Ruiwen Wu, Liping Zhang, Lili Liu, Junli Jia, Xiongjun Liu
Accurate phylogenetic reconstructions are crucial for comprehending the evolutionary histories, reproductive traits, and ecological habits of organisms. The subfamily Gonideinae of freshwater mussels is currently thought to include eight tribes. However, due to inadequate taxon sampling and molecular data, the assignment of the freshwater mussel genus Inversidens at the tribe level has been unstable. Additionally, the lack of phylogenetic data has hindered efforts to understand the basic biology and implementation of conservation efforts of Inversidens rentianensis, an endemic species to China. Here, we first present the complete mitochondrial genome of Inversidens rentianensis and offer a detailed description of its anatomical morphology. Based on DNA sequence data from five genes (COI, ND1, 16S rRNA, 18S rRNA, and 28S rRNA) and complete mitochondrial genomes, we investigated the phylogenetic position of Inversidens using various analytical methods. Both the concatenated five-gene and mitogenome datasets strongly supported that Inversidens classified to the tribe Gonideini in Gonideinae and formed a basal clade within the tribe Gonideini. Molecular dating analysis suggested that Inversidens originated during the mid-Cretaceous era (102.73 Mya, 95% highest posterior density (HPD) = 72.22-137.03 Mya) and underwent diversification in the Late Paleogene era (37.92 Mya, 95% HPD = 20.39-60.59 Mya). Moreover, based on the Quantitative Assessment of Species for Conservation (QASCP), Inversidens rentianensis is ranked as second priority, providing valuable insights for its management and conservation efforts. Taken together, this study provides a comprehensive understanding of the systematic position and evolutionary history of Inversidens within the currently accepted subfamily Gonideinae classification framework. These findings establish a solid foundation for future investigations on the ecology, reproductive behavior patterns, and conservation biology of this taxonomic group.
{"title":"Unraveling the Phylogenetic Relationships and Taxonomic Status of a Puzzling Freshwater Mussel Genus Inversidens (Bivalvia, Unionidae) through Multilocus Phylogeny and Mitochondrial Phylogenomics","authors":"Ruiwen Wu, Liping Zhang, Lili Liu, Junli Jia, Xiongjun Liu","doi":"10.1155/2024/1499508","DOIUrl":"10.1155/2024/1499508","url":null,"abstract":"<div>\u0000 <p>Accurate phylogenetic reconstructions are crucial for comprehending the evolutionary histories, reproductive traits, and ecological habits of organisms. The subfamily Gonideinae of freshwater mussels is currently thought to include eight tribes. However, due to inadequate taxon sampling and molecular data, the assignment of the freshwater mussel genus <i>Inversidens</i> at the tribe level has been unstable. Additionally, the lack of phylogenetic data has hindered efforts to understand the basic biology and implementation of conservation efforts of <i>Inversidens rentianensis</i>, an endemic species to China. Here, we first present the complete mitochondrial genome of <i>Inversidens rentianensis</i> and offer a detailed description of its anatomical morphology. Based on DNA sequence data from five genes (COI, ND1, 16S rRNA, 18S rRNA, and 28S rRNA) and complete mitochondrial genomes, we investigated the phylogenetic position of <i>Inversidens</i> using various analytical methods. Both the concatenated five-gene and mitogenome datasets strongly supported that <i>Inversidens</i> classified to the tribe Gonideini in Gonideinae and formed a basal clade within the tribe Gonideini. Molecular dating analysis suggested that <i>Inversidens</i> originated during the mid-Cretaceous era (102.73 Mya, 95% highest posterior density (HPD) = 72.22-137.03 Mya) and underwent diversification in the Late Paleogene era (37.92 Mya, 95% HPD = 20.39-60.59 Mya). Moreover, based on the Quantitative Assessment of Species for Conservation (QASCP), <i>Inversidens rentianensis</i> is ranked as second priority, providing valuable insights for its management and conservation efforts. Taken together, this study provides a comprehensive understanding of the systematic position and evolutionary history of <i>Inversidens</i> within the currently accepted subfamily Gonideinae classification framework. These findings establish a solid foundation for future investigations on the ecology, reproductive behavior patterns, and conservation biology of this taxonomic group.</p>\u0000 </div>","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/1499508","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139397015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ahmad Zaman, Azhar Rafique, Asma Ashraf, Muhammad Shahid Mahmood, Nazia Nahid, Farhat Jabeen, Salma Sultana, Tayyaba Sultana, Sultan Ali, S. M. Neamul Kabir Zihad, Shaikh Jamal Uddin
