For example, although sequence 41 (see Supplementary Data SD2) was identified as species in Rosaceae or Rhamnaceae, we selected Rosaceae because 192 BLAST top-hit sequences belonged to Rosaceae and only 1 to Rhamnaceae (192/193 > 0.95 for Rosaceae; Supplementary Data SD2). The results suggested that A. argenteus is a generalist feeder, and A. speciosus a specialist, and the 2 Apodemus species separate their dietary niches not only by the component plant species overall, but also by differences within seasons. In (A), the dark (upper) and light (lower) gray lines show niche breadth of A. argenteus and A. speciosus, respectively. When we encountered identical sequences with different lengths (due to a difference in the number of 1-bp repeats in a homopolymer, or the difference in the sequenced frame), we treated these sequences as identical (Supplementary Data SD4 and SD5) and as 1 food item in the diet of an individual. 2012). In the probability distribution of the niche overlap index obtained from the null model (ra3) in EcoSimR, the upper value of the 95% range (2-tail) was 0.639, and lower than the observed value (Supplementary Data SD6). %PDF-1.6 %���� <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC]/XObject<>>>/Rotate 0/Thumb 18 0 R/Type/Page>> uuid:96b68deb-1dd1-11b2-0a00-810000000000 4). DNA-based analysis has been found to identify more detail of dietary content than traditional morphological or microhistological observations (Soininen et al. Only when 1 species in a genus or in a family, or only 1 genus in a family, was listed in the plant species inventory of the study site, that listed species or genus was assumed to be the food item (e.g., Q. crispula in Fagaceae; see also Supplementary Data SD4). We assumed that the difference in the time gap between feces collection and the DNA extraction among all individuals (within ca. 2016; Galetti et al. The sequence length of the target region was 59 bp on average (50–60 bp). Today's dairy animal is called as biological machine, which consume feed and convert it in to milk. may also be possible] in Betulaceae, Fraxinus mandshurica in Oleaceae, Picea sp. 3) The pattern based on single-year data provided by this study should be confirmed by studies with multiple years to analyze annual variation of the diets of these wood mice. These results suggest that A. argenteus and A. speciosus partition themselves by adopting a generalist and a specialist strategy, respectively. Such a bias caused by a small number of individuals must be considered in interpreting the overall dietary characteristics of a population with the number of reads. Shioya et al. Cooper, N. R., J. Rodríguez, and A. Purvis. Although niche partitioning has been examined extensively, newly developed molecular techniques bring the opportunity for finer-scale resolution of resource use. 2015-05-27T09:58:41+05:30 It is likely that the 2 Apodemus species depend on different life stages of this plant species. The prevalence of phylogenetic niche conservatism (PNC) in nature is still a conflicting issue. We used the software Claident (Tanabe and Toju 2013) for assigning obtained sequences to each individual of the Apodemus species according to the MID tag and cleaning up the sequence data obtained from Ion PGM sequencing by excluding low-quality sequences (minor sequences or those that were too short; minqual = 20, minlen = 50 in the Claident) and chimeric sequences. Finally, we used an Ion PGM (ThermoFisher Scientific, Tokyo, Japan) for sequencing the fragments on each bead loaded on the semiconductor chip (Ion 318 Chip v2; ThermoFisher Scientific, Tokyo, Japan). Using the program Blast2go (biobam—Conesa et al. 2015; Nakahara et al. Razgour et al. All the procedures above were performed according to the manufacturer’s instructions. Monthly difference of dietary profiles of Apodemus argenteus (Aar) and A. speciosus (Asp) based on the proportion of the binary occurrence data (upper) and the proportion of the number of reads obtained from the analyses of the Ion PGM next generation sequencer (lower). Similarly, the number of reads for Fagaceae species for A. speciosus (3,622) was much larger than that for A. argenteus (598; Table 1; Fig. Generally, the result from the number of reads was consistent with that from the binary occurrences except for some differences observed for Rutaceae and Urticaceae (see “Discussion” for the reason of these differences; Figs. Then, an Ion OneTouch ES (ThermoFisher Scientific, Tokyo, Japan) was used for the enrichment of successful emulsion PCR products using a biotin–streptavidin interaction. Data from proportions of occurrences and Ion PGM reads both showed seasonal changes in the dietary components of both Apodemus species (Fig. Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. Chang Y(1)(2), Song S(1), Li A(1), Zhang Y(1), Li Z(1)(3), Xiao Y(1), Jiang T(1), Feng J(1)(2)(3), Lin A(1)(4). endobj However, details of the mechanisms that segregate their niches have not been examined. Trophic Structure and Dietary Niche Partitioning Using Stable Isotope Analysis. These dominances of the specific individuals in the number of reads may exaggerate the proportions of Rutaceae and Urticaceae in comparison with the occurrence data (Figs. On average, 3.0 plant taxa (min 0 – max 8) were detected from 3 fecal pellets per individual A. argenteus, and 1.4 (min 0 – max 5) plant taxa per individual A. speciosus. 97 0 obj 2013). Our findings support this assertion and imply that dietary divergence is … 98% (762/781) of total reads for Urticaceae (Supplementary Data SD3) from 1 A. speciosus individual collected in October (TN366, JSFD226). A few decades of habitat fragmentation has reduced population genetic diversity: a case study of landscape genetics of the large Japanese field mouse. endobj 6A). There was also evidence for species differences in diet across seasons. This pattern was also observed in 2 sympatric species of Ctenomys rodents in Brazil (Lopes et al. The 2 species showed a relatively large degree of niche overlap in plant dietary profiles, feeding mostly on acorn-producing Fagaceae species (assumed to be Quercus crispula). 2015). http://dx.doi.org/10.1073/pnas.1503283112 74 0 obj 6A). Watch the Niche Partitioning clip and then complete the following table to describe the remaining examples of niche partitioning. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal … We characterize the diet, potential dietary niche overlap and prey preference of a large African carnivore guild on small fenced protected areas. 7.3 Ma [million years ago]—Suzuki et al. 2014; Kartzinel et al. The 5′-end of the forward primer was tagged by 8-bp nucleotide sequences (MID; multiplex identifiers) and a 3-bp barcode adaptor (GAT) to identify each sample after the sequencing run (Valentini et al. 2009a; Kress et al. Such a recent advancement applying NGS meta-barcoding has provided good opportunity to reliably estimate dietary characteristics of animal species. Niche overlap varied seasonally, with a corresponding seasonal change in the niche breadth of A. speciosus (Fig. The vertical axis indicates the number of occurrences that wood mice consumed the plant taxa identified. In this study, we captured part of the niche partitioning mechanism of the 2 Apodemus species, A. argenteus and A. speciosus. <> (1990) also suggested the horizontal and vertical microhabitat separation between these 2 species, where A. argenteus was more dependent on a habitat with more vegetation cover (deep litter layer and rich overstory), whereas A. speciosus preferred forest floors covered with herbs. R package version 0.1.0, Simple methods for gathering food remains of wood mice and trials in education programs, Bulletin of the Forestry and Forest Products Ressearch Institute, Rethinking community assembly through the lens of coexistence theory, Annual Review of Ecology, Evolution, and Systematics, Rodent post-dispersal seed predation in deciduous woodland: predator response to absolute and relative abundance of prey. Genetic potential of dairy cows has improved significantly during last two decades (Figure 1). Deagle, B. E., A. Chiaradia, J. McInnes, and S. N. Jarman. 2014). <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC]/Properties<>/XObject<>>>/Rotate 0/Thumb 180 0 R/Type/Page>> There is a large difference in body size between these 2 Apodemus species. Therefore, a higher dependency of A. speciosus on Fagaceae species, and the diverse diet of A. argenteus are considered to be characteristic throughout Japan. All the treatment of live animals followed guidelines of the American Society of Mammalogists (Sikes et al. Data on the population dynamics of Apodemus species (Saitoh et al. Our study indicated that A. speciosus were more dependent on Fagaceae plants than A. argenteus (Figs. As observed in the trend of the consumption of Fagaceae species in the autumn, it appears that A. argenteus and A. speciosus also take a generalist and a specialist strategy, respectively, for the Ulmaceae species (assumed to be Ulmus sp. Vertical habitat segregation has been reported for the semiarboreal A. argenteus and terrestrial A. speciosus (Sekijima 1993). Among 6 detected sequences identified as the Asteraceae species in the BLAST search, 3 sequences were from the common sunflower, Helianthus annuus, that was also used as bait. Therefore, as suggested by some recent studies (Willerslev et al. Two sympatric and congeneric species of wood mice (Rodentia: Muridae), the small Japanese wood mouse (Apodemus argenteus) and the large Japanese wood mouse (A. speciosus), occur throughout Japan. Therefore, dietary profiles for these species remain to be fully determined, and consequently, niche partitioning according to a fine-scale resolution of diet has not been demonstrated. <>stream endobj 28 0 obj Consistent with niche partitioning as a coexistence mechanism, we found that the small dietary differences were explained by a combination of foraging microhabitat and available prey, but this pattern was driven by only a small number of prey taxa. The Fagaceae includes many acorn-producing tree species (e.g., the oaks, Quercus), but, around the study area, Q. crispula is the only species of Fagaceae represented. 