{"id":97,"date":"2019-04-07T09:00:21","date_gmt":"2019-04-07T13:00:21","guid":{"rendered":"https:\/\/ibol.org\/barcodebulletin\/?p=97"},"modified":"2020-07-16T11:15:01","modified_gmt":"2020-07-16T15:15:01","slug":"dna-barcoding-and-genomics-in-the-megadiverse-amazon-altitude-fields","status":"publish","type":"post","link":"https:\/\/ibol.org\/barcodebulletin\/research\/dna-barcoding-and-genomics-in-the-megadiverse-amazon-altitude-fields\/","title":{"rendered":"DNA Barcoding and Genomics in the Megadiverse Amazon Altitude Fields"},"content":{"rendered":"\n[et_pb_section fb_built=”1″ fullwidth=”on” _builder_version=”3.22″ background_blend=”multiply”][et_pb_fullwidth_header title=”DNA BARCODING AND GENOMICS IN THE MEGADIVERSE AMAZON ALTITUDE FIELDS” subhead=”Scientists are contributing to the most profound molecular representation of biodiversity in any Brazilian environment.” _builder_version=”3.21.4″ content_font=”||||||||” content_text_color=”rgba(0,0,0,0.8)” subhead_font=”||on||||||” subhead_text_color=”#ffffff” subhead_font_size=”16px” background_color=”rgba(168,211,103,0)” use_background_color_gradient=”on” background_color_gradient_start=”#000000″ background_color_gradient_end=”#a8d367″ background_color_gradient_end_position=”70%” background_image=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/04\/v4.boldsystems.org_7125_animalia.png” custom_margin_tablet=”” custom_margin_phone=”” custom_margin_last_edited=”on|desktop”][\/et_pb_fullwidth_header][et_pb_fullwidth_image src=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/06\/Oliviera-FigMain.png” _builder_version=”4.4.7″ max_width=”95%” module_alignment=”center” custom_margin=”-20px||20px” hover_enabled=”0″ box_shadow_style=”preset1″ alt=”Entrance of a ferruginous cave” title_text=”Oliviera-FigMain”][\/et_pb_fullwidth_image][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.22″ custom_padding=”0|0px|7px|0px|false|false”][et_pb_row module_class=” et_pb_row_fullwidth” _builder_version=”3.25″ width=”89%” 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” 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_text _builder_version=”3.27.4″ text_font=”||on||||||” text_text_color=”#646564″]

The entrance of a ferruginous cave at the Bocaina mountain in the Caraj\u00e1s region, Par\u00e1 State, Brazil.\n\nPHOTO CREDIT: Jo\u00e3o Marcos Rosa.<\/p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”2_3,1_3″ _builder_version=”3.25″][et_pb_column type=”2_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”3.27.4″]I<\/span>ndustrial activities in the Brazilian Amazon are highly regulated by governmental agencies. However, the lack of knowledge about megadiverse areas is a problem for the establishment of best conservation practices; this is the case for mining operations in the eastern Amazonian Caraj\u00e1s, a region comprised of a mosaic of national parks, indigenous peoples\u2019 conservation areas, and nature reserves. Of particular interest are the ferruginous altitude fields known as the Canga. Our floristic survey described the presence of 1,094 species from just over 200 previously known1<\/sup>. The lack of biodiversity data is even more significant for the ferruginous caves where only around 10 invertebrate species are identified to the species level. Unfortunately, this is typical for the Amazon basin.[\/et_pb_text][et_pb_text _builder_version=”3.27.4″ text_font=”||||||||”]

To provide reliable scientific data that contributes to the implementation of best conservation practices, Instituto Tecnol\u00f3gico Vale is developing DNA barcode reference libraries for the flora, cave invertebrates, and bats of the region, and providing deeper genomic references for species that are endangered or difficult to identify. To achieve this goal, we established the necessary infrastructure to conduct DNA sequencing using Sanger, Illumina, and PacBio technologies, coupled with high-performance computing, artificial intelligence algorithms, and highly trained personnel.<\/p>\n