The present study was conducted from March 2021 to February 2022 in the Thal desert and Trimmu barrage of district Jhang located in the Punjab province of Pakistan to find out the diversity, abundance, and distribution of birds. The point count method was used for the Trimmu barrage, and the line transect method was used for the collection of data in the Thal desert area. We recorded 31,696 individuals belonging to 67 species of birds from two distinct types of habitats (Thal desert and Trimmu barrage) of district Jhang. Among these species, 39 species were residents, 18 species were winter visitors, 9 species were summer breeders, and a single species (Terek sandpiper) was a passage migrant. Highly significant differences (,, and
{"title":"Diversity, Abundance, and Distribution of Avifauna in District Jhang, Pakistan","authors":"Ahmad Zaman, Azhar Rafique, Asma Ashraf, Muhammad Shahid Mahmood, Nazia Nahid, Farhat Jabeen, Salma Sultana, Tayyaba Sultana, Sultan Ali, S. M. Neamul Kabir Zihad, Shaikh Jamal Uddin","doi":"10.1155/2023/3308651","DOIUrl":"https://doi.org/10.1155/2023/3308651","url":null,"abstract":"The present study was conducted from March 2021 to February 2022 in the Thal desert and Trimmu barrage of district Jhang located in the Punjab province of Pakistan to find out the diversity, abundance, and distribution of birds. The point count method was used for the Trimmu barrage, and the line transect method was used for the collection of data in the Thal desert area. We recorded 31,696 individuals belonging to 67 species of birds from two distinct types of habitats (Thal desert and Trimmu barrage) of district Jhang. Among these species, 39 species were residents, 18 species were winter visitors, 9 species were summer breeders, and a single species (Terek sandpiper) was a passage migrant. Highly significant differences (<span><svg height=\"11.7978pt\" style=\"vertical-align:-0.2063999pt\" version=\"1.1\" viewbox=\"-0.0498162 -11.5914 26.155 11.7978\" width=\"26.155pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"><g transform=\"matrix(.013,0,0,-0.013,0,0)\"></path></g><g transform=\"matrix(.0091,0,0,-0.0091,9.945,-5.741)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,18.524,0)\"></path></g></svg><span></span><span><svg height=\"11.7978pt\" style=\"vertical-align:-0.2063999pt\" version=\"1.1\" viewbox=\"29.736183800000003 -11.5914 40.721 11.7978\" width=\"40.721pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"><g transform=\"matrix(.013,0,0,-0.013,29.786,0)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,36.026,0)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,42.267,0)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,48.508,0)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,54.75,0)\"><use xlink:href=\"#g113-58\"></use></g><g transform=\"matrix(.013,0,0,-0.013,60.991,0)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,63.955,0)\"><use xlink:href=\"#g113-56\"></use></g></svg>,</span></span> <span><svg height=\"9.48819pt\" style=\"vertical-align:-0.1802893pt\" version=\"1.1\" viewbox=\"-0.0498162 -9.3079 22.015 9.48819\" width=\"22.015pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"><g transform=\"matrix(.013,0,0,-0.013,0,0)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,6.864,0)\"></path></g><g transform=\"matrix(.013,0,0,-0.013,14.384,0)\"><use xlink:href=\"#g117-34\"></use></g></svg><span></span><span><svg height=\"9.48819pt\" style=\"vertical-align:-0.1802893pt\" version=\"1.1\" viewbox=\"25.5971838 -9.3079 12.655 9.48819\" width=\"12.655pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"><g transform=\"matrix(.013,0,0,-0.013,25.647,0)\"><use xlink:href=\"#g113-50\"></use></g><g transform=\"matrix(.013,0,0,-0.013,31.887,0)\"><use xlink:href=\"#g113-50\"></use></g></svg>,</span></span> and <span><svg height=\"9.2729pt\" style=\"vertical-align:-0.6370001pt\" version=\"1.1\" viewbox=\"-0.0498162 -8.6359 19.289 9.2729\" width=\"19.289pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"><g transform=\"matrix(.013,0,0,-0.013,0,0)\"></path></g><g transform=\"","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138507614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Du, Shu-Jing Li, Fei Xu, T. Luo, F. Luo, Guo-Hua Yu, Jiang Zhou
Nostril structures are important characteristics for generic diagnosis in Nemacheilidae and Cobitidae. Based on phylogenetic analysis, we found that 10 genera within Nemacheilidae (Eonemachilus, Guinemachilus, Lefua, Micronemacheilus, Oreonectes, Paranemachilus, Protonemacheilus, Traccatichthys, Troglonectes, and Yunnanilus) shared tube-shaped anterior nostrils and formed a monophyletic group. Morphologically, the location between the anterior and posterior nostrils was divided into three types: (i) separated, i.e., a distance greater than 1.5 times the diameter of the posterior nostril; (ii) adjacent, i.e., a distance shorter than the diameter of the posterior nostril; and (iii) closely set, i.e., posterior margin of the anterior nostril connected to the anterior margin of the posterior nostril. Thus, the 10 genera can be distinguished based on nostril features. Additionally, we describe one new genus, Guinemachilus gen. nov., and two new species, Guinemachilus pseudopulcherrimus sp. nov. and Paranemachilus chongzuo sp. nov.
