Our paper among the top downloaded papers in Evolutionary Biology

Glad to see our paper Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens among the top downloaded papers in Evolutionary Biology of Wiley journals. This paper was published in Molecular Ecology Resources and has been the most downloaded article in this journal in 2014.

Here is the link to Wiley’s announcement page. And the link to our paper.

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Bio2 Team co-hosts major biomonitoring science forum

The Environment Canada Canadian Aquatic Biomonitoring Network (CABIN) Team and the Biodiversity Institute of Ontario, University of Guelph, co-hosted the 3nd biennial CABIN Science Forum on December 2-3, 2014 in Guelph, Ontario. Previous science forums were held in Vancouver, BC in 2010 and Fredericton, NB in 2012. The 2-day forum (agenda) included themed sessions with short presentations by CABIN partners, followed by discussion periods. The forum also included tours of the facilities of the University of Guelph’s Biodiversity Institute and Centre for Biodiversity Genomics. One of the main themes was “Biomonitoring 2.0: Genomics and its application in Biomonitoring”. In total, over 70 attendees from industry, government, and academia were in attendance with nearly 100 more participating via web conference.

Plenary speakers from Canada, USA, and China came to present some of their recent genomic biomonitoring research and participate in the discussion, including:

  • Xiaowei Zhang; Nanjing University; “Environmental Genomics Reveal Environmental Threshold of Ammonia for the Protection of Zooplankton in Freshwater Ecosystem”
  • Eric Stein; Southern California Coastal Water Research Project; “Application of eDNA and Metabarcoding to Routine Stream and Wetland Biomonitoring Programs in California”
  • Erik Pilgrim; US EPA; “Expanding Bioassessment into Understudied or Novel Communities through DNA Metabarcoding”
  • Joel Gibson; University of Guelph; “Assessing Boreal Aquatic Ecosystems using DNA Metasystematics and Next-generation Sequencing”
  • Shadi Shokralla; University of Guelph; “Biomonitoring 2.0: a New Implementation of Next-generation Sequencing Technologies for Environmental DNA Research and Ecosystem Assessment”


The discussion of genomics and biomonitoring gets lively.


Bio2 team member, Shadi Shokralla, leads forum attendees through a tour of the University of Guelph lab facilities.

Hajibabaei and King present at Latornell Conservation Symposium

Mehrdad Hajibabaei and Ian King gave talks at the 2014 Latornell Conservation Symposium on Wednesday, Nov. 19th. They were part of the session “What’s in Your Water? Ecological Applications of eDNA for Species Detection and Monitoring”.


Dr. Mehrdad Hajibabaei

Mehrdad Hajibabaei: “Biodiversity Analysis through Environmental DNA: From Microbes to Mammals”

 Ian King: “Using environmental DNA (eDNA) for monitoring Jefferson Salamander (Ambystoma jeffersonianum) and the Ambystoma species complex in southern Ontario”

DNA metasystematics in the Maquenque National Wildlife Refuge of Costa Rica

Ph.D. student Katie McGee recently returned from a six-week field research trip of the humid Atlantic lowland rainforests of the Maquenque National Wildlife Refuge (MNWLR) located in the Northern Zone of Costa Rica.

She was there under a National Science Foundation Research Experience for Undergraduates (REU) grant, serving as the Graduate Student Mentor/Research Scientist, and was also completing her thesis project field research.

View of the dense rainforest along the trails of the Laguna del Lagarto Lodge

Katie’s current research in the Hajibabaei lab involves the use of Next-Generation Sequencing (NGS) to study the effects of a chrono-sequence on soil microbial, invertebrate, plant phylogenetic, and functional gene diversity, along with Carbon and Nitrogen cycle dynamics, and how these metrics change over a land-use gradient. The ultimate goal is to determine whether these metrics can serve as good candidates for indicators of ecosystem functioning. Another area of interest for Katie’s research project is to determine—via NGS and several other molecular tools—whether or not a dominant Nitrogen-fixing tree in the MNWLR, Pentaclethra macroloba (Fabaceae), has a particular soil microbial fingerprint associated with it. If so, how do different life stages of this tree species affect the soil microbial communities, as well as time since disturbance and seasonality; and do these soil microbial communities along with Carbon and Nitrogen cycle dynamics change as distance away from the base of the tree increases?

