Pub Date : 2024-09-16DOI: 10.1101/2024.09.13.612884
Erin S. Morrison, Guinevere P. Pandolfi, Stepfanie M. Aguillon, Jarome R. Ali, Olivia Archard, Daniel T Baldassarre, Illeana Baquero, Kevin F.P. Bennett, Kevin M. Bonney, Riley Bryant, Rosanne M. Catanach, Therese A. Catanach, Ida Chavoshan, Sarah N. Davis, Brooke D. Goodman, Eric R. Gulson-Castillo, Matthew Hack, Jocelyn Hudon, Gavin M. Leighton, Kira M. Long, Ziqi Ma, Dakota E. McCoy, J. F. McLaughlin, Gaia Rueda Moreno, Talia M. Mota, Lara Noguchi, Ugo Nwigwe, Teresa Pegan, Kaiya Provost, Shauna Ann Rasband, Jessie F Salter, Lauren C. Silvernail, Jared A. Simard, Heather R. Skeen, Juliana Soto-Patino, Young Ha Suh, Qingyue Wang, Matthew E. Warshauer, Sissy Yan, Betsy Zalinski, Ziqi Zhao, Allison J. Shultz
Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The official common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a particular issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the common names of species and their frequency of use, we used a crowdsourcing approach and recruited a total of 85 professional ornithologists and non-professional participants to classify unique descriptors in the English common names of all recognized bird species from around the world. Each species' common name was assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% had names describing the biology of the species, while the remaining 11% of species had names derived from human cultural references or local non-English languages. Species with common names based on features of avian biology were more likely to share an evolutionary history or be from the same geographic region, in comparison to species with common names derived from human culture. The crowdsourced data collection also revealed that many common names contained specialized or historic terminology unknown to many of the participants. As the first comprehensive assessment of the state of terminology in English common names of birds, the dataset sheds light on historical approaches to nomenclature and provides insight into how the general public currently engages with species through their names.
{"title":"Bird Name-a-thon: Categorizing English bird names using crowdsourcing","authors":"Erin S. Morrison, Guinevere P. Pandolfi, Stepfanie M. Aguillon, Jarome R. Ali, Olivia Archard, Daniel T Baldassarre, Illeana Baquero, Kevin F.P. Bennett, Kevin M. Bonney, Riley Bryant, Rosanne M. Catanach, Therese A. Catanach, Ida Chavoshan, Sarah N. Davis, Brooke D. Goodman, Eric R. Gulson-Castillo, Matthew Hack, Jocelyn Hudon, Gavin M. Leighton, Kira M. Long, Ziqi Ma, Dakota E. McCoy, J. F. McLaughlin, Gaia Rueda Moreno, Talia M. Mota, Lara Noguchi, Ugo Nwigwe, Teresa Pegan, Kaiya Provost, Shauna Ann Rasband, Jessie F Salter, Lauren C. Silvernail, Jared A. Simard, Heather R. Skeen, Juliana Soto-Patino, Young Ha Suh, Qingyue Wang, Matthew E. Warshauer, Sissy Yan, Betsy Zalinski, Ziqi Zhao, Allison J. Shultz","doi":"10.1101/2024.09.13.612884","DOIUrl":"https://doi.org/10.1101/2024.09.13.612884","url":null,"abstract":"Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The official common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a particular issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the common names of species and their frequency of use, we used a crowdsourcing approach and recruited a total of 85 professional ornithologists and non-professional participants to classify unique descriptors in the English common names of all recognized bird species from around the world. Each species' common name was assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% had names describing the biology of the species, while the remaining 11% of species had names derived from human cultural references or local non-English languages. Species with common names based on features of avian biology were more likely to share an evolutionary history or be from the same geographic region, in comparison to species with common names derived from human culture. The crowdsourced data collection also revealed that many common names contained specialized or historic terminology unknown to many of the participants. As the first comprehensive assessment of the state of terminology in English common names of birds, the dataset sheds light on historical approaches to nomenclature and provides insight into how the general public currently engages with species through their names.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-14DOI: 10.1101/2024.09.11.612409