鼻孔结构是线虫科和蠓科属诊断的重要特征。通过系统发育分析发现，nemachelidae科10个属(Eonemachilus、Guinemachilus、Lefua、Micronemacheilus、Oreonectes、Paranemachilus、Protonemacheilus、Traccatichthys、Troglonectes和Yunnanilus)共有管状前鼻孔，形成一个单系类群。在形态学上，前鼻孔和后鼻孔之间的位置分为三种类型:(i)分开，即距离大于后鼻孔直径的1.5倍;(ii)邻近，即距离小于后鼻孔的直径;(三)紧密相连，即前鼻孔的后缘与后鼻孔的前缘相连。因此，可以根据鼻孔特征来区分这10个属。此外，还发现了1个新属(Guinemachilus gen. nov.)和2个新种(Guinemachilus pseudopulcherrimus sp. nov.)和2个新种(Paranemachilus chongzuo sp. nov.)。
{"title":"Clarification of Phylogenetic Relationships among Chinese Nemacheilids with Tube-Shaped Anterior Nostrils, with a Description of a New Genus and Two New Species","authors":"L. Du, Shu-Jing Li, Fei Xu, T. Luo, F. Luo, Guo-Hua Yu, Jiang Zhou","doi":"10.1155/2023/3600085","DOIUrl":"https://doi.org/10.1155/2023/3600085","url":null,"abstract":"Nostril structures are important characteristics for generic diagnosis in Nemacheilidae and Cobitidae. Based on phylogenetic analysis, we found that 10 genera within Nemacheilidae (Eonemachilus, Guinemachilus, Lefua, Micronemacheilus, Oreonectes, Paranemachilus, Protonemacheilus, Traccatichthys, Troglonectes, and Yunnanilus) shared tube-shaped anterior nostrils and formed a monophyletic group. Morphologically, the location between the anterior and posterior nostrils was divided into three types: (i) separated, i.e., a distance greater than 1.5 times the diameter of the posterior nostril; (ii) adjacent, i.e., a distance shorter than the diameter of the posterior nostril; and (iii) closely set, i.e., posterior margin of the anterior nostril connected to the anterior margin of the posterior nostril. Thus, the 10 genera can be distinguished based on nostril features. Additionally, we describe one new genus, Guinemachilus gen. nov., and two new species, Guinemachilus pseudopulcherrimus sp. nov. and Paranemachilus chongzuo sp. nov.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47021394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mahboob Ali, Palwasha Khan, Mahreen Mahmood, Jilong Han, G. Afzal, Iram Qadeer, S. Azmal, N. El-Mouhty, S. Mahmoud, Ibrahim Jafri, Muhammad Ali, Nighat Hashmi
Positive selection refers to the process by which certain genetic variations are more likely to be passed on to future generations because they confer some advantage in terms of survival or reproduction. Zinc finger proteins are a type of transcription factor that plays a role in regulating gene expression, particularly in undifferentiated stem cells. Suppose it has been found that certain zinc finger proteins show genetic signatures of positive selection in mammals. In that case, it suggests that these proteins may have played a role in adaptive evolution in undifferentiated stem cells. This could mean that the specific genetic changes in these zinc finger proteins gave an advantage to the organisms that possessed them, helping them survive and reproduce more effectively. These genetic changes may have allowed the organisms to adapt to changing environments or to develop new abilities, such as increased resistance to disease or faster growth. Undifferentiated stem cells that underwent adaptive evolution during the evolution of mammals can be identified genetically by the outcomes of positive selection on zinc finger proteins. Because of selection pressures like environmental shifts or the introduction of novel pathogens, it is plausible that some zinc finger proteins have experienced fast evolution. The emergence of novel activities or higher expression levels of these proteins as a result of this quick evolution may have given the creatures that possessed them a survival edge. Another possible outcome of positive selection in zinc finger proteins is the emergence of new genetic variations that allow for increased diversity and plasticity in stem cells. This increased diversity and plasticity could have allowed for more efficient adaptation to changing environments and could have played a role in the evolution of new organisms or new characteristics in existing organisms. Overall, the results of positive selection in zinc finger proteins can provide insight into how adaptive evolution occurred in undifferentiated stem cells during the evolution of mammals and how this evolution may have contributed to the development of new organisms and new characteristics and adaptations to changing environments.
