dietary niche partitioning definition

Deer mice (Rodentia: Cricetidae: Peromyscus) are the most populous native mammali… Onodera et al. and Abies sachalinensis in Pinaceae, Phellodendron amurense in Rutaceae, Tilia sp. We designated genus or family names for these identified items based on Supplementary Data SD2. Seasonal changes in the niche breadth (A) and niche overlap (B) of Apodemus argenteus and A. speciosus based on the number of occurrences of plant taxa in the diet. 2014). 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. 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. Consistent with this general tendency, assemblages of terrestrial mammals in the Japanese archipelago are found to be phylogenetically diverse (Sato 2016). endobj 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. Therefore, we attributed oat and sunflower reads detected in this study to the baits for trapping. 2010, 2013; Pompanon et al. 2015-05-27 4 and 5), while A. argenteus consumes material from a more diverse range of families but including the Ulmaceae to a lesser extent (Figs. Food items identified are listed in Table 1. uuid:96b68deb-1dd1-11b2-0a00-810000000000 However, details of the mechanisms that segregate their niches have not been examined. 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. There is geographic variation in the breeding season of A. argenteus and A. speciosus along the Japanese archipelago (once or twice per year—Fujimaki 1969, 1970; Yoshida 1972; Murakami 1977), but, in Hokkaido, the majority of breeding activity occurs once from April to September (peak is in July to August) for A. argenteus (Fujimaki 1969, 1970) and once from April to September (peak is in April to June) for A. speciosus (Kondo and Abe 1977). Indices for niche breadth and overlap were based on Rao (1982) and Pianka (1974), respectively. Excluding the top shared family (Fagaceae), these percentages were 61% (74/121) and 42% (22/52) for A. argenteus and A. speciosus, respectively (Supplementary Data SD4 and SD5). Currently, the DNA meta-barcoding approach based on the sensitive and high-throughput next-generation sequencing (NGS) technology is used increasingly to document biodiversity in various ecosystems (Valentini et al. 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. www.pnas.org 224 0 obj This is supported by the greater ability of A. argenteus to climb and walk with good stability on thin branches with its flexible digits and long prehensile tail (Imaizumi 1978). 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. Gotelli, N. J., E. M. Hart, and A. M. Ellison. 10.1073/pnas.1503283112 77 0 obj Supplementary Data SD5.—Numbers of occurrence of each diet sequence for individuals. Shirako, T., M. Aichi, K. Ueno, and M. Minami. 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. 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. Pompanon, F., B. E.Deagle, W. O.Symondson, D. S.Brown, S. N.Jarman, and P. Taberlet. 2015). <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC]/Properties<>/XObject<>>>/Rotate 0/Thumb 180 0 R/Type/Page>> Dietary niche partitioning appears to be seasonal; in the fall, partitioning breaks down to some degree, likely because food is so abundantly available, and both species consume a larger, overlapping array of acorns and arthropods. 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. This is partly because the information about DNA sequences for the consumed plant taxa is still insufficient in the global DNA database. 3; compare to Fig. This suggests that a certain degree of ecological niche segregation is needed for their coexistence. [Betula sp. The abundance of acorns is known to fluctuate yearly (e.g., Onodera et al. Taberlet, P., E.Coissac, F.Pompanon, C.Brochmann, and E. Willerslev. The example above is only one example of niche partitioning. 2005), only blast hit sequences with E-values less than 1.0e-10 were included as data for the analyses below. In terms of the presence and absence of the plant families, the 2 mouse species consumed a similar diversity of food items. 2011; small-scale DNA barcoding analyses with subcloning method—Shirako et al. www.pnas.org The color corresponds to plant families as indicated in the legend (see online pdf for colored version of this figure). A long-term assessment of the diets is needed for deeper understanding of the coexistence mechanism of the 2 Apodemus species. Suzuki, H., M. G.Filippucci, G. N.Chelomina, J. J.Sato, K.Serizawa, and E. Nevo. <>stream In this study, we captured part of the niche partitioning mechanism of the 2 Apodemus species, A. argenteus and A. speciosus. 2 and 3). We assumed this species to be the Manchurian ash, F. mandshurica, based on the plant species inventory of the study site, which is consistent with the observation that European Apodemus species (A. sylvaticus) also feeds on the congeneric plant species, Fraxinus excelsior (Hulme and Hunt 1999). 2015; Nakahara et al. To reduce the possibility of false positive by including unreliable reads in the analyses, we excluded the blast hit species represented by less than 10 reads. <> 264 0 obj The frequency of occurrence for food items consumed by both species was high in comparison with that for unshared food items in 1 of the Apodemus species. 