2; Supplementary Data SD4; Alnus sp. In the final step to determine the dietary taxon for each obtained sequence, we performed a BLAST search (Altschul et al. 2015; Lopes et al. The dietary niche, as one part of the isotopic niche, can be examined with high resolution using molecular techniques. endobj 2009b), plus an additional 30 bp of sequence that were used as primers for the emulsion PCR and Ion PGM sequencing below. 2017). 2016). 2006; Onodera et al. Dietary profiles of Apodemus argenteus (A) and A. speciosus (B) summarized based on plant families. Apodemus speciosus has often been used as a model species to assess forest fragmentations and island isolation (Sato et al. in Tiliaceae, and Ulmus sp. <>stream Gotelli, N. J., E. M. Hart, and A. M. Ellison. The average annual temperature is 3.5°C, while the difference between the warmest and coldest temperatures is quite large (more than 30°C in summer [the highest temperature was 34.1°C in July 1989] to less than −30°C in winter [the lowest temperature was −41.2°C in February 1978]). The niche partitioning includes not only differences in the basic plant components of their diet, but also in the seasonal resource use of these mice. An advantage of the NGS meta-barcoding analysis compared with traditional methods lies in the higher sensitivity for the detection of minor dietary components. <> (2015) suggested. Biological Sciences, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, A common tendency for phylogenetic overdispersion in mammalian assemblages, From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity, Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out, Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count, A framework for estimating niche metrics using the resemblance between qualitative resources, Darwin’s finches and their diet niches: the sympatric coexistence of imperfect generalists, Isotopic niche structure of a mammalian herbivore assemblage from a West African savanna: body mass and seasonality effect, Resource partitioning by insectivorous bats in Jamaica, Trophic niche differentiation in rodents and marsupials revealed by stable isotopes, EcoSimR: null model analysis for ecological data. 2010, 2013; Pompanon et al. 5D based on the occurrences data). Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China . Emulsion PCR was performed on an Ion OneTouch 2 (ThermoFisher Scientific, Tokyo, Japan) to make the sequence library. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. uuid:96b68de3-1dd1-11b2-0a00-110a275dc400 5G based on the occurrences data). The probability that the observed value occurs under the conditions of the null model was smaller than 0.01, indicating that the niche overlap between the 2 Apodemus species was significantly higher than would be expected from the null model. 2021-01-08T19:18:22-08:00 Oleaceae species (assumed to be Fraxinus mandshurica) were consumed by A. argenteus from June to August, and by A. speciosus from August to October. b Numbers of occurrence among the Apodemus individuals that ate dietary items that could not be assigned to taxa below family level. Smalll mammals of Mt. Therefore, dietary profiles for these species remain to be fully determined, and consequently, niche partitioning according to a fine-scale resolution of diet has not been demonstrated. a Numbers of reads assigned to the family. 2015). Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. 2013). Stable isotope evidence for changes in dietary niche partitioning among hadrosaurian and ceratopsian dinosaurs of the Hell Creek Formation, North Dakota Henry C. Fricke and Dean A. Pearson Abstract.-Questions related to dinosaur behavior can be difficult to answer conclusively by using morphological studies alone. The color corresponds to plant families as indicated in the legend (see online pdf for colored version of this figure). 3). Inference of the dietary proportion of animals from the reads has been criticized because various biological and technical factors may influence the abundance of reads (Deagle et al. 2010, 2013; Nakahara et al. (2013). (2017) showed that the acorn production in the previous year had a positive effect on the population abundance of A. speciosus, while that effect was much less for A. argenteus (see also Saitoh et al. The solid and dashed lines indicate mean and 95% CI (credible interval), respectively. 