Biology subjects

Rodgers, T. W.

Publications and source records attributed to Rodgers, T. W..

10 recordsLinked to original sources

bioRxiv2026

Distribution and diet of Central American Clouded Tiger Cat Leopardus pardinoides oncilla via noninvasive genetics

The Clouded Tiger Cat Leopardus pardinoides is a recently recognized Neotropical species for which ecological and natural history data are sparse. Knowledge of species distribution and elevational range are largely based upon camera trap studies, and its diet has not been examined. The objective of this study was to better define the geographical and elevational distribution of the subspecies L. pardinoides oncilla in Central America using genetically confirmed records. We also provide the first diet analysis for L. pardinoides. We conducted extensive surveys for scat samples by visual means and with a scent detection dog across mountain ranges in Panama and Costa Rica, confirmed species identity using Sanger sequencing of mitochondrial DNA, and analyzed diet composition via DNA metabarcoding. Altogether, we collected 195 confirmed L. pardinoides scats. Records were strongly associated with high elevations, with a median elevation of 2805 m, and a maximum of 3422 m. Our findings highlight core habitat for L. pardinoides in the Cordillera Talamanca mountains in the border region of Panama and Costa Rica, and we identified isolated populations from the Central Volcanic Cordillera of Costa Rica and the Central Cordillera of Panama. DNA metabarcoding detected 59 vertebrate taxa. Diet was dominated by small mammals (74% of samples), especially cricetid rodents and shrews. Birds were also commonly detected (35% of samples), while reptiles (13%) and amphibians (1.9%) were less frequent. Estimated median adult prey mass was low (25 g), indicating that the species specializes on small prey. Most vertebrate prey identified were species endemic to montane regions of Panama and Costa Rica. These findings provide valuable ecological and natural history data on Clouded Tiger Cats in Central America that will inform conservation and management of this recently recognized species.

zoology↗

bioRxiv2026

Extraction-free iDNA metabarcoding of small dung beetles is an efficient method for surveying arboreal mammals in tropical forests

Surveying mammals in tropical rainforests, particularly those that inhabit the rainforest canopy, can be challenging. We tested a novel method for detecting rainforest mammals with metabarcoding of iDNA at Los Amigos Biological Station in the Peruvian Amazon. We used an extraction-free, direct PCR approach to metabarcode vertebrate DNA, whereby buffer from tubes that contained dung beetles for 24 hours was used directly in PCR, negating the need for labor-intensive dissection and DNA extraction. We used a mammal-specific marker targeting the mitochondrial 16S gene and a general metazoan marker targeting the mitochondrial COI gene. From just 105 dung beetles, mostly small beetles from the genus Sylvicanthon, we detected 42 vertebrate species from 16 orders and 26 families, including 33 mammal species and 10 primates. Of the mammals, more than half were arboreal species. The mammal-specific 16S marker detected more mammal species, but the general COI marker detected some mammals not detected by 16S plus eight avian and one fish species, and, in most cases, yielded sequences from the dung beetles themselves. Because small dung beetles are often abundant and easy to catch in tropical forests, this extraction-free direct PCR method provides a powerful and efficient tool for monitoring mammalian diversity. Our results demonstrate that this method works particularly well for primates and other arboreal mammals that are challenging to detect with traditional methods.

ecology↗

bioRxiv2025

An efficient iDNA method for surveying rainforest mammals with carrion flies

Metabarcoding of vertebrate DNA derived from invertebrates (iDNA) is a promising method for monitoring of mammal populations However, optimization of field and laboratory methods for efficient and economical sampling and analysis is needed. We used metabarcoding of carrion flies to survey for mammals at Los Amigos Biological Station in the Peruvian Amazon. We used an extraction-free, direct PCR approach to metabarcode vertebrate DNA, whereby buffer from tubes that contained flies for 3-5 hours was used directly in PCR, negating the need for labor-intensive DNA extraction. We also examined two different pooling methods to investigate the efficacy of pooling multiple fly samples to economize sequencing of large numbers of samples. Metabarcoding detected 27 mammalian taxa from 9 orders and 18 families plus four anuran taxa from three families from just 240 carrion flies collected over 3 days. Pooling of buffer from multiple flies prior to PCR resulted in the loss of many species compared to sequencing of individual flies. However, pooling of PCR product after an initial PCR from individual flies, but prior to indexing, resulted in species detection nearly identical to sequencing of individual flies. These methodological findings will contribute to the feasibility of iDNA metabarcoding for vertebrate monitoring and biodiversity conservation.

ecology↗

bioRxiv2025

Understanding detection probability in a low-density population to inform optimal eDNA sampling for freshwater mussels

Environmental DNA (eDNA) offers a sensitive tool for detecting aquatic species, including those at low population densities. However, effective use of eDNA in conservation and monitoring efforts requires an understanding of detection probabilities and optimal replication effort necessary to minimize false negatives. This study assessed the probability of detecting Anodonta nuttalliana, a native freshwater mussel, in two Utah populations with contrasting densities (medium and low). We conducted traditional visual sampling alongside highly replicated eDNA sampling at both sites. In the medium-density population, eDNA provided high detection probabilities with minimal replication. However, in the low-density population, substantially greater replication was needed to achieve similar detection probabilities. Despite the increased eDNA replication effort needed to detect the low-density population, eDNA outperformed traditional visual sampling, which failed to detect live mussels at the low-density site. Our findings highlight the critical balance between sampling effort and detection success, offering guidance for optimizing eDNA sampling strategies in monitoring efforts, especially for species which occur at low densities.