 <\/p>[\/et_pb_text][et_pb_blurb image=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/06\/Oliviera-Fig1.png” _builder_version=”4.4.7″ body_font=”||||||||” body_text_align=”right” body_text_color=”#646564″ body_font_size=”16px” custom_padding=”||50px” hover_enabled=”0″ border_color_all=”#929292″ alt=”Botanists collecting samples” title_text=”Oliviera-Fig1″]

Botanists collecting samples in a temporary lake in ferruginous altitude fields in the Caraj\u00e1s region, Par\u00e1 State, Brazil.
PHOTO CREDIT: Jo\u00e3o Marcos Rosa<\/span><\/p>\n[\/et_pb_blurb][et_pb_text _builder_version=”3.27.4″ module_alignment=”right”]

To date, over 8,575 barcodes for 3,548 specimens of plants and invertebrates have been produced, while a large number of species remain to be identified by morphological attributes. Morphological specimen determination is conducted by in-house specialists, as well as by an extensive network of specialists in universities and museums across Brazil and abroad.<\/p>\n

For this purpose, nuclear and chloroplast or mitochondrial markers as well as low coverage to whole genome sequencing or restriction site-associated DNA sequencing (RADSeq) are being employed to unravel the vast genetic diversity of the biota of Caraj\u00e1s2-4<\/sup>. For several endemic plants, such as species of Asteraceae, Melastomataceae5<\/sup>, Convolvulaceae6<\/sup>, and Isoetaceae2<\/sup>, diversity analyses, based on next-generation sequencing, aim to characterize the genetic variability among and within populations, as well as the identification of markers under selective pressure. These methods also contribute to the understanding of population structure and the process of gene flow between populations affected by natural factors and industrial operations.\u00a0Models of environmental distribution, including parameters sensitive to climate change, were determined for several taxonomic groups, including plants and bats7<\/sup>.[\/et_pb_text][et_pb_blurb image=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2020\/06\/Oliviera_Fig3.jpg” _builder_version=”4.4.7″ body_font=”||||||||” body_text_align=”right” body_text_color=”#646564″ body_font_size=”16px” custom_margin=”||50px” hover_enabled=”0″ border_color_all=”#929292″ title_text=”Oliviera_Fig3″]

Specimens of the pinheirinho-da-canga (Paepalanthus fasciculoides<\/em>) highly adapted to inhabit the canga (ancient ferruginous rock outcrops) at the altitude fields in the Caraj\u00e1s region, Par\u00e1 State, Brazil.
PHOTO CREDIT<\/span>: Jo\u00e3o Marcos Rosa<\/p>\n[\/et_pb_blurb][et_pb_text _builder_version=”3.27.4″ module_alignment=”right” custom_padding=”||80px|||”]We are also establishing eDNA methods, as well as metagenomics and metaproteomics data for environmental monitoring of ferruginous fields phytophysiognomies, areas under rehabilitation processes, and caves8<\/sup>. Together these data constitute the most profound molecular representation of any environment in Brazil. We have contributed a total of 3,072 specimens to the Barcode of Life Data System (BOLD)<\/a> comprising 398 genera (291 new) in addition to the 408 different genera collected through the national effort for angiosperms in Brazil. We have also provided 571 cave fauna specimens.\n\nIt is important to highlight that all of these data generated are being provided to the public and its use will be critical to the conservation of such a unique collection of species.[\/et_pb_text][et_pb_text disabled_on=”off|off|off” _builder_version=”3.27.4″ text_font=”||||||||” text_font_size=”15px” custom_padding=”||72px|||”]

References:<\/h4>\n

1. Brazil Flora Group (2018) Growing knowledge: an overview of Seed Plant diversity in Brazil. Rodrigu\u00e9sia<\/em> 66(4): 1085\u20131113. http:\/\/dx.doi.org\/10.1590\/2175-7860201566411<\/a><\/p>\n

