Resident or invasive species? Environmental DNA can provide reliable answers

Resident or invasive species? Environmental DNA can provide reliable answers

Resident or invasive species? Environmental DNA can provide reliable answers

Environmental DNA can be successfully applied to identify vertebrates in a tropical lake improving our capacity to map and monitor species.
Panoramic view of Bacalar Lake including the 40-m deep Esmeralda sinkhole. PHOTO CREDIT: Manuel Elías-Gutiérrez

Monitoring life within large bodies of water – those species that should and shouldn’t live there – can be very expensive and time consuming. To overcome these limitations, efforts in many temperate regions employ methods that use environmental DNA (eDNA), enabling effective and targeted detection of invasive and resident endangered species.

Our study is the first to demonstrate that eDNA-based monitoring can be successfully applied to target the whole fish community in a tropical freshwater system and its adjacent wetlands.

Between 1980 -1990, eDNA was the term introduced to define particulate DNA and it was used to detect and describe microbial communities in marine sediments and phytoplankton communities in the water column1. However, eDNA is presently defined as the genetic material left behind by eukaryotic organisms in the environment, reflecting a rise in the use of eDNA for the detection of vertebrate and invertebrate species in aquatic systems1. The popularity of using eDNA has increased following the development of next-generation sequencing, advances in quantitative PCR (qPCR), and the growth of DNA barcodes libraries such as the Barcode of Life Data System (BOLD), providing a quicker and more taxonomically comprehensive tool for biodiversity assessments.

 

South end of lake Bacalar with the sinkhole Cenote Azul.
PHOTO CREDIT: Manuel Elías-Gutiérrez

Lake Bacalar is the largest epicontinental habitat in Mexico’s Yucatan Peninsula, and it is renowned for its striking blue color, clarity of the water, and for the world’s largest occurrence of living stromatolites, a calcareous mound built up of layers of lime-secreting cyanobacteria. Due to the presence of sediments derived from karst limestone, it represents the world’s largest fresh groundwater-feed ecosystem. The northern part of Lake Bacalar is connected to a complex system of lagoons and the southern part has an indirect connection to the sea via a wetland system that connects with Hondo River and enters Chetumal Bay. This river has been heavily impacted by the discharge of organic waste and pesticides, by vegetation clearing, and by the introduction of invasive fish such as tilapia and the Amazon sailfin catfish (Pterygoplichthys pardalis) 2-4, first detected in 2013 4. The Amazon sailfin catfish is a serious threat to the fragile stromatolite ecosystem due to its burrowing habits and competition with local fish. The impact of declining water quality and the rise of invasive species on the native fish fauna needs to be carefully monitored in aid of conservation efforts of Lake Bacalar.

A team of researchers from the Instituto Tecnológico de Chetumal and El Colegio de la Frontera Sur sampled eight localities in December 2015, and January and April 2016. After each of 14 sampling events, water and sediment samples were immediately placed on ice before transportation to the lab in Chetumal. To minimize eDNA degradation, we filtered water samples within seven hours of collection. All filters and sediments were stored at -18°C before being transported on ice from Chetumal to the Centre for Biodiversity Genomics in Guelph, Canada, where DNA extraction was undertaken.

 

Water sampling between stromatolites.
PHOTO CREDIT: Miguel Valadez

We sequenced short fragments (<200 bp) of the cytochrome c oxidase I (COI) gene on Ion Torrent PGM or S5 platforms. In total, we recovered eDNA sequences from 75 species of vertebrates including 47 fishes, 15 birds, seven mammals, five reptiles, and one amphibian. Although all species are known from this region, six fish species represent new records for the study area, while two require verification (Vieja fenestrata and Cyprinodon beltrani /simus), because their presence is unlikely in this ecosystem. While there were species (two birds, two mammals, one reptile) only detected from sediments, water samples recovered a much higher diversity (52 species), indicating better eDNA preservation in the slightly alkaline Bacalar water.  Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment that confirmed our methods were effective.

Interesting findings include the detection of rare species, such as an anteater Tamandua mexicana, which was detected by both PGM and S5 instruments from a river sample (Juan Sarabia), and migratory birds, such as warbler Oreothlypis peregrina known to overwinter in the Yucatan Peninsula.