Rebecca A Brociek, Dongfang Li, Richard Broughton, David S Gardner
Background: Adoption of a plant-based diet is a popular lifestyle choice for many owners of canine companion animals. Increasingly, owners would like to feed their canine companions a similar diet. A plant-based dietary pattern has been reported to be associated with some micronutrient deficiencies. Complete dog foods are, by definition, supposed to be nutritionally replete in all macro- and micronutrients. Few studies have reported a full nutritional analysis of complete, dry plant- versus meat-based dog foods. Method: Here, 31 pet foods (n=19 meat-based, n=6 veterinary and n=6 plant-based) were analysed for total protein content and individual amino acids, fatty acids, major and trace elements, vitamin D and all B-vitamins. Results: Nutritional composition of meat and plant-based foods were similar, except for iodine and B-vitamins, which were lower in plant-based foods. The majority (66%) of veterinary diets with lower total protein by design, were also deficient in one or more essential amino acids. Isolated instances of non-compliance to nutritional guidelines were observed across all food-groups. Of the tested nutrients 55%, 16%, 24% and 100% of foods met all amino acid, mineral, B-vitamin, and vitamin D guidelines, respectively. Conclusions: Adopting a plant-based dietary pattern for your companion canine can provide nutritional adequacy with respect to the majority of macro- and micronutrients, but feeding supplemental iodine and B-vitamins should be considered. Veterinary diets, purposely low in crude protein, often have less than optimal essential amino acid composition. These data provide important new information for owners of companion canines being fed plant-based or veterinary diets.
背景：采用以植物为基础的饮食是许多犬科伴侣动物主人选择的一种流行生活方式。越来越多的主人希望给他们的犬类伴侣喂食类似的食物。据报道，植物性饮食模式与某些微量营养素缺乏症有关。根据定义，完整的狗粮应该富含所有宏量和微量营养素。很少有研究报告对以植物为基础的全营养干狗粮和以肉类为基础的全营养干狗粮进行全面的营养分析。方法：对 31 种宠物食品（19 种肉类食品、6 种兽医食品和 6 种植物食品）的总蛋白质含量、单个氨基酸、脂肪酸、主要元素和微量元素、维生素 D 和所有 B 族维生素进行了分析。结果肉类食品和植物性食品的营养成分相似，但植物性食品中的碘和 B 族维生素含量较低。总蛋白质含量较低的兽粮中，大多数（66%）还缺乏一种或多种必需氨基酸。在所有食品类别中都发现了个别不符合营养指南的情况。在检测的营养素中，分别有55%、16%、24%和100%的食品符合所有氨基酸、矿物质、B族维生素和维生素D的标准。结论为伴侣犬采用以植物为基础的膳食模式可以提供充足的大部分宏量和微量营养素，但应考虑喂食补充碘和 B 族维生素。兽粮的粗蛋白质含量较低，其必需氨基酸的组成往往达不到最佳水平。这些数据为饲养以植物饲料或兽医饲料为主食的伴侣犬的主人提供了重要的新信息。
{"title":"Nutritional analysis of commercially available, complete plant- and meat-based dry dog foods in the UK","authors":"Rebecca A Brociek, Dongfang Li, Richard Broughton, David S Gardner","doi":"10.1101/2024.09.11.612409","DOIUrl":"https://doi.org/10.1101/2024.09.11.612409","url":null,"abstract":"Background: Adoption of a plant-based diet is a popular lifestyle choice for many owners of canine companion animals. Increasingly, owners would like to feed their canine companions a similar diet. A plant-based dietary pattern has been reported to be associated with some micronutrient deficiencies. Complete dog foods are, by definition, supposed to be nutritionally replete in all macro- and micronutrients. Few studies have reported a full nutritional analysis of complete, dry plant- versus meat-based dog foods. Method: Here, 31 pet foods (n=19 meat-based, n=6 veterinary and n=6 plant-based) were analysed for total protein content and individual amino acids, fatty acids, major and trace elements, vitamin D and all B-vitamins. Results: Nutritional composition of meat and plant-based foods were similar, except for iodine and B-vitamins, which were lower in plant-based foods. The majority (66%) of veterinary diets with lower total protein by design, were also deficient in one or more essential amino acids. Isolated instances of non-compliance to nutritional guidelines were observed across all food-groups. Of the tested nutrients 55%, 16%, 24% and 100% of foods met all amino acid, mineral, B-vitamin, and vitamin D guidelines, respectively. Conclusions: Adopting a plant-based dietary pattern for your companion canine can provide nutritional adequacy with respect to the majority of macro- and micronutrients, but feeding supplemental iodine and B-vitamins should be considered. Veterinary diets, purposely low in crude protein, often have less than optimal essential amino acid composition. These data provide important new information for owners of companion canines being fed plant-based or veterinary diets.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.08.611910
