Browsing by Subject "Biodiversity"
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Item Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats(PLOS, 2017-05-11) Price, James T.; Paladino, Frank V.; Lamont, Margaret M.; Witherington, Blair E.; Bates, Scott T.; Soule, Tanya; Biology, School of ScienceThe gut microbiome of herbivorous animals consists of organisms that efficiently digest the structural carbohydrates of ingested plant material. Green turtles (Chelonia mydas) provide an interesting model of change in these microbial communities because they undergo a pronounced shift from a surface-pelagic distribution and omnivorous diet to a neritic distribution and herbivorous diet. As an alternative to direct sampling of the gut, we investigated the cloacal microbiomes of juvenile green turtles before and after recruitment to neritic waters to observe any changes in their microbial community structure. Cloacal swabs were taken from individual turtles for analysis of the 16S rRNA gene sequences using Illumina sequencing. One fecal sample was also obtained, allowing for a preliminary comparison with the bacterial community of the cloaca. We found significant variation in the juvenile green turtle bacterial communities between pelagic and neritic habitats, suggesting that environmental and dietary factors support different bacterial communities in green turtles from these habitats. This is the first study to characterize the cloacal microbiome of green turtles in the context of their ontogenetic shifts, which could provide valuable insight into the origins of their gut bacteria and how the microbial community supports their shift to herbivory.Item Classifying the unknown: Insect identification with deep hierarchical Bayesian learning(Wiley, 2023) Badirli, Sarkhan; Picard, Christine Johanna; Mohler, George; Richert, Frannie; Akata, Zeynep; Dundar, Murat1. Classifying insect species involves a tedious process of identifying distinctive morphological insect characters by taxonomic experts. Machine learning can harness the power of computers to potentially create an accurate and efficient method for performing this task at scale, given that its analytical processing can be more sensitive to subtle physical differences in insects, which experts may not perceive. However, existing machine learning methods are designed to only classify insect samples into described species, thus failing to identify samples from undescribed species. 2. We propose a novel deep hierarchical Bayesian model for insect classification, given the taxonomic hierarchy inherent in insects. This model can classify samples of both described and undescribed species; described samples are assigned a species while undescribed samples are assigned a genus, which is a pivotal advancement over just identifying them as outliers. We demonstrated this proof of concept on a new database containing paired insect image and DNA barcode data from four insect orders, including 1040 species, which far exceeds the number of species used in existing work. A quarter of the species were excluded from the training set to simulate undescribed species. 3. With the proposed classification framework using combined image and DNA data in the model, species classification accuracy for described species was 96.66% and genus classification accuracy for undescribed species was 81.39%. Including both data sources in the model resulted in significant improvement over including image data only (39.11% accuracy for described species and 35.88% genus accuracy for undescribed species), and modest improvement over including DNA data only (73.39% genus accuracy for undescribed species). 4. Unlike current machine learning methods, the proposed deep hierarchical Bayesian learning approach can simultaneously classify samples of both described and undescribed species, a functionality that could become instrumental in biodiversity monitoring across the globe. This framework can be customized for any taxonomic classification problem for which image and DNA data can be obtained, thus making it relevant for use across all biological kingdoms.Item Correction to: Inaugural BMC Ecology and Evolution image competition: the winning images(Springer Nature, 2021-09-09) Harman, Jennifer L.; Cuff, Alison L.; Settele, Josef; Jacobus, Luke M.; Liberles, David A.; Traulsen, Arne; IUPUC Division of ScienceFollowing the publication of the original article [1], we were notified that: The description of Fig. 2 was incorrect: This image shows "an amphipod crustacean of the species E. verrucosus densely covered with an overgrown colony of parasitic ciliates. Ciliates living on weakened crustaceans are capable of forming vast