Article
Agriculture, Dairy & Animal Science
Mitsuki Kondo, Yoshinori Ikenaka, Shouta M. M. Nakayama, Yusuke K. Kawai, Mayumi Ishizuka
Summary: In this study, the evolutional features of the UGT gene family in Carnivora were clarified. Specific gene expansions of UGT1As in Canidae, brown bear, and black bear, as well as genetic duplications of UGT2Bs in Canidae, some Mustelidae, and Ursidae were identified. Additionally, gene contractions or complete loss of UGT1A7-12 were observed in phocids, some otariids, felids, and some Mustelids. These findings suggest significant evolutionary differences of UGTs even among closely related species and emphasize the importance of appropriate approaches for assessing pharmacokinetics and toxicokinetics in wildlife carnivores.
Article
Biochemistry & Molecular Biology
Daniel Wong, Hannah Norman, Thomas J. Creedy, Kurt Jordaens, Kevin M. Moran, Andrew Young, Ximo Mengual, Jeffrey H. Skevington, Alfried P. Vogler
Summary: Using genome skimming, researchers generated mitochondrial genomes for 91 species of hoverflies, revealing their phylogenetic relationships and the evolution of their larval life history traits. The study identified a basal split and several deep clades within the family, shedding light on the diversity and evolution of hoverflies.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Entomology
Xin Li, Xiaodong Cai, Shuangmei Ding, Liang Wang, Wenliang Li, Xiaoyan Liu, Chuntian Zhang, Ding Yang
Summary: Reconstructing the phylogenetic relationship within Muscidae using 43 mitochondrial genomes identified three major groups. The best phylogenetic tree supported the monophyly of all subfamilies except Mydaeinae. The merging of Helina Robineau-Desvoidy, 1830 with Phaonia Robineau-Desvoidy, 1830 was preferred. We also advocated for the subfamily status of Azeliinae and Reinwardtiinae and the separation of Stomoxyinae from Muscinae. Muscidae diverged in the early Eocene (51.59 Ma) and most subfamilies diverged around 41 Ma. The study provided new insights into the phylogenetic relationships and divergence time estimation of Muscidae using mitochondrial genomes.
Article
Biodiversity Conservation
Marina O. Favarini, Taiz L. L. Simao, Gabriel S. Macedo, Fabricio S. Garcez, Larissa R. Oliveira, Susana Cardenas-Alayza, Marco Cardena Mormontoy, Fernando Angulo, Carlos Benhur Kasper, Warren E. Johnson, Eduardo Eizirik
Summary: The canid genus Lycalopex, consisting of six South American species, has posed challenges in determining their evolutionary relationships. In this study, mitochondrial DNA (mtDNA) analysis was conducted on Lycalopex individuals, as well as specimens from closely related species, to reconstruct their phylogenetic relationships. The results confirmed the monophyly of most species based on mtDNA, with one case suggesting potential interspecies admixture. Additionally, nuclear marker analysis revealed examples of intra-specific variation and lack of species monophyly, indicating incomplete lineage sorting and hybridization. This study provides robust mitochondrial resolution of this complex radiation and highlights the difficulties in using traditional nuclear markers.
Article
Zoology
Jia-Chen Zhu, Xuan-Kun Li, Chao-Dong Zhu, Qiong Wu, Jin-Hua Xiao, Cornelis van Achterberg, Da-Wei Huang, Xue-Xin Chen
Summary: Using mitochondrial phylogenomic analyses of 139 mitochondrial genomes, the study reveals the major interfamilial phylogeny of Chalcidoidea. The results suggest that Chalcidoidea arose near the Jurassic/Cretaceous boundary and underwent two dynamic shifts in diversification. The potential codiversification between chalcidoids and their hosts may have played a crucial role in accelerating the diversification of Chalcidoidea.
ZOOLOGICAL RESEARCH
(2023)
Article
Biology
Jiaming Hu, Michael V. Westbury, Junxia Yuan, Zhen Zhang, Shungang Chen, Bo Xiao, Xindong Hou, Hailong Ji, Xulong Lai, Michael Hofreiter, Guilian Sheng
Summary: Cave hyenas, extinct bone-cracking carnivores from the family Hyaenidae, were widespread across Eurasia during the Pleistocene and became extinct at the end of the Late Pleistocene. A study of two cave hyena fossils from northeastern China suggests a split of the Asian cave hyena mitochondrial lineage from their European and African relatives around 1.85 million years ago, in line with the earliest Crocuta fossil dating to approximately 2 million years ago. Comparisons of genetic diversity indicate cave hyenas had higher diversity than extant species, likely due to non-monophyletic lineages. The joint female effective population size of Crocuta experienced declines during the Late Pleistocene.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Christoph Stritt, Elena L. Gimmi, Michele Wyler, Abdelmonaim H. Bakali, Aleksandra Skalska, Robert Hasterok, Luis A. J. Mur, Nicola Pecchioni, Anne C. Roulin
Summary: Wild plant populations of Brachypodium distachyon exhibit extensive genetic subdivision, influenced by the interplay of high selfing and seed dispersal rates. The species' evolution is characterized by the independent expansion of three lineages during the Upper Pleistocene, with selfing and dispersal maintaining high genotypic diversity at regional scales.