Tanvir Ahmed, Md. Abul Hashem, Afifa Afrin, Ankon Lahiry, Shahina Rahman, Takashi Bungo, Shubash Chandra Das
The current study aimed to optimize the fasting duration in order to mitigate the detrimental effects of heat stress on broilers raised in hot and humid climatic environments. A total of 500 broiler DOCs were assigned to five distinct treatment groups: T0= Non-fasted controlled temperature (24-26 oC) (NF-CT), T1= Non-fasted heat stressed (30-38 oC) (NF-HS), T2= 6 hours fasted heat stressed (6-h FHS), T3= 8 hours fasted heat stressed (8-h FHS), and T4= 10 hours fasted heat stressed (10-h FHS). Each treatment was replicated five times, with 20 birds in each replicate group. As expected, the birds in NF-CT group showed significantly better performances for all the growth parameters, although birds who fasted for 8-h under heat stress exerted better growth and FCR in comparison to the other HS groups. Fasting of birds under heat stress significantly showed the lowest mortality. Like the NF-CT group, birds in 8-h FHS achieved significantly higher dressing percentage, breast meat, liver yields, and the lowest abdominal fat. Fasting for 8- and 10-h significantly increased breast meat pH and water holding capacity and thus reduced cooking loss. Fasting also improved the breast meat color quality by increasing redness (a*) and reducing the hue angle values comparable with the NF-CT group. A significantly upward trend in villi height (VH), width (VW) and crypt depth (CD) of gut segments was also observed in the birds of the 8-h FHS group. Total bacterial and coliform counts in cecum contents were reduced significantly with the increase in the fasting period. Benefit-cost analysis showed better profitability in the 8-h FHS group than other HS groups. Taken altogether, it can be concluded that broiler chicken exposed to 8-h fasting period is an effective approach to mitigate heat stress under hot and humid climatic conditions.
{"title":"Effects of fasting on heat-stressed broiler chickens: part I- growth performance, meat quality, gut histomorphological and microbial responses","authors":"Tanvir Ahmed, Md. Abul Hashem, Afifa Afrin, Ankon Lahiry, Shahina Rahman, Takashi Bungo, Shubash Chandra Das","doi":"10.1101/2024.09.08.611910","DOIUrl":"https://doi.org/10.1101/2024.09.08.611910","url":null,"abstract":"The current study aimed to optimize the fasting duration in order to mitigate the detrimental effects of heat stress on broilers raised in hot and humid climatic environments. A total of 500 broiler DOCs were assigned to five distinct treatment groups: T0= Non-fasted controlled temperature (24-26 oC) (NF-CT), T1= Non-fasted heat stressed (30-38 oC) (NF-HS), T2= 6 hours fasted heat stressed (6-h FHS), T3= 8 hours fasted heat stressed (8-h FHS), and T4= 10 hours fasted heat stressed (10-h FHS). Each treatment was replicated five times, with 20 birds in each replicate group. As expected, the birds in NF-CT group showed significantly better performances for all the growth parameters, although birds who fasted for 8-h under heat stress exerted better growth and FCR in comparison to the other HS groups. Fasting of birds under heat stress significantly showed the lowest mortality. Like the NF-CT group, birds in 8-h FHS achieved significantly higher dressing percentage, breast meat, liver yields, and the lowest abdominal fat. Fasting for 8- and 10-h significantly increased breast meat pH and water holding capacity and thus reduced cooking loss. Fasting also improved the breast meat color quality by increasing redness (a*) and reducing the hue angle values comparable with the NF-CT group. A significantly upward trend in villi height (VH), width (VW) and crypt depth (CD) of gut segments was also observed in the birds of the 8-h FHS group. Total bacterial and coliform counts in cecum contents were reduced significantly with the increase in the fasting period. Benefit-cost analysis showed better profitability in the 8-h FHS group than other HS groups. Taken altogether, it can be concluded that broiler chicken exposed to 8-h fasting period is an effective approach to mitigate heat stress under hot and humid climatic conditions.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1101/2024.09.08.611911
Saima Naz, Qudrat Ullah, Dalia Fouad, Abdul Qadeer, Maria Lateef, Muhammad Waqar Hassan, Ahmad Manan Mustafa Chatha