2. Nunes GL, Oliveira RRM, Guimar\u00e3es JTF, Giulietti AM, Caldeira C, Vasconcelos S, et al., (2018) Quillworts from the Amazon: A multidisciplinary populational study on\u00a0Isoetes serracarajensis<\/em>\u00a0and\u00a0Isoetes cangae<\/em>. PLoS ONE<\/em> 13(8): e0201417. https:\/\/doi.org\/10.1371\/journal.pone.0201417<\/a><\/p>\n

3. Ramalho AJ, Zappi DC, Nunes GL, Watanabe MTC, Vasconcelos S, Dias MC, Jaff\u00e9 R, Prous X, Giannini TC, Oliveira G and Giulietti AM (2018) Blind testing: DNA barcoding sheds light upon the identity of plant fragments as a subsidy for cave conservation.\u00a0Frontiers in Plant Science<\/em> 9:1052. https:\/\/doi.org\/10.3389\/fpls.2018.01052<\/a><\/p>\n

4. Oliveira RRMO, Vasconcelos S, Pires ES, Pietrobon T, Prous X and Oliveira G (2019) Complete mitochondrial genomes of three troglophile cave spiders (Mesabolivar, pholcidae<\/em>), Mitochondrial DNA Part B 4(1): 251\u2013252. https:\/\/doi.org\/10.1080\/23802359.2018.1547139<\/a><\/p>\n

5. Carvalho CdS,\u00a0Lanes ECM,\u00a0Silva AR,\u00a0Caldeira CF,\u00a0Carvalho-Filho N,\u00a0Gastauer M,\u00a0Imperatriz-Fonseca VL,\u00a0Nascimento W,\u00a0Oliveira G, Siqueira JO, Viana PL,\u00a0Jaffe R (2019) Habitat loss does not always entail negative genetic consequences. bioRxiv<\/em>\u00a0528430.\u00a0https:\/\/doi.org\/10.1101\/528430<\/a><\/p>\n

6. Lanes \u00c9C, Pope NS, Alves R, Carvalho Filho NM, Giannini TC, Giulietti AM, Imperatriz-Fonseca VL, Monteiro W, Oliveira G, Silva AR, Siqueira JO, Souza-Filho PW, Vasconcelos S and Jaff\u00e9 R (2018) Landscape genomic conservation assessment of a narrow-endemic and a widespread morning glory from Amazonian Savannas.\u00a0Frontiers in Plant Science<\/em> 9:532. https:\/\/doi.org\/10.3389\/fpls.2018.00532<\/a><\/p>\n

7. Costa WF, Ribeiro M, Saraiva AM, Imperatriz-Fonseca VL, Giannini TC (2018) Bat diversity in Caraj\u00e1s National Forest (Eastern Amazon) and potential impacts on ecosystem services under climate change. Biological Conservation<\/em> 218: 200\u2013210. https:\/\/doi.org\/10.1016\/j.biocon.2017.12.034<\/a><\/p>\n

8. Gastauer M, Vero MPO, de Souza KP, Pires ES, Alves R, Caldeira CF, Ramos SJ, Oliveira G (2019) A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining. Scientific Data <\/em>6:190008. https:\/\/doi.org\/10.1038\/sdata.2019.8<\/span><\/p>[\/et_pb_text][\/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”]