{"title":"Positive Selection in Zinc Finger Protein Reveals Genetic Signatures of Adaptive Evolution in Undifferentiated Stem Cells during Evolution in Mammals","authors":"Mahboob Ali, Palwasha Khan, Mahreen Mahmood, Jilong Han, G. Afzal, Iram Qadeer, S. Azmal, N. El-Mouhty, S. Mahmoud, Ibrahim Jafri, Muhammad Ali, Nighat Hashmi","doi":"10.1155/2023/6693488","DOIUrl":"https://doi.org/10.1155/2023/6693488","url":null,"abstract":"Positive selection refers to the process by which certain genetic variations are more likely to be passed on to future generations because they confer some advantage in terms of survival or reproduction. Zinc finger proteins are a type of transcription factor that plays a role in regulating gene expression, particularly in undifferentiated stem cells. Suppose it has been found that certain zinc finger proteins show genetic signatures of positive selection in mammals. In that case, it suggests that these proteins may have played a role in adaptive evolution in undifferentiated stem cells. This could mean that the specific genetic changes in these zinc finger proteins gave an advantage to the organisms that possessed them, helping them survive and reproduce more effectively. These genetic changes may have allowed the organisms to adapt to changing environments or to develop new abilities, such as increased resistance to disease or faster growth. Undifferentiated stem cells that underwent adaptive evolution during the evolution of mammals can be identified genetically by the outcomes of positive selection on zinc finger proteins. Because of selection pressures like environmental shifts or the introduction of novel pathogens, it is plausible that some zinc finger proteins have experienced fast evolution. The emergence of novel activities or higher expression levels of these proteins as a result of this quick evolution may have given the creatures that possessed them a survival edge. Another possible outcome of positive selection in zinc finger proteins is the emergence of new genetic variations that allow for increased diversity and plasticity in stem cells. This increased diversity and plasticity could have allowed for more efficient adaptation to changing environments and could have played a role in the evolution of new organisms or new characteristics in existing organisms. Overall, the results of positive selection in zinc finger proteins can provide insight into how adaptive evolution occurred in undifferentiated stem cells during the evolution of mammals and how this evolution may have contributed to the development of new organisms and new characteristics and adaptations to changing environments.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49370756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The genus Holosticha s. l. is a typical “melting pot” group with an intricate history, and so far, it has been divided into eleven genera. Both newly obtained taxonomic and molecular data provide the opportunity to gain more insights to outline the taxa in it and to understand their systematic and evolutionary relationship. Here, we describe Caudikeronopsis monilata sp. nov. from intertidal sediment on the China coast of the Yellow Sea and analyze the phylogenetic relationships of Holosticha s. l. by obtaining a total of 16 new sequences of seven isolates. The results demonstrate that (1) the morphological features of Holosticha s. str. are outlined very well, but its systematic relationship with Uncinata is still puzzling; (2) based on both morphological and molecular databases, the genera Adumbratosticha, Arcuseries, Caudikeronopsis, Extraholosticha, and “Holosticha + Uncinata” complex are separated clearly from each other in the phylogenetic analyses; and (3) the Anteholosticha isolates are dispersed among the urostylids in the phylogenetic analyses, even though its generic diagnostic features are described very clearly. In the present work, however, the secondary structure predictions do not provide better resolutions for understanding the systematic and evolutionary relationships among the holostichids. And the genus Anteholosticha becomes a new “melting pot” taxon.
{"title":"Refining the “Melting Pot” Genus Holosticha s. l. (Protozoa, Ciliophora, Hypotrichia) Based on Multigene Datasets with Establishment of a New Species Caudikeronopsis monilata sp. nov.","authors":"Xumiao Chen, Ju Li, Kuidong Xu","doi":"10.1155/2023/3411188","DOIUrl":"https://doi.org/10.1155/2023/3411188","url":null,"abstract":"The genus Holosticha s. l. is a typical “melting pot” group with an intricate history, and so far, it has been divided into eleven genera. Both newly obtained taxonomic and molecular data provide the opportunity to gain more insights to outline the taxa in it and to understand their systematic and evolutionary relationship. Here, we describe Caudikeronopsis monilata sp. nov. from intertidal sediment on the China coast of the Yellow Sea and analyze the phylogenetic relationships of Holosticha s. l. by obtaining a total of 16 new sequences of seven isolates. The results demonstrate that (1) the morphological features of Holosticha s. str. are outlined very well, but its systematic relationship with Uncinata is still puzzling; (2) based on both morphological and molecular databases, the genera Adumbratosticha, Arcuseries, Caudikeronopsis, Extraholosticha, and “Holosticha + Uncinata” complex are separated clearly from each other in the phylogenetic analyses; and (3) the Anteholosticha isolates are dispersed among the urostylids in the phylogenetic analyses, even though its generic diagnostic features are described very clearly. In the present work, however, the secondary structure predictions do not provide better resolutions for understanding the systematic and evolutionary relationships among the holostichids. And the genus Anteholosticha becomes a new “melting pot” taxon.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45016033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
H. I. Ahmad, Laraib Jameel, Quratulain Zahra, Jia-Bin Zhou, Linmiao Li, Xiujuan Zhang, Shakeel Ahmed, D. Ali, G. Kumar, Aleena Safdar, Farhan Abbas, Jinping Chen
Interferon-Epsilon (IFNε) is a type of interferon, a protein that plays a role in the immune response to viral infections. This study is aimed at examining the molecular evolution of the IFNε pseudogene in Manis javanica, and it has been found to modulate the innate and specific antiviral immunity in this species. In this study, we identified that IFNε gene has undergone rapid evolution in Manis javanica, with the human and primate IFNε genes showing evidence of positive selection. This suggests that IFNε has played an important role in the evolution of the immune system, possibly in response to coevolution with viral pathogens. Comparative genomic analysis revealed that the IFNε pseudogene in pangolins originated from a gene duplication event approximately 48 million years ago. It subsequently lost its protein-coding function due to multiple deleterious mutations. However, the IFNε pseudogene exhibits a high degree of conservation in its promoter region, suggesting it may still play a regulatory role in antiviral immunity. This suggests that the pseudogene may have evolved to serve an important function in the pangolin’s immune system, potentially helping to protect it from viral infections. The molecular evolution of IFNε provides insights into the coevolutionary dynamics between host immune systems and viral pathogens and may have implications for developing new antiviral therapies.