Industrial and agricultural water run-off are polluting the aquatic ecosystem by depositing different toxic trace elements (TTEs) in riverine system. It has become a global concern impacting not only the well-being of aquatic organisms but human health as well. Current study evaluated the impact of four TTEs (Cadmium (Cd), copper (Cu), lead (Pb), and nickel (Ni)) in three organs (liver, gills, and muscles) of five fish species viz, Rita rita, Sperata sarwari, Wallago attu, Mastacembelus armatus, and Cirrhinus mrigala collected from right and left banks of Punjnad headworks during winter, spring and summer. We investigated accumulation (mg/kg) of these TTEs in fish in addition to the human health risk assessment by estimating exposure hazards, hazardous index (THQ and TTHQ) and metal pollution index (MPI). The obtained results showed that W. attu accumulated significantly more TTEs (p < 0.00) as compared to other fish. Among seasons, summer had significantly more (p < 0.00) accumulation of TTEs than other seasons. Lead (Pb) accumulation was highest across TTEs in fish liver as compared to gills and muscles. Right bank showed higher accumulation (p < 0.00) of all TTEs in all fish species in contrast to the left bank. The human health risk assessment showed that Cd and Pb had higher exposure levels than Cu and Ni. Furthermore, the THQ was in the order of Cd > Pb > Ni > Cu. All fish species had THQ 1 for Cd and Pb and TTHQ > 1 for all fish. MPI index showed moderate to high level of TTE contamination if all fish species. The study concluded that right bank has higher metal accumulation than left bank. However, fish consumption from both of the study site was not safe for human consumption.
{"title":"Trace Elements in Fish: Assessment of bioaccumulation and associated health risks.","authors":"Saima Naz, Qudrat Ullah, Dalia Fouad, Abdul Qadeer, Maria Lateef, Muhammad Waqar Hassan, Ahmad Manan Mustafa Chatha","doi":"10.1101/2024.09.08.611911","DOIUrl":"https://doi.org/10.1101/2024.09.08.611911","url":null,"abstract":"Industrial and agricultural water run-off are polluting the aquatic ecosystem by depositing different toxic trace elements (TTEs) in riverine system. It has become a global concern impacting not only the well-being of aquatic organisms but human health as well. Current study evaluated the impact of four TTEs (Cadmium (Cd), copper (Cu), lead (Pb), and nickel (Ni)) in three organs (liver, gills, and muscles) of five fish species viz, Rita rita, Sperata sarwari, Wallago attu, Mastacembelus armatus, and Cirrhinus mrigala collected from right and left banks of Punjnad headworks during winter, spring and summer. We investigated accumulation (mg/kg) of these TTEs in fish in addition to the human health risk assessment by estimating exposure hazards, hazardous index (THQ and TTHQ) and metal pollution index (MPI). The obtained results showed that W. attu accumulated significantly more TTEs (p < 0.00) as compared to other fish. Among seasons, summer had significantly more (p < 0.00) accumulation of TTEs than other seasons. Lead (Pb) accumulation was highest across TTEs in fish liver as compared to gills and muscles. Right bank showed higher accumulation (p < 0.00) of all TTEs in all fish species in contrast to the left bank. The human health risk assessment showed that Cd and Pb had higher exposure levels than Cu and Ni. Furthermore, the THQ was in the order of Cd > Pb > Ni > Cu. All fish species had THQ 1 for Cd and Pb and TTHQ > 1 for all fish. MPI index showed moderate to high level of TTE contamination if all fish species. The study concluded that right bank has higher metal accumulation than left bank. However, fish consumption from both of the study site was not safe for human consumption.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1101/2024.09.03.610934
Samuel Nibouche, Joëlle Sadeyen, Sébastien Dervin, Mirana Gauche, Sabine Mérion, Janice Minatchy, Romuald Fontaine, Philippe Reynaud, Bruno Michel
This work is a synthesis of new taxa for the Reunion Island identified between 1963 and 2022 and not published to date. The collections were carried out mainly by researchers and technicians from CIRAD or FDGDON. Sampling mainly targeted at crop pests and their natural enemies. The list includes 101 taxa new for Reunion. The Hymenoptera and Hemiptera are the most represented orders.
