Reduction of Automobile and Aircraft Collisions with Wildlife in Indiana

Conflicts between wildlife and human interests have increased in recent decades due to growing human populations and the resulting expansion of anthropogenic pressures into wildlife habitat. Our overall objectives were to evaluate the the potential impacts of wildlife on transportation in Indiana and vice-versa. The results presented in this final report summarize two aspects of our research: the impact of automotive traffic on wildlife (“road kill”; Part I), and the wildlife hazards present at general aviation airports around the state (“airstrike”; Part II). The road kill dataset indicated that at 13 survey routes traversing 180 linear km of road, 11,068 animals were killed by traffic. These animals included mammals, birds, reptiles, and (mostly) amphibians. GIS data indicates that nearby wetlands were typically associated with a high incidence of road kill. While road kills were detected in all months, there were obvious seasonal and weather related patterns in the data. Most road kills occurred from July through September, which was concurrent with peak temperatures and precipitation levels. We highlight a variety of animal-friendly engineering options that can be used to effectively reduce encounters between wildlife and drivers, resulting in fewer accidents and less road kill. With regard to the airstrike dataset, airport habitats consisted mainly of short grass (40.2% of total airport area), soybean fields (10.3%), corn fields (9.5%), runway systems (8.1%), other development (6.6%), woodlots (5.2%), medium grass (4.8%), tall grass (4.6%), and hayfields (3.2%). At least two types of wildlife attractants were present at each airport property, and the most common wildlife attractants included standing water (ephemeral), open culverts, crop fields, woodlot refugia, and gravel piles. Proportion of airport perimeters fenced ranged from 7.5% to 100%, but most airport perimeters were \u3e40% fenced. Most airports with \u3e25% of the perimeter enclosed by chain-link fencing had 0.2-0.5 openings per 100 m of fence, with gaps and dig-holes being the most common openings. Considering the most hazardous species, 0-92 white-tailed deer and 0-28 coyotes were observed at individual airports combining all survey methods across a year. Of 16 bird species groups identified as hazardous to aircraft, American kestrel, blackbirds-starling, crows-ravens, mourning dove, shorebirds, sparrows, and swallows were present at 9-10 of the airport properties; geese, hawks (buteos), and vultures were present at 7-8 of the airport properties; and ducks, herons, and rock doves were present at 5-6. Questionnaires indicated that pilots using focal airports were accustomed to wildlife hazards: 69% of respondents reported that they had altered aircraft operation due to wildlife within the past year, and 25% reported involvement in a wildlife strike during the past year. Furthermore, 88% of respondents felt that wildlife populations at Indiana airports were at least “somewhat hazardous”. Despite pilots’ awareness of wildlife hazards, less than 70% of respondents supported the use of fencing or wildlife deterrents, 43% supported modification/elimination of wildlife habitat, and only 38% of respondents supported for lethal removal of wildlife on airport properties. Hazards associated with deer and coyotes can be alleviated by installing suitable fencing; for airports with extant fences, care should be taken to monitor fences regularly and repair gaps as soon as they are discovered. Presence of deer and coyotes inside airport fences should not be tolerated. Birds are best managed by maintaining airport habitats in a manner that minimizes availability and/or quality of food, water, cover, and loafing sites for hazardous species. Furthermore, several new technologies and refinements in techniques for wildlife damage management at airports have emerged recently and may benefit small airports, such as advancements in electric fencing and the use of dead bird effigies to repel some hazardous bird species

A review of mitigation measures for reducing wildlife mortality on roadways

A growing literature in the field of road ecology suggests that vehicle/wildlife collisions are important to biologists and transportation officials alike. Roads can affect the quality and quantity of available wildlife habitat, most notably through fragmentation. Likewise, vehicular traffic on roads can be direct sources of wildlife mortality and in some instances, can be catastrophic to populations. Thus, connectivity of habitat and permeability of road systems are important factors to consider when developing road mortality mitigation systems. There are a variety of approaches that can be used to reduce the effects of roads and road mortality on wildlife populations. Here, we briefly review wildlife-crossing structures, summarize previous wildlife road mortality mitigation studies, describe common mitigation measures, and discuss factors that influence the overall effectiveness of mitigation strategies. Because there are very few road mortality studies “before” and “after” the installation of wildlife-crossing structures, their efficiency is nearly impossible to evaluate. However, simple and relatively inexpensive measures reviewed herein can almost certainly reduce the number of collisions between wildlife and automobile

Captive Breeding Protocols and Their Impact on Genetic Diversity in White-footed Mice (Peromyscus leucopus): Implications for Threatened and Endangered Species

