bioRxiv - Zoology最新文献

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"title":"Ancient DNA Clarifies the Identity and Geographic Origin of the holotype of the genus Ctenomys","authors":"Renan Maestri, Gislene L Goncalves, Violaine Nicolas-Colin, Anna Bryjova, Rodrigo Fornel, Eric Coissac, Pierre Taberlet, Gilson RP Moreira, Thales Renato Ochotorena de Freitas","doi":"10.1101/2024.09.10.612281","DOIUrl":"https://doi.org/10.1101/2024.09.10.612281","url":null,"abstract":"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.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181089","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}

{"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}

{"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}

{"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}