{"title":"Molecular Evolution of Interferon-Epsilon (IFNε) Pseudogene Modulates Innate and Specific Antiviral Immunity in Manis javanica","authors":"H. I. Ahmad, Laraib Jameel, Quratulain Zahra, Jia-Bin Zhou, Linmiao Li, Xiujuan Zhang, Shakeel Ahmed, D. Ali, G. Kumar, Aleena Safdar, Farhan Abbas, Jinping Chen","doi":"10.1155/2023/2949008","DOIUrl":"https://doi.org/10.1155/2023/2949008","url":null,"abstract":"Interferon-Epsilon (IFNε) is a type of interferon, a protein that plays a role in the immune response to viral infections. This study is aimed at examining the molecular evolution of the IFNε pseudogene in Manis javanica, and it has been found to modulate the innate and specific antiviral immunity in this species. In this study, we identified that IFNε gene has undergone rapid evolution in Manis javanica, with the human and primate IFNε genes showing evidence of positive selection. This suggests that IFNε has played an important role in the evolution of the immune system, possibly in response to coevolution with viral pathogens. Comparative genomic analysis revealed that the IFNε pseudogene in pangolins originated from a gene duplication event approximately 48 million years ago. It subsequently lost its protein-coding function due to multiple deleterious mutations. However, the IFNε pseudogene exhibits a high degree of conservation in its promoter region, suggesting it may still play a regulatory role in antiviral immunity. This suggests that the pseudogene may have evolved to serve an important function in the pangolin’s immune system, potentially helping to protect it from viral infections. The molecular evolution of IFNε provides insights into the coevolutionary dynamics between host immune systems and viral pathogens and may have implications for developing new antiviral therapies.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48821635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Luis Fernando da Silva Rodrigues-Filho, Paula da Costa Nogueira, D. Sodré, José Rafael da Silva Leal, J. Nunes, G. Rincon, R. Lessa, I. Sampaio, M. Vallinoto, J. Ready, J. Sales
The family Carcharhinidae includes the most typical and recognizable sharks, although its internal classification is the subject of extensive debate. In particular, the type genus, Carcharhinus Blainville, 1816, which is also the most speciose, appears to be paraphyletic in relation to a number of morphologically distinct taxa. Isogomphodon oxyrhynchus (Valenciennes, 1839) (the daggernose shark) is a carcharinid, which is endemic to a limited area of the Western Atlantic between Trinidad and Tobago and the Gulf of Maranhão in northern Brazil, one of the smallest ranges of any New World elasmobranch species. In recent decades, I. oxyrhynchus populations have been decimated by anthropogenic impacts, which has led to the classification of the species as critically endangered by the IUCN. However, there is considerable debate on both the validity of the species (I. oxyrhynchus) and the status of Isogomphodon Gill, 1862 as a distinct entity from the genus Carcharhinus. The present study is based on a molecular assessment of the genetic validity of the I. oxyrhynchus that combines mitochondrial and nuclear markers, which were used to identify the biogeographic events responsible for the emergence and dispersal of the species in northern Brazil. The genetic distance analyses and phylogenetic trees confirmed the paraphyly of the genus Carcharhinus, recovering a clade comprising Carcharhinus+I. oxyrhynchus+Prionace glauca (Linnaeus, 1758). Our results indicate not only that the daggernose shark is actually a member of the genus Carcharhinus, but that it is genetically more closely related to Carcharhinus porosus (Ranzani, 1839) than it is to the other Carcharhinus species analyzed. Given this, I. oxyrhynchus and P. glauca are therefore reclassified and recognized as Carcharhinus oxyrhynchus and Carcharhinus glaucus. The daggernose shark, Carcharhinus oxyrhynchus, diverged from C. porosus during the Miocene, when significant geomorphological processes occurred on the northern coast of South America, in particular in relation to the configuration of the Amazon River. It is closely associated with the area of the Amazon plume, and its distinctive morphological features represent autapomorphic ecological adaptations to this unique habitat and do not reflect systematic distinction from Carcharhinus.