Docks in front of Bacalar town
PHOTO CREDIT: Miguel Valadez

Our study indicates that eDNA can be successfully applied to monitor vertebrates in a tropical oligotrophic lake as well as more eutrophic (higher primary production) wetlands and can aid conservation and monitoring programs in tropical areas by improving our capacity to map occurrence records for resident and invasive species.

Our next step is to convince Mexican and international stakeholders to implement these methodologies and establish a permanent biomonitoring system for this and other pristine freshwater ecosystems found in Yucatan Peninsula. This work is necessary to detect effects of climate change, declining water quality, and the increasing tourism activities in this region.

References:

1. Díaz-Ferguson EE, Moyer GR (2014) History, applications, methodological issues and perspectives for the use of environmental DNA (eDNA) in marine and freshwater environments. Revista de Biología Tropical 62: 1273-1284. DOI: 10.15517/RBT.V62I4.13231

2. Wakida-Kusunoki AT, Luis Enrique Amador-del Ángel (2011) Aspectos biológicos del pleco invasor Pterygoplichthys pardalis (Teleostei : Loricariidae) en el río Palizada, Campeche, México. Revista Mexicana de Biodiversidad 82: 870-878

3. Alfaro REM, Fisher JP, Courtenay W, Ramírez Martínez C, Orbe-Mendoza A, Escalera Gallardo C, et al. (2009) Armored catfish (Loricariidae) trinational risk assessment guidlines for aquatic alien invasive species. Test cases for the snakeheads (Channidae) and armored catfishes (Loricariidae) in North American inland waters. Montreal, Canada: Commission for Environmental Cooperation. pp. 25-49.

4. Schmitter-Soto JJ, Quintana R, Valdéz-Moreno ME, Herrera-Pavón RL, Esselman PC (2015) Armoured catfish (Pterygoplichthys pardalis) in the Hondo River basin, Mexico-Belize. Mesoamericana 19: 9-19.

Written by

Natalia V. Ivanova

Natalia V. Ivanova

Centre for Biodiversity Genomics, Guelph, ON, Canada

Martha Valdez-Moreno

Martha Valdez-Moreno

El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico

Manuel Elías-Gutiérrez

Manuel Elías-Gutiérrez

El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico

May 15, 2019
doi: 10.21083/ibol.v9i1.5474

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Diagnosing a rare human disease in Mexico’s lowlands

Diagnosing a rare human disease in Mexico’s lowlands

Diagnosing a rare human disease in Mexico’s lowlands

The first multidisciplinary study using DNA barcodes as a medical diagnostic tool forms a unique collaborative group comprised of medical practitioners and scientists.

Scanning electron micrograph of the anterior part of Lagochilascaris minor.
PHOTO CREDIT: Manuel Elías-Gutiérrez

Roundworms (Nematoda) are one of the most diverse groups of invertebrates. Lagochilascaris minor, a parasitic nematode often found in wild cats such as jaguars and pumas, as well as in domestic cats and dogs, has only rarely been known to infect humans. However, a recent case in the Yucatan Peninsula has brought about a very unique collaboration between medical practitioners and scientists. Lagochilascaris minor has been reported in the Americas, commonly in South America where the eggs have been found in public parks1. However, identifying L. minor with conventional methods can be misleading as they resemble other ascaridoid eggs. When a 23-year old man from a village in the forests of southern Quintana Roo state (Yucatan Peninsula) came into the local hospital in July 2016, physicians were surprised to find that a parasite had destroyed the mastoid apophysis, the lateral sinus, and part of the cerebellum. After a radical mastoidectomy and medical treatment for 63 days, the patient made a full recovery. After removal, the parasite was identified as L. minor using DNA barcodes and morphology. While the method of infection is uncertain, it is thought to be through direct exposure to the eggs or through the consumption of uncooked meat from wild animals.