Written by<\/p>[\/et_pb_text][et_pb_team_member name=”Guilherme Oliveira” position=”Environmental Genomics Group, Instituto Tecnol\u00f3gico Vale, Bel\u00e9m, Brazil” image_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/04\/Guilherme_Oliveira.png” _builder_version=”3.22.2″ header_font=”||||||||” header_text_align=”center” header_font_size=”19px” body_font=”||||||||” body_font_size=”15px” text_orientation=”center”][\/et_pb_team_member][et_pb_team_member name=”Gisele Nunes Lopes” position=”Environmental Genomics Group, Instituto Tecnol\u00f3gico Vale, Bel\u00e9m, Brazil” image_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/04\/Gisele-Nunes.png” _builder_version=”3.27.4″ header_font=”||||||||” header_font_size=”19px” body_font=”||||||||” body_font_size=”15px” text_orientation=”center”][\/et_pb_team_member][et_pb_team_member name=”Rafael Valadares” position=”Environmental Genomics Group, Instituto Tecnol\u00f3gico Vale, Bel\u00e9m, Brazil” image_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/04\/Rafael_Valadares.png” _builder_version=”3.22.2″ header_font=”||||||||” header_font_size=”19px” body_font=”||||||||” body_font_size=”15px” text_orientation=”center”][\/et_pb_team_member][et_pb_team_member name=”Ronnie Alves” position=”Environmental Genomics Group, Instituto Tecnol\u00f3gico Vale, Bel\u00e9m, Brazil” image_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/04\/Ronnie_Alves.png” _builder_version=”3.22.2″ header_font=”||||||||” header_font_size=”19px” body_font=”||||||||” body_font_size=”15px” text_orientation=”center”][\/et_pb_team_member][et_pb_team_member name=”Santelmo Vasconcelos” position=”Environmental Genomics Group, Instituto Tecnol\u00f3gico Vale, Bel\u00e9m, Brazil” image_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/04\/Santelmo_Vasconcelos.png” _builder_version=”3.22.2″ header_font=”||||||||” header_font_size=”19px” body_font=”||||||||” body_font_size=”15px” text_orientation=”center”][\/et_pb_team_member][et_pb_divider _builder_version=”3.21.4″ custom_margin=”26px||5px”][\/et_pb_divider][et_pb_text _builder_version=”3.27.4″ _dynamic_attributes=”content” text_font=”||||||||” text_orientation=”center”]@ET-DC@eyJkeW5hbWljIjp0cnVlLCJjb250ZW50IjoicG9zdF9kYXRlIiwic2V0dGluZ3MiOnsiYmVmb3JlIjoiIiwiYWZ0ZXIiOiIiLCJkYXRlX2Zvcm1hdCI6ImRlZmF1bHQiLCJjdXN0b21fZGF0ZV9mb3JtYXQiOiIifX0=@[\/et_pb_text][et_pb_button button_url=”https:\/\/ibol.org\/barcodebulletin\/wp-content\/uploads\/2019\/09\/2019_Oliveira.pdf” url_new_window=”on” button_text=”Download PDF” button_alignment=”center” _builder_version=”4.4.7″ custom_button=”on” button_text_size=”12px” button_text_color=”#ffffff” button_bg_color=”#003254″ button_icon=”%%26%%” button_icon_color=”#ffffff” hover_enabled=”0″ box_shadow_style=”preset3″ box_shadow_horizontal=”3px” box_shadow_vertical=”11px”][\/et_pb_button][et_pb_text _builder_version=”4.4.7″ text_font_size=”14px” text_orientation=”center” hover_enabled=”0″]