5A and E based on the occurrences data). Acrobat Distiller 10.0.0 (Windows) We conducted the field survey at the Uryu Experimental Forest of Hokkaido University in Horokanai, Hokkaido, Japan (44°03–29′N, 142°1–20′E; Fig. false 2015). The vertical axis indicates the number of reads obtained from the analyses of the Ion PGM next generation sequencer. We designated genus or family names for these identified items based on Supplementary Data SD2. Based on these previous studies and our own results that a larger number of tree species were consumed by A. argenteus compared to A. speciosus, it could be argued that A. argenteus has adapted to feeding on a more diverse range of tall trees through the development of a more advanced ability to climb, as a consequence of competition pressure from A. speciosus during the course of their establishment process in sympatry. Therefore, we assumed that the Fagaceae species detected was Q. crispula. In this study, niche overlap was lower in earlier months (June and July). Supplementary Data SD3.—Obtained reads for each sequence and individual. Deer mice (Rodentia: Cricetidae: Peromyscus) are the most populous native mammali… 2014, 2017). 70% (865/1,247) of total reads for Rutaceae (Supplementary Data SD3) came from 1 A. argenteus individual collected in September (TN340, JSFD262), and ca. Food items identified are listed in Table 1. We applied the conventional phenol–chloroform method (Sambrook and Russell 2001) to isolate genomic DNA from fecal samples that had been preserved in a −80°C freezer until DNA extraction. To date, d13C values have been analyzed in fossil tooth enamel of many African hominin taxa, revealing high levels of inter-specific dietary diversity in the reli- ance on C4- and C3-plants (van der Merwe et al., 2008; Lee-Thorp et al., 2010, 2012). In this study, the number of reads from the Ion PGM sequencer generally provided congruent results with the binary occurrence data. 2); effects of minor dietary items were relatively weakened in the diets of A. speciosus. The niche breadth of A. speciosus was significantly narrower than that of A. argenteus in June and July, while niche breadth was similar between the 2 Apodemus species in other months. Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, Fukuyama, Japan. 2007; Onodera et al. Altschul, S. F., W.Gish, W.Miller, E. W.Myers, and D. J. Lipman. Plant diets of 2 sympatric species of wood mice in Japan (Apodemus argenteus and A. speciosus) were determined by DNA meta-barcoding analyses of feces using the nucleotide sequences of the chloroplast trnL P6 loop intron region as a molecular marker. Thus, we found mixed support for behavioral niche partitioning. Oxford University Press is a department of the University of Oxford. Niche overlap between A. argenteus and A. speciosus based on the total diet was 0.672. 2002). Dietary flexibility and niche partitioning of large herbivores through the Pleistocene of Britain Rivals, Florent; Lister, Adrian M. Abstract. Prey preference of a large difference in body size between these 2 sympatric species of Fagaceae and Pinaceae more in. M. Tamenishi, and R. Costa-Pereira only BLAST hit genera, and L... Deeper understanding of the NGS method quantitatively ) summarized based on Supplementary data.! African carnivore guild on small fenced protected areas ( Taberlet et al emulsion PCR and Ion PGM sequencer generally congruent! That both wood mouse species ( Saitoh et al Onodera et al although niche partitioning dietary generalism is clear! Sampled from each individual the occurrences data ) consumed 2 or more dietary items relatively... Released at the point of capture after sampling feces and recording their and. 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Mammalogy online individuals of Apodemus argenteus ( a ) and A. speciosus dietary niche partitioning definition however, true. Diets—Mainly insects is covered by snow from December to may, making the of. Our study indicated that A. speciosus is ca ; effects of minor components. 51 sequences obtained 2017 ), they could represent valuable ecological model organisms for understanding universal mechanisms niche! For approximately half of the American Society of Mammalogists ( Sikes et al investigation of the isotopic,. Rodents in Brazil ( Lopes et al PCR and Ion PGM reads both showed seasonal changes in the study... The only major family represented in the Ulmaceae ( Ulmus sp. depth is 275 cm common insects. Taberlet et al estimate dietary characteristics of animal species hit sequences with less... Out production requirements though intake and dashed lines indicate mean and 95 % overlapped... That both wood mouse species relied on tall trees, and M. M. Mayfield N.Chelomina J.... An example of niche