Coronal computerized tomography scan of the human patient. Arrow indicates destruction of the left mastoid bone.
PHOTO CREDIT: Hospital General de Chetumal, Mexico

While it has been a challenge to successful identify Nematoda using genetic markers in the past, high-quality DNA barcode sequences were obtained using semi-degenerate primers designed for micro-crustaceans2. A comparison with 81 ascaridoids obtained from the Barcode of Life Data System (BOLD) revealed its position in a unique clade, most closely related to Baylisascaris procyonis. This is the first multidisciplinary study involving DNA barcodes as a diagnostic medical tool in a human patient. This field of research can be promising because we can get a precise identification of the parasites in any stage of their life cycle. Diagnosis using DNA barcoding will allow the recognition of the infection parameters, transmission, and more precise epidemiology of parasites. With this information, we can not only diagnose the disease but also prevent it by finding the infectious stages, the intermediate hosts, or the vectors in the environment. All sequences of Lagochilascaris are in the public project ‘NECHE Lagochilascaris from Yucatan’ in BOLD. This study is published in the Journal of Parasitology.

References:

  1. de Moura MQ, Jeske S, Gallina T, Borsuk S, Berne MEA, Villela MM (2012) First report of Lagochilascaris (Nematoda: Ascarididae) eggs in a public park in Southern Brazil. Veterinary Parasitology 184(2-4): 359-361. https://doi.org/10.1016/j.vetpar.2011.09.019
  2. Prosser SW, Velarde-Aguilar MG, Leon-Regagnon V, Hebert PD (2013) Advancing nematode barcoding: A primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes. Molecular Ecology Resources 13(6): 1108-1115. https://doi.org/10.1111/1755-0998.12082

Written by

David González-Solís

David González-Solís

El Colegio de la Frontera Sur, Chetumal, México

Manuel Elías-Gutiérrez

Manuel Elías-Gutiérrez

El Colegio de la Frontera Sur, Chetumal, México

Jenny Alejandra Prado-Bernal

Clínica Carranza, Chetumal, México

Miguel Alfredo García-de la Cruz

Hospital General Dr. Manuel Gea González, Ciudad de México, México

April 30, 2019
doi: 10.21083/ibol.v9i1.5475

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DNA Barcoding Wild Flora in Pakistan’s Forests

DNA Barcoding Wild Flora in Pakistan’s Forests

DNA Barcoding Wild Flora in Pakistan’s Forests

Preserving voucher specimens and creating a virtual herbarium to understand and protect some of the oldest living trees on the planet.
Juniper Forest of Ziarat, Balochistan, Pakistan. PHOTO CREDIT: Nazeer Ahmed
Balochistan, the largest province of Pakistan, is endowed with a variety of natural forests. Juniper (Juniperus excelsa), Pinus (Pinus gerardiana), wild Olive (Olea sp.) and mangroves are the predominant forest ecosystems of the province. The versatility of life forms in these forests support dynamic ecosystems and provide several important ‘ecosystem services’ like food, medicines, climate regulation, genetic resources, recreation facilities, etc. Biodiversity conservation, in the face of such benefits, becomes imperative. Comprehensive cataloguing of flora and fauna is, by all means, at the heart of such conservation endeavours.

The Juniper forest of Ziarat, Balochistan, declared a UNESCO Man and Biosphere Reserve, is considered one of the world’s largest compact forests of its kind spreading over an area of 100,000 ha. Being some of the oldest living trees on earth, they are termed “Living Fossils”. The Chilgoza (Pinus gerardiana), also known as the Chilgoza Pine, on the other hand, are listed as lower risk, near threatened forest. Anthropogenic interferences have further aggravated the situation in this ecosystem and a more focused study about their current status is needed.

Juniper Forest of Ziarat, Balochistan, Pakistan. PHOTO CREDIT: Nazeer Ahmed

Fragmented studies exist attempting to document the associated flora of these forests; however, a more comprehensive approach is needed. The use of DNA barcoding techniques, duly augmented by classical taxonomy, is necessary for the creation of a reference library to inventory, assess, and describe the biodiversity of these forests. To fill this gap, a study was designed to provide a foundation for future biodiversity assessment and conservation efforts.

