Morphometric and Genetic Determination of Age Class and Sex for Fecal Pellets of Sika Deer (<i>Cervus nippon</i>)

Hanya, Goro; Naito, Senri; Namioka, Erina; Ueda, Yosuke; Sato, Y.; Pastrana, J. A.; He, Tianmeng; Yan, Xiao‐Xin; Saito, Miho; Costa, Raquel; Allanic, Morgane; Honda, Takeshi; Kurihara, Yosuke; Yumoto, Takakazu; Hayakawa, T.

doi:10.3106/041.042.0406

Cited by 3 publications

(3 citation statements)

References 26 publications

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“…Regarding age groups, the average of the morphometric variables was always higher in the adults than in the yearlings and fawns. This assumption agrees with the findings by MacCracken & Van (2011) for reindeer, Woodruff et al (2016) for Sonoran pronghorn, and Hanya et al (2017) for sika deer. Sánchez-Rojas et al (2004) found that in mule deer, the faecal pellets belonging to the yearlings were more rounded, and the length/width proportion was lower in the yearlings than in the adults, but no significant differences were observed.…”

Section: Discussionsupporting

confidence: 93%

White-tailed deer sex identification from faecal DNA and pellet morphometry by neural network and fuzzy logic analyses

et al. 2019

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Knowing the sex of white-tailed deer (Odocoileus virginianus) individuals can provide information to set harvesting rates and management activities. Therefore, the aim of this study is to identify the sex through classification function by using faecal pellet morphometry. Faeces were collected for 12 months in Durango, Mexico; their morphometric variables were measured, the faecal DNA was extracted, and the SRY gene marker was amplified to identify sex. A neural network and fuzzy logic sex classification functions were obtained. The outputs were validated with the SRY gene results. Data from adults in the winter were used to obtain the classification functions. Classification functions could accurately classify sex in 94.4% with neural networks and 86.9% with fuzzy logic. The neural network classified more accurately the sex of adult white-tailed deer studied in winter with the faecal pellets morphometry than with the fuzzy logic analysis. This technique can be a tool for non-invasive studies and monitoring of populations.

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Section: Discussionsupporting

confidence: 93%

White-tailed deer sex identification from faecal DNA and pellet morphometry by neural network and fuzzy logic analyses

et al. 2019

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“…Traditional detection-based monitoring is timeconsuming and labor-intensive (Hanya, Yoshihiro, Zamma, Kubo, & Takahata, 2003;Whitesides, Oates, Green, & Kluberdanz, 1988), and the precision of identifying species or age-sex classes may depend on the ability of the observers. Methods based on animal traces, such as feces, nests or footprints, enable researchers to collect more data per unit effort than detection-based methods (Delibes et al, 2012;Hanya et al, 2017;Kanamori, Kuze, Bernard, Malim, & Kohshima, 2017). However, one can only obtain limited information on the individual animal that left the trace compared with direct observation (Hanya et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Methods based on animal traces, such as feces, nests or footprints, enable researchers to collect more data per unit effort than detection-based methods (Delibes et al, 2012;Hanya et al, 2017;Kanamori, Kuze, Bernard, Malim, & Kohshima, 2017). However, one can only obtain limited information on the individual animal that left the trace compared with direct observation (Hanya et al, 2017). Camera trapping is a powerful method that can reveal not only the species or age-sex classes but also the behavior of the filmed animals (Pebsworth & LaFleur, 2014), and it requires minimum effort in the field.…”

Section: Introductionmentioning

confidence: 99%

Host selection of hematophagous leeches (Haemadipsa japonica): Implications for iDNA studies

Hanya

Morishima

Koide³

et al. 2019

Ecological Research

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The development of an efficient and cost‐effective method for monitoring animal populations or biodiversity is urgently needed, and invertebrate‐derived DNA (iDNA) may offer a promising tool for assessing the diversity and other ecological information of vertebrates. We studied the host species of a hematophagous leech (Haemadipsa japonica) in Yakushima by genetic barcoding and compared the results with those for mammal composition revealed by camera trapping. We analyzed 119 samples using two sets of primers by Sanger sequencing and one set of primer by next generation sequencing. The proportion of the samples that were successfully sequenced and identified to at least one species was 11.8–24.3%, depending on the three different methods. In all of these three methods, most of the samples were identified as sika deer (18/20, 6/15 and 16/29) or human (2/20, 7/15 and 21/29). The nonhuman mammal host species composition was significantly different from that estimated by camera trapping. Sika deer was the main host, which may be related with their high abundance, large body size and terrestriality. Ten samples included DNA derived from multiple species of vertebrates. This may be due to the contamination of human DNA, but we also found DNA from deer, Japanese macaque and a frog in the same samples, suggesting the mixture of the two meals in the gut of the leech. Using H. japonica‐derived iDNA would not be suitable to make an inventory of species, but it may be useful to collect genetic information on the targeted species, due to their high host selectivity.

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Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island

et al. 2018

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Fecal DNA-based 16S ribosomal RNA (rRNA) gene sequencing using next-generation sequencers allows us to understand the dynamic gut microbiome adaptation of animals to their specific habitats. Conventional techniques of fecal microbiome analysis have been developed within the broad contexts defined by human biology; hence, many of these techniques are not immediately applicable to wild nonhuman primates. In order to establish a standard experimental protocol for the analysis of the gut microbiomes of wild animals, we selected the Japanese macaques (Macaca fuscata yakui) on Yakushima Island. We tested different protocols for each stage of fecal sample processing: storage, DNA extraction, and choice of the sequencing region in the bacterial 16S rRNA gene. We also analyzed the gut microbiome of captive Japanese macaques as the control. The comparison of samples obtained from identical macaques but subjected to different protocols showed that the tested storage methods (RNAlater and lysis buffer) produced effectively the same composition of bacterial operational taxonomic units (OTUs) as the standard frozen storage method, although the relative abundance of each OTU was quantitatively affected. Taxonomic assignment of the detected bacterial groups was also significantly affected by the region being sequenced, indicating that sequencing regions and the corresponding polymerase chain reaction (PCR) primer pairs for the 16S rRNA gene should be carefully selected. This study improves the current standard methods for microbiome analysis in wild nonhuman primates. Japanese macaques were shown to be a suitable model for understanding microbiome adaptation to various environments.

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Morphometric and Genetic Determination of Age Class and Sex for Fecal Pellets of Sika Deer (Cervus nippon)

Cited by 3 publications

References 26 publications

White-tailed deer sex identification from faecal DNA and pellet morphometry by neural network and fuzzy logic analyses

White-tailed deer sex identification from faecal DNA and pellet morphometry by neural network and fuzzy logic analyses

Host selection of hematophagous leeches (Haemadipsa japonica): Implications for iDNA studies

Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island

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