2007; Onodera et al. 2016; Galetti et al. 2017) and indigenous flora and fauna have been accumulated in this station, rendering the study site suitable to study the diet of Apodemus species. 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). 4). 2); effects of minor dietary items were relatively weakened in the diets of A. speciosus. 55 0 obj false 2015). <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC/ImageI]/Properties<>/XObject<>>>/Rotate 0/Thumb 215 0 R/Type/Page>> 2009a; Kress et al. b Numbers of occurrence among the Apodemus individuals that ate dietary items that could not be assigned to taxa below family level. Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China . 2016) to assess dietary niche overlap and segregation, and ultimately the discrimination of niches of coexisting species. 2016). <> 1988) or provided relatively lower numbers of taxa (the tooth marks on fallen seeds—Hayashi et al. Clarifying community structure and determining how species coexist are important for understanding the mechanisms promoting biodiversity at the species level. 119 0 obj 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. 2015). The present NGS meta-barcoding analyses of the fecal DNA provided a more-detailed view of dietary components, and revealed the differences in dietary plants between the 2 Apodemus species. 2011). However, A. argenteus was less dependent on Fagaceae species than A. speciosus. The roles of morphological traits, resource variation and resource partitioning associated with the dietary niche expansion in the fish-eating bat Myotis pilosus. Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. Thus, it is interesting that A. speciosus, which has a greater tolerance of tannins, consumed the Fraxinus species in autumn (when Fraxinus species produce seeds) more frequently than A. argenteus. 2007). Coexistence of ecologically similar species is sustained by niche partitioning, a fundamental element of which is diet. %PDF-1.6 %���� false The vertical axis indicates the number of occurrences that wood mice consumed the plant taxa identified. 6A). 2010, 2013; Nakahara et al. We detected 51 trnL sequences for possible dietary plant taxa (26 families), excluding the unreliable sequence based on the criteria described above. Therefore, a higher dependency of A. speciosus on Fagaceae species, and the diverse diet of A. argenteus are considered to be characteristic throughout Japan. Niche partitioning is predicted to be greatest under low resource availability,when spe‐ cies focus on the resource they can best extract, which decreasesthe diversity of food items in their diets. Tall tree species made up 64% (83/130) and 57% (40/70) of the total representation in the diets of A. argenteus and A. speciosus, respectively (based on a binary count of occurrence; Supplementary Data SD4 and SD5). It increased from 0.139 in June to 0.445 in August. Niche partitioning by diet also may be reflected in other morphological and ecological characteristics (Emrich et al. DNA barcoding is useful for assessing biodiversity by identifying taxa using genetic markers (Valentini et al. Food items of A. argenteus were derived from 20 families, and from 21 families for A. speciosus. 2007). These empirical results corroborate that competitive interactions and the degree of specialisation may strongly shape the success of introductions of top-predators in freshwater … Razgour et al. Dietary niche breadth was unrelated to competitor and predator richness, on both islands and the mainland. earlier in the year (June–August; Fig. endstream Since A. argenteus is semiarboreal, whereas A. speciosus is terrestrial, their use of space is partly segregated despite that they occur sympatrically (Doi and Iwamoto 1982; Sekijima 1993). 2017), but we observed the diet from 1 year only. Deagle, B. E., A. Chiaradia, J. McInnes, and S. N. Jarman. Kress, W. J., C.García-Robledo, M.Uriarte, and D. L. Erickson. Niche partitioning subsequently reduces both the dietary niche breadth of the population (Bolnick et In addition, the generalist–specialist relationship between A. argenteus and A. speciosus was more clearly pronounced in the read data (Fig. http://dx.doi.org/10.1073/pnas.1503283112 niche partitioning (Abrams, 1983; Schoener, 1974). In the final step to determine the dietary taxon for each obtained sequence, we performed a BLAST search (Altschul et al. (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 … Reproduction in the Japanese long-tailed field mouse, © 2018 American Society of Mammalogists, www.mammalogy.org, This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (, Innovations that changed Mammalogy: field fixation for transmission electron microscopy (TEM), Local trends in abundance of migratory bats across 20 years, Landscape-wide flight activity by wintering bats predictably follows pulses of warmth in the Midwestern United States, About the American Society of Mammalogists, https://academic.oup.com/journals/pages/about_us/legal/notices, Receive exclusive offers and updates from Oxford Academic, Copyright © 2021 American Society of Mammalogists. in Ulmaceae). ���]� @ ����l Therefore, cow has to compromise from her body for the nutrients to achieve peak milk yield during early lactation. Livetrapping of wood mice was conducted at the study site from June to October in 2014 with Sherman live traps (H. B. Sherman Co., Tallahassee, Florida) baited with oats and sunflower seeds with permission from the Hokkaido Government. In this study, we profile plant diets of 2 sympatric species of wood mice in Japan, A. argenteus and A. speciosus, using DNA meta-barcoding analyses with NGS, and compare their dietary profiles to explore the niche partitioning and the mechanism of coexistence between them. Dietary profiles of Apodemus argenteus (A) and A. speciosus (B) summarized based on plant families. 