 

Funded by Pakistan Agricultural Research Council and Higher Education Commission of Pakistan, our research group at the Balochistan University of Information Technology, Engineering & Management Sciences, Quetta is expecting to barcode and acquire samples of approximately 1,000 wild plant species. 

To date, 730 samples of 525 different species have been collected and 29% (150 of 525) have been barcoded. Besides maintaining voucher specimens, a virtual herbarium will be made available to the global scientific community interested in the flora of these forest ecosystems.

Read more about Pakistan:

SMALL STEPS LEAD TO BIG INITIATIVES: PAKISTAN REAFFIRMS SUPPORT FOR IBOL BY LAUNCHING PAKBOL

From economically important insect species to plants to food security, Pakistani researchers are working to barcode all life in their country through a national initiative – PakBOL.

UNIVERSITY OF SINDH JAMSHORO BARCODES GRASSHOPPERS IN PAKISTAN’S THAR DESERT

Tracking the shift of non-pests to crop pests, a phenomenon accelerated by anthropogenic pressures in the Thar Desert.

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The Diversification and Evolution of Marine Invertebrates in Oceanic Islands

The Diversification and Evolution of Marine Invertebrates in Oceanic Islands

The Diversification and Evolution of Marine Invertebrates in Oceanic Islands

Unravelling long-established divergence patterns and remarkable geographic segregation that has endured over millions of years in marine invertebrates.

Macaronesian rocky shores. PHOTO CREDIT: Pedro Vieira, Mafalda Tavares, Henrique Queiroga

Oceanic islands constitute prime evolutionary grounds for terrestrial organisms, promoting extensive isolation and harboring exceptional levels of diversity and endemism. Marine organisms, on the contrary, are not expected to experience evolutionary forces with the same intensity and, therefore, their diversification and evolution in oceanic landscapes has been somewhat disregarded.

Shore-dwelling marine benthic invertebrates are unique relative to both terrestrial organisms and other marine taxa. Most shore species have planktonic larvae that facilitate dispersal over open water. However, some small invertebrates, such as free-living peracarids (Peracarida: Crustacea), are more prone to isolation due to life histories characterized by direct development and putatively reduced vagility.

As a result of a DNA barcode-based screening of the diversity of littoral peracarids along Macaronesia and nearby continental shores, we have found an exceptional amount of cryptic diversity, together with a very structured geographic assortment within multiple morphospecies. We investigated, with particular detail, two common and distinct peracarid taxa present in the Macaronesian archipelagos of Azores, Madeira, and Canaries, namely 3 morphospecies of the isopod genus Dynamene1 and 7 morphospecies of the amphipod family Hyalidae2. We unraveled an additional 34 suspected new species (75% endemic of Macaronesia) with no apparent discriminative morphological features, including the noteworthy cases of the isopod Dynamene edwardsi and the amphipod Apohyale stebbingi comprising 9 and 13 putative species, respectively. Adding to this surprising cryptic diversity, lineages within each morphospecies were also frequently exclusive to one island (50%), despite the general geographic proximity of the islands within each archipelago (e.g., from as little as 50 km between Porto Santo and Madeira). Globally, the genetic divergences among lineages within a morphospecies were also comparatively high (e.g., D. edwardsi up to 22% and A. stebbingi up to 21%), indicating a very deep evolutionary history in the region which pre-dates the Pleistocene glacial cycles (D. edwardsi lineages probably started diverging between 20 and 30 MYA).  

Representative study species; not to scale.
PHOTO CREDIT: Pedro Vieira

There were several noteworthy findings in these studies. First, the unexpectedly high amount of diversity and endemism in these Macaronesian marine invertebrates, even within the same archipelago. Although peracarids can be assumed to have comparatively low vagility, since they lack a planktonic larval stage, there is extensive evidence for their dispersal capability and population connectivity. Namely, both our and other authors’ studies report peracarid morphospecies displaying little genetic structure over wide geographic ranges, for example, along the European continental Atlantic coasts.

Second, we were surprised to find marked geographic segregation among the newly found species. They were frequently restricted to a single island where they constituted the only representative of the cryptic complex. To a certain extent, the geographical segregation of these peracarids more closely resemble what would be expected for terrestrial organisms than marine invertebrates.

