By Physilia Chua<\/p>[\/et_pb_fullwidth_header][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.22.3″ custom_padding=”0|0px|7px|0px|false|false”][et_pb_row module_class=” et_pb_row_fullwidth” _builder_version=”4.0.4″ width=”65%” width_tablet=”80%” width_phone=”” width_last_edited=”on|desktop” max_width=”89%” max_width_tablet=”80%” max_width_phone=”” max_width_last_edited=”on|desktop” module_alignment=”right” custom_padding=”0|0px|27px|0px|false|false” make_fullwidth=”on”][et_pb_column type=”4_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_divider color=”rgba(100,101,100,0.18)” _builder_version=”4.0.4″ width=”80%” custom_margin=”||1px|||”][\/et_pb_divider][et_pb_text _builder_version=”4.0.4″ text_font=”||||||||” text_text_color=”#646564″ text_font_size=”14px” text_line_height=”0.8em” text_line_height_tablet=”” text_line_height_phone=”1.3em” text_line_height_last_edited=”on|phone”]
Spotted! A male capercaillie displaying its magnificent tail feathers<\/p>\n
PHOTO CREDIT: Per G\u00e4tzschmann<\/span><\/p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_4,3_4″ use_custom_gutter=”on” gutter_width=”4″ _builder_version=”4.0.4″ module_alignment=”center”][et_pb_column type=”1_4″ _builder_version=”4.0.4″][\/et_pb_column][et_pb_column type=”3_4″ _builder_version=”4.0.4″][et_pb_text _builder_version=”4.0.4″ text_font=”||||||||” custom_padding=”||0px|||”] G<\/span>one are the days when researchers needed to spend countless hours observing an animal in the wild to understand its behaviour and ecology. As we demonstrate with our study, valuable data can be gathered by simply examining faecal samples with powerful metagenomics approaches.<\/p>\n The need for data that effectively informs biological conservation is intensifying as the rate of biodiversity loss increases. Traditionally, scientists have endured long hours in the field, often hiding uncomfortably in bushes or traversing dangerous and hard-to-reach places, all for the purpose of observing elusive animals.<\/p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.0.4″ background_image=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/Chua-Figure2.jpg” parallax=”on”][et_pb_row column_structure=”3_4,1_4″ _builder_version=”4.0.4″ custom_padding=”||600px||false|false”][et_pb_column type=”3_4″ _builder_version=”4.0.4″][\/et_pb_column][et_pb_column type=”1_4″ _builder_version=”4.0.4″][et_pb_text _builder_version=”4.0.6″ text_font=”||on||||||” text_text_color=”#ffffff” text_font_size=”13px” header_5_text_color=”#ffffff”] With the advent of next-generation sequencing (NGS) technologies \u2013 those that effectively provide large amounts of DNA sequence data \u2013 it is now possible to obtain a wealth of ecological information from just a single faecal sample. The ease of collecting such samples circumvents some of the challenges of studying animals otherwise hard to find.<\/p>\n One such NGS approach is metagenomics shotgun sequencing (MSS), which determines the nucleotide composition of large amounts of random DNA molecules recovered from complex samples of DNA from various sources. This method makes it possible to simultaneously retrieve information about the host\u2019s diet, microbiome, gut parasites, as well as the population structure of the species1<\/sup>. While it has vast potential for conservation biology, few studies have utilised MSS to reconstruct the diet of animals, and none have done so for herbivorous birds.<\/p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.0.4″ background_image=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/Chua-Figure3.jpg” parallax=”on”][et_pb_row column_structure=”3_4,1_4″ _builder_version=”4.0.4″ custom_padding=”||600px||false|false”][et_pb_column type=”3_4″ _builder_version=”4.0.4″][\/et_pb_column][et_pb_column type=”1_4″ _builder_version=”4.0.4″][et_pb_text _builder_version=”4.0.6″ text_font=”||on||||||” text_text_color=”#646564″ text_font_size=”13px” header_5_text_color=”#000000″] The western capercaillie (Tetrao urogallus<\/em>), or wood grouse, is an emblematic species which can be found in the coniferous forest of Eurasia. Highly susceptible to the increased levels