Captive breeding protocols used in zoos often are aimed at increasing population sizes and retaining genetic diversity of endangered species. However, captive breeding causes genetic adaptation to captivity that can lead to an overall decrease in genetic diversity and reduce chances of a successful reintroduction to the wild. In this study, we assess how 3 different breeding protocols—random mating, preferential breeding of individuals with the lowest mean kinship scores, and selection for docility—affect the variability of mitochondrial DNA in white-footed mice (Peromyscus leucopus). We used mice that were captured from the wild but were mated for up to 20 generations using one of the aforementioned breeding protocols. Using animals from generations 0, 6, and 19, as well as the wild source population, we sequenced the mitochondrial D-loop in 2 replicate populations representing each of the 3 breeding protocols. Initial sequences indicate there is genetic variation at this mitochondrial locus, and further sequencing will allow us to quantify the genetic diversity maintained under each breeding protocol. These results will increase our understanding of the decline in genetic diversity due to adaptation to captivity. Thus, our results will have direct relevance for the maintenance and growth of zoo populations of critically endangered species

Genetic relationships of Caribbean lowland spiny pocket mice (Heteromys desmarestianus: Rodentia; Heteromyidae): evidence of a distinct mitochondrial lineage

Genetic studies provide important insights into the evolutionary history and taxonomy of species, allowing us to identify lineages dif-ficult to distinguish morphologically. The relationships among species in the genus Heteromys have been in flux as new species have been described, and candidate species have been suggested in the H. desmarestianus group. One new potential species may be in Costa Rica’s Carib-bean lowlands. Herein, we test the phylogenetic relationships of individuals from Costa Rica’s Caribbean lowlands to individuals from through-out the species’ range using mitochondrial sequences from cytochrome-b (cytb). We captured 116 individuals from the lowlands, sequenced their cytb gene, and incorporated 74 GenBank sequences from throughout the species’ range to test if individuals from Costa Rica’s Caribbean lowlands potentially constitute an undescribed species. Our results document a distinct mitochondrial lineage in the Caribbean lowlands of Costa Rica. Our results from extensive sampling within the lowlands show a unique mitochondrial DNA lineage, which suggests the presence of an undescribed species. The Caribbean lowlands of Costa Rica may hold other cryptic diversity, and further phylogenetic studies should incorporate samples from this area, as it may have a unique evolutionary history. Los estudios genéticos proporcionan información importante sobre la historia evolutiva y la taxonomía de las especies, lo que nos permite identificar linajes difíciles de distinguir morfológicamente. Las relaciones filogenéticas entre las especies del género Heteromys han estado cambiando a medida que se han descrito nuevas especies y se han sugerido especies candidatas en el grupo H. desmarestianus. Una nueva especie potencial podría encontrarse en las tierras bajas del Caribe de Costa Rica. En este trabajo analizamos las relaciones filogenéticas entre individuos de las tierras bajas del Caribe de Costa Rica con individuos de todo el rango de la especie utilizando secuencias mitocondriales del citocromo-b (cytb). Capturamos 116 individuos de las tierras bajas, secuenciamos su gen cytb e incorporamos 74 secuencias GenBank de todo el área de distribución de la especie para probar si los individuos de las tierras bajas del Caribe de Costa Rica constituyen potencialmente una especie no descrita. Nuestros resultados indican la presencia de un linaje distinto basado en el ADN mitocondrial, que sugiere que los indivi-duos de las tierras bajas del Caribe de Costa Rica probablemente son una especie distinta. Las tierras bajas del Caribe de Costa Rica pueden tener una diversidad críptica significativa. Por ello sugerimos que estudios filogenéticos adicionales deberían incorporar muestras de esta área, ya que puede tener una historia evolutiva única

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (<it>Acipenser fulvescens</it>) gonads.</p> <p>Results</p> <p>Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (~19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 candidate SNPs were identified from > 50 different genes. We employed an analytical approach from theoretical ecology (rarefaction) to evaluate depth of sequencing coverage relative to gene discovery. We also considered the relative merits of normalized versus native cDNA libraries when using next-generation sequencing platforms. Not surprisingly, fewer genes from the normalized libraries were rRNA subunits. Rarefaction suggests that normalization has little influence on the efficiency of gene discovery, at least when working with thousands of reads from a single tissue type.</p> <p>Conclusion</p> <p>Our data indicate that titration runs on 454 sequencers can characterize thousands of expressed sequence tags which can be used to identify SNPs, gene ontologies, and levels of gene expression in species of conservation concern. We anticipate that rarefaction will be useful in evaluations of gene discovery and that next-generation sequencing technologies hold great potential for the study of other non-model organisms.</p