Article
Evolutionary Biology
Ruie Nie, Alfried P. Vogler, Xing-Ke Yang, Meiying Lin
Summary: Cerambycidae (longhorn beetles) and related families in the superfamily Chrysomeloidea are important components of forest ecosystems, playing key roles in nutrient cycling and pollination. Through the study of mitochondrial genomes and taxon sampling, the phylogeny of Chrysomeloidea reveals the division into a 'lamiine' clade and a 'cerambycine' clade. The diversification of families within Chrysomeloidea coincides with the radiation of angiosperms during the Early Cretaceous.
SYSTEMATIC ENTOMOLOGY
(2021)
Article
Genetics & Heredity
Xiaofeng Zheng, Rusong Zhang, Bisong Yue, Yongjie Wu, Nan Yang, Chuang Zhou
Summary: This study sequenced and characterized the nearly complete mitochondrial genomes of moths from six major lineages, providing insights into their phylogenetic relationships. The analysis revealed a slightly different pattern from previous studies and identified previously unassigned tribes within the Geometridae family. The study contributes to our understanding of moth phylogeny and has implications for further research in phylogeography and pest control.
Article
Genetics & Heredity
John King N. Layos, Cyrill John P. Godinez, Lawrence M. Liao, Yoshio Yamamoto, Joseph S. Masangkay, Hideyuki Mannen, Masahide Nishibori
Summary: This study provides a comprehensive analysis of the early dispersal history of Philippine pigs by analyzing their mitochondrial DNA. The results suggest a close genetic relationship between Philippine pigs and pigs from mainland Southeast Asia and Northeast Asia, indicating gene flow possibly resulting from human migration and trade. Despite geographic barriers, numerous genetic lineages have persisted across the Philippine islands. The study also reveals intriguing discrepancies between the ancestral pattern and distribution range of endemic Philippine wild pigs, offering new insights into the complexity of these animals.
FRONTIERS IN GENETICS
(2022)
Article
Evolutionary Biology
Ying Wang, Jinjun Cao, David Muranyi, Xuan Guo, Caiyue Guo, Weihai Li
Summary: This study investigates the phylogeny of Systellognatha families by sequencing mitochondrial genomes of different families. The results reveal the effectiveness of using site-heterogeneous models in recovering the monophyly of the Perloidea family and provide new insights into the phylogeny of Systellognatha.
Article
Biochemistry & Molecular Biology
Weidong Huang, Changhua Zhang, Tingzhen Zhang, Ye Xu, Shiwen Xu, Li Tian, Hu Li, Wanzhi Cai, Fan Song
Summary: This study investigates the characteristics and evolution of the control region (CR) in Tortricidae, a type of moth. Through mitochondrial genome analysis, the researchers found that the CR sequences in Tortricidae exhibit high structural diversity, indicating the plasticity of the mitochondrial DNA molecule in this insect group.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Plant Sciences
Lijuan Feng, Zenghui Wang, Chuanzeng Wang, Xuemei Yang, Mengmeng An, Yanlei Yin
Summary: The mitochondrial genome of Punica granatum was sequenced and assembled in this study. The results showed the genome structure, variation, and evolution of this species. The mitogenome contained 74 genes, including protein-coding genes, tRNA genes, and rRNA genes. Various analyses, such as codon usage, nucleotide diversity, and gene migration, were conducted to further understand the evolutionary biology of pomegranate.
Article
Plant Sciences
Hao Liu, Junping Yu, Xiaoxia Yu, Dan Zhang, Han Chang, Wei Li, Haifeng Song, Zheng Cui, Peng Wang, Yixin Luo, Fei Wang, Dagang Wang, Zhi Li, Zhiping Huang, Aigen Fu, Min Xu
Summary: This study delves into the architecture and genetic diversity of mitogenome in cultivated soybeans, revealing differences compared to wild soybeans. Classification of wild and cultivated soybeans globally into five cytoplasmic groups sheds light on soybean cultivation history.