of habitat destruction and fragmentation, their declining population has placed them on the International Union for Conservation of Nature (IUCN) Red-list throughout most of western and central Europe2<\/sup>. By studying the wood grouse\u2019s diet, we could gain clues about the resources it requires and the other species it interacts with in its habitat, informing better conservation strategies. By observing the animal and morphologically identifying plant remains from their faecal samples, it was determined that the capercaillie\u2019s diet consists of mostly pine needles in the winter, and Vaccinium<\/em> species in the summer3<\/sup>.<\/p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.0.4″ background_enable_image=”off”][et_pb_column type=”4_4″ _builder_version=”4.0.4″][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/Chua-Figure4.jpg” _builder_version=”4.0.4″][\/et_pb_image][et_pb_text _builder_version=”4.0.4″ text_font=”||on||||||” text_text_color=”#646564″ text_font_size=”13px” header_text_color=”#646564″ header_5_text_color=”#646564″ custom_margin=”||||false|false”] Photo credit: Physilia Chua<\/p>[\/et_pb_text][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.0.4″ custom_css_main_element=”margin:auto;”][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/Chua-Figure5b.jpg” _builder_version=”4.0.4″][\/et_pb_image][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_4,3_4″ _builder_version=”4.0.4″][et_pb_column type=”1_4″ _builder_version=”4.0.4″][\/et_pb_column][et_pb_column type=”3_4″ _builder_version=”4.0.4″][et_pb_text _builder_version=”4.0.4″]However, preliminary results from our study show promising signs that the capercaillie\u2019s diet is more diverse than once thought. Other than plants, we have also discovered parasitoid wasps and several species of mites, which could have been accidental ingestion while feeding or preening. And with the use of metagenomics, there is also the possibility of obtaining more detailed quantitative information about its diet that can be used to inform habitat management choices. Their gut microbiome, intestinal parasites, and population genetics are also currently being analysed. \n\nUnexpectedly, we were also able to detect the presence of plant-pathogenic fungus and nematodes from their faecal samples, providing some interesting ecological insights about the capercaillie\u2019s habitat. Even though our research is still in its infancy, by using metagenomics shotgun sequencing on faecal samples, our initial study has already yielded a wealth of data. There is truly an untapped potential for its application in conservation biology and biomonitoring, which should be further explored. [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.0.4″ background_image=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/Chua-Figure6.jpg” parallax=”on”][et_pb_row column_structure=”3_4,1_4″ _builder_version=”4.0.4″ custom_padding=”||600px||false|false”][et_pb_column type=”3_4″ _builder_version=”4.0.4″][\/et_pb_column][et_pb_column type=”1_4″ _builder_version=”4.0.4″][et_pb_text _builder_version=”4.0.4″ text_font=”||on||||||” text_text_color=”#000000″ text_font_size=”13px” header_5_text_color=”#000000″ background_color=”rgba(255,255,255,0.66)” custom_padding=”10px|10px|10px|10px|false|false”] Written by<\/p>[\/et_pb_text][et_pb_team_member name=”Physilia Chua ” position=”Department of Biology, University of Copenhagen, Copenhagen, Denmark. ” image_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/Physilia_Chua.png” _builder_version=”4.0.4″ header_font=”||||||||” header_text_align=”center” header_font_size=”17px” body_font=”||||||||” body_font_size=”15px” text_orientation=”center” width=”85%” module_alignment=”center”][\/et_pb_team_member][et_pb_divider divider_position=”center” _builder_version=”3.27.4″ custom_margin=”50px||1px||false|false”][\/et_pb_divider][et_pb_text _builder_version=”4.0.6″ text_font=”||||||||” text_text_color=”#003254″ text_orientation=”center”]November 12, 2019[\/et_pb_text][et_pb_button button_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/2019-Chua.pdf” url_new_window=”on” button_text=”Download PDF” button_alignment=”center” _builder_version=”4.0.6″ custom_button=”on” button_text_size=”12px” button_text_color=”#ffffff” button_bg_color=”#003254″ button_icon=”%%26%%” button_icon_color=”#ffffff” box_shadow_style=”preset3″ box_shadow_horizontal=”3px” box_shadow_vertical=”11px”][\/et_pb_button][et_pb_text _builder_version=”4.0.4″ text_font_size=”14px” text_orientation=”center”] Subscribe to the iBOL Barcode Bulletin for updates on DNA barcoding efforts, the iBOL Consortium, and more.