Article
Evolutionary Biology
Xiang Ji, Alexander A. Fisher, Shuo Su, Jeffrey L. Thorne, Barney Potter, Philippe Lemey, Guy Baele, Marc A. Suchard
Summary: Divergence time estimation is crucial for dating important events. With the advent of high-throughput sequencing, Bayesian phylogenetic studies have analyzed large-scale data, challenging divergence time reconstruction. To overcome this limitation, a ratio transformation is explored to map internal node heights, and linear-time algorithms are developed to compute the terms of the log-likelihood. Hamiltonian Monte Carlo sampling with the ratio transform is then used to learn divergence times in 4 pathogenic viruses and coralline red algae, improving inference efficiency and confirming previous findings.
SYSTEMATIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Giobbe Forni, Federico Plazzi, Alex Cussigh, Oskar Conle, Frank Hennemann, Andrea Luchetti, Barbara Mantovani
Summary: The study found that the diversity of Phasmatodea species is mainly concentrated in the suborder Euphasmatodea, which has a pantropical distribution and is believed to have originated from a recent rapid evolutionary radiation. By analyzing the mitogenomes of 17 species and other available mitogenomes, researchers sought to uncover the origins and diversification of Euphasmatodea. The divergence time analysis suggested that Euphasmatodea diversification began around 187 million years ago, potentially influenced by the Triassic-Jurassic mass extinction and the breakup of Pangea.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Evolutionary Biology
Tom Carruthers, Robert W. Scotland
Summary: Understanding and representing uncertainty is crucial in academic research to enable robust advances, especially in divergence time estimation which has been underestimated, affecting inferences about macroevolution. The assumptions underlying methods may not adequately reflect uncertainty, leading to potential contradiction by subsequent findings, while the interpretation of time-calibrated phylogenies for reconstructing general evolutionary timescales is highly sensitive to methodological limitations. However, using time-calibrated phylogenies to test specific hypotheses leads to inferences that are less sensitive to methodological limitations.
SYSTEMATIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Min Zhao, J. Gordon Burleigh, Urban Olsson, Per Alstrom, Rebecca T. Kimball
Summary: The Old World flycatchers, robins and chats are a diverse songbird family, and a comprehensive and well-resolved species-level phylogeny for this family is still lacking. In this study, a supermatrix phylogeny was constructed using data from multiple genetic loci, including previously unsampled taxa. The results provide insights into the evolutionary relationships within the Muscicapidae family.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Zoology
M. Alejandra Camacho, Daniel Cadar, Balazs Horvath, Andres Merino-Viteri, Jerome Murienne
Summary: By analyzing the mitochondrial genomes of 26 bat species, we obtained reliable results on the evolutionary relationships between Phyllostomid subfamilies, and clarified previously uncertain relationships between certain subfamilies.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Ecology
Santiago Claramunt
Summary: CladeDate is an R package that generates calibration information from the fossil record using simple mathematical models to estimate clade age and uncertainty, fitting standard probability density functions for time-tree inference software.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Paleontology
Joseph E. O'Reilly, Philip C. J. Donoghue
Summary: The impact of systematically distributed missing data resulting from taphonomic processes on clade age estimates is negative, with different stages of taphonomy introducing greater differences in age estimates. However, the general influence of missing data is weak, likely due to the compensatory effect of extensive morphological data from extant taxa.
Article
Plant Sciences
Jing Wang, Jun Qian, Yuan Jiang, Xiaochen Chen, Baojiang Zheng, Shilin Chen, Fajian Yang, Zhichao Xu, Baozhong Duan
Summary: This study investigates the phylogenetic relationships and intrageneric taxonomy within Polygonatum by analyzing the complete chloroplast genomes of 26 species of Trib. Polygonateae. It identifies eight highly variable regions that could serve as potential molecular markers for identifying Polygonatum species. The molecular clock analysis suggests that Polygonatum diverged around 14.71 million years ago, and the phylogenetic analysis supports the monophyly of Polygonatum.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biodiversity Conservation
Antoine Fouquet, Pedro Marinho, Alexandre Rejaud, Thiago R. Carvalho, Marcel A. Caminer, Martin Jansen, Raissa N. Rainha, Miguel T. Rodrigues, Fernanda P. Werneck, Albertina P. Lima, Tomas Hrbek, Ariovaldo A. Giaretta, Pablo J. Venegas, German Chavez, Santiago Ron
Summary: The diverse anuran clades in the Amazon region have recently diversified, with two new species being described. The dispersal of these species occurred relatively late compared to other terrestrial anurans, but in parallel with more mobile vertebrates, and was largely influenced by the region's geological evolution and the specific dispersal abilities of the species.
SYSTEMATICS AND BIODIVERSITY
(2021)
Article
Geochemistry & Geophysics
Naihao Liu, Shengtao Wei, Rongchang Liu, Yang Yang, Nan Zhang, Jinghuai Gao
Summary: In this study, an unscaled generalized S-transform (UGST) and a Q estimation method based on the weighted Kullback-Leibler divergence are proposed, and an estimation workflow is built. Compared with contrastive methods, the proposed workflow achieves more accurate estimation results and demonstrates better noise immunity.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2022)
Article
Thermodynamics
Wonjun Choi, Sangwon Lee, Ba Huu Dinh, Young -Sang Kim
Summary: This study proposes a real-time probabilistic estimation method for determining the thermal properties of backfill used in underground power transmission lines and ground heat exchangers. The method enables real-time monitoring of temporal changes in the estimated probability distribution of the thermal property and quantifies the estimation uncertainty. It also allows for immediate decision-making regarding experiment termination by evaluating real-time convergence using the Jensen-Shannon divergence.
