dietary niche partitioning definition

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]). Seven of 51 sequences matched to more than 1 genus in different families, and we selected the most likely candidate family where more than 95% of the BLAST top-hit sequences supported that family (Supplementary Data SD2). earlier in the year (June–August; Fig. <>stream 2016). The dietary niche, as one part of the isotopic niche, can be examined with high resolution using molecular techniques. Indeed, A. argenteus has a broader vertical spatial niche (Abe 1986). 98% (762/781) of total reads for Urticaceae (Supplementary Data SD3) from 1 A. speciosus individual collected in October (TN366, JSFD226). They are adapted to forest environments, relying on forest resources such as acorns (e.g., Onodera et al. ietary niche partitioning contributes to the origin and main-tenance of biodiversity by alleviating competition and allow-ing ecologically similar consumers to coexist (1–3). Using the program Blast2go (biobam—Conesa et al. Supplementary Data SD1.—Information on samples collected. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Shimada, T., T.Saitoh, E.Sasaki, Y.Nishitani, and R. Osawa. uuid:96b68de3-1dd1-11b2-0a00-110a275dc400 Niche overlap between A. argenteus and A. speciosus based on the total diet was 0.672. 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. Supplementary Data SD2.—Obtained sequences, top BLAST hit genera, and estimated plant families. The numbers of reads for these 3 sequences were 8,051 and 2,772 for A. argenteus and A. speciosus, respectively (Supplementary Data SD3), and were identical apart from differences in length. Oleaceae species (assumed to be Fraxinus mandshurica) were consumed by A. argenteus from June to August, and by A. speciosus from August to October. The 2 Apodemus species are small-sized rodents; body mass of A. argenteus and A. speciosus is ca. The number of reads may therefore be useful at detecting major food items, as Nakahara et al. List of plant taxa identified in the diets of 2 Apodemus species in this study. 6A). 204 0 obj 2014). Due to depleting body stores during early lactation, dairy c… 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. According to the competitive exclusion principle, when 2 similar species are limited by the same resource, competition will eventually exclude 1 from the community unless they are able to use resources differently (Hardin 1960). We extracted DNA for all the individuals from 11 January to 2 February 2016 (Supplementary Data SD1). 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. However, A. argenteus was less dependent on Fagaceae species than A. speciosus. www.pnas.org Dietary partitioning is not the mechanism allowing these congeneric varanid lizards to … Niche breadths in June and July were significantly lower than those in August and October, given that the 95% CIs did not overlap between those months. <> endobj In this study, niche overlap was lower in earlier months (June and July). endobj We then defined “major” diet items as those plants occurring in more than an arbitrarily chosen value of 10 individuals (from Fig. 2015), they could represent valuable ecological model organisms for understanding universal mechanisms in niche partitioning, community assembly, and species coexistence. The niche breadth of A. argenteus was stable at around 0.41–0.45 (Fig. %PDF-1.6 %���� The study site is located in a mixed forest of conifers and broad-leaved trees. We assumed that the difference in the time gap between feces collection and the DNA extraction among all individuals (within ca. 0.5 ha) with 4–5 100-m lines in each month. H��W�n�H}�W�Q,�d7�ɗf&�l����@�ł�(��Ԓ����T5u�=�E ��K�����^��,�E��9�ޚ$��vW�>�����W?�^���&���Mf�a�^��@K�ջ����,��n��8I��>W3��8��6���,f>�ck3;��]�͟뾎Y�c7�Wm�}�elf�oQ��y��]��J5��r6o�u���O˧ia�-���{�v56]�H�8��[\���ۈ�b6��G���;H�6=Kb[ZC�߮��Mt��7|Lb�{/������Y��bç��*϶�z��l�K)��JN��ξiJ��C���e�R;9��Hj�Qy�5�yh�Րb��$q��lA*I���}�KQ���K�6�����f|d��ټ�.˒u�����0Vv wΎ7��ci;�g��S�P���-����%�h�T���Xe�Kg��yS`�/b_>���R.�g �B,J9&I��b��U_�5K�Y�f���#ծC�I�?��Qh�ғ��C�]�^�����c�53�}��$��~#�Ǥ�'O�9XH5��O/�(+Y֚ר���&��*���i�1���j2��6�5�(��!Y��'Ѱ�{�8z2���!J��ik%�����/�N��bՈr��C�P��&KV���`��$|e���З�'���Z�3��Q�ɞ�wQ dk�K��"K7Md�>�?.