 

A. Sampling locations for each Dynamene species. B. Reduced median network of COI data from the genus Dynamene. Size of the circles are proportional to the number of similar haplotypes. Number of mutations separating each haplotype and inferred ancestors (median vectors) are displayed in black. Links displaying a single mutation do not display the number.

PHOTO CREDIT: Pedro Vieira

Finally, the combined evidence on diversity, geographic segregation, and divergence times, unraveled long-established divergence patterns and a remarkable geographic segregation that endured over millions of years till present. Therefore, the current distribution patterns of many of these peracarids cannot be elucidated through common accounts of marine invertebrates in the north-eastern Atlantic, namely processes involving dispersal, geographic proximity or Pleistocene glacial cycles. We propose alternative mechanisms for the speciation of these invertebrates in Macaronesia, such as those involving priority effects and pre-emptive exclusion, which have been seldom evoked to explain the deep segregation in the open ocean.

In the near future, we intend to investigate the genetic variability of taxa with planktonic larvae from these oceanic islands to verify if the long-term segregation patterns are exclusive of peracarid crustaceans or, instead, are more widespread patterns in marine invertebrates in Macaronesia.

References

  1. Vieira PE, Desiderato A, Holdich DM, Soares P, Creer S, Carvalho GR, Costa FO, Queiroga H (2019) Deep segregation in the open ocean: Macaronesia as an evolutionary hotspot for low dispersal marine invertebrates. Molecular Ecology. https://doi.org/10.1111/mec.15052
  2. Desiderato A, Costa FO, Serejo CS, Abbiati M, Queiroga H, Vieira PE (2019) Macaronesian islands as promoters of diversification in amphipods: The remarkable case of the family Hyalidae (Crustacea, Amphipoda). Zoologica Scripta. https://doi.org/10.1111/zsc.12339

Written by

Pedro Vieira

Pedro Vieira

University of Minho, Braga, Portugal

Filipe Costa

Filipe Costa

University of Minho, Braga, Portugal

April 7, 2019
doi: 10.21083/ibol.v9i1.5477

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Discovering Fiji’s native bees: hidden secrets in a biodiversity hotspot

Discovering Fiji’s native bees: hidden secrets in a biodiversity hotspot

Discovering Fiji’s native bees: hidden secrets in a biodiversity hotspot

Researchers provide new insights into biodiversity using DNA barcoding in Fiji's topographically complex archipelago.

Homalictus hadrander, one of the four described species previously known from Fiji.
PHOTO CREDIT: James Dorey

Fiji’s entomological diversity has historically been considered depauperate. Recent widespread DNA barcoding efforts, however, from the South Australian Museum, Flinders University, and University of South Australia, along with a flurry of undergraduate, honours, and PhD students, have helped to uncover some of the hidden secrets of biodiversity within this topographically complex archipelago. Since 2010, funding from the Australian & Pacific Science Foundation and Australian Commonwealth New Colombo Plan, along with support from students, has enabled fieldwork focused on collecting bees, wasps, and butterflies across all the major Fijian islands. Trekking up the tallest mountains, four-wheel driving across challenging terrain, and following the meandering rivers of inland Fiji has revealed that initial estimations of Fiji’s entomological fauna have been severely underestimated. 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. Interestingly, 60% of these new species are only found above 800 m elevation which comprise a mere 2% of land area of Fiji, and they are often restricted to single mountain tops (Figure 1). From extensive DNA barcoding, mitochondrial haplotype diversity was used to explore the level of intraspecific gene flow in the widespread species of the genus (Figure 2).

Figure 1: (a) The number of species (species richness) plotted against land area available at each elevational gradient. (b) Map of Fiji showing the land area available. Colours correspond to those used in (a).

CREATED BY: Cale Matthews

These results also indicate that gene flow is being restricted within highland localities of the most widespread Homalictus 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 colonisation, which would result in the genus being present for several glacial cycles. During glacial maxima, cooler climates 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.

 

Figure 2: (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.