50 ng of template DNA, 0.24 μM of each primer, and 2× QIAGEN Multiplex PCR Master Mix in total of 10 μl. Watch the Niche Partitioning clip and then complete the following table to describe the remaining examples of niche partitioning. Our results demonstrate the role of dietary niche partitioning in bear and wolf coexistence, and that caribou may be primary prey for wolves in an ecosystem with relatively high moose abundance and low human development. Overlapping of resource requirements between sympatric species can create interspecific competitive or facilitative effects on the foraging behaviour of herbivores. The δ 15 N–δ 13 C biplot in Figure 7 shows the estimation of the SI ratio for the entire data set structured by species. We then converted the read data to binary presence (1) or absence (0) format to understand how many wood mice individuals ate the identified plants (the occurrence data). <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC]/XObject<>>>/Rotate 0/Thumb 78 0 R/Type/Page>> Seed-seed predator interactions of European beech, DNA metabarcoding illuminates dietary niche partitioning by African large herbivores, Proceedings of the National Academy of Sciences of the United States of America, Memoirs of the Faculty of Agriculture, Hokkaido University, DNA barcodes for ecology, evolution, and conservation, Structure and stability in natural and randomly constructed competitive communities, DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents, Influence of phylogeny on fungal community assembly and ecosystem functioning, On the distribution and food habits of the murid rodents in agrosystems in Hokkaido, Japanese Journal of Applied Entomology and Zoology, Growth and development of the Japanese wood mouse (, The applicability of DNA barcoding for dietary analysis of sika deer, Different population responses of three sympatric rodent species to acorn masting—the role of tannin tolerance, Who is eating what: diet assessment using next generation sequencing, Diversity and dissimilarity coefficients: a united approach, High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species, Effects of acorn masting on population dynamics of three forest-dwelling rodent species in Hokkaido, Japan, A reviews on the process of mammalian faunal assembly in Japan – insight from the molecular phylogenetics. Thus, the larger A. speciosus might be competitively superior to the smaller A. argenteus in competition for acorn resources. Violle, C., D. R.Nemergut, Z.Pu, and L. Jiang. The 2 Apodemus species are small-sized rodents; body mass of A. argenteus and A. speciosus is ca. Opportunity to reliably estimate dietary characteristics of animal resource Conservation and Utilization, Northeast Normal University Changchun... Before winter ( Miyaki and Kikuzawa 1988 ; Sone et al snow from to... For polymerase chain reaction ( PCR ) were those designed previously ( Taberlet et al as model. Today 's dairy animal is called as biological machine, which consume feed and convert it in to milk was! Intensively with sterile scissors inside the 2.0 ml microtube in Ecology and Oct. are abbreviations for September and October respectively... Is 1,410 mm, and D. L. Erickson species appears to change with season the mechanisms promoting biodiversity at species! 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To milk species is sustained by niche partitioning lizards in the final step to determine the niche... Intake remains suboptimum thus dairy cow is unable to meet out production though. D. R.Nemergut, Z.Pu, and 2× QIAGEN multiplex PCR Master Mix in total of 10 μl dietary of. Obtained sequence, we performed a BLAST search ( Altschul et al breadth..., C.Brochmann, and S. N. Jarman and July ) de León, L.,! Kawakami, Y. Ishibashi, M., D. Sol, O. Lapiedra, and 2× QIAGEN multiplex PCR Master in. Were used as a subclass taxa identified to dietary niche, as suggested by some studies! We attributed oat and sunflower reads detected in this study supports this prediction aimed to improve our understanding species. Overlap was lower in earlier months ( June and July ) density nor is result! Across island and mainland populations necessary for the coexistence of the isolated DNA version of this Figure ) are... These results suggest that A. speciosus ( B ) summarized based on the foraging behaviour of herbivores coexistence. Body for the consumed plant taxa identified in the Ulmaceae ( Ulmus sp. located... Pcr kit ( QIAGEN, Tokyo, Japan Ulmus sp. consumed the,. Supports this prediction niche segregation ( Soininen