Avian genetic ecotoxicology: DNA of the canary in a coalmine

Abstract Genotoxic chemicals, through damage and alteration of the genetic material of wild organisms, pose significant threats to the persistence of wild animal populations. Their damaging effects can ultimately impair the health of the ecosystem and its provision of services to human society. Bird species are good candidates for the role of sentinels of the effects of genotox-ins, thanks to (i) the diversity of their ecological niches, (ii) their ubiquity across environments, (iii) their conspicuousness, abundance and approachability, together with (iv) their well-known life histories and the availability of historical data series. Avian diversity increases the likelihood that adequate model species be available for monitoring genotoxicants and assessing their impact. This paper reviews the methods utilized by genetic ecotoxicological studies of wild birds, highlighting their benefits and shortcomings. It also summarizes the genetic ecotoxicological studies so far conducted. In spite of a paucity of studies, several classes of genotoxicants have already been investigated across a variety of species and environments, thus supporting the versatility of birds as monitors of genotoxic contamination. Future technical advancements and applications are suggested, with particular reference to the analysis of mutational events, gene expression and methylation patterns. Finally, I argue that the development of avian genetic ecotoxicology will contribute to the understanding of natural variation in the underlying machinery for coping with DNA damage and oxidative stress, both of which are increasingly recognized as proximate factors in the evolution of life history adaptations.

Download Full-text

Limited Dispersal, Deleterious Mutations and the Evolution of Sex

Genetics ◽

10.1093/genetics/142.3.1053 ◽

1996 ◽

Vol 142 (3) ◽

pp. 1053-1060

Author(s):

Joel R Peck

Keyword(s):

Mathematical Model ◽

Sexual Reproduction ◽

Genetic Locus ◽

Genetic Material ◽

Plant Population ◽

Deleterious Mutations ◽

Animal Populations ◽

Offspring Sex ◽

Limited Dispersal ◽

Hermaphroditic Plant

Abstract This study presents a mathematical model that allows for some offspring to be dispersed at random, while others stay close to their mothers. A single genetic locus is assumed to control fertility, and this locus is subject to the occurrence of deleterious mutations. It is shown that, at equilibrium, the frequency of deleterious mutations in the population is inversely related to the rate of dispersal. This is because dispersal of offspring leads to enhanced competition among adults. The results also show that sexual reproduction can lead to a decrease in the equilibrium frequency of deleterious mutations. The reason for this relationship is that sex involves the dispersal of genetic material, and thus, like the dispersal of offspring, sex enhances competition among adults. The model is described using the example of a hermaphroditic plant population. However, the results should apply to animal populations as well.

Download Full-text

Morwell Coal Mine Fire as a Cascading Disaster: A Case Study

Prehospital and Disaster Medicine ◽

10.1017/s1049023x19000360 ◽

2019 ◽

Vol 34 (s1) ◽

pp. s8-s8 ◽

Cited By ~ 1

Author(s):

Dudley McArdle ◽

Caroline Spencer ◽

Frank Archer

Keyword(s):

Coal Mine ◽

Core Structure ◽

Disaster Mitigation ◽

Alternative View ◽

Human Society ◽

Adequate Model ◽

Mine Fire ◽

Sequence Of Events ◽

Coal Mine Fire

Introduction:Despite the influential Hyogo and Sendai Frameworks, risk remains poorly understood in the emergency preparedness sector. Hazard assessment and risk management are usually considered before events. An alternative view considers risk as a cascade of potential consequences throughout an event. The 2014 fire in the Victorian rural community of Morwell included a three-phased event: a small bush fire, from which embers ignited a persistent fire in a disused open cut brown coal mine fire. The consequent air pollution precipitated a public health emergency in the nearby community of 15,000 people.Aim:To examine this event as a case study to investigate concordance with accepted definitions and key elements of a cascading event.Methods:Selected literature informed a risk cascade definition and model as a framework to examine the key post-event public inquiries available in the public domain.Results:Informed by a Conceptual Framework for a Hazard Evolving into a Disaster (Birnbaum et al., 2015), Wong and colleagues promote a Core Structure of a Comprehensive Framework for Disaster Evaluation Typologies (Wong, 2017). This Core Structure provided an adequate model to examine the sequence of events in the Morwell event. Definitions of cascading effects is more complex (Zuccaro et al., 2018). Our analysis of the Morwell event used the authoritative definition of cascading disasters published by Pescaroli and Alexander (2015). Using this definition, the Morwell event increased in progression over time and generated unexpected secondary events of strong impact. The secondary events could be distinguished from the original source of disaster, and demonstrated failures of physical structures as well as inadequacy of disaster mitigation strategies, while highlighting unresolved vulnerabilities in human society.Discussion:The Morwell coal mine fire of 2014 reflects the key criteria of a cascading disaster and provides understandings to mitigate the consequences of similar events in the future.