CREATED BY: Cale Matthews

Further to the work on bees, we have also started barcoding Fiji’s butterfly fauna, along with the first-ever species of Gasteruption, a parasitoid wasp genus, found in Fiji. The species, Gasteruption tomanivi (Published in Zootaxa by PhD student Ben Parslow), was found at the peak of Fiji’s 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’s hidden secrets of biodiversity.

 

Written by

Cale Matthews

Cale Matthews

School of Biological Sciences, Flinders University, Adelaide, Australia

James Dorey

James Dorey

School of Biological Sciences, Flinders University, Adelaide, Australia

Scott Groom

Scott Groom

School of Agriculture, University of Adelaide, Australia

Olivia Davies

School of Biological Sciences, Flinders University, Adelaide, Australia

Elisha Freedman

Elisha Freedman

School of Biological Sciences, Flinders University, Adelaide, Australia

Justin Holder

School of Biological Sciences, Flinders University, Adelaide, Australia

Ben Parslow

School of Biological Sciences, Flinders University, Adelaide, Australia

Michael Schwarz

School of Biological Sciences, Flinders University, Adelaide, Australia

Mark Stevens

Mark Stevens

School of Biological Sciences, Flinders University, Adelaide, Australia

April 7, 2019
PDF
https://doi.org/10.21083/ibol.v9i1.5482

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Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

Using DNA dietary analysis on Eastern Mediterranean wildlife to explore the role of animals in ecological restoration processes.
Plant collection in Ehden Nature Reserve – north Lebanon. PHOTO CREDIT: Saint Joseph University

Lebanon is considered a hotspot for biodiversity in the Mediterranean basin likely due to its geographic position at the transition of two major landmasses (that is Eurasia and Africa). The Lebanese territory is divided between mountainous slopes with fertile valleys separating the two mountain chains that run parallel with the sea and the steppe areas in the north-east. Deep canyons and numerous rivers characterize this mountainous landscape.

These geomorphological regions give rise to many bio-climatic zones and several habitat types that are home to more than 9,116 described species (4,486 for fauna and 4,630 for flora from which 91 are endemic). However, major taxonomic groups like insects and fungi are understudied and taxa are underrepresented within public data platforms. For example, according to the Barcode of Life Data System (BOLD), only 345 Lebanese specimens with sequences are published, forming 151 BINs and, of these records, only 108 have species names.

In September 2018, the Faculty of Science at Saint Joseph University of Beirut joined the iBOL Consortium providing us with the opportunity to unravel Lebanese biodiversity by DNA barcoding both small and large mammals as well as the main trees and shrubs used in reforestation programs. We will also target endemic plant species.

Animals are a crucial component for the resilience of forest ecosystems and an important factor in forest restoration projects as they promote the sustainability of reintroduced plants, as well as seed dispersal. However, we still need to identify the animals present in restored areas.

Animal scat collection. PHOTO CREDIT: Saint Joseph University

In addition, knowing what each animal eats and which plant seeds are being dispersed is crucial for reforestation schemes that promote wildlife and ensure ecosystem sustainability. The information needed to study the diets of animals can be found hidden in their scat which contains not only the animal’s DNA, but also what that animal has eaten. With the powerful technique of DNA metabarcoding, we now have the necessary tool to efficiently unravel the genetic information hidden in animal scat. The DNA sequences obtained from such material are identified by comparison to a reference library of animals and plants of the Eastern Mediterranean countries.

 

Constructing the Reference Library: DNA isolation Photo credit: Université Saint-Joseph

Constructing the Reference Library – DNA isolation.
PHOTO CREDIT: Saint Joseph University

This reference library was prepared from leaves collected in the wild and from DNA isolated from dead animals found along roads or from private museums. Thus, we have generated sequences for 51 plants and 18 mammals. This study conducted in collaboration with the Smithsonian Conservation Biology Institute and the University of Otago is the first to employ a DNA dietary analysis on wildlife in the Eastern Mediterranean Region and explicitly considering the role of wildlife in ecological restoration processes. Our results will inform management strategies to help with the conservation efforts of these imperiled species.