{"title":"Additions to the list of arthropods of Reunion Island","authors":"Samuel Nibouche, Joëlle Sadeyen, Sébastien Dervin, Mirana Gauche, Sabine Mérion, Janice Minatchy, Romuald Fontaine, Philippe Reynaud, Bruno Michel","doi":"10.1101/2024.09.03.610934","DOIUrl":"https://doi.org/10.1101/2024.09.03.610934","url":null,"abstract":"This work is a synthesis of new taxa for the Reunion Island identified between 1963 and 2022 and not published to date. The collections were carried out mainly by researchers and technicians from CIRAD or FDGDON. Sampling mainly targeted at crop pests and their natural enemies. The list includes 101 taxa new for Reunion. The Hymenoptera and Hemiptera are the most represented orders.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.1101/2024.09.10.612189
SREENATH KANNANCHERY RAMANATHAN, Pradeep B, Aju K Raju, Sandhya Sukumaran, Wilson Sebastian, Alvin Anto
Pangio juhuae sp nov, a new species of subterranean eel loach, is described from Kerala, India. It is distinguished from its subterranean congeners by the presence of a dorsal fin, four pectoral rays and five segmented anal fin rays. Genetic analyses suggest that P. juhuae is closely related to P. bhujia but is distinct in morphology, particularly by the presence of a dorsal fin. The low genetic distance and significant morphological difference between these two Pangio species suggest that they have diverged from an immediate common ancestor and evolved distinct adaptations to subterranean niches. P. juhuae exhibits less evolved troglobitic traits compared to P. bhujia and P. pathala, suggesting it could be a connecting species in the evolutionary transition from terrestrial to subterranean loaches. This discovery provides evidence for possible subterranean speciation of fishes in underground habitats.
Pangio juhuae sp nov 是一种产于印度喀拉拉邦的地下鳗鳅新品种。它与地下同类的区别在于背鳍、四条胸鳍和五条分节臀鳍。遗传分析表明，P. juhuae 与 P. bhujia 亲缘关系密切，但在形态上，尤其是背鳍的存在，与 P. bhujia 截然不同。这两个庞然大物物种之间的遗传距离很低，形态差异很大，这表明它们是从一个直接的共同祖先那里分化出来的，并进化出了对地下壁龛的不同适应。与P. bhujia和P. pathala相比，P. juhuae表现出较少的进化蛙足性状，这表明它可能是陆生泥鳅向地下泥鳅进化过渡过程中的一个连接物种。这一发现为地下栖息地鱼类可能的地下物种提供了证据。
{"title":"Discovery of a new species of subterranean eel loach from southern India","authors":"SREENATH KANNANCHERY RAMANATHAN, Pradeep B, Aju K Raju, Sandhya Sukumaran, Wilson Sebastian, Alvin Anto","doi":"10.1101/2024.09.10.612189","DOIUrl":"https://doi.org/10.1101/2024.09.10.612189","url":null,"abstract":"Pangio juhuae sp nov, a new species of subterranean eel loach, is described from Kerala, India. It is distinguished from its subterranean congeners by the presence of a dorsal fin, four pectoral rays and five segmented anal fin rays. Genetic analyses suggest that P. juhuae is closely related to P. bhujia but is distinct in morphology, particularly by the presence of a dorsal fin. The low genetic distance and significant morphological difference between these two Pangio species suggest that they have diverged from an immediate common ancestor and evolved distinct adaptations to subterranean niches. P. juhuae exhibits less evolved troglobitic traits compared to P. bhujia and P. pathala, suggesting it could be a connecting species in the evolutionary transition from terrestrial to subterranean loaches. This discovery provides evidence for possible subterranean speciation of fishes in underground habitats.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"115 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.10.612281
Renan Maestri, Gislene L Goncalves, Violaine Nicolas-Colin, Anna Bryjova, Rodrigo Fornel, Eric Coissac, Pierre Taberlet, Gilson RP Moreira, Thales Renato Ochotorena de Freitas