Download Full-text

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

10.21203/rs.3.rs-20034/v3 ◽

2020 ◽

Author(s):

Agata Motyka-Pomagruk ◽

Sabina Zoledowska ◽

Agnieszka Emilia Misztak ◽

Wojciech Sledz ◽

Alessio Mengoni ◽

...

Keyword(s):

Comparative Genomics ◽

Large Scale ◽

De Novo ◽

Genetic Material ◽

Soft Rot ◽

Potato Production ◽

Core Gene ◽

Ecological Niches ◽

Dickeya Solani ◽

High Level

Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

Download Full-text

Urine as a high-quality source of host genomic DNA from wild populations

10.1101/2020.02.18.955377 ◽

2020 ◽

Author(s):

Andrew T. Ozga ◽

Timothy H. Webster ◽

Ian C. Gilby ◽

Melissa A. Wilson ◽

Rebecca S. Nockerts ◽

...

Keyword(s):

Genetic Material ◽

Population History ◽

Whole Genome ◽

Dental Calculus ◽

Wild Populations ◽

Multiple Sources ◽

Allelic Dropout ◽

Natural Habitats ◽

High Quality ◽

Animal Populations

AbstractThe ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as feces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.

Download Full-text

The emergence of tolerance of human disturbance in Neotropical birds

Journal of Tropical Ecology ◽

10.1017/s0266467419000282 ◽

2019 ◽

Vol 36 (1) ◽

pp. 1-5 ◽

Cited By ~ 2

Author(s):

Piotr Tryjanowski ◽

Jakub Z. Kosicki ◽

Martin Hromada ◽

Peter Mikula

Keyword(s):

North America ◽

Human Disturbance ◽

Escape Response ◽

Bird Species ◽

Small Scale ◽

Behavioural Plasticity ◽

Mato Grosso ◽

Animal Populations ◽

History Of ◽

Rapid Emergence

AbstractAnimals living close to human settlements more often experience disturbance, but also reduced predation risk. Because an escape response is costly, behavioural adjustments of animals in terms of increased tolerance of humans occurs and is often reported in the literature. However, most such studies have been conducted in and around long-existing cities in Europe and North America, on well-established animal populations. Here, we investigate the degree of tolerance of human disturbance across 132 bird species occurring in disturbed (small farms) and undisturbed (intact wetlands and grasslands) areas in Pantanal, Mato Grosso (Brazil), a region with only a very recent history of human-induced disturbance. We found a clear across-species trend toward higher tolerance of human disturbance in birds near farms when compared with birds in wild areas. Such a flexible and perhaps also rapid emergence of tolerance when facing small-scale and very recent human disturbance presumably involves learning and might be attributed to behavioural plasticity. The ability of birds to modify their degree of tolerance of human disturbance may play a key role in the facilitation of wildlife–human coexistence.

Download Full-text

The impact of novel lyssavirus discovery

Microbiology Australia ◽

10.1071/ma17006 ◽

2017 ◽

Vol 38 (1) ◽

pp. 17 ◽

Cited By ~ 18

Author(s):

Ashley C Banyard ◽

Anthony R Fooks

Keyword(s):

Rabies Virus ◽

Human Exposure ◽

Animal Health ◽

Potential Effect ◽

Human Populations ◽

Human Society ◽

Scientific Interest ◽

Animal Populations ◽

Potential Impact ◽

The Impact

The global discovery of novel lyssaviruses is of continued scientific interest through its importance to both public and animal health. Lyssaviruses cause an invariably fatal encephalitis that is more commonly known as rabies. The term rabies has a long history in human society, as rabies virus (RABV) is the only pathogen that is associated with 100% fatality once the onset of clinical disease has started. Although predominantly associated across the globe with domestic and feral dog populations, the association of bats is clear. Whilst evolutionarily associated with bats, RABV is most commonly transmitted to human populations through the bite of an infected dog and dogs are considered the primary reservoir of disease. Indeed, RABV does cause more than an estimated 70000 deaths every year globally in human populations and whilst this is largely in areas where the disease is endemic, areas that remain free of rabies must remain vigilant to the risk of re-incursion of disease. Characterisation of novel lyssaviruses is of importance on several levels. Not least to investigate the pathogenesis and potential transmission routes of different lyssavirus species but also to assess the potential effect of post-exposure treatments and vaccination should human exposure occur. Bat lyssaviruses and the problems associated with novel discoveries and the potential impact they have on both human and animal populations are discussed.

Download Full-text

Site-Use Intensity, Cultural Modification of the Environment, and the Development of Agricultural Communities in Southern Arizona

American Antiquity ◽

10.2307/40035307 ◽

2005 ◽

Vol 70 (3) ◽

pp. 403-431 ◽

Cited By ~ 13

Author(s):

Rebecca M. Dean

Keyword(s):

Human Impacts ◽

Bird Species ◽

Food Sources ◽

Ecological Niches ◽

Agricultural Communities ◽

Local Environments ◽

Middle Archaic ◽

Site Use ◽

Transition To Agriculture ◽

Cultural Modification

Some non-prey animals, including certain rodent and bird species, are particularly good indicators of local environments, and are argued to provide an alternative way to look at the emergence of sedentism before, during, and after the transition to agriculture. With the first villages and irrigated fields, human impacts on the environment opened new ecological niches and affected the composition of local pest populations. Some of these animals would have been attracted to the new food sources available in village environments, while others may have been driven away by the destruction of their habitat. In southern Arizona, changes in archaeological pest assemblages are a source of information on the degree of site-use intensity prehistorically and how it changed through the Archaic and Hohokam cultural sequence. Faunal data from the Hohokam region suggest that the earliest farmers in the region were not significantly more sedentary than their Middle Archaic predecessors, and indeed site-use intensity did not increase substantially until well after the introduction of domestic plants.