{"title":"Evolutionary History and Taxonomic Reclassification of the Critically Endangered Daggernose Shark, a Species Endemic to the Western Atlantic","authors":"Luis Fernando da Silva Rodrigues-Filho, Paula da Costa Nogueira, D. Sodré, José Rafael da Silva Leal, J. Nunes, G. Rincon, R. Lessa, I. Sampaio, M. Vallinoto, J. Ready, J. Sales","doi":"10.1155/2023/4798805","DOIUrl":"https://doi.org/10.1155/2023/4798805","url":null,"abstract":"The family Carcharhinidae includes the most typical and recognizable sharks, although its internal classification is the subject of extensive debate. In particular, the type genus, Carcharhinus Blainville, 1816, which is also the most speciose, appears to be paraphyletic in relation to a number of morphologically distinct taxa. Isogomphodon oxyrhynchus (Valenciennes, 1839) (the daggernose shark) is a carcharinid, which is endemic to a limited area of the Western Atlantic between Trinidad and Tobago and the Gulf of Maranhão in northern Brazil, one of the smallest ranges of any New World elasmobranch species. In recent decades, I. oxyrhynchus populations have been decimated by anthropogenic impacts, which has led to the classification of the species as critically endangered by the IUCN. However, there is considerable debate on both the validity of the species (I. oxyrhynchus) and the status of Isogomphodon Gill, 1862 as a distinct entity from the genus Carcharhinus. The present study is based on a molecular assessment of the genetic validity of the I. oxyrhynchus that combines mitochondrial and nuclear markers, which were used to identify the biogeographic events responsible for the emergence and dispersal of the species in northern Brazil. The genetic distance analyses and phylogenetic trees confirmed the paraphyly of the genus Carcharhinus, recovering a clade comprising Carcharhinus+I. oxyrhynchus+Prionace glauca (Linnaeus, 1758). Our results indicate not only that the daggernose shark is actually a member of the genus Carcharhinus, but that it is genetically more closely related to Carcharhinus porosus (Ranzani, 1839) than it is to the other Carcharhinus species analyzed. Given this, I. oxyrhynchus and P. glauca are therefore reclassified and recognized as Carcharhinus oxyrhynchus and Carcharhinus glaucus. The daggernose shark, Carcharhinus oxyrhynchus, diverged from C. porosus during the Miocene, when significant geomorphological processes occurred on the northern coast of South America, in particular in relation to the configuration of the Amazon River. It is closely associated with the area of the Amazon plume, and its distinctive morphological features represent autapomorphic ecological adaptations to this unique habitat and do not reflect systematic distinction from Carcharhinus.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44655418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Navarro, Sergio Jiménez Pinadero, T. Decaëns, M. Hedde, M. Novo, D. Trigo, D. Marchán
The taxonomy of earthworms has been riddled by instability, lack of systematically useful characters, and lax diagnoses of some genera. This has led to the use of some genera such as Allolobophora Eisen, 1874 as taxonomic wastebaskets, blurring their evolution and biogeographical history. The implementation of molecular techniques has revolutionized the systematics of the genus; however, some of its species have not been previously included in molecular phylogenetic analyses. Thus, the molecular markers COI, 16S, ND1, 12S, and 28S were sequenced for six endemic species including several taxa of Allolobophora and Aporrectodea Örely, 1885 (another related catch-all genus). Phylogenetic relationships determined by Bayesian inference and maximum likelihood analyses support the status of two of the six taxa examined (Allolobophora burgondiae Bouché, 1972 and Aporrectodea icterica Savigny, 1826) as part of Allolobophora sensu stricto and a presumed synonymy between Allolobophora and Heraclescolex Qiu and Bouché, 1998. Branch lengths and average pairwise genetic distances support the transfer of Allolobophora satchelli Bouché, 1972 to the genus Panoniona Mršić and Šapkarev, 1988 and the emergence of two new genera, Heraultia gen. nov. and Vosgesia gen. nov., endemic to France, hosting Allolobophora tiginosa Bouché, 1972 and Allolobophora zicsii Bouché, 1972, respectively. The aforementioned changes of status and the diagnosis for Heraultia and Vosgesia are presented. These results provided more evolutionarily and biogeographically coherent earthworm groups and highlighted that the Maghreb and the area around the Alps are potential key locations for the diversification of Allolobophora and several lineages of Lumbricidae.
