Biology subjects

Harris, N. C.

Publications and source records attributed to Harris, N. C..

13 recordsLinked to original sources

bioRxiv2024

Key unprotected areas for carnivore conservation in Mexico

Area-based conservation remains a pivotal component of global wildlife protection efforts. Mexico hosts a diverse array of area-based approaches, encompassing protected areas (PAs) and other effective area-based conservation measures (OECMs) such as voluntary conservation areas (VCAs) and wildlife management units (UMAs). Indigenous Territories (ITs) also provide heightened conservation potential through traditional ecological knowledge systems. These conservation spaces exhibit significant variations in community involvement, national coverage, and governance. Here, we evaluate the conservation potential of these land management types for 29 terrestrial carnivores, focusing on spatial co-occurrence. We determine areas in Mexico lacking area-based protection and calculate carnivore richness per land management type. Analyzing overlap between land management types and carnivore ranges, we employ heat maps to visualize overlap occurrence and key unprotected areas. We found that across all carnivore ranges, 87% of the area remains unprotected under designated protection areas (PAs & VCAs), decreasing to 65.2% after including non-designated types (ITs and UMAs). We identified several key gaps in the protection estate for Mexican carnivores, most notably on the eastern Mexican coast in the state of Veracruz. Our findings corroborate the importance of including Indigenous Peoples and Local Communities in conservation efforts, emphasizing their contributions to the stewardship of Mexican ecosystems. As the global protected area estate continues to expand under the post-2020 global biodiversity targets, and the importance of a well-designed and diverse portfolio of practices for conservation is recognized, the need for collective action, increased collaboration and inclusivity, and effective communication amongst stakeholders becomes necessary for carnivore conservation.

ecology↗

bioRxiv2020

Downtown Diet: a global meta-analysis of urbanization on consumption patterns of vertebrate predators

Predation is a fundamental ecological process that shapes communities and drives long-term evolutionary dynamics. As the world rapidly urbanizes, it is critical to understand how the built environment and other human perturbations alter predation across taxa. We conducted a meta-analysis to quantify the effects of urban environments on three components of trophic ecology in predators: dietary species richness (DSR), dietary evenness (DEV), and stable isotopic ratios ({delta}13C and {delta}15N IR). We then evaluated whether intensity of anthropogenic pressure, using the human footprint index (HFI), explained variation in the effect sizes of dietary attributes using a meta-regression. We calculated Hedges g effect sizes from 44 studies including 11,986 samples across 40 predatory species in 39 cities globally. The direction and magnitude of effect sizes varied between predator taxonomic groups with reptile diets exhibiting the most sensitivity to urbanization. Effect sizes revealed that predators in cities had comparable DSR, DEV, and nitrogen ratios, though carbon consumption was significantly higher. We found that HFI did not explain variation in effect sizes, a result consistent between the 1993 and 2009 editions of this metric. Our study provides the first assessment of how urbanization has perturbed predator-prey interactions for multiple taxa at a global scale, revealing that the functional role of predators is conserved in cities and urbanization does not inherently relax predation.

ecology↗

bioRxiv2020

Patch characteristics and domestic dogs differentially affect carnivore space use in fragmented landscapes in Southern Chile

In an increasingly anthropogenic world, native species face multiple interacting threats. Habitat fragmentation and domestic dogs are two such perturbations threatening terrestrial mammals globally. Here, we implemented a camera trap survey in the fragmented central valley/Andean foothills transition of the Los Lagos Region in Southern Chile to evaluate space use of native carnivores in a landscape comprised of patches of native forest amidst a matrix of pastureland. Using an occupancy modeling framework to account for imperfect detection, we examined the impacts of dogs and landscape metrics of fragmentation on three mesocarnivores - the foxes culpeo (Lycalopex culpaeus) and chilla (Lycalopex griseus) and the wild cat guina (Leopardus guigna). Factors driving occupancy differed for each of the native species, while detection rates for both canid species increased with dog occupancy. We found that a small (12%) simulated increase in dog occupancy negatively impacted the spatial use of the culpeo. Habitat loss and fragmentation were positive drivers for the chilla and the dog, and indirectly impacted the culpeo through the domestic dog. The guina did not respond to fragmentation and other habitat covariates or dog occupancy. Instead, all native carnivore species temporally partitioned diel activity with dogs. We highlight that the effects of dogs or fragmentation are not ubiquitous across the carnivore guild with varied tolerance. However, future conditions of increased fragmentation and habitat loss will likely increase the potential contact between domestic dogs and native carnivores.

