Biology subjects

Mock, K. E.

Publications and source records attributed to Mock, K. E..

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↗

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

Mosaic of Somatic Mutations in the Ancient and Still-Living Aspen Clone, Pando

While evolutionary biology traditionally focuses on the spread of mutations within populations, the dynamics of mutational spread within individuals, particularly in long-lived clonally-spreading organisms, remain poorly understood. Here we examine the genetic structure of Pando, Earths largest known quaking aspen (Populus tremuloides) clone. We sequenced over 500 samples across Pando and neighboring clones, including multiple tissue types. At fine spatial scales, we detected significant genetic structure, particularly in leaf tissue, but this signal weakened across larger distances, suggesting either rapid root growth homogenizes the system over time or mechanisms exist that prevent widespread mutation transmission. Phylogenetic analyses date Pando between [~]12,000 and 37,000 years old, supported by continuous aspen pollen presence in nearby lake sediments. Tissues accumulated mutations at different rates, with leaves showing significantly higher mutation loads than roots or branches. This work provides the first quantitative age estimate for this remarkable organism and offers initial insights into the spatial dynamics of somatic mutation in a massive clonal plant. While our reduced-representation sequencing approach limits detection of rare variants, these findings establish a foundation for understanding how long-lived modular organisms accumulate and distribute genetic variation, questions that will benefit from future high-coverage whole-genome sequencing across tissues.

evolutionary biology↗

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

Genetic variation at the species and population levels in the Rocky Mountain ridged mussel (Gonidea angulata)

Freshwater mussels in western North America are threatened by water diversions, climate change, loss of required host fish, and other factors, and have experienced marked decline in the past several decades. All four of the primary lineages (potentially species) of freshwater mussels in the western U.S. and Canada are widespread and have somewhat generalist host fish requirements. Of these lineages, perhaps the most poorly understood and of greatest conservation concern is Gonidea angulata (Rocky Mountain ridged mussel). Gonidea is a monotypic genus occurring only in the western continental U.S. and southern Canada. Here we describe the patterns of genetic variation across the species range, including several populations in the Okanagan Valley at the northern edge of the range. We detected only ten mitochondrial cytochrome oxidase I haplotypes, three of which ere commonly found across major hydrologic basins, and the remainder of which were basin-specific variants. Haplotypes differed by a maximum of 5 of 537 nucleotides. New microsatellite loci were developed for G. angulata as a part of this study. Data from these microsatellite loci indicated that the population in the Chehalis River, Washington, was distinct from other locations, and that the Okanagan lake population was somewhat diverged from the remaining populations in the Columbia River and Klamath Lake. Only low levels of inbreeding were detected, in contrast to previous findings in Margartifera falcata, suggesting that hermaphroditism is not common. The population with the least diversity, according to microsatellite data, was the northernmost known population in Okanagan Lake We discuss the biogeographic and conservation implications of our findings.

ecology↗

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

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↗