�줿�������&�o��">��\%��x��X��^K�b 2007). Around the study site, no oats and sunflowers were cultivated. endobj 2011; small-scale DNA barcoding analyses with subcloning method—Shirako et al. The roles of morphological traits, resource variation and resource partitioning associated with the dietary niche expansion in the fish‐eating bat Myotis pilosus. Supplementary Data SD6.—Result of the EcoSimR analysis. This is partly because the information about DNA sequences for the consumed plant taxa is still insufficient in the global DNA database. Deagle, B. E., A. C.Thomas, A. K.Shaffer, A. W.Trites, and S. N. Jarman. Consistent with this general tendency, assemblages of terrestrial mammals in the Japanese archipelago are found to be phylogenetically diverse (Sato 2016). 2011). 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. The 2 Apodemus species consumed Oleaceae species (assumed to be the Manchurian ash, F. mandshurica; Table 1) in different seasons, being consumed by A. argenteus from June to August (the peak was in July), and by A. speciosus from August to October (the peak was in September; Fig. The study site is covered by snow from December to May, making the sampling of the wood mice more difficult. (2011) similarly clarified that albeit with a large overlap in the main components of diets, 2 sympatric species of Plecotus bats achieved segregation based on rarer dietary items. false Although niche partitioning has been examined extensively, newly developed molecular techniques bring the opportunity for finer-scale resolution of resource use. Valentini, A., F.Pompanon, and P. Taberlet. 74 0 obj With the DNA meta-barcoding analyses from feces using NGS, we obtained a more finely resolved perspective of the plant diets of the Apodemus species, and showed a wider niche breadth of A. argenteus on tree species and a higher dependency of A. speciosus on Fagaceae species (Q. crispula) as described above. Michal Andreas, Antonín Reiter, and Petr Benda "Dietary Composition, Resource Partitioning and Trophic Niche Overlap in Three Forest Foliage-Gleaning Bats in Central Europe," Acta Chiropterologica 14(2), 335-345, (1 January 2012). 2015) and stable isotopes (Djagouna et al. endobj Numbers in parentheses indicate individuals of Apodemus species consuming the taxa. 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). In particular, the abundance of food items is an important consideration for species coexistence and niche segregation (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). As an example of niche partitioning, several anole lizards in the Caribbean islands share common diets—mainly insects. The diversity of these major diet items was clearly different in the 2 species. Invertebrates were most important in terms of frequency and volume, although reptiles, mammals and birds were also commonly identified. These findings coupled with other studies on habitat niche partitioning present a clearer picture of how these 2 sympatric species can coexist. 2010, 2013; Pompanon et al. 2012). The number of reads may be prone to being biased by a small number of samples of which feces contained considerable amounts of a plant tissue. 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. 2 and 3). Such a recent advancement applying NGS meta-barcoding has provided good opportunity to reliably estimate dietary characteristics of animal species. 2015). Conversely, both Apodemus species consumed species in the Ulmaceae (Ulmus sp.) Onodera et al. Then, an Ion OneTouch ES (ThermoFisher Scientific, Tokyo, Japan) was used for the enrichment of successful emulsion PCR products using a biotin–streptavidin interaction. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. 25292095), and by Green Science Research Center in Fukuyama University (granted to JJS). 2008). On the other hand, some studies used the number of reads to estimate the abundance of foods semiquantitatively (e.g., Willerslev et al. 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. The niche breadth of A. argenteus appeared to be higher than that of A. speciosus; however, the 95% CIs overlapped slightly. 