ecology↗

bioRxiv2020

Living in the concrete jungle: carnivore spatial ecology in urban parks

People and wildlife are living in an increasingly urban world, replete with unprecedented human densities, sprawling built environments, and altered landscapes. Such anthropogenic pressures can affect multiple processes within an ecological community, from spatial patterns to interspecific interactions. We tested two competing hypotheses, human shields versus human competitors, to characterize how humans affect the carnivore community using multi-species occupancy models. From 2017-2020, we conducted the first camera survey of city parks in Detroit, Michigan, and collected spatial occurrence data of the local native carnivore community. Our 12,106-trap night survey captured detected data for coyotes (Canis latrans), red foxes (Vulpes vulpes), gray foxes (Urocyon cinereoargenteus), raccoons (Procyon lotor), and striped skunks (Mephitis mephitis). Overall occupancy varied across species ({Psi}coyote=0.40, {Psi} raccoon=0.54, {Psi}red fox =0.19, {Psi}striped skunk =0.09). Contrary to expectations, humans did not significantly affect individual occupancy for these urban carnivores. However, co-occurrence between coyote and skunk only increased with human activity. The observed positive spatial association between an apex and subordinate pair supports the human shield hypothesis. Our findings demonstrate how urban carnivores can exploit spatial refugia and coexist with humans in the cityscape.

ecology↗

bioRxiv2020

Vigilance response of a key prey species to anthropogenic and natural threats in Detroit

Rapid urbanization coupled with increased human activity induces pressures that affect predator-prey relations through a suite of behavioral mechanisms, including alteration of avoidance and coexistence dynamics. Synergisms of natural and anthropogenic threats existing within urban environments exacerbate the necessity for species to differentially modify behavior to each risk. Here, we explore the behavioral response of a key prey species, cottontail rabbits (Sylvilagus floridanus), to pressures from humans, domestic dogs, and a natural predator, coyotes (Canis latrans) in a human-dominated landscape. We conducted the first camera survey in urban parks throughout Detroit, Michigan in 2017-2020 to assess vigilance response corresponding to a heterogeneous landscape created from variation in the occupancy of threats. We predicted a scaled response where cottontail rabbits would be most vigilant in areas with high coyote activity, moderately vigilant in areas with high domestic dog activity, and the least vigilant in areas of high human activity. From 8,165 independent cottontail rabbit detections in Detroit across 11,616 trap nights, one-third were classified as vigilant. We found vigilance behavior increased with coyote occupancy and in locations with significantly high domestic dog activity, but found no significant impact of human occupancy or their spatial hotspots. We also found little spatial overlap between rabbits and threats, suggesting rabbits invest more in spatial avoidance; thus, less effort is required for vigilance. Our results elucidate strategies of a prey species coping with various risks to advance our understanding of the adaptability of wildlife in urban environments. In order to promote coexistence between people and wildlife in urban greenspaces, we must understand and anticipate the ecological implications of human-induced behavioral modifications.

ecology↗

bioRxiv2020

Humans induce differential access to prey for large African carnivores

Wildlife adaptively respond to human presence by adjusting their temporal niche, possibly modifying encounter rates among species and trophic dynamics that structure communities. Here we show that these human-induced modifications to behaviours are prolific among species and alter apex predators access to prey resources. We assessed human-induced changes to wildlife diel activity and consequential changes in predator-prey overlap using 11,954 detections of three apex predators and 13 ungulates across 21,430 trap-nights in West Africa. Over two-thirds of species altered their diel use in response to human presence, and ungulate nocturnal activity increased by 6.8%. Rather than traditional pairwise predator-prey comparisons, we considered spatiotemporally explicit predator access to a suite of prey resources to evaluate community-level trophic responses to human presence. Although leopard prey access was not affected, lion and hyena access to 3 prey species significantly increased when prey increased their nocturnal temporal niche to avoid humans. Ultimately, humans considerably altered the composition of available prey, with implications for prey selection, demonstrating how humans perturb ecological processes via behavioural modifications.