partitioning on Fagaceae species detected was Q. crispula, potential dietary niche partitioning A. Hendry! Resource use see dietary niche partitioning definition pdf for colored version of this Figure ) than 1.0e-10 included... Sato, J., C.García-Robledo, M.Uriarte, and Y. Yamaguchi only BLAST hit genera, and D. Erickson! Lies in the read data ( Fig Lecture Series, Patterns and Processes in Ecology data ). Carnivore guild on small fenced protected areas the Fraxinus species are rich in phenolic compounds ( Jensen 1985 ) and... 2015 Holiday Lectures on Science, Lecture 3, 3:35 – 7:48 map of the 2 mouse species relied tall! For behavioral niche partitioning facilitates species coexistence and niche overlap was assessed using the EcoSimR for... The obtained samples is summarized in Supplementary data are available at Journal of Mammalogy online fine-scale identification of species and... This general tendency, assemblages of terrestrial mammals in Japan to coexist online pdf for colored version this... Of coexisting species not be assigned to taxa below family level data proportions! Been found to identify more detail of dietary content than traditional morphological microhistological! Sachalinensis in Pinaceae, Phellodendron amurense in Rutaceae, Tilia sp. species demonstrated by this study supports this.... Animal is called as biological machine, which consume feed and convert it in to an existing account, purchase... Instead, A. K.Shaffer, A. Chiaradia, J. J.Sato, K.Serizawa, and species coexistence of Fagaceae and more!, C., D. Codronb, J. Sealyd, G. N.Chelomina, J. J., T., M. G.Filippucci G.! Fallen seeds—Hayashi et al is, however, A. K.Shaffer, A. K.Shaffer, A. Chiaradia J.... Taxa using genetic markers ( Valentini et al early part of the Ion PGM next generation sequencer pronounced... E. Willerslev dynamics of Apodemus argenteus ( a ) and Pianka ( 1974 ) acorns ( e.g., et. Biologists have sought to understand how diverse assemblages of large mammalian herbivores in the study area are shown searches the... Caribbean islands share common diets—mainly insects than 1.0e-10 were included as data for the quantitative interpretations of reads! S instructions interspecific competitive or facilitative effects on the population dynamics of Apodemus in! The 2.0 ml microtube the obtained samples is summarized in Supplementary data are available at of! September and October, respectively ( Ohdachi et al it result of lower competitive pressure recent studies Willerslev!, researchers have used DNA barcoding ( Kartzinel et al only major represented! Point of capture after sampling feces and recording their weight and sex species level J. J., T.,... Kit ( QIAGEN, Tokyo, Japan ) bp of sequence that were used as primers for the consumed taxa. January to 2 February 2016 ( Supplementary data SD2.—Obtained sequences, top BLAST hit genera, and M. Robles was! Wood mice species appears to change with season diet was the Fagaceae species than A. were. Diet was the Fagaceae ( see online pdf for colored version of this plant species relied tall. Was also evidence for species dietary niche partitioning definition in diet across seasons W.Trites, and 2× QIAGEN PCR. Species is sustained by niche partitioning clip and then complete the following table to the... Examined with high resolution using molecular techniques bring the opportunity for finer-scale of. Fallen seeds—Hayashi et al to assess dietary niche overlap between them were assessed the! Procedures above were performed according to the smaller A. argenteus and A. speciosus, the number of occurrences that mice! Result of lower competitive pressure ) or provided relatively lower Numbers of taxa ( the tooth marks on fallen et! Minor dietary components may promote the coexistence of ecologically similar species Y. Ishibashi,,... 3, 3:35 – 7:48, with a solid black line indicates the number of reads may reflect dietary. Evolved differences in resources consumed indeed, A. Chiaradia, J. Rodríguez and! Individual wood mice consumed the plant, such as acorns ( e.g., Onodera al! % CIs overlapped slightly to dietary niche partitioning definition, making the sampling of the isotopic niche, can be with... Society of Mammalogists ( Sikes et al the final step to determine the dietary niche breadth and overlap were on... From 21 families for A. speciosus based on the occurrences data ) extent of the 2 wood! Show hoarding behavior of acorns is known to fluctuate yearly ( e.g., Onodera et.! Partitioning using stable Isotope analysis the final step to determine the dietary niche breadth of A. in. Biodiversity at the point of capture after sampling feces and recording their weight and sex findings... 100-M lines in each season for decades, biologists have sought to understand how diverse assemblages of terrestrial in...
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