{"title":"Catch-All No More: Integrative Systematic Revision of the Genus Allolobophora Eisen, 1874 (Crassiclitellata, Lumbricidae) with the Description of Two New Relict Earthworm Genera","authors":"A. Navarro, Sergio Jiménez Pinadero, T. Decaëns, M. Hedde, M. Novo, D. Trigo, D. Marchán","doi":"10.1155/2023/5479917","DOIUrl":"https://doi.org/10.1155/2023/5479917","url":null,"abstract":"The taxonomy of earthworms has been riddled by instability, lack of systematically useful characters, and lax diagnoses of some genera. This has led to the use of some genera such as Allolobophora Eisen, 1874 as taxonomic wastebaskets, blurring their evolution and biogeographical history. The implementation of molecular techniques has revolutionized the systematics of the genus; however, some of its species have not been previously included in molecular phylogenetic analyses. Thus, the molecular markers COI, 16S, ND1, 12S, and 28S were sequenced for six endemic species including several taxa of Allolobophora and Aporrectodea Örely, 1885 (another related catch-all genus). Phylogenetic relationships determined by Bayesian inference and maximum likelihood analyses support the status of two of the six taxa examined (Allolobophora burgondiae Bouché, 1972 and Aporrectodea icterica Savigny, 1826) as part of Allolobophora sensu stricto and a presumed synonymy between Allolobophora and Heraclescolex Qiu and Bouché, 1998. Branch lengths and average pairwise genetic distances support the transfer of Allolobophora satchelli Bouché, 1972 to the genus Panoniona Mršić and Šapkarev, 1988 and the emergence of two new genera, Heraultia gen. nov. and Vosgesia gen. nov., endemic to France, hosting Allolobophora tiginosa Bouché, 1972 and Allolobophora zicsii Bouché, 1972, respectively. The aforementioned changes of status and the diagnosis for Heraultia and Vosgesia are presented. These results provided more evolutionarily and biogeographically coherent earthworm groups and highlighted that the Maghreb and the area around the Alps are potential key locations for the diversification of Allolobophora and several lineages of Lumbricidae.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48415743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Branchinotogluma is one of the most diverse genera among the polynoids inhabiting deep-sea chemosynthetic environments. A total of 14 species have been described from the hydrothermal vents and cold seeps worldwide. Our phylogenetic analyses based on four genes (COI, 16S, 18S, and 28S rRNA) recovered the current Branchinotogluma as paraphyletic, with seven clades scattered in two main clades. The monophyly of the main clade composed of Branchinotogluma (except Branchinotogluma segonzaci), Branchipolynoe, and Peinaleopolynoe is supported by the presence of 20–21 segments with 9–10 pairs of elytra, ventral papillae starting from segment 12 in males, and arborescent branchiae. The monophyly of another main clade composed of B. segonzaci, Bathykurila, Lepidonotopodium, Levensteiniella, and Thermopolynoe is supported by the presence of usually 22–30 segments with 11 pairs of elytra and the lack of ventral papillae in females. In addition, our study recognized two new species, Branchinotogluma nanhaiensis sp. nov. and B. robusta sp. nov., based on specimens collected from the deep-sea cold seeps in the South China Sea. Both the morphology and molecular phylogenetic analyses support the validity of the two new species and the sister relationships between B. nanhaiensis and B. japonicus and between B. robusta and B. pettiboneae as well.