CASE STUDIES IN THERMAL ENGINEERING
(2023)
Article
Microbiology
Zhaoxue Zhang, Xinye Liu, Mengfei Tao, Xiaoyong Liu, Jiwen Xia, Xiuguo Zhang, Zhe Meng
Summary: Based on multi-locus phylogenies and morphological characteristics, three new species were discovered, namely Pseudoplagiostoma alsophilae, P. bambusae, and P. machili. Molecular clock analysis revealed that the ancestor of Pseudoplagiostomataceae and Apoharknessiaceae emerged in the Cretaceous period, with most species appearing in the Paleogene and Neogene periods. Historical biogeography reconstruction suggested that Asia, especially Southeast Asia, was likely the ancestral area for Pseudoplagiostomataceae.
Article
Multidisciplinary Sciences
Chase D. Brownstein, Tiago R. Simoes, Michael W. Caldwell, Michael S. Y. Lee, Dalton L. Meyer, Simon G. Scarpetta
Summary: Most reptile diversity is found in lizards (including snakes), but their origins are poorly understood. A recent study claimed that a fossil called Cryptovaranoides microlanius from the Late Triassic is the oldest known lizard. However, using computed tomography scans and expanded phylogenetic datasets, researchers have refuted this claim and instead proposed that Cryptovaranoides is a potential member of the bird and crocodylian total clade, Archosauromorpha. Bayesian total evidence dating supports a Jurassic origin of modern lizards, contradicting the previous Triassic origin hypothesis.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Zoology
Wenqian Wang, Rui Meng, Yixin Huang, Wei Fang, Huan Zhang, Huizhen Liu, Adam Stroinski, Thierry Bourgoin, Daozheng Qin
Summary: This study reconstructed the phylogenetic relationship of the planthopper superfamily Fulgoroidea based on whole mitogenome sequences. The results showed the classification relationships between different families and the timing of their origin. However, the sampling of taxa needs improvement to address controversial issues.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Avas Pakrashi, Vikas Kumar, David A. C. Stanford-Beale, Stephen L. Cameron, Kaomud Tyagi
Summary: This study provides new insights into the mitogenomic features, gene arrangement, phylogeny, and divergence time estimation of thrips belonging to the order Thysanoptera.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Multidisciplinary Sciences
Matthew A. Campbell, Thaddaeus J. Buser, Michael E. Alfaro, J. Andres Lopez
Article
Evolutionary Biology
Richard C. Harrington, Matt Friedman, Masaki Miya, Thomas J. Near, Matthew A. Campbell
Summary: Amarsipus carlsbergi is a rare mesopelagic fish that is closely related to Tetragonurus and belongs to a clade that questions the monophyly of Stromateoidei. The study provides a taxonomically comprehensive phylogenomic framework and strong support for stromateoid paraphyly, casting uncertainty on previous hypotheses of morphological evolution within Pelagiaria.
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
Evolutionary Biology
Matthew A. Campbell, Eric C. Anderson, John Carlos Garza, Devon E. Pearse
Summary: Genetic changes underlying adaptation in different populations of rainbow trout show diversity, with variations mainly occurring in chromosomal inversion regions and other genetic areas, leading to distinct differences in selection among populations.
JOURNAL OF HEREDITY
(2021)
Article
Genetics & Heredity
Matthew C. Hale, Matthew A. Campbell, Garrett J. McKinney
Summary: The genomics era has enabled researchers to ask questions about genome organization and architecture in non-model species at an unprecedented rate. Analysis of genome-wide datasets has revealed novel structural variants (SVs) in many species, some of which are linked to adaptation. Despite the abundance of genome-wide datasets in salmonids, the number of documented SVs is surprisingly low, likely due to the removal of loci in high linkage disequilibrium during analysis. Re-analyzing RAD-seq data from different populations of Arctic charr, a novel 1.2 MB SV was discovered at the distal end of LG12, containing 15 protein-coding genes associated with various functions, with frequency variations found only in the Nunavut population, suggesting recent evolution of the polymorphism.
G3-GENES GENOMES GENETICS
(2021)
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
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
Ecology
Ava Ghezelayagh, Richard C. Harrington, Edward D. Burress, Matthew A. Campbell, Janet C. Buckner, Prosanta Chakrabarty, Jessica R. Glass, W. Tyler McCraney, Peter J. Unmack, Christine E. Thacker, Michael E. Alfaro, Sarah T. Friedman, William B. Ludt, Peter F. Cowman, Matt Friedman, Samantha A. Price, Alex Dornburg, Brant C. Faircloth, Peter C. Wainwright, Thomas J. Near
Summary: The study constructs a time-calibrated phylogeny to explore patterns of body shape disparity within spiny-rayed fishes. The authors find a steady accumulation of lineages throughout the Cenozoic, with an increase in morphological disparity after the Cretaceous-Palaeogene event, facilitating the radiation and diversification of spiny-rayed fishes.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Fisheries
Yingxin Su, Peter B. B. Moyle, Matthew A. A. Campbell, Amanda J. J. Finger, Sean M. M. O'Rourke, Jason Baumsteiger, Michael R. R. Miller
Summary: Using population genetic and genomic information, this study identified three major lineages of Speckled Dace in California that align with geography. These distinct evolutionary lineages highlight the importance of managing Speckled Dace with distinct population segments to preserve within-species diversity. This study emphasizes the significance of genetic analyses for conservation and management of freshwater fishes.
TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY
(2022)
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
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
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.
