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Genetics based topics
HM330 Barcoding the diversity of Cusuco cloud forest in Honduras (Weeks 3 - 8; need to have completed HM001 and HM003) So many taxonomists have worked in the Cusuco Park now as part of the Opwall teams that substantial species lists have been obtained for many taxa. The next stage is to complete genetic barcoding for these species and submit these data to GenBank. This is an ideal project for dissertation students who can isolate and amplify the cytochrome C oxidase subunit 1 (COI) gene sequence for taxa such as dung beetles, jewel scarab beetles, amphibians, small mammals, birds or bats to determine levels of genetic diversity and the possible presence of previously undescribed cryptic species. There are 6 endemic species of amphibian in the Park none of which have been sequenced and there are suspected cryptic species of dung beetle, frog and small mammal that have yet to be fully analyzed and described. The project could compare the species identified from the gene sequencing with the morphometric data, potentially describe cryptic species and compare the sequences of species found in Cusuco that have been deposited in public databases. Generally, it will be expected that you collect your samples from at least three camps, and work with the appropriate biodiversity team. Students working on this project will be isolating and amplifying the relevant section of the COI gene and testing that there is viable DNA using agarose electrophoresis. The DNA samples will then be returned to the home institutions on FTA Whatman cards so that sequencing can be done. DNA sequencing cannot be done in the field, and students wanting to do projects of this type will need to ensure that they or their institution can cover the cost of the sequencing (approx $6 per sample).
HM331 Landscape genetics of amphibian species in Honduras (Weeks 3 - 8; need to have completed HM001 and HM003) A new field in population genetics, Landscape Genetics, investigates population structure and connectivity in the context of barriers and facilitators within the environment. The detailed satellite imagery and habitat mapping which exists within Cusuco allows a particularly fine-grained analysis of gene flow among populations of species within the park. Inter Simple Sequence Repeat (ISSR) polymorphisms provide a practical and relatively inexpensive alternative to microsatellites that can be utilised in the field for examining within species genetic diversity and gene flow. With the Chytrid fungus widespread within Cusuco, many species of amphibian endemic to cloud forests have suffered declines. Determining how these species move through the landscape and how populations are connected is extremely important for directing conservation effort. This project will use ISSR polymorphisms to examine genetic diversity, population structure and gene flow in amphibian populations in relation to landscape features within the park.
HM332 Prevalence of Chytrid in amphibian populations within the Cusuco National Park, Honduras (Weeks 3 - 8; need to have completed HM001 and HM003) The spread of chytrid fungus has caused severe declines in many amphibian populations and is a major concern for global amphibian conservation. Chytrid is known to have been present within the amphibian populations of Cusuco for at least 15 years, but its prevalence within specific areas of the forest and the extent to which different species are affected are not well known. Amphibian species will be encountered during diurnal and nocturnal transects and swabbed for chytrid. Swabs will be taken back to the lab at base camp and tested for the presence of chytrid using polymerase chain reaction (PCR) and visualised using agarose gel electrophoresis. Individuals will also be assessed for visual signs of infection. Prevalence of chytrid will be mapped in the park using multiple years data to assess whether the disease is continuing to spread to previously uninfected areas.
HM333 Carnivore patch occupancy in Cusuco National Park, Honduras: Comparing genetic and traditional techniques (Weeks 3 - 8; need to have completed HM001 and HM003) Carnivores can readily be attracted to a baited hair trap. Using a broad-spectrum hair trap capable of attracting most carnivorous mammals in the park, it will be possible to compare patch occupancy derived from tracks, feeding signs and scat with those from baited traps. Students could also look at how genetic estimates of the carnivore community composition differ from those of spoor analysis. This project would involve the use of baited hair traps set up in a grid in a sector of forest. Species will be identified by hair follicle characteristics under the microscope and DNA will be extracted from the shed hairs in the Base Camp genetics lab. Students working on this project will be isolating and amplifying the relevant section of the COI gene and testing that there is viable DNA using agarose electrophoresis. The DNA samples will then be returned to the home institutions on FTA Whatman cards so that sequencing can be done. DNA sequencing cannot be done in the field, and students wanting to do projects of this type will need to ensure that they or their institution can cover the cost of the sequencing (approx $6 per sample).
HM334 Genetic diversity and possible divergence of island and mainland populations of the Honduran Curlyhair Tarantula (Brachypelma albopilosum) (Weeks 3 - 8; need to have completed HM001 and HM003) The Honduran Curlyhair tarantula (Brachypelma albopilosum) is widespread through Central America from Honduras to Costa Rica. The species also occurs on a number of islands throughout its range, with particularly high densities found in the Cayos Cochinos. It has been observed that this species, although typically terrestrial, may be more arboreal in the Cayos Cochinos. A wide range of research questions may be pursued around the differences between island and mainland populations of this species, with students spending time both in Cusuco and the Cayos Cochinos. Projects could focus on intraspecific genetic variation and population structure using Inter Simple Sequence Repeat (ISSR) polymorphisms, with analysis being performed in the genetics laboratory in Cusuco. In addition to genetic variation, students can look at differences in habitat use, prey choice and availability as well as potential differences in body size and morphology between insular and mainland populations.
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