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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":"
Scientists are contributing to the most profound molecular representation of biodiversity in any Brazilian environment.<\/p>\n","protected":false},"author":9,"featured_media":4582,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"\n
C. Matthews<\/em>1<\/em><\/sup>, J. Dorey<\/em>1<\/em><\/sup>, S. Groom<\/em>2<\/em><\/sup>, O. Davies<\/em>1<\/em><\/sup>, E. Freedman<\/em>1<\/em><\/sup>, J. Holder<\/em>1<\/em><\/sup>, B. Parslow<\/em>1<\/em><\/sup>, M. Schwarz<\/em>1<\/em><\/sup>, M. Stevens<\/em>3,4<\/em><\/sup><\/p>\n\n\n\n
1 <\/sup>School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia 
2 <\/sup>School of Agriculture, Food and Wine, University of Adelaide, SA 5005, Australia 
3 <\/sup>South Australian Museum, GPO Box 234, Adelaide SA 5001, Australia 
4 <\/sup>School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia<\/p>\n\n\n\n
Fiji\u2019s entomological diversity has historically\nbeen considered depauperate. Recent widespread DNA barcoding efforts, however,\nfrom the South Australian Museum, Flinders University and University of South\nAustralia, along with a flurry of undergraduate, honours and PhD students, have\nhelped to uncover some of the hidden secrets of biodiversity within this\ntopographically complex archipelago.<\/p>\n\n\n\n
Since 2010, funding from the Australian\n& Pacific Science Foundation and Australian Commonwealth New Colombo Plan, along\nwith support from students, has enabled fieldwork focused on collecting bees,\nwasps, and butterflies across all the major Fijian islands. Trekking up the\ntallest mountains, four wheel driving across challenging terrain, and following\nthe meandering rivers of inland Fiji has revealed that initial estimations of\nFiji\u2019s entomological fauna have been severely underestimated. <\/p>\n\n\n\n
DNA barcoding over 1,000 bee specimens has increased species richness estimates from 4 species (known since 1979) up to 26 endemic species in the genus Homalictus. <\/em>Interestingly, 60% of these new species are only found above 800 m elevation which comprise a mere 2% of land area of Fiji, and often restricted to single mountain tops. From extensive barcoding, mitochondrial haplotype diversity was used to explore the level of intraspecific gene flow in the widespread species of the genus. <\/p>\n\n\n\n
\"Haplotype<\/a>
Haplotype network of all sequenced HOMALICTUS fijiensis (N=358) coloured by sampling locality. Hash marks represent nucleotide changes between each haplotype. Shared haplotypes represented by circles with multiple colours. Circle outline representing highland or lowland sampling. (b) Sampling map of H. fijiensis coloured by geographic sampling locality.<\/figcaption><\/figure><\/div>\n\n\n\n
These results also indicate that gene flow is being restricted within highland localities of the most widespread Homalictus <\/em>species. Dispersal from a species home range does not appear to be occurring in Fiji, which may be presenting a contemporary model of speciation that is predominantly influenced by past climatic fluctuations. There is an estimated crown age of 400 ka for the initial Fijian Homalictus <\/em>colonisation, which would result in the genus being present for several glacial cycles. During glacial maxima, cooler climate would be ubiquitous throughout Fiji, however during glacial minima and interglacial periods there is a distinction between cool highland and warm lowland climate. DNA barcoding results indicate that the largest diversification of this genus is concordant with the most recent glacial minima, as species that were freely dispersing during glacial maxima are forced to retreat into highland refugia. Combined with the inferred haplotype networks, these results indicate that restriction due to low thermal tolerance of lowland climate is driving the extraordinary highland species richness in Fiji. Further to the work on bees, we have also started barcoding Fiji\u2019s butterfly fauna, along with the first ever species of Gasteruption<\/em>, a parasitoid wasp genus, found in Fiji. The species, Gasteruption tomanivi<\/em> (Published in Zootaxa by PhD student Ben Parslow), was found at the peak of Fiji\u2019s highest mountain. These discoveries have highlighted how little is known about the entomofauna of Fiji and how the use of DNA barcoding has helped to uncover Fiji\u2019s hidden secrets of biodiversity. <\/p>\n","_et_gb_content_width":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"categories":[2],"tags":[20,19,23,28,107,29,24,27,108,25,45],"coauthors":[132,128,129,130,131],"class_list":["post-97","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-research","tag-amazon","tag-brazil","tag-caves","tag-conservation","tag-edna","tag-environmental-assessment","tag-invertebrates","tag-mammalia","tag-metagenomics","tag-plantae","tag-reference-library"],"_links":{"self":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/97","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\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/comments?post=97"}],"version-history":[{"count":58,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/97\/revisions"}],"predecessor-version":[{"id":4584,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/posts\/97\/revisions\/4584"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/media\/4582"}],"wp:attachment":[{"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/media?parent=97"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/categories?post=97"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/tags?post=97"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/ibol.org\/barcodebulletin\/wp-json\/wp\/v2\/coauthors?post=97"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}