Influences of multilocus heterozygosity on size during early life

Genetic diversity has been hypothesized to promote fitness of individuals and populations, but few studies have examined how genetic diversity varies with ontogeny. We examined patterns in population and individual genetic diversity and the effect of genetic diversity on individual fitness among life stages (adults and juveniles) and populations of captive yellow perch (Perca flavescens) stocked into two ponds and allowed to spawn naturally. Significant genetic structure developed between adults and offspring in a single generation, even as heterozygosity and allelic richness remained relatively constant. Heterozygosity had no effect on adult growth or survival, but was significantly and consistently positively related to offspring length throughout the first year of life in one pond but not the other. The largest individuals in the pond exhibiting this positive relationship were more outbred than averaged size individuals and also more closely related to one another than they were to average‐sized individuals, suggesting potential heritability of body size or spawn timing effects. These results indicate that the influence of heterozygosity may be mediated through an interaction, likely viability selection, between ontogeny and environment that is most important during early life. In addition, populations may experience significant genetic change within a single generation in captive environments, even when allowed to reproduce naturally. Accounting for the dynamic influences of genetic diversity on early life fitness could lead to improved understanding of recruitment and population dynamics in both wild and captive populations.Heterozygosity is assumed to increase the fitness of individuals throughout life, but ontogenetic variance in heterozygosity–fitness correlations (HFCs) is poorly understood. We observed significant differences in HFCs between yellow perch populations and among life stages, suggesting the influence of heterozygosity may be mediated through an interaction, likely viability selection, between ontogeny and environment that is most important during early life. Accounting for the dynamic influences of genetic diversity on early life fitness could lead to improved understanding of recruitment and population dynamics in both wild and captive populations.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136477/1/ece32781.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136477/2/ece32781_am.pd

Next-generation metrics for monitoring genetic erosion within populations of conservation concern

This work was conducted as a part of the Next-generation Genetic Monitoring Working Group at the National Institute for Mathematical and Biological Synthesis, sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Emma Carrol was supported by a Marie Slodowska Curie Fellowship, (Behaviour-Connect) funded by the EU Horizon2020 program. MWB was supported by a Royal Society Wolfson research merit award. LW was supported by the University of Idaho. This research was supported in part by NSF awards 1355106 and 1357386 to AES.Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene-flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management-relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.Publisher PDFPeer reviewe

Is Sexual Monomorphism a Predictor of Polygynandry? Evidence from a Social Mammal, the Collared Peccary

Sexual dimorphism is common in polygynous species, and there is clear evidence that both intra-sexual competition and female preferences can drive the evolution of large body size in males. In contrast, sexual monomorphism is often argued to reflect a relaxation of male mate competition or an intensification of resource competition among females. Alternatively, it might imply opportunities for females to circumvent or counteract male mate competition in a polygynandrous mating system. We test the prediction that sexual monorphism is associated with polygynandry in the collared peccary (Pecari tajacu, Tayassuidae), a social ungulate closely related to the old-world suids. The genetic mating system in the Tayassuidae is unknown, but its sexual monomorphism presents a striking contrast to the strong size dimorphism found in most Suidae, so that a departure from the polygynous system common in Suidae would be noteworthy. We characterized genetic relationships among adults within herds in three geographically distinct populations, assigned parents to 75 offspring, and tested for skew in individual reproductive success. Parentage assignment data indicated that multiple males sire offspring within a herd, and in the population for which genetic data were most complete, 19% of parentage assignments were potentially sired by extra-herd males. Some litters have multiple sires, and neither males nor females monopolized reproduction, even in small herds. This result supports our prediction and suggests that sexual monomorphism may either select for or be an evolutionary consequence of a promiscuous mating system

High-Pitched Notes during Vocal Contests Signal Genetic Diversity in Ocellated Antbirds

Animals use honest signals to assess the quality of competitors during aggressive interactions. Current theory predicts that honest signals should be costly to produce and thus reveal some aspects of the phenotypic or genetic quality of the sender. In songbirds, research indicates that biomechanical constraints make the production of some acoustic features costly. Furthermore, recent studies have found that vocal features are related to genetic diversity. We linked these two lines of research by evaluating if constrained acoustic features reveal male genetic diversity during aggressive interactions in ocellated antbirds (Phaenostictus mcleannani). We recorded the aggressive vocalizations of radiotagged males at La Selva Biological Station in Costa Rica, and found significant variation in the highest frequency produced among individuals. Moreover, we detected a negative relationship between the frequency of the highest pitched note and vocalization duration, suggesting that high pitched notes might constrain the duration of vocalizations through biomechanical and/or energetic limitations. When we experimentally exposed wild radiotagged males to simulated acoustic challenges, the birds increased the pitch of their vocalization. We also found that individuals with higher genetic diversity (as measured by zygosity across 9 microsatellite loci) produced notes of higher pitch during aggressive interactions. Overall, our results suggest that the ability to produce high pitched notes is an honest indicator of male genetic diversity in male-male aggressive interactions