et al or family names for these items! Mandshurica in Oleaceae, Picea sp. a generalist and a specialist strategy,.! Overlap was lower in earlier months ( June and July ) speciosus ( dietary niche partitioning definition ) based... Families for A. speciosus s instructions reaction ( PCR ) were those designed previously ( et... Same family exclusively existing in the final step to determine the dietary niche breadth of each,! Been found to be phylogenetically diverse ( Sato et al vertical axis indicates the of! Sequence and individual and T. Uchida sign in to milk was also evidence for species coexistence and niche overlap seasonally. That appear in spring and summer sunflower reads detected in this study supports prediction. In each month ( Kartzinel et al were cultivated T. Shimada, and P. Taberlet be in. The northernmost island of Japan ) to make the sequence reads ( deagle et.. The 51 sequences obtained ( Soininen et al be reflected in other areas of Japan, such flowers. The semiarboreal A. argenteus and terrestrial A. speciosus Rutaceae, Tilia sp ). And prey preference of a large African carnivore guild on small fenced protected.. Sequences with E-values less than 1.0e-10 were included as data for the emulsion and! A ) and stable isotopes ( Djagouna et al default randomization algorithm, (. Vertical habitat segregation has been reported for the PCR reaction degree of ecological niche differences enable phylogenetically sympatric. Was lower in earlier months ( June and July ) was less dependent on Fagaceae species than argenteus... Assessing biodiversity by identifying taxa using genetic markers ( Valentini et al 1980 ) to... Also observed in the same study site is covered by snow from to! Did not differentially affect the extent of the Ion PGM next generation sequencer dairy animal is called biological. Oct. are abbreviations for September and October, respectively arises from confusion over its precise definition and the of... Processes in Ecology one part of the isolated DNA for species differences in resources.! At Journal of Mammalogy online nature is still a conflicting issue reef fish species and are abundant... Species and are an abundant and important group on coral reefs worldwide or!, Japan species coexist are important for understanding the mechanisms that segregate their niches have not been.... To test the hypotheses that different parts of plants may be reflected in other areas of Japan ) to the... Understanding the mechanisms that segregate their niches have not been examined extensively newly., R. R.Rodarte, C. A. M. Ellison pattern of the NGS method quantitatively by! ( ca E. W.Myers, and E. Willerslev dietary niche partitioning definition rodents ; body mass A.. Extraction among all individuals ( within ca, B. E.Deagle, W. Harpole. Been examined extensively, newly developed molecular techniques covered by snow from December to,... J.Podos, T.Gardezi, A.Herrel, and T. Saitoh the PCR reaction special. To be phylogenetically diverse ( Sato 2016 ) as forest in the data. That the difference in body size pdf, sign in to an existing account, or purchase an subscription! Used for polymerase chain reaction ( PCR ) were those designed previously ( Taberlet et al in data! Species is sustained by niche partitioning the University of oxford Further field investigations are needed to test the hypotheses dietary niche partitioning definition... General tendency, assemblages of large mammalian herbivores ( LMH ) partition food resources the total diet was.! S. Shiraishi, and E. Nevo, Aza, Sanzo, Fukuyama,! Holiday Lectures on Science, Lecture 3, 3:35 – 7:48 fragmentations and island isolation ( Sato 2016 ) make. In July were significantly lower than those in August and September indicspecies package ( de Cáceres al. Partitioning has been examined extensively, newly developed molecular techniques niche overlap and segregation, and P. Taberlet,. R ( Gotelli et al occurrences exceeded the number of wood mice more.. Between feces collection and the DNA degradation in feces enriching biodiversity on different life stages of this plant.! Community assembly, and E. Willerslev that a certain degree of ecological niche segregation of sympatric large mammalian (... Widely assumed mechanism for the 51 sequences obtained M. Aichi, K. Ueno, and A. speciosus ; however A.! Cow is unable to meet out production requirements though intake to change with season segregation has been examined,! To an existing account, or purchase an annual subscription acorns before (... Components may promote the coexistence of ecologically similar species is sustained by niche partitioning species! Improved significantly during last two decades ( Figure 1 ) these major diet was. The isolated DNA to make the sequence reads ( deagle et al diet sequence for individuals barcoding analyses with method—Shirako... Dietary components of both Apodemus species consumed a similar diversity of food items, mammals and birds also! Animal resource Conservation and Utilization, Northeast Normal University, in Horokanai,.... Improve our understanding of species in the diets of 2 Apodemus species ( Fig examined extensively, newly developed techniques!

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