<\/p>[\/et_pb_text][et_pb_code _builder_version=”3.21″][mc4wp_form][\/et_pb_code][\/et_pb_column][et_pb_column type=”1_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.29.3″ background_color=”#000000″][et_pb_row _builder_version=”3.29.3″][et_pb_column type=”4_4″ _builder_version=”3.29.3″][et_pb_text _builder_version=”3.29.3″ text_font=”||on||||||” text_text_color=”#ffffff” text_font_size=”13px” header_3_text_align=”center” header_3_text_color=”#a8d367″ header_3_font_size=”27px” text_orientation=”center”] The Barcode Bulletin moderates comments to\u00a0promote an informed and courteous conversation. Abusive, profane, self-promotional, or incoherent comments will be rejected.\u00a0<\/em><\/p>[\/et_pb_text][et_pb_comments show_avatar=”off” show_reply=”off” show_count=”off” disabled_on=”off|off|off” _builder_version=”3.29.3″ header_font=”||||||||” header_text_color=”#000000″ form_field_font=”||on||||||” form_field_text_align=”left” custom_button=”on” button_text_size=”13px” button_font=”||||||||” custom_padding=”|50px||50px|false|false”][\/et_pb_comments][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.21.3″ custom_padding=”0|0px|0|0px|false|false” border_width_all=”-2px” border_width_top=”3px” border_color_top=”#a8d367″ global_module=”532″ saved_tabs=”all”][et_pb_row column_structure=”1_3,2_3″ make_equal=”on” _builder_version=”3.25″][et_pb_column type=”1_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/10\/BarcodeBulletin.png” align_tablet=”center” align_phone=”” align_last_edited=”on|desktop” _builder_version=”3.29.3″ max_width_tablet=”38%” max_width_phone=”” max_width_last_edited=”on|phone”][\/et_pb_image][\/et_pb_column][et_pb_column type=”2_3″ _builder_version=”3.25″ custom_padding=”|||” custom_css_main_element=”margin:auto;” custom_padding__hover=”|||”][et_pb_text _builder_version=”3.27.4″ text_font=”||||||||” text_font_size=”16px”] About the Bulletin<\/a>\u00a0|\u00a0Glossary<\/a><\/a> | Archive<\/a> | iBOL Consortium<\/a> | iBOL News<\/a> | Contact Us<\/a><\/p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]\n","protected":false},"excerpt":{"rendered":" Environmental DNA provides a non-invasive and simple means of biomonitoring<\/p>\n","protected":false},"author":38,"featured_media":3167,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"categories":[253],"tags":[43,249,245,248,246,173,247,250,251,244],"coauthors":[252],"class_list":["post-3166","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-illuminations","tag-diet","tag-gut-parasites","tag-iucn","tag-microbiome","tag-nematodes","tag-next-generation-sequencing","tag-population-structure","tag-tetrao-urogallus","tag-western-capercaillie","tag-wood-grouse"],"_links":{"self":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/3166","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/users\/38"}],"replies":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/comments?post=3166"}],"version-history":[{"count":27,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/3166\/revisions"}],"predecessor-version":[{"id":4559,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/3166\/revisions\/4559"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/media\/3167"}],"wp:attachment":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/media?parent=3166"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/categories?post=3166"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/tags?post=3166"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/coauthors?post=3166"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Searching for capercaillies in the midst of a snow storm in the Norwegian boreal forests<\/h5>\n<\/div>\nPhoto credit: Physilia Chua[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.0.4″][et_pb_row column_structure=”1_4,3_4″ use_custom_gutter=”on” gutter_width=”4″ _builder_version=”4.0.4″ module_alignment=”center”][et_pb_column type=”1_4″ _builder_version=”4.0.4″][\/et_pb_column][et_pb_column type=”3_4″ _builder_version=”4.0.4″][et_pb_text _builder_version=”4.0.4″ text_font=”||||||||” custom_padding=”||0px|||”]