Ctenomys Blainville 1826 ranks among the top ten most diverse mammal genera in terms of species richness. However, the taxonomic history of Ctenomys brasiliensis Blainville,1826, the corresponding type species, has long been obscured by a dearth of information regarding the collection data of the type material, compounded by an elusive geographic origin. Here, employing ancient DNA methodology, we sequenced the complete mitogenome of the remaining type specimen and conducted an extensive historical investigation to correlate originally described locality names with present-day locales in South America. Our analysis unequivocally confirms that the type specimen corresponds to the species currently designated as Ctenomys minutus Nehring, 1887. This resolution lays to rest a century-old debate surrounding the provenance of the type specimen, rejecting prior hypotheses that placed its collection site in southeastern Brazil or Uruguay. Instead, our evidence suggests it was likely obtained from a third location in southernmost Brazil. Previous analyses overlooked this new location due to confusion surrounding geographic nomenclature and labeling errors, issues rectified by our combined mitogenomic and historical approach. Furthermore, quantitative morphological analyses boost our findings, demonstrating a closer affinity between C. brasiliensis and C. minutus within the same species group. Accordingly, we validate C. brasiliensis and propose C. minutus as its junior synonym. Our study underscores the importance of robust DNA analyses in confirming the identity and geographic origins of type specimens, especially for Ctenomys species with similar phenotypes, and specimens collected centuries ago.
就物种丰富度而言，Ctenomys Blainville 1826 是十大最多样化的哺乳动物属之一。然而，由于缺乏有关模式标本采集数据的信息，再加上难以捉摸的地理起源，Ctenomys brasiliensis Blainville,1826（相应的模式种）的分类历史长期以来一直模糊不清。在此，我们采用古老的 DNA 方法，对剩余模式标本的完整有丝分裂基因组进行了测序，并进行了广泛的历史调查，以将最初描述的地点名称与当今南美洲的地点名称联系起来。我们的分析明确证实，该模式标本与目前被指定为 Ctenomys minutus Nehring, 1887 的物种相对应。这一结论平息了一个世纪以来围绕模式标本来源的争论，否定了之前将其采集地点置于巴西东南部或乌拉圭的假设。相反，我们的证据表明，它很可能来自巴西最南端的第三个地点。之前的分析由于地理命名的混乱和标签错误而忽略了这一新的地点，而我们结合有丝分裂基因组学和历史方法纠正了这些问题。此外，定量形态学分析也促进了我们的研究结果，证明在同一物种组中，C. brasiliensis 与 C. minutus 的亲缘关系更为密切。因此，我们验证了 C. brasiliensis，并提议将 C. minutus 作为它的小异名。我们的研究强调了强有力的 DNA 分析在确认模式标本的身份和地理起源方面的重要性，尤其是对于表型相似的栉水母物种和数百年前采集的标本。
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Pub Date : 2024-09-09DOI: 10.1101/2024.09.04.611334
Leonid L. Voyta, Daniel A. Melnikov
Our paper is the first contribution to the comprehensive analysis of the complicated evolution of cranial and mandibular parts connected by pterygoid muscles, as part of more global investigation into adaptive evolution of Arvicolinae. The analysis was performed on 90 micro-computed-tomography-scanned specimens from 33 species from 19 genera of Arvicolinae as well as two species from two genera of Cricetinae as an outgroup. We revised 11 morphological traits of the 'palato-spheno-pterygoid' complex, including key features of the palatine that are highly important for defining Arvicolinae taxa according to the micro-computed-tomography data. We also homologized characters of the posterior palatal margin and categorized the composition of the palatal elements into two main morphotypes: morphotype 'A' is unique to Clethrionomyini and morphotype 'B' was subdivided into three additional types and was found to occur in the outgroup (cricetines), voles (B2), and lemmings (B3). Morphospace analysis of the palato-spheno-pterygoid complex by means of the three-dimensional dataset revealed a mode of transformation of morphotype 'A' into morphotype 'B2.' A separate task was the development of a protocol for the preparation of morphological data for subsequent evaluation of genotype-phenotype relationships using specialized software applications (e.g., RERconverge).