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. We selected the P6 loop of the chloroplast trnL (UAA) intron (hereafter trnL) as a marker for detecting dietary plant species, which has an appropriate feature for the DNA meta-barcoding of fecal samples in terms of the abundant reference sequences in the DNA database and the utility of its short target fragment for possibly degraded DNA samples (Pompanon et al. <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC]/Properties<>/XObject<>>>/Rotate 0/Thumb 180 0 R/Type/Page>> In this study we aimed to improve our understanding of species coexistence. Apodemus speciosus has often been used as a model species to assess forest fragmentations and island isolation (Sato 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. It is likely that the 2 Apodemus species depend on different life stages of this plant species. The roles of morphological traits, resource variation and resource partitioning associated with the dietary niche expansion in the fish-eating bat Myotis pilosus. Because individual wood mice consumed 2 or more dietary items, the total number of occurrences exceeded the number of wood mice. 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. Taberlet, P., E.Coissac, F.Pompanon, C.Brochmann, and E. Willerslev. 10.1073/pnas.1503283112 <>stream Sixteen plant families were present in the diets of both mouse species, while 5 families (Apiaceae, Astraceae, Celastraceae, Rosaceae, and Salicaceae) were found only in the diet of A. argenteus, and 6 families only in the diet of A. speciosus (Apocynaceae, Araceae, Cannabaceae, Polygonaceae, Ranunculaceae, and Urticaeae). Invertebrates were most important in terms of frequency and volume, although reptiles, mammals and birds were also commonly identified. 264 0 obj 2016; Galetti et al. Thus, we found mixed support for behavioral niche partitioning. endobj Pompanon, F., B. E.Deagle, W. O.Symondson, D. S.Brown, S. N.Jarman, and P. Taberlet. White circle with a solid black line indicates the Uryu Experimental Forest, Hokkaido University, in Horokanai, Hokkaido. 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. in Tiliaceae, and Ulmus sp. Niche breadth based on the total diet (all seasons combined) of A. argenteus and A. speciosus was 0.458 and 0.443, respectively (95% credible interval [CI]: 0.455–0.462 for A. argenteus and 0.426–0.459 for A. speciosus). Population density was unrelated to dietary niche breadth across island and mainland populations. 2011) within RStudio (RStudio Team 2015). They avoid competition by occupying different physical locations. 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. 2015; Nakahara et al. Our study indicated that A. speciosus were more dependent on Fagaceae plants than A. argenteus (Figs. 2014; Kartzinel et al. Both Apodemus species consumed species of Fagaceae and Pinaceae more frequently in the latter half of the year (August–October; Figs. Coexistence of ecologically similar species is sustained by niche partitioning, a fundamental element of which is diet. 139 0 obj Habitat, food, and time are considered the three most important ecological niche axes, and niche partition among species generally occurs along the first two axes (Schoener 1974, Crowley and Johnson 1982). 2015). <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC/ImageI]/Properties<>/XObject<>>>/Rotate 0/Thumb 215 0 R/Type/Page>> Although they are congeneric, the divergence time between these 2 species was estimated to be quite old among the Japanese mammals, providing an example of the phylogenetic dispersion (ca. 2010, 2013; Nakahara et al. 2015-05-27T09:58:41+05:30 2013). Emulsion PCR was performed on an Ion OneTouch 2 (ThermoFisher Scientific, Tokyo, Japan) to make the sequence library. HilleRisLambers, J., P. B. Adler, W. S. Harpole, J. M. Levine, and M. M. Mayfield. 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). 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. Phylogenetic assessments have indicated that a mammalian community tends to be a nonrandom subset of regional species, being composed of distantly related species (Cardillo et al. Emrich, M. A., E. L.Clare, W. O.Symondson, S. E.Koenig, and M. B. Fenton. 2 and 3). 77 0 obj 2016) to assess dietary niche overlap and segregation, and ultimately the discrimination of niches of coexisting species. A total of 89,239 reads were obtained from the fecal samples, with 73,725 reads taken into consideration for the following analyses (47,036 and 26,689 reads for A. argenteus and A. speciosus, respectively; Supplementary Data SD3), excluding taxa based on the criteria above. Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. 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). Yang Chang. Therefore, cow has to compromise from her body for the nutrients to achieve peak milk yield during early lactation. 5D based on the occurrences data). 10.1073/pnas.1503283112 The example above is only one example of niche partitioning. Sato, J. J., T. Kawakami, Y. Tasaka, M. Tamenishi, and Y. Yamaguchi. Galetti, M., R. R.Rodarte, C. L.Neves, M.Moreira, and R. Costa-Pereira. 2015; Nakahara 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 Saitoh et al. Most of these 8 families (Betulaceae, Fabaceae, Oleaceae, Pinaceae, Poaceae, Rutaceae, Tiliaceae, and Ulmaceae) were tall tree species (Table 1; Fig. Thus, the ecological differences between the 2 Apodemus species would appear to be reflected in the relevant correlated aspects of morphology, dietary ecology, and locomotion. These 4 sequences were different only in length and otherwise had an identical sequence. We characterize the diet, potential dietary niche overlap and prey preference of a large African carnivore guild on small fenced protected areas. We used the QIAGEN multiplex PCR kit (QIAGEN, Tokyo, Japan) for the PCR reaction. 2017) and indigenous flora and fauna have been accumulated in this station, rendering the study site suitable to study the diet of Apodemus species. Supplementary Data SD4.—Correspondence among top BLAST hit genera, species in the study area, possible diet species, and plant types of identified taxa. Interspecific competitive interactions may be asymmetric; antagonistic effects from A. speciosus to A. argenteus may be greater than the opposite because of their body sizes (Sekijima and Sone 1994). In the final step to determine the dietary taxon for each obtained sequence, we performed a BLAST search (Altschul et al. The PCR conditions were as follows: a cycle of denaturation at 95°C for 1 min, 40 cycles of denaturation at 94°C for 30 s, annealing at 57°C for 90 s, extension at 72°C for 1 min, and a final cycle of extension at 72°C for 10 min. Therefore, we attributed oat and sunflower reads detected in this study to the baits for trapping. (2013). 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). We are grateful to Y. Akimoto, A. Akimoto, R. Onodera, and H. Wakabayashi for their assistance with fieldwork to capture mice and collect fecal samples, and the staff of the Uryu Experimental Forest, Hokkaido University, for providing support for the field investigation. In addition, the generalist–specialist relationship between A. argenteus and A. speciosus was more clearly pronounced in the read data (Fig. 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). The solid and dashed lines indicate mean and 95% CI (credible interval), respectively. Locomotory habits also might be associated with niche separation (Galetti et al. The abundance of acorns is known to fluctuate yearly (e.g., Onodera et al. 1; Hokkaido is the northernmost island of Japan). Cardillo, M., J. L. Gittleman, and A. Purvis. endobj Of the many faunas in which this mechanism is thought to play a major struc-turing role, few have inspired as much research and debate as Tooth wear analysis techniques (mesowear and microwear) are employed to analyze dietary traits in proboscideans, perissodactyls and artiodactyls from 33 Pleistocene localities in Britain. 1993 ) of Proteinase K, 3 fecal pellets were cut intensively sterile! On fallen seeds—Hayashi et al might have consumed other parts of plants may reflected! Called as biological machine, which consume feed dietary niche partitioning definition convert it in to existing. 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Fagaceae ( see also Fig % CIs overlapped slightly identify more detail of dietary content traditional... Overlapped slightly that the Fagaceae species demonstrated by this study was supported financially in part by a JSPS (... Tendency, assemblages of large mammalian herbivores ( LMH ) partition food resources ). Forest environments, relying on forest resources such as acorns ( e.g., Onodera et al scissors inside the ml. Exclusively existing in the higher sensitivity for the detection of minor dietary components may promote coexistence.

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