{"title":"Reevaluation of the Systematic Status of Branchinotogluma (Annelida, Polynoidae), with the Establishment of Two New Species","authors":"Xuwen Wu, Wenquan Zhen, Qi Kou, Kuidong Xu","doi":"10.1155/2023/1490800","DOIUrl":"https://doi.org/10.1155/2023/1490800","url":null,"abstract":"Branchinotogluma is one of the most diverse genera among the polynoids inhabiting deep-sea chemosynthetic environments. A total of 14 species have been described from the hydrothermal vents and cold seeps worldwide. Our phylogenetic analyses based on four genes (COI, 16S, 18S, and 28S rRNA) recovered the current Branchinotogluma as paraphyletic, with seven clades scattered in two main clades. The monophyly of the main clade composed of Branchinotogluma (except Branchinotogluma segonzaci), Branchipolynoe, and Peinaleopolynoe is supported by the presence of 20–21 segments with 9–10 pairs of elytra, ventral papillae starting from segment 12 in males, and arborescent branchiae. The monophyly of another main clade composed of B. segonzaci, Bathykurila, Lepidonotopodium, Levensteiniella, and Thermopolynoe is supported by the presence of usually 22–30 segments with 11 pairs of elytra and the lack of ventral papillae in females. In addition, our study recognized two new species, Branchinotogluma nanhaiensis sp. nov. and B. robusta sp. nov., based on specimens collected from the deep-sea cold seeps in the South China Sea. Both the morphology and molecular phylogenetic analyses support the validity of the two new species and the sister relationships between B. nanhaiensis and B. japonicus and between B. robusta and B. pettiboneae as well.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43263082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Iván Ballester-Torres, A. Ricarte, Zorica Nedeljković, M. Marcos-garcía
Comprising nearly 500 species worldwide, Cheilosia Meigen is the largest genus of Syrphidae in the Palaearctic region. Within Cheilosia, phenotypic diversity has been assessed in different species groups, including the group of Cheilosia longula (Zetterstedt, 1838). However, the phenotypic variability of Cheilosia soror (Zetterstedt, 1843), a highly variable member of the C. longula group, has never been assessed in western Europe. In the present work, morphological and molecular analyses were conducted to assess the phenotypic variability found in 300+ specimens of C. soror from the Iberian Peninsula. A total of 16 variable characters were identified and defined for the C. soror morphology, with the highest variation found in the colour of the mesonotum pilosity and the metatibia colour. Morphological variation was assessed against molecular variation based on two molecular markers, one mitochondrial, the 5 ′ end of the cytochrome c oxidase subunit I (COI-5 ′ ), and one nuclear, the large subunit ribosomal DNA (28S). Phylogenetic analyses rendered trees with topologies in disagreement with the defined morphological variation. Two haplotypes were identified amongst the analysed specimens of C. soror, together with a haplotypic variant exclusive to the Iberian region. Potential distributions were used to identify unexplored areas of occurrence of C. soror and other species of the C. longula group in the Iberian Peninsula. Unassessed areas of occurrence of C. soror should be surveyed in the future to confirm the absence of hidden taxonomic diversity within the range of phenotypic variation for this species. Phenotypic variation of the other two Iberian species of the C. longula group, C. longula and C. scutellata (Fallén, 1817), was also assessed to find that they are species with less-variable morphology than C. soror and with molecular characters in accordance with other conspecific populations in Europe. New distributional data are provided for C. soror and C. scutellata from Spain, and a leg abnormality is identified for the first time in C. soror.
{"title":"High Phenotypic Diversity Does Not Always Hide Taxonomic Diversity: A Study Case with Cheilosia soror (Zetterstedt, 1843) (Diptera: Syrphidae) in the Iberian Peninsula","authors":"Iván Ballester-Torres, A. Ricarte, Zorica Nedeljković, M. Marcos-garcía","doi":"10.1155/2022/8378483","DOIUrl":"https://doi.org/10.1155/2022/8378483","url":null,"abstract":"Comprising nearly 500 species worldwide, Cheilosia Meigen is the largest genus of Syrphidae in the Palaearctic region. Within Cheilosia, phenotypic diversity has been assessed in different species groups, including the group of Cheilosia longula (Zetterstedt, 1838). However, the phenotypic variability of Cheilosia soror (Zetterstedt, 1843), a highly variable member of the C. longula group, has never been assessed in western Europe. In the present work, morphological and molecular analyses were conducted to assess the phenotypic variability found in 300+ specimens of C. soror from the Iberian Peninsula. A total of 16 variable characters were identified and defined for the C. soror morphology, with the highest variation found in the colour of the mesonotum pilosity and the metatibia colour. Morphological variation was assessed against molecular variation based on two molecular markers, one mitochondrial, the 5\u0000 \u0000 ′\u0000 \u0000 end of the cytochrome c oxidase subunit I (COI-5\u0000 \u0000 ′\u0000 \u0000 ), and one nuclear, the large subunit ribosomal DNA (28S). Phylogenetic analyses rendered trees with topologies in disagreement with the defined morphological variation. Two haplotypes were identified amongst the analysed specimens of C. soror, together with a haplotypic variant exclusive to the Iberian region. Potential distributions were used to identify unexplored areas of occurrence of C. soror and other species of the C. longula group in the Iberian Peninsula. Unassessed areas of occurrence of C. soror should be surveyed in the future to confirm the absence of hidden taxonomic diversity within the range of phenotypic variation for this species. Phenotypic variation of the other two Iberian species of the C. longula group, C. longula and C. scutellata (Fallén, 1817), was also assessed to find that they are species with less-variable morphology than C. soror and with molecular characters in accordance with other conspecific populations in Europe. New distributional data are provided for C. soror and C. scutellata from Spain, and a leg abnormality is identified for the first time in C. soror.","PeriodicalId":54751,"journal":{"name":"Journal of Zoological Systematics and Evolutionary Research","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43010809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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