我们的论文是对翼状肌连接的颅骨和下颌骨复杂进化过程进行全面分析的首次贡献，是对弧齿兽科适应性进化进行更全面研究的一部分。该分析是通过对来自19个Arvicolinae属的33个物种以及作为外群的2个Cricetinae属的2个物种的90个显微计算机断层扫描标本进行的。我们对 "腭-鼻-翼 "复合体的 11 个形态特征进行了修订，其中包括腭部的关键特征，这些特征对于根据显微计算机断层成像数据界定 Arvicolinae 类群非常重要。我们还对腭后缘的特征进行了同源分析，并将腭元素的组成分为两个主要形态类型：形态类型 "A "是Clethrionomyini特有的，而形态类型 "B "则被细分为另外三种类型，并发现它们出现在外群（鹤嘴蟾）、田鼠（B2）和旅鼠（B3）中。通过三维数据集对腭-鼻-翼复合体进行形态空间分析，发现了形态类型 "A "向形态类型 "B2 "转化的模式。另一项任务是制定形态学数据准备规程，以便随后使用专业软件应用程序（如 RERconverge）评估基因型与表型的关系。
{"title":"Evolution of the skull in arvicoline cricetids (Rodentia) according to 3D morphometric insights: Part 1. Morphological disparity of the palato-spheno-pterygoid complex","authors":"Leonid L. Voyta, Daniel A. Melnikov","doi":"10.1101/2024.09.04.611334","DOIUrl":"https://doi.org/10.1101/2024.09.04.611334","url":null,"abstract":"Our paper is the first contribution to the comprehensive analysis of the complicated evolution of cranial and mandibular parts connected by pterygoid muscles, as part of more global investigation into adaptive evolution of Arvicolinae. The analysis was performed on 90 micro-computed-tomography-scanned specimens from 33 species from 19 genera of Arvicolinae as well as two species from two genera of Cricetinae as an outgroup. We revised 11 morphological traits of the 'palato-spheno-pterygoid' complex, including key features of the palatine that are highly important for defining Arvicolinae taxa according to the micro-computed-tomography data. We also homologized characters of the posterior palatal margin and categorized the composition of the palatal elements into two main morphotypes: morphotype 'A' is unique to Clethrionomyini and morphotype 'B' was subdivided into three additional types and was found to occur in the outgroup (cricetines), voles (B2), and lemmings (B3). Morphospace analysis of the palato-spheno-pterygoid complex by means of the three-dimensional dataset revealed a mode of transformation of morphotype 'A' into morphotype 'B2.' A separate task was the development of a protocol for the preparation of morphological data for subsequent evaluation of genotype-phenotype relationships using specialized software applications (e.g., RERconverge).","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.05.610699
Joseph McClure
The study of cetacean size and growth aids in research about their energetics, ecology, evolution, and taxonomy. Data on total body length and weight of large cetaceans is retained in an overwhelming amount of literature and previous reviews are limited in their discussing variation in both length and weight. Nearly all the known published literature was examined to provide a brief but comprehensive summary of the adult size of four large odontocetes. To supplement the existing literature, data from the International Whaling Commission catch database were reviewed and incorporated into analyses to improve descriptions of intraspecific variation in adult size for Physeter macrocephalus. Regional comparisons of commercial data for P. macrocephalus revealed apparent differences in adult size that are likely more attributable to catch biases rather than a diagnostic difference in size between populations.