colonies resembling a "fur coat" Should read: This image shows "an amphipod crustacean of the species E. verrucosus densely covered with an overgrown colony of parasitic ciliates and unknown oomycetes or fungi. These organisms on weakened crustaceans are capable of forming vast colonies resembling a "fur coat". The caption of Fig. 2 was changed from “Eulimnogammarus verrucosus, a species of crustacean endemic to the UNESCO World Heritage Site Lake Baikal, suffering from a parasitic ciliate infection. Attribution: Kseniya Vereshchagina” to “Eulimnogammarus verrucosus, a species of crustacean endemic to the UNESCO World Heritage Site Lake Baikal, suffering from a parasitic ciliate and unknown oomycete (water mold) or fungi infection. Attribution: Kseniya Vereshchagina”. The affiliations of the 3rd and 4th authors had been swapped by mistake. The original article has been corrected.Item Female Blow Flies As Vertebrate Resource Indicators(Springer Nature, 2019-07-22) Owings, Charity G.; Banerjee, Aniruddha; Asher, Travis M. D.; Gilhooly, William P.; Tuceryan, Anais; Huffine, Mary; Skaggs, Christine L.; Adebowale, Iyun M.; Manicke, Nicholas E.; Picard, Christine J.; Biology, School of ScienceRapid vertebrate diversity evaluation is invaluable for monitoring changing ecosystems worldwide. Wild blow flies naturally recover DNA and chemical signatures from animal carcasses and feces. We demonstrate the power of blow flies as biodiversity monitors through sampling of flies in three environments with varying human influences: Indianapolis, IN and two national parks (the Great Smoky Mountains and Yellowstone). Dissected fly guts underwent vertebrate DNA sequencing (12S and 16S rRNA genes) and fecal metabolite screening. Integrated Nested Laplace Approximation (INLA) was used to determine the most important abiotic factor influencing fly-derived vertebrate richness. In 720 min total sampling time, 28 vertebrate species were identified, with 42% of flies containing vertebrate resources: 23% DNA, 5% feces, and 14% contained both. The species of blow fly used was not important for vertebrate DNA recovery, however the use of female flies versus male flies directly influenced DNA detection. Temperature was statistically relevant across environments in maximizing vertebrate detection (mean = 0.098, sd = 0.048). This method will empower ecologists to test vertebrate community ecology theories previously out of reach due practical challenges associated with traditional sampling.Item Inaugural BMC Ecology and Evolution image competition: the winning images(Springer Nature, 2021-08-13) Harman, Jennifer L.; Cuff, Alison L.; Settele, Josef; Jacobus, Luke M.; Liberles, David A.; Traulse, Arne; IUPUC Division of ScienceThe inaugural BMC Ecology and Evolution image competition attracted entries from talented ecologists and evolutionary biologists worldwide. Together, these photos beautifully capture biodiversity, how it arose and why we should conserve it. This editorial celebrates the winning images as selected by the Editor of BMC Ecology and Evolution and senior members of the journal's editorial board.Item Mediators of Fine-Scale Population Genetic Structure in the Black Blow Fly, Phormia regina (Meigen) (Diptera: Calliphoridae)(2019-08) Owings, Charity Grace; Picard, Christine J.; Walsh, Susan; Wang, Xianzhong; Holland, Jeffery D.; Gilhooly, William, IIIPopulation genetic structure is difficult to assess in blow flies (Diptera: Calliphoridae) due to high connectivity and genetic diversity of subpopulations. Previous studies revealed high relatedness among individuals within wild samples of blow fly populations, however broad geographic structure was absent. The aim of this research was to determine if blow fly genetic structure exists at a fine spatiotemporal resolution and, if so, to elucidate the influence of environmental factors and resource availability on fly genetics. Specifically, blow fly population genetic patterns were tested against a null hypothesis that flies adhere to a patchy population model with high genetic diversity (i.e. no structure) and high resource availability. Samples of the black blow fly, Phormia regina Meigen (Diptera: Calliphoridae), were collected at six urban parks in Indiana, USA (=urban) in 2016 and 2017 (N = 14 and 16 timepoints, respectively). Additional sampling in different ecoregions was performed to determine if trends observed at a high-resolution scale were also present at a broad geographic scale. Therefore, P. regina were also collected at four sites within two national parks (the Great Smoky Mountains and Yellowstone National Parks) over a three-day period. Randomly selected females (N = 10) from each sample