Download Full-text

Chytridiomycosis as a cause of global amphibian declines

Microbiology Australia ◽

10.1071/ma16063 ◽

2016 ◽

Vol 37 (4) ◽

pp. 190

Author(s):

Thomas J. Burns ◽

Mark S. Greener ◽

Paul A. Hoskisson

Keyword(s):

Environmental Health ◽

Life Histories ◽

Amphibian Declines ◽

Environmental Toxins ◽

Ecological Niches ◽

Sensitive Skin ◽

The Earth ◽

Highly Sensitive ◽

Terrestrial Environments

Amphibians are remarkable creatures that have inhabited the Earth for over 350 million years, and exhibit some of the most amazing and diverse life histories. The planet is home to around 7,500 species of amphibian, which occupy an extraordinary number of ecological niches. They are often viewed as indicators of environmental health by ecologists due to their reliance on both aquatic and terrestrial environments to complete their lifecycles. Furthermore, their thin and highly sensitive skin, where much of their respiration occurs, makes them highly susceptible to environmental toxins, disease and radiation.

Download Full-text

Short-Lived Species Move Uphill Faster Under Climate Change

10.21203/rs.3.rs-389565/v1 ◽

2021 ◽

Author(s):

Joséphine Couet ◽

Emma-Liina Marjakangas ◽

Andrea Santangeli ◽

John Atle Kålås ◽

Åke Lindström ◽

...

Keyword(s):

Climate Change ◽

Life Histories ◽

Bird Species ◽

Species Traits ◽

Climatic Conditions ◽

Range Shift ◽

Mountain Range ◽

Large Spatial Scale ◽

Altitudinal Range ◽

Species Abundances

Abstract Climate change is pushing species ranges towards poles and mountain tops. Although many studies have documented local altitudinal shifts, knowledge of general patterns at a large spatial scale, such as a whole mountain range, is very limited. From a conservation perspective, studying altitudinal shifts is particularly important as mountain regions often represent biodiversity hotspots and are among the most vulnerable ecosystems. Here, we examine whether altitudinal shifts have occurred among birds in the Scandinavian mountains over 13 years and assess whether such shifts are related to species’ traits. Using abundance data, we show a clear pattern of uphill shifts in the mean altitudes of the bird species’ abundances across the Scandinavian mountains, with an average speed of 0.9 m per year. Out of 77 species, 54 shifted their ranges uphill. In general, the range shift was faster when the altitudinal range within the area was wider. Importantly, the altitudinal shift was strongly related to species’ longevity: short-lived species showed more pronounced altitudinal uphill shifts than long-lived species. Our results show that the altitudinal range shifts are not only driven by a small number of individuals at the range boundaries, but the overall bird abundances are on the move. This highlights the wide-ranging impact of climate change and the potential vulnerability of species with slow life-histories, as they appear unable to timely respond to rapidly changing climatic conditions.

Download Full-text

Interactive Communication Between Male and Female Great Tits (Parus Major) During the Dawn Chorus

The Auk ◽

10.1093/auk/121.1.184 ◽

2004 ◽

Vol 121 (1) ◽

pp. 184-191 ◽

Cited By ~ 4

Author(s):

Leen Gorissen ◽

Marcel Eens

Keyword(s):

Life Histories ◽

Bird Species ◽

Parus Major ◽

Egg Laying ◽

Interactive Communication ◽

Dawn Chorus ◽

Nest Box ◽

Interactive Behavior ◽

Song Birds ◽

Dawn Song

Abstract Studies of the dawn chorus in birds have focused mainly on the behavior and song output of males and on the function(s) of male song. Less attention has been paid to the females' behavior and to communication between members of a pair. In Great Tits (Parus major), males sing vigorously at dawn in the vicinity of the female's nest hole just before and during egg laying. We studied the female's vocal behavior during the dawn chorus as well as communication between pair members. All females vocally interacted with their mates from inside the nest box. Females produced a sound with a very low sound-pressure level only audible from few meters, which we have named the “quiet call.” This quiet call was unique to females and was only produced from inside the nest box. To our knowledge, our study is the first to show that both members of a pair vocally interact during the dawn chorus. Given that many temperate-zone bird species have similar life histories as the Great Tit, it is very likely that similar interactive behavior occurs in other (song)birds. This interactive behavior may provide a new and manipulable