A typical day out in the fields high above the Arctic Circle in Troms\u00f8, Dividalen National Park, Norway<\/h5>\n\nPhoto credit: Physilia Chua[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.0.4″][et_pb_row column_structure=”1_4,3_4″ use_custom_gutter=”on” gutter_width=”4″ _builder_version=”4.0.4″ module_alignment=”center”][et_pb_column type=”1_4″ _builder_version=”4.0.4″][\/et_pb_column][et_pb_column type=”3_4″ _builder_version=”4.0.4″][et_pb_text _builder_version=”4.0.4″ text_font=”||||||||” custom_padding=”||0px|||”]
A pile of capercaillie scat<\/h5>\nPhoto credit: Physilia Chua[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ use_custom_gutter=”on” gutter_width=”2″ _builder_version=”4.0.4″][et_pb_column type=”1_2″ _builder_version=”4.0.4″][et_pb_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/11\/Chua-Figure5.jpg” _builder_version=”4.0.4″][\/et_pb_image][et_pb_text _builder_version=”4.0.4″ text_font=”||on||||||” text_text_color=”#646564″ text_font_size=”13px” header_text_color=”#646564″ header_5_text_color=”#646564″ custom_margin=”-4px||||false|false”]
Capercaillie\u2019s favourite food? Pine needles (left) and\u00a0Vaccinium<\/em> sp. (right)<\/h5>\n
The road less travelled might lead to unexpected discoveries<\/h5>\n\nPhoto credit: Physilia Chua[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ use_custom_gutter=”on” gutter_width=”2″ specialty=”on” _builder_version=”3.23.3″][et_pb_column type=”2_3″ specialty_columns=”2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_row_inner _builder_version=”3.25″][et_pb_column_inner saved_specialty_column_type=”2_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text disabled_on=”off|off|off” _builder_version=”4.0.4″ text_font=”||||||||” text_font_size=”15px” custom_padding=”43px|||||”]
AcknowledgementS:<\/h4>\nI thank my supervisors Kristine Bohmann, Sanne Boessenkool, and Inger Greve Alsos for their guidance in every step of this research, without whom this study would not have been possible. I am deeply grateful to Torbj\u00f8rn Ekrem for his invaluable support both in and outside of fieldwork. I am indebted to my collaborators Kat Bruce and Alex Crampton-Platt for taking me into their team at NatureMetrics and making bioinformatics look so easy. Lastly, my sincere gratitude to the members of the eDNA group at the Section for Evolutionary Genomics, University of Copenhagen, and also to my fellow Plant.ID ESRs for keeping me in the right headspace. This project is part of the H2020 MSCA-ITN-ETN Plant.ID network and has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement No 765000. [\/et_pb_text][et_pb_text disabled_on=”off|off|off” _builder_version=”4.0.6″ text_font=”||||||||” text_font_size=”15px” custom_padding=”43px|||||” hover_enabled=”0″]
References:<\/h4>\n1. Srivathsan A, Sha JCM, Vogler A, Meier R (2015) Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus<\/em>). Molecular Ecology Resources<\/em> 15<\/em>(2): 250\u2013261. https:\/\/doi.org\/10.1111\/1755-0998.12302\n\n2. Storch I (2000) Grouse: status survey and conservation action plan 2000-2004. IUCN\/SSC Action Plans for the Conservation of Biological Diversity. Retrieved from http:\/\/www.iucn.org\/dbtw-wpd\/edocs\/2000-031.pdf\n\n3. Picozzi N, Moss R, Catt DC (1996) Capercaillie habitat, diet and management in a Sitka spruce plantation in central Scotland. International Journal of Agriculture and Forestry<\/em>. 69(4): 373 \u2013 388. https:\/\/doi.org\/10.1093\/forestry\/69.4.373[\/et_pb_text][\/et_pb_column_inner][\/et_pb_row_inner][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”3.27.4″ text_font=”||on||||||” text_text_color=”#646564″ text_orientation=”center”]
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