underwent the following analyses: 1) gut DNA extraction, 2) molecular analysis at 6 microsatellite loci, 3) vertebrate-specific 12S and 16S rRNA sequencing, and, 4) vertebrate fecal metabolite screening. Flies from the national parks and a comparable subset of urban data also underwent stable isotope analysis (SIA) to determine larval food source. Overall, strong seasonal population genetic structure was observed over both years in the urban environment (2016 F’ST = 0.47, 2017 F’ST 0.34), however spatial structure was lacking, as seen in previous studies (2016 F’ST = 0.04, 2017 F’ST 0.03). Weather conditions prior to and on the day of blow fly collections, interspecific competition, and resource availability greatly impacted the genetic diversity and kinship of P. regina. A total of 17 and 19 vertebrate species were detected by flies in 2016 and 2017, respectively, and many flies tested positive for vertebrate feces, suggesting that many varied resources are important for maintaining high gene flow among geographic locations. Genetic diversity was non-existent in flies collected from the Smokies (F’ST = 0.00), while very slight spatial structure existed in the Yellowstone populations (F’ST = 0.07). Environmental factors such as temperature, humidity, and wind speed were all statistically relevant in maximizing fly collections with vertebrate resources. In 720 min of total sampling time in the national parks and a subset of urban data, 28 vertebrate species were identified, and fecal resources appeared to be the most abundant in Yellowstone. Stable isotope analysis revealed a majority of larval resources in the national parks were herbivores, with a more even distribution of carnivore and herbivore carcasses present in the urban environment, which likely explains the high genetic diversity of adult flies in these regions. Overall, the null hypothesis that P. regina adheres to a patchy population model could not be rejected for the Smokies populations. However, the urban and Yellowstone populations appear to adhere to a Levins metapopulation model in which variable availability in resources leads to random bottleneck events in the local populations. Overall, environmental conditions, competition, and resource availability are all important factors influencing P. regina population genetic structure in different environments.Item A role for gut microbiota in host niche differentiation(Springer Nature, 2020-07) Greene, Lydia K.; Williams, Cathy V.; Junge, Randall E.; Mahefarisoa, Karine L.; Rajaonarivelo, Tsiky; Rakotondrainibe, Hajanirina; O’Connell, Thomas M.; Drea, Christine M.; Otolaryngology -- Head and Neck Surgery, School of MedicineIf gut microbes influence host behavioral ecology in the short term, over evolutionary time, they could drive host niche differentiation. We explored this possibility by comparing the gut microbiota of Madagascar's folivorous lemurs from Indriidae and Lepilemuridae. Occurring sympatrically in the eastern rainforest, our four, target species have different dietary specializations, including frugo-folivory (sifakas), young-leaf folivory (indri and woolly lemurs), and mature-leaf folivory (sportive lemurs). We collected fecal samples, from 2013 to 2017, and used amplicon sequencing, metagenomic sequencing, and nuclear magnetic resonance spectroscopy, respectively, to integrate analyses of gut microbiome structure and function with analysis of the colonic metabolome. The lemurs harbored species-specific microbiomes, metagenomes, and metabolomes that were tuned to their dietary specializations: Frugo-folivores had greater microbial and metagenomic diversity, and harbored generalist taxa. Mature-leaf folivores had greater individual microbiome variation, and taxa and metabolites putatively involved in cellulolysis. The consortia even differed between related, young-leaf specialists, with indri prioritizing metabolism of fiber and plant secondary compounds, and woolly lemurs prioritizing amino-acid cycling. Specialized gut microbiota and associated gastrointestinal morphologies enable folivores to variably tolerate resource fluctuation and support nutrient extraction from challenging resources (e.g., by metabolizing plant secondary compounds or recalcitrant fibers), perhaps ultimately facilitating host species' diversity and specialized feeding ecologies.Item Successful cryopreservation of coral larvae using vitrification and laser warming(Springer Nature, 2018-10-24) Daly, Jonathan; Zuchowicz, Nikolas; Lendo, C. Isabel Nuñez; Khosla, Kanav; Lager, Claire; Henley, E. Michael; Bischof, John; Kleinhans, F.W.; Lin, Chiahsin; Peters, Esther C.; Hagedorn, Mary; Physics, School of ScienceClimate change has increased