Article
Microbiology
Peng Wu, Tian Yao, Yuanhang Ren, Jinghua Ye, Yuan Qing, Qiang Li, Mingying Gui
Summary: This study sequenced and compared the mitochondrial genomes of two Pisolithus species, revealing certain characteristics and differences. The research on Pisolithus mitochondrial genomes contributes to a better understanding of the evolutionary history of these fungal species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mario Mairal, Steven L. Chown, Justine Shaw, Desalegn Chala, John H. Chau, Cang Hui, Jesse M. Kalwij, Zuzana Munzbergova, Bettine Jansen van Vuuren, Johannes J. Le Roux
Summary: The study reveals that human activity significantly impacts the post-introduction dynamics of invasive species, leading to high genetic diversity and admixture of P. annua on Marion Island, while populations on unoccupied Prince Edward Island show low genetic diversity and structure. High genetic variation and admixture facilitated by human activity, coupled with high habitat suitability, suggest that P. annua is likely to increase its distribution and abundance in the future.
Article
Environmental Sciences
Sven-Erick Weiss, Arsalan Emami-Khoyi, Horst Kaiser, Paul D. Cowley, Nicola C. James, Bettine Jansen van Vuuren, Alan K. Whitfield, Peter R. Teske
Summary: The critically endangered estuarine pipefish, Syngnathus watermeyeri, is facing a significant risk of extinction due to anthropogenic and natural factors. This study found that the remaining populations in two South African estuaries are highly inbred and there is no significant genetic difference between them. The small population sizes of the estuarine pipefish lead to adverse genetic effects. The creation of additional populations may help prevent further loss of genetic diversity and minimize the overall extinction risk.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Evolutionary Biology
Laura Tensen, John Power, Gerrie Camacho, Raquel Godinho, Bettine Jansen van Vuuren, Klaus Fischer
Summary: The red leopard colour morph is a unique variant found only in South Africa's Central Bushveld bioregion. The increasing prevalence of this phenotype is believed to be due to the low dispersal of young individuals caused by high levels of human-induced mortality and selective hunting, leading to an increase in rare genetic variants.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Joana L. Rocha, Pedro Vaz Pinto, Hans R. Siegismund, Matthias Meyer, Bettine Jansen van Vuuren, Luis Verissimo, Nuno Ferrand, Raquel Godinho
Summary: The study explores the factors driving the evolution of the sable antelope in southcentral Africa by analyzing complete mitogenomes. The results suggest that both climatic events and geomorphological barriers have shaped the species' patterns of diversification and vicariance. The use of comprehensive mitogenomic data sets contributes to a better understanding of environmental, geomorphological, and evolutionary patterns in Africa throughout the Quaternary.
Article
Zoology
Geraldine Veron, Caroline Daniel, Paolo Pagani, Emmanuel Do Linh San, Andrew C. Kitchener, Alexandre Hassanin
Summary: Phylogeographical patterns of African mammals are influenced by Pleistocene environmental fluctuations and geographical barriers, impacting species differently based on habitat preferences and dispersal capabilities. The marsh mongoose and white-tailed mongoose were studied to compare their phylogeographical patterns, revealing differences in genetic structure based on their habitat preferences and dispersal abilities.
Article
Biochemistry & Molecular Biology
Devon C. Main, Bettine Jansen van Vuuren, Colin R. Tilbury, Krystal A. Tolley
Summary: The application of molecular phylogenetics and species delimitation methods has helped to address limitations in morphology-based taxonomy and highlight inconsistencies in current taxonomy. This study focused on the genus Chamaeleo, which consists of 14 species distributed across Africa and Eurasia, and aimed to construct a comprehensive phylogeny, identify potential cryptic diversity, and determine the biogeographic origin and diversification of the genus. The results revealed the presence of at least 18 taxa within Chamaeleo and suggested a southern African/Zambezian origin for the genus, with diversification occurring during the cooling and aridification of Africa in the Oligocene Epoch. Species-level diversification began in the Miocene Epoch, possibly driven by aridification and tectonic events. These findings lay the groundwork for future taxonomic re-evaluation of Chamaeleo.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Genetics & Heredity
Stefano Porrelli, Michele Gerbault-Seureau, Roberto Rozzi, Rayan Chikhi, Manon Curaudeau, Anne Ropiquet, Alexandre Hassanin
Summary: This study sequenced and compared the genome of a wild endangered dwarf buffalo, the lowland anoa, to address the lack of genomic data for wild species of the genus Bubalus. The draft genome assembly of the lowland anoa showed good completeness and is expected to contribute to comparative genome analyses among bovid species.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Mario Mairal, Carlos Garcia-Verdugo, Johannes J. Le Roux, John H. Chau, Bettine Jansen van Vuuren, Cang Hui, Zuzana Munzbergova, Steven L. Chown, Justine D. Shaw
Summary: This study investigates the invasive plant species Poa annua in the isolated islands of the Southern Ocean. The results show that P. annua exhibits high genetic diversity, low population structure, and low selfing rates in the sub-Antarctic archipelagos. It suggests multiple independent introductions of P. annua into the sub-Antarctic and convergent reproductive strategies in each major archipelago.