{"title":"A summary of intraspecific size variation for large odontocetes","authors":"Joseph McClure","doi":"10.1101/2024.09.05.610699","DOIUrl":"https://doi.org/10.1101/2024.09.05.610699","url":null,"abstract":"The study of cetacean size and growth aids in research about their energetics, ecology, evolution, and taxonomy. Data on total body length and weight of large cetaceans is retained in an overwhelming amount of literature and previous reviews are limited in their discussing variation in both length and weight. Nearly all the known published literature was examined to provide a brief but comprehensive summary of the adult size of four large odontocetes. To supplement the existing literature, data from the International Whaling Commission catch database were reviewed and incorporated into analyses to improve descriptions of intraspecific variation in adult size for Physeter macrocephalus. Regional comparisons of commercial data for P. macrocephalus revealed apparent differences in adult size that are likely more attributable to catch biases rather than a diagnostic difference in size between populations.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"388 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Under the current context of intensive farming, small-horned animals are more suitable for large-scale breeding. The CASP14 gene, closely associated with skin and keratin formation, may influence horn size due to its link with skin development. This study comprehensively analyzed the tissue-specific expression of CASP14 using RNA-Seq data, identified functional sites through whole-genome sequencing (WGS), and investigated allele-specific expression (ASE) validated by KASP assays. Results showed significantly higher CASP14 expression in the scurred group com-pared to the SHE group, with pronounced expression in the skin. Interbreed comparisons also revealed elevated CASP14 levels in the scurred group. Analysis of potential functional sites indicated structural similarities in the CASP14 protein among horned mammals. Five ASE events were discovered, and intersecting these with SNPs and high fixation index loci (Fst > 0.05) identified three potential functional sites: 7941628, 7941817, and 7941830. The SNP site 7944295 was selected for T-test analysis and further validated through KASP assays, corroborating the role of CASP14 in sheep horn phenotypes. Our findings suggest that CASP14 plays a significant role in horn development, offering insights into breeding strategies for small-horned animals.
在当前集约化养殖的背景下，小角动物更适合大规模养殖。CASP14基因与皮肤和角蛋白的形成密切相关，它与皮肤发育的关系可能会影响角的大小。本研究利用RNA-Seq数据全面分析了CASP14的组织特异性表达，通过全基因组测序（WGS）确定了其功能位点，并通过KASP检测验证了等位基因特异性表达（ASE）。结果显示，与SHE组相比，鳞屑组的CASP14表达量明显较高，且在皮肤中的表达量明显高于SHE组。种间比较也显示，毛发稀疏组的 CASP14 水平较高。对潜在功能位点的分析表明，有角哺乳动物的 CASP14 蛋白结构相似。发现了五个 ASE 事件，并将这些事件与 SNP 和高固定指数位点（Fst > 0.05）相交，确定了三个潜在的功能位点：7941628、7941817 和 7941830。我们选择了 SNP 位点 7944295 进行 T 检验分析，并通过 KASP 检测进一步验证了 CASP14 在羊角表型中的作用。我们的研究结果表明，CASP14 在绵羊角的发育过程中起着重要作用，为小角羊的育种策略提供了启示。
{"title":"Tissue-specific and functional loci analysis of CASP14 gene in the sheep horn","authors":"Xiaoning Lu, Guoqing Zhang, Hao Yang, Mingzhu Shan, Xiaoxu Zhang, Yuqin Wang, Junyan Bai, Zhangyuan Pan","doi":"10.1101/2024.09.03.611085","DOIUrl":"https://doi.org/10.1101/2024.09.03.611085","url":null,"abstract":"Under the current context of intensive farming, small-horned animals are more suitable for large-scale breeding. The CASP14 gene, closely associated with skin and keratin formation, may influence horn size due to its link with skin development. This study comprehensively analyzed the tissue-specific expression of CASP14 using RNA-Seq data, identified functional sites through whole-genome sequencing (WGS), and investigated allele-specific expression (ASE) validated by KASP assays. Results showed significantly higher CASP14 expression in the scurred group com-pared to the SHE group, with pronounced expression in the skin. Interbreed comparisons also revealed elevated CASP14 levels in the scurred group. Analysis of potential functional sites indicated structural similarities in the CASP14 protein among horned mammals. Five ASE events were discovered, and intersecting these with SNPs and high fixation index loci (Fst > 0.05) identified three potential functional sites: 7941628, 7941817, and 7941830. The SNP site 7944295 was selected for T-test analysis and further validated through KASP assays, corroborating the role of CASP14 in sheep horn phenotypes. Our findings suggest that CASP14 plays a significant role in horn development, offering insights into breeding strategies for small-horned animals.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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