The “DNA metasystematics” approach that Katie will be using builds on the advances made possible by traditional DNA barcoding, but avoids the limitation of barcoding individual specimens one-by-one. With the advances afforded by the development of NGS technologies (e.g., Roche 454 FLX and Illumina MiSeq machines used in the Hajibabaei lab), DNA can be extracted from bulk soil samples and multiple markers can be sequenced using multiple primers for each marker.

This research initiative is the first of its kind in this particular area of Costa Rica (the MNWLR) to examine multiple trophic levels along with Carbon and Nitrogen cycle dynamics through NGS to develop indicators of habitat condition. Recent remediation strategies in this area have included the development of an extensive array of secondary forests, however, regional scientists are concerned these mosaics of secondary forests are not regenerating in a healthy manner conducive to ecosystem functioning. Cleared forests used as pasture often suffer degradation of soils because suppression of forest successional processes is occurring, which leads to colonization of scrub growth, and invasive grasses and ferns, rather than indigenous tree growth.

Chestnut Mandibled Toucan

In 2001, the Costa Rican Ministry of Environment and Energy established the San Juan-La-Selva Biological Corridor (SJLSBC) to connect six protected areas into a single integrated biological unit of 1,204,812 ha, and to protect the Northern Zone Ecosystems from further legal and illegal extraction-based land management practices. In 2005, the MNWLR was created by executive decree by the Costa Rican government and is the core conservation unit of the SJLBC. This particular biological portion of the SJLBC protects more than 50,000 ha of humid Atlantic lowland primary and secondary tropical forests, and other diverse ecosystems such as wetlands, lagoons, and rivers. It also conserves the highest percentage of forest cover that contains the most valuable habitats for biodiversity. Thus, this provides a unique opportunity to study the impact that decades of prior land-use history may have on vegetation and soil ecosystem structure and function.

Spider monkeys are common throughout this area

The study site of Katie’s research project is located within the private lands of the Laguna del Lagarto Lodge in the MNWLR, which has been involved in a long-standing 10+ years relationship between the owners, Vinzenz and Kurt Schmack, and Dr. Bill Eaton (Co-PI of NSF REU grant; Pace University). The habitats used for Katie’s current research project consist of an existing chrono-sequence containing six, 1,000 m2 study plots in each habitat type that were permanently established by Katie and Dr. Eaton in August, 2012. Each of the three habitat types was originally part of a large tract of upland primary forest with the same topography and soil type. These plots were established within a primary forest, 32-year-old secondary forest, and a 22-year-old secondary forest.


Katie McGee (left), Olivia Karas (middle) and Dr. Bill Eaton (right)

The Laguna del Lagarto Lodge contains 1,275 ha of forested land, and is home to over 350 bird species, including the endangered Great Green Macaw (Ara ambigua). The rare, majestic, tropical, hardwood giant, the Almendro tree (Dipteryx panamensis), is also in large abundance there. The lodge has provided economic opportunity through eco-tourism for the local town of Boca Tapada, and has helped Boca Tapada receive electricity in 1997 and internet in 2013.

In total, the six-week research trip involved 12+ hour days, over 400 soil cores being taken, over 400 soil DNA extractions performed, sieving over 100 soil samples, and over 20 days of Substrate-Induced Respiration. To help maintain sanity given this punishing work schedule, team building and camaraderie were nurtured by introducing the infamous “Hawaiian Shirt Wednesday”, along with guitar-filled nights with students, faculty members, and residents from the local community of Boca Tapada.