Article
Virology
Alexandre Hassanin, Opale Rambaud
Summary: A new method called coloured genomic bootstrap (CGB) barcodes is proposed to study the origins of coronaviruses and understand their host and geographic origins. The study reveals that SARS-CoV and SARS-CoV-2 contain genomic regions of mixed ancestry from horseshoe bat viruses. Different regions of the viruses share exclusive ancestry with various Rhinolophus viruses from different regions of China and Southeast Asia, supporting their emergence in these bat species. However, further research is needed to investigate the diversity of coronaviruses in bats from other Southeast Asian countries.
Article
Plant Sciences
Romain Sabroux, Alexandre Hassanin, Laure Corbari
Summary: This study presents the inventory and classification of sea spiders from the Madibenthos Expedition in Martinique, using morphological and molecular data. A total of 72 species, 16 genera, and nine families were identified, including 13 new species. The study reveals that Martinique now has 79 species of sea spiders, with most being endemic to the Tropical Northwestern Atlantic or cosmopolitan/shared with the South America Atlantic coast. The study also highlights the presence of potentially introduced species and the underestimated diversity of sea spiders in the Tropical Northwestern Atlantic. It calls for a wider use of barcoding in sea spider research.
EUROPEAN JOURNAL OF TAXONOMY
(2022)
Article
Biochemistry & Molecular Biology
Romain Sabroux, Laure Corbari, Alexandre Hassanin
Summary: The phylogeny of sea spiders is still debated, but this study supports the monophyly of most accepted families. The research also discusses the morphological evolution of sea spiders and provides arguments for their origin during the Jurassic period or earlier.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Virology
Manon Curaudeau, Camille Besombes, Emmanuel Nakoune, Arnaud Fontanet, Antoine Gessain, Alexandre Hassanin
Summary: This study identified the distribution of Monkeypox virus in African mammal genera and predicted the geographic distributions of these species. By analyzing niche overlap with MPXV, the most probable animal reservoir was determined to be the red-cheeked squirrel.
Article
Zoology
Vuong Tan Tu, Neil M. Furey, Tamas Gorfol, Alexandre Hassanin, Satoru Arai, Daisuke Koyabu, Bounsavane Douangboubpha, Gabor Csorba
Summary: This study integrates multiple data sources to re-evaluate the taxonomic status of Rhinolophus rex rex, R. r. paradoxolophus and R. schnitzleri. Contrary to the current taxonomic view, the results indicate that these taxa are actually representatives of a single, widely distributed and morphologically variable species, R. rex. The recognition of different subspecies or distinct species based on morphological and acoustic data should be regarded as invalid.
VERTEBRATE ZOOLOGY
(2023)
Article
Environmental Sciences
Conny P. Serite, Arsalan Emami-Khoyi, Ofentse K. Ntshudisane, Nicola C. James, Bettine Jansen van Vuuren, Taryn Bodill, Paul D. Cowley, Alan K. Whitfield, Peter R. Teske
Summary: Understanding the dietary preferences of endangered species is important for conservation strategies. The study compared metabarcoding and metagenomics to analyze the diets of endangered pipefish species. Metabarcoding showed a difference in prey preference between the two species, while metagenomics identified additional copepod species in one species' diet. Metagenomics was found to be a useful complementary method for dietary analysis, although it is more affected by a lack of reference sequences.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Ecology
Arsalan Emami-Khoyi, Candice M. Jooste, Ryan J. Wasserman, Tatenda Dalu, Morgan J. J. Raath-Kruger, Bettine Jansen van Vuuren, Peter R. Teske
Summary: This study investigated the spatial genetic structure and dispersal history of a calanoid copepod species in temporary wetlands in the Eastern Cape province of South Africa. The wetland populations were highly structured across the landscape and potentially represent cryptic speciation. The dispersal history of these populations was affected by a postulated barrier, which eventually disappeared, allowing the species to spread into coastal regions.
FRESHWATER BIOLOGY
(2023)