ecology↗

bioRxiv2020

Fear not: avoidance behavior missing in species sympatric with the critically endangered West African lion

Predators are major regulators in communities through trophic and non-trophic pathways. However, as human pressures continue to threaten apex predators, including Africas iconic lion, predators functional role in their ecosystems may be compromised. Where lions are critically endangered, we found no evidence of avoidance behavior in either competitor or prey species from a camera survey in the largest protected area complex in West Africa. Our findings raise concerns that lions have already become functionally extinct in portions of their West African range, highlighting the urgency of restorative efforts and environmental investments to reverse current declining population trends and the loss of regulatory roles.

ecology↗

bioRxiv2020

Gastrointestinal parasite community in the critically endangered West African lion

Large carnivores of Africa, such as lions (Panthera leo), suffer from prey depletion and habitat fragmentation, that possibly impact the composition of the gastrointestinal parasite community. West African lions are particularly important, as this population is critically endangered and yet little is known of their gastrointestinal parasite community, which can reflect the health and resilience of the host population. From fecal samples collected in the W-Arly-Pendjari (WAP) transboundary protected area complex in Burkina Faso and Niger, we identified 309 oocysts of at least five different species using fecal flotation and sedimentation tests. We also compared these gastrointestinal parasites to other results from surveys of lions from Southern and East African regions and found similar taxa to previous surveys, but lower species richness across West African samples.

ecology↗

bioRxiv2020

Michigan ZoomIN: validating crowd-sourcing to identify mammals from camera surveys

Camera trap studies have become a popular medium to assess many ecological phenomena including population dynamics, patterns of biodiversity, and monitoring of endangered species. In conjunction with the benefit to scientists, camera traps present an unprecedented opportunity to involve the public in scientific research via image classifications. However, this engagement strategy comes with a myriad of complications. Volunteers vary in their familiarity with wildlife, and thus, the accuracy of user-derived classifications may be biased by the commonness or popularity of species and user-experience. From an extensive multi-site camera trap study across Michigan U.S.A, images were compiled and identified through a public science platform called Michigan ZoomIN. We aggregated responses from 15 independent users per image using multiple consensus methods to assess accuracy by comparing to species identification completed by wildlife experts. We also evaluated how different factors including consensus algorithms, study area, wildlife species, user support, and camera type influenced the accuracy of user-derived classifications. Overall accuracy of user-derived classification was 97%; although, several canid (e.g., Canis lupus, Vulpes vulpes) and mustelid (e.g., Neovison vison) species were repeatedly difficult to identify by users and had lower accuracy. When validating user-derived classification, we found that study area, consensus method, and user support best explained accuracy. To continue to overcome stigma associated with data from untrained participants, we demonstrated their value by showing the accuracy from volunteers was comparable to experts when classifying North American mammals. Our hierarchical workflow that integrated multiple consensus methods lead to more image classifications without extensive training and even when the expertise of the volunteer was unknown. Ultimately, adopting such an approach can harness broader participation, expedite future camera trap data synthesis, and improve allocation of resources by scholars to enhance performance of public participants and increase accuracy of user-derived data.

ecology↗

bioRxiv2020

Temporal refuges differ between anthropogenic and natural top down pressures in a subordinate carnivore

Apex predators structure communities through consumptive and non-consumptive pathways. In the carnivore guild, this can result in a within-guild cascade through the suppression of mesocarnivores. As the top-down influences of apex predators wane due to human-driven declines, landscape level anthropogenic pressures are rising. Human impacts can be analogous to apex predators in that humans can drive increased mortality in both prey species and carnivores, and impact communities through indirect fear effects and food subsidies. Here, we evaluate whether anthropogenic top-down pressures can structure communities in a similar manner as apex predators in shaping the interactions of mesocarnivores. Specifically, we expect anthropogenic forces to induce comparable effects as occurrence of apex predators in driving spatiotemporal partitioning between two mesocarnivores. Using multiple camera-trap surveys, we compared the temporal response of a small carnivore, the raccoon (Procyon lotor), to the larger coyote (Canis latrans) at four sites across Michigan that represented opposing gradients of pressure from humans and apex predators. Contrary to our expectations, we found that raccoons shifted their activity pattern in response to coyotes at sites with higher anthropogenic pressures and exhibited no temporal response at sites with apex predators. Temporal shifts were characterized by raccoons being more diurnal in areas of high coyote activity. We conclude that despite superficial similarities, anthropogenic forces do not replace the function of native apex predators in structuring the mesocarnivore guild. As such, an intact and functioning native predator guild remains necessary to preserve spatiotemporal community structure, in natural and disturbed systems alike.

