow levels, with Arctic grayling and Dolly Varden char potentially excluding Chinook salmon in certain situations. This highlights the importance of considering predation risk in efforts to support Chinook salmon recovery through climate adaptation, fisheries management, and habitat restoration decisions.
ECOLOGY OF FRESHWATER FISH
(2022)
Article
Zoology
Hsin Lee, Nicolas Puillandre, Yasunori Kano, Wei-Jen Chen, Sarah Samadi
Summary: This study investigates the species diversity of the family Cocculinidae using an integrated approach. The results reveal high diversity in the Indo-West Pacific region, with many species not assigned to known names. Additionally, a previously unknown copulatory structure and ten main clades in the family were discovered.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Genetics & Heredity
Matthew A. Campbell, Shannon E. K. Joslin, Alisha M. Goodbla, Malte Willmes, James A. Hobbs, Levi S. Lewis, Amanda J. Finger
Summary: This study investigated life history variation in the critically endangered Delta Smelt and found evidence of associations between genetic variants and life history phenotypes. Using DNA sequencing data, the researchers accurately assigned fish into freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within the Delta Smelt population.
G3-GENES GENOMES GENETICS
(2022)
Article
Ecology
Yuting Vicky Lin, Wanchien Victoria Hsiao, Wei-Jen Chen, Vianney Denis
Summary: This study examines the responses of fish to temperature and benthic habitat changes, and identifies potential sentinels of environmental changes. The distribution of some fish species is constrained by temperature, while others also depend on the availability of benthic habitats. Global warming may lead to shifts in the distribution of certain fish species, and the tropicalization process may occur in different waves.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Zoology
Peter B. Moyle, Matthew A. Campbell
Summary: Using population genomics and other genetic, distributional, and meristic studies, it has been discovered that the Riffle Sculpin actually consists of three cryptic species and four subspecies, most of which are endemic to California.
Article
Fisheries
Fumihito Tashiro, Wei-Jen Chen
Summary: The new synaphobranchid eel, Ilyophis singularis, is described based on specimens collected from the northeastern South China Sea. It is distinguished by its low number of vertebrae and several other characteristics, and the uncertainties in defining the subgroups in the Ilyophis genus are also discussed.
ICHTHYOLOGICAL RESEARCH
(2023)
Article
Biodiversity Conservation
Tsai-Hsuan Tony Hsu, Wei-Jen Chen, Vianney Denis
Summary: eDNA metabarcoding method is powerful for investigating fish fauna, but its replacement of traditional methods is still debatable. This study compared fish diversity assessments using eDNA, UVC, and DOV surveys in northern Taiwan. The results showed that eDNA can explore the regional species pool effectively, while all methods revealed the same spatial patterns of beta diversity. Visual surveys were more suitable for studying fish-benthos interactions. Specific surveys should be implemented based on ecological questions of interest, rather than recommending a combination of eDNA with traditional methods indiscriminately.
ECOLOGICAL INDICATORS
(2023)
Article
Evolutionary Biology
Matthew A. Campbell, Matthew C. Hale, Chase S. Jalbert, Kristine Dunker, Adam J. Sepulveda, J. Andres Lopez, Jeffrey A. Falke, Peter A. H. Westley
Summary: Invasive species pose a major threat to biodiversity, but they also provide opportunities for ecological and evolutionary research. This study analyzed the genetic variation of native and invasive populations of northern pike and found low levels of genetic diversity, indicating bottleneck effects. The results suggest that invasive pike likely came from multiple introductions from different native populations in Alaska, and genetic admixture may have mitigated the negative effects of genetic bottlenecks. Additionally, the study identified a small isolated population of pike in Southeast Alaska that is native in origin. Although lack of genetic variation may limit colonization success, this genetically depauperate apex predator does not seem to be affected.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Multidisciplinary Sciences
Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Celine Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cecile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cedric Cabau, Christophe Klopp, Andrew Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius, Yann Guiguen
Summary: Through the study of gene sequence and chromosomal rearrangement in teleosts, it was found that Elopomorpha and Osteoglossomorpha are sister groups to all other teleosts, resolving over 50 years of controversy on their evolutionary relationships.