Written by

Carole Saliba

Carole Saliba

Faculty of Science, Saint-Joseph University

Liliane Boukhdoud

Liliane Boukhdoud

Faculty of Science, Saint-Joseph University

Magda Bou Dagher Kharrat

Magda Bou Dagher Kharrat

Faculty of Science, Saint-Joseph University

April 7, 2019
doi: 10.21083/ibol.v9i1.5489

Read more about Lebanon:

iBOL SCIENCE COMMITTEE MEMBER RECOGNIZED AS “FACE OF EXCHANGE” BY U.S. STATE DEPARTMENT

Magda Bou Dagher Kharrat, a leader in DNA barcoding and conservation in Lebanon, has been named as a notable alumnus of the U.S. State Department’s International Visitor Leadership Program.

HOW BIOSCAN IS INSPIRING THE NEXT GENERATION OF RESEARCHERS

They were enlightened by the idea of discovering new species and by the possibility of doing so using DNA barcoding tools.”

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Saving the Pangolin: Philippines’ Fight Against the Illegal Wildlife Trade

Saving the Pangolin: Philippines’ Fight Against the Illegal Wildlife Trade

Saving the Pangolin: Philippines’ Fight Against the Illegal Wildlife Trade

Governments, scientists, and enforcement agencies join forces to formally incorporate molecular identification of trafficked species within wildlife forensics.
The Palawan Pangolin, Manis culionensis. PHOTO CREDIT: Renz Angelo Duco

On April 8, 2013, a Chinese-registered fishing vessel ran aground on Tubbataha Reef, a marine protected area southeast of the island province of Palawan, Philippines. When the ship was towed to port at Puerto Princesa City, it was found to contain 400 concealed boxes with more than 3,000 frozen pangolins. These specimens were initially thought to be the Palawan Pangolin (Manis culionensis), an IUCN-listed endangered species. This and many other pangolin species have been described as some of the most trafficked animals on Earth as they are priced for their ‘scales’ for supposed medicinal value as well as for their exotic meat, both of which fetch a high value in the Chinese market.

The Palawan Pangolin and many other Philippine endemic species are protected by the Philippine Wildlife Resources Conservation and Protection Act (Republic Act 9147), which prohibits the capture, sale and transport of threatened species. However, Philippine Wildlife Enforcement Officers (WEOs) are hindered from carrying out their duties because they are limited in their ability to correctly identify confiscated species, which is often based on morphology alone. More often, WEOs have to deal with specimens that are not intact (e.g. tissue, blood, bone, etc.), rendering a taxonomic identification impossible. This poses a significant challenge for WEOs who need to correctly identify confiscated specimens and prosecute poachers.

Going back to the Tubbataha case, the Department of Environment and Natural Resources (DENR) sought the help of the University of the Philippines Diliman, Institute of Biology (UPD-IB) through its DNA Barcoding Laboratory to identify the pangolin specimens. Adrian Luczon, the lead investigator for the molecular identification of the specimens, utilized the COI gene and two reference Manis culionensis samples. His team’s results demonstrated that the Tubbataha specimens actually belonged to another critically endangered species, the Sunda Pangolin (M. javanica) native to mainland Southeast Asia, Borneo, Java, Sumatra, and nearby islands. Despite the DNA barcoding results indicating the specimens to be from another species outside the Philippines, the trafficking of the Palawan Pangolin remains unabated. In fact, within the same year, several batches of confiscations involving these pangolins have taken place, which Luczon’s team identified as the Palawan Pangolin through DNA barcoding. Clearly, there was an urgent need to formally incorporate molecular identification of trafficked species within the wildlife forensics work in the Philippines.

In 2015, UPD-IB entered a collaboration with the DENR through its Biodiversity Management Bureau to establish the first Molecular Wildlife Forensics (WILDFORCE) Lab in the Philippines. Through this partnership, DENR provides samples of Philippine endemic species to populate the Philippine DNA barcode database. These samples are to be processed at the Biodiversity Research Laboratory, headed by Dr. Perry Ong, and the DNA Barcoding Laboratory of UPD-IB. Other specimens brought to the lab for proper identification through DNA barcoding include the Philippine Duck (Anas luzonica), the Philippine Tarsier (Tarsius syrichta), the Gray’s Monitor Lizard (Varanus olivaceus), and the Philippine Sailfin Lizard (Hydrosaurus pustulatus), among others.