ecology↗

bioRxiv2018

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

The lysine metabolism of Pseudomonas putida can produce multiple important commodity chemicals and is implicated in rhizosphere colonization. However, despite intensive study, the biochemical and genetic links between lysine metabolism and central metabolism remain unresolved in P. putida. Here, we leverage Random Barcode Transposon Sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes in both L- and D-lysine metabolism. We first describe three pathway enzymes that catabolize 2-aminoadipate (2AA) to 2-ketoglutarate (2KG) connecting D-lysine to the TCA cycle. One of these enzymes, PP_5260, contains a DUF1338 domain, a family without a previously described biological function. We demonstrate PP_5260 converts 2-oxoadipate (2OA) to 2-hydroxyglutarate (2HG), a novel biochemical reaction. We expand on recent work showing that the glutarate hydroxylase, CsiD, can co-utilize both 2OA and 2KG as a co-substrate in the hydroxylation of glutarate. Finally we demonstrate that the cellular abundance of D- and L-lysine pathway proteins are highly sensitive to pathway specific substrates. This work demonstrates the utility of RB-TnSeq for discovering novel metabolic pathways in even well-studied bacteria.\n\nImportanceO_LIP. putida is an attractive host for metabolic engineering as its lysine metabolism can be utilized for the production of multiple important commodity chemicals.\nC_LIO_LIWe demonstrate the first biochemical evidence of a bacterial 2OA catabolic pathway to central metabolites.\nC_LIO_LIDUF1338 proteins are widely dispersed across many kingdoms of life. Here we demonstrate the first biochemical evidence of function for a member of this protein family.\nC_LI

microbiology↗

bioRxiv2018

Isonitrile Formation by a Non-heme Iron(II)-dependent Oxidase/Decarboxylase

The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We here provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, members of which are critical for the virulence of pathogenic mycobacteria.

biochemistry↗

bioRxiv2017

Biosynthesis of Isonitrile Lipopeptides by Conserved Non-ribosomal Peptide Synthetase Gene Clusters in Actinobacteria

A putative lipopeptide biosynthetic gene cluster is conserved in many species of Actinobacteria, including Mycobacterium tuberculosis and M. marinum, but the specific function of the encoding proteins has been elusive. Using both in vivo heterologous reconstitution and in intro biochemical analyses, we have revealed that the five encoding biosynthetic enzymes are capable of synthesizing a new family of isonitrile lipopeptides (INLPs) through a thio-template mechanism. The biosynthesis features the generation of isonitrile from a single precursor Gly promoted by a thioesterase and a non-heme iron(II)-dependent oxidase homologue, and the acylation of both amino groups of Lys by the same isonitrile acyl chain facilitated by a single condensation domain of a non-ribosomal peptide synthetase (NRPS). In addition, the deletion of INLP biosynthetic genes in M. marinum has decreased the intracellular metal concentration, suggesting the role of this biosynthetic gene cluster in metal transport.\n\nSignificance StatementMycobacterium tuberculosis is the leading causative agent of tuberculosis (TB), of which millions of deaths occur annually. A putative lipopeptide biosynthetic gene cluster has been shown to be essential for the survival of this pathogen in hosts, and homologous gene clusters have also been found in all pathogenic mycobacteria and other species of Actinobacteria. We have identified the function of these gene clusters in making a new family of isonitrile lipopeptides. The biosynthesis has several unique features, including an unprecedented mechanism for isonitrile synthesis. Our results have further suggested that these biosynthetic gene clusters play a role in metal transport, and thus have shed light on a new metal transport system that is crucial for virulence of pathogenic mycobacteria.

biochemistry↗