Article
Fisheries
Matthew A. Campbell, Mary E. Badger, Nick Buckmaster, Andrew B. Starostka, Travis Hawks, Amanda J. Finger
Summary: This study confirms the Wall Canyon Sucker as a distinct species through genome-wide sampling and analysis. It is closely related to the Warner Sucker and exhibits high genetic isolation. The results support the recognition of the Wall Canyon Sucker as a separate species and suggest the need for a formal taxonomic description.
TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY
(2023)
Article
Zoology
Matthew A. Campbell, Ensieh Habibi, Grace Auringer, Molly Stephens, Jeff Rodzen, Kevin W. Conway, Amanda J. Finger
Summary: Rainbow Trout, Oncorhynchus mykiss, show high levels of phenotypic diversity, with Coastal Rainbow Trout (O. m. irideus) found west of the Cascade and Sierra Nevada mountain ranges, and interior Redband Trout (O. mykiss sspp.) distributed to the east. The study analyzed DNA sequence data from Sacramento Redband Trout O. m. stonei, Rainbow Trout, and Golden Trout, and identified that O. m. stonei is polyphyletic with populations in the Pit River and Upper McCloud River. Isolated populations in the Upper McCloud River Basin represent a distinct lineage of Rainbow Trout, not closely related to interior Redband Trout lineages, leading to the formal description of a new subspecies, McCloud River Redband Trout O. mykiss calisulat.
Article
Multidisciplinary Sciences
Hsin Lee, Kwen-Shen Lee, Chia-Hsin Hsu, Chen-Wei Lee, Ching-En Li, Jia-Kang Wang, Chien-Chia Tseng, Wei-Jen Chen, Ching-Chang Horng, Colby T. Ford, Andreas Kroh, Omri Bronstein, Hayate Tanaka, Tatsuo Oji, Jih-Pai Lin, Daniel Janies
Summary: The classification of the Class Echinoidea is being revised based on emerging molecular phylogenetic evidence, particularly concerning the sister-group relationships within the superorder Luminacea. The placement of many families remains unresolved due to incongruent evidence from different data sources. This study investigates the phylogenetic relationships of 25 taxa, proposing three new superfamilies and revealing the importance of the tropical western Pacific and eastern Indian Oceans in the early diversification of sand dollars. The study also highlights the role of Taiwan fauna in understanding the historical migration and dispersal events in the evolutionary history of Luminacea.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Ben A. Potter, Carrin M. Halffman, Holly J. McKinney, Joshua D. Reuther, Bruce P. Finney, Francois B. Lanoe, J. Andres Lopez, Charles E. Holmes, Erica Palmer, Marie Capps, Brian M. Kemp
Summary: The earliest known use of freshwater and anadromous fish in North America by humans was documented to be 13,000 and 11,800 years ago, respectively, in central Alaska. This suggests that fishing as an economic resource originated during this time period and was influenced by climatic factors.
Article
Environmental Sciences
Andrew P. Cyr, Katie A. Drew, Sierra Corsetti, Andrew C. Seitz, Trent M. Sutton, J. Andres Lopez, Matthew J. Wooller, Todd O'Hara
Summary: Arctic lamprey is an important dietary resource in Alaska, but concerns about mercury levels in their tissues and potential impact on human health exist. This study investigated the feeding ecology of Arctic lamprey and found that their diet mainly consists of capelin, Pacific sand lance, and Pacific herring, with diet composition varying with size class. Results suggest that feeding location and biomagnification are not significant factors in mercury levels in Arctic lamprey, and the current mercury levels do not pose a human health risk.
ENVIRONMENTAL RESEARCH
(2023)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.