In 2018, with financial support from the Japan Biodiversity Fund and endorsement from the Secretariat of the Convention on Biological Diversity, and in support of the Global Taxonomy Initiative, WILDFORCE was able to train 18 individuals among researchers from higher educational institutions (HEIs) and WEOs from regional DENR offices. The training aimed to capacitate these personnel on the basic principles of DNA barcoding and eventually allow them to set up their own labs. These efforts are envisioned to contribute to building a robust Philippine DNA barcode database and decentralize the processing of evidence towards the DENR regional offices and local HEIs.

Wildlife enforcement officers and researchers from higher educational institutions receive training on DNA barcoding.

PHOTO CREDIT: Adrian Luczon

The sad reality of illegal trafficking of endangered species, as manifested by the Tubbataha case, has prompted the Philippine government and various stakeholders to join forces to combat illegal wildlife trade. It is only through collective effort grounded in science that we can have a chance to protect biodiversity.

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University of Sindh Jamshoro Barcodes Grasshoppers in Pakistan’s Thar Desert

University of Sindh Jamshoro Barcodes Grasshoppers in Pakistan’s Thar Desert

University of Sindh Jamshoro Barcodes Grasshoppers in Pakistan’s Thar Desert

Tracking the shift of non-pests to crop pests, a phenomenon accelerated by anthropogenic pressures in the Thar Desert.
The Thar Desert is considered the seventh largest desert in the world and the third largest in Asia. Although this desert is rich in unique biodiversity, efforts to explore and analyze its fauna and flora have been minimal. The desert harbours some important crop pests, particularly orthopterans, by providing them alternate host plants, overwintering space, and environments for reproduction. The region provides favourable soil and environmental conditions for the survival of Acridids (grasshoppers and locusts). In particular, it supports the reproduction, development, and outbreak of the desert locust; the gregarious phase of locusts results in attacks on neighbouring regions that cause severe loss to crops and forests.

Cattle grazing in the Thar region.
Photo credit: Ahmed Ali Samejo

Around 20,000 orthopterans have been described in the world including 1,750 from India, but the number of known species in Pakistan is merely 161. Our recent surveys of the Thar region have revealed 29 species of grasshoppers that are new to the country indicating the rich grasshopper diversity of this desert.

With expanding agricultural fields, overgrazing and desertification, and changing ecological conditions, biodiversity is also changing. These changes are pushing non-pests to become crop pests, a phenomenon that warrants further investigation using reliable identification methods. An effective, preventive management strategy of these pests relies on an improved knowledge of their biology and ecology, and on more efficient monitoring and control techniques. The Department of Zoology at the University of Sindh Jamshoro has taken initiative to document and understand the grasshopper fauna in the Thar Desert by coupling DNA barcoding with conventional taxonomy.

Field surveys in the Thar Desert with Kumar, Riffat, & Samejo (left to right).
PHOTO CREDIT: Ahmed Ali Samejo

With funding support from the Higher Education Commission (HEC) Pakistan, the department plans to develop a DNA barcode reference library for grasshoppers in the Thar Desert of Pakistan. Grasshopper collection and specimen identification is already in progress and, so far, 2,334 specimens have been identified to 22 species while the identity of 300 specimens is yet to be resolved. After the front-end processing (data-basing, imaging, tissue sampling) at the University of Sindh Jamshoro is complete, the identified specimens will be barcoded at the Centre for Biodiversity Genomics, University of Guelph.

This is the first effort towards understanding grasshopper diversity in the Thar using DNA methods and developing a reliable reference library for this important group of pest insects. The generated data will not only be used for the rapid identification of grasshoppers and locusts, it will also provide a useful tool for pest management and biodiversity conservation.

Written by

Riffat Sultana

Riffat Sultana

Department of Zoology, University of Sindh Jamshoro, Pakistan

April 7, 2019
doi: 10.21083/ibol.v9i1.5491

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