zoology↗

bioRxiv2024

A novel degenerate primer set for eDNA metabarcoding of amphibians, turtles and fish

Metabarcoding of environmental DNA (eDNA) has revolutionized the detection of aquatic species across large geographic scales. However, the effectiveness of eDNA metabarcoding across taxa is marker-dependent, often requiring multiple markers to detect divergent taxonomic groups. Here, we introduce a novel metabarcoding marker designed to simultaneously detect amphibians, turtles, and fish from eDNA samples. We initially optimized this marker to match species from central and southern California, USA, and conducted validation on 525 field-collected eDNA samples from central California, while also testing an existing published amphibian marker from the literature. Additionally, we assessed the global applicability of the marker with in-silico analysis through comparison with 11,350 amphibian, turtle, and fish mitochondrial genomes downloaded from GenBank. Field validation demonstrated the markers robustness in detecting aquatic vertebrates, outperforming the published marker in sensitivity, particularly for turtles and fish. In-silico evaluation demonstrated the potential for global use of this marker, indicating broad applicability for amplifying eDNA from amphibians, turtles, and fish worldwide. Our findings highlight the utility of this novel marker for monitoring of aquatic vertebrate communities, with implications for conservation, management, and ecological research.

ecology↗

bioRxiv2022

Multiplex qPCR assays for detection of Anaxyrus californicus and Spea hammondii from environmental DNA

We developed a species-specific, quantitative PCR assay multiplex for the detection of two threatened and endangered anuran species, arroyo toad (Anaxyrus californicus) and western spadefoot (Spea hammondii), from environmental DNA (eDNA). Both species have experienced range wide declines over the last century, mostly as a result of habitat loss. Given these declines and their cryptic life histories, improved tools for detecting and monitoring both species are needed. Species-specificity and sensitivity of assays were empirically tested in the lab, and the multiplexed assays were validated with field-collected eDNA samples. Both assays were species-specific, sensitive, and effectively detected the target species from streams, rivers and ponds, although detection was imperfect. These assays provide an efficient and economical tool that will aid in the detection, monitoring, management, and conservation of these at-risk species.

zoology↗

bioRxiv2020

Detection of four imperiled western North American freshwater mussel species from environmental DNA with multiplex qPCR assays

We developed multiplexed, species-specific, quantitative PCR assays for the detection of four freshwater mussel species native to western North America, Gonidea angulata, Margaritifera falcata, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA (eDNA). These species have experienced dramatic declines over the last century and are currently threatened in many portions of their ranges. Therefore, improved tools for detecting and monitoring these species are needed. Species-specificity and sensitivity of assays were empirically tested in the lab, and multiplex assays were also validated with field collected eDNA samples. All assays were species-specific, sensitive, and effective for detection from eDNA samples collected from streams and rivers. These assays will aid in the detection, monitoring, management, and conservation of these vulnerable species.View Full Text

zoology↗

bioRxiv2018

qPCR assays for the detection of two western North American freshwater mussel species, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA

We developed species-specific quantitative PCR assays for the detection of two freshwater mussel species native to the western North America, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA. These species have experienced dramatic declines over the last century, and are currently threatened in many portions of their range. Improved tools for detecting and monitoring these species are needed. Species-specificity and sensitivity of the assays was empirically tested in the lab, and both assays were also validated with field collected eDNA samples. We found that the assays we designed are species-specific, sensitive, and are effective for detecting Anodonta nuttalliana and Anodonta oregonensis from environmental DNA samples collected from streams and rivers. These assays will aid in the detection, monitoring, management, and conservation of these threatened species.

zoology↗

bioRxiv2017

Carrion Fly-Derived DNA Metabarcoding Is An Effective Tool For Mammal Surveys: Evidence From A Known Tropical Mammal Community

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, which were pooled into 102 DNA extractions. We then conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers targeting mtDNA, and sequenced these amplicons on Illumina MiSeq. For taxonomic assignment, we compared BLAST with the new program PROTAX, and we found PROTAX significantly improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which were previously known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera-trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera-trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys, and has the potential to detect a broader range of species than more commonly used methods.

zoology↗

bioRxiv2017

Quantitative PCR assays for detection of five Alaskan fish species: Lota lota, Salvelinus alpinus, Salvelinus malma, Thymallus arcticus, and Cottus cognatus from environmental DNA

The North Slope of Alaska contains arctic fish populations that are important for subsistence of local human populations, and are under threat from natural resource extraction and climate change. We designed and evaluated four quantitative PCR assays for the detection of environmental DNA from five Alaskan fish species present on the North Slope of Alaska: burbot (Lota lota), arctic char (Salvelinus alpinus), Dolly Varden (Salvelinus malma), arctic grayling (Thymallus arcticus), and slimy sculpin (Cottus cognatus). All assays were designed and tested for species specificity and sensitivity, and all assays detected target species from filtered water samples collected from the field. These assays will enable efficient and economical detection and monitoring of these species in lakes and rivers. This in turn will provide managers with improved knowledge of current distributions and future range shifts associated with climate and development threats, enabling more timely management.

zoology↗