the incidence of coral bleaching events, resulting in the loss of ecosystem function and biodiversity on reefs around the world. As reef degradation accelerates, the need for innovative restoration tools has become acute. Despite past successes with ultra-low temperature storage of coral sperm to conserve genetic diversity, cryopreservation of larvae has remained elusive due to their large volume, membrane complexity, and sensitivity to chilling injury. Here we show for the first time that coral larvae can survive cryopreservation and resume swimming after warming. Vitrification in a 3.5 M cryoprotectant solution (10% v/v propylene glycol, 5% v/v dimethyl sulfoxide, and 1 M trehalose in phosphate buffered saline) followed by warming at a rate of approximately 4,500,000 °C/min with an infrared laser resulted in up to 43% survival of Fungia scutaria larvae on day 2 post-fertilization. Surviving larvae swam and continued to develop for at least 12 hours after laser-warming. This technology will enable biobanking of coral larvae to secure biodiversity, and, if managed in a high-throughput manner where millions of larvae in a species are frozen at one time, could become an invaluable research and conservation tool to help restore and diversify wild reef habitats.Item Utilization of Blow Flies (Phormia regina) as Vertebrate Resource Diversity Indicators(2022-08) Jones, Ashton Brooke; Picard, Christine; Walsh, Susan; Wells, JeffreyBlow flies are often utilized in the field of forensic science due to their ability to aid in the estimation of time since death. Currently, estimations of postmortem interval require assumptions to be made and are prone to a margin of error, prompting research that may contribute to more accurate postmortem interval estimations and help to fill in the gaps of unknown information. Blow flies are necrophagous, feeding on feces and carrion, and therefore, are constantly sampling the environment. This behavior can be exploited in order to monitor the biodiversity in an environment. Through analysis of DNA isolated from the guts of blow flies, information can be obtained regarding what animals have died in an environment, what animals are still living in that environment, and the abundance and diversity of the animals present in a specific environment. Using fly-derived ingested DNA is a viable method for vertebrate resource identification and biodiversity monitoring. Over the course of a two-summer sampling period, in and around two national parks, a total of 162 blow fly (Phormia regina) samples returned a positive vertebrate DNA identification, with 33 species identified from five animal orders. Of the total number of flies collected and analyzed, 23.58% returned a positive vertebrate species identification. The method detected both abundant and common species based on National Park surveys, as well as some uncommon or unknown to the park species. In the SE region, 9 individuals belonging to the Rodentia order, 12 individuals belonging to the Artiodactyla order, 21 individuals belonging to the Carnivora order, 1 individual belonging to the Cingulata order, and 3 individuals belonging to the Lagomorph order were detected. In the SE region, 63% of the individuals detected belonged to the common category, 14% of the individuals detected belonged to the uncommon category, and 23% of the individuals detected belonged to the not in park/unknown category. In the NW region, 42 individuals belonging to the Rodentia order, 46 individuals belonging to the Artiodactyla order, and 28 individuals belonging to the Carnivora order were detected. In the NW region, 52% of the individuals detected belonged to the abundant category, 36% of the individuals detected belonged to the common category, and 12% of the individuals detected belonged to the uncommon category. The relative biodiversity of the sampled environment can be inferred. In the SE region, the Shannon Biodiversity Index was calculated to be 2.28 with an evenness of 0.844, while in the NW region, the Shannon Biodiversity Index was calculated to be 2.79 with an evenness of 0.855. Unsurprisingly, there was greater biodiversity in the Northwest Park samples than in the Southeast Park samples. Additionally, the ideal weather conditions for blow fly collection were determined be at a temperature of between 60- and 80-degrees Fahrenheit, a relative humidity between 50% and 60%, no precipitation, and a wind speed between 2 and 8 miles per hour. This information has further implications in the field of forensic science, specifically dealing with wildlife forensics, pathogen distributions, and can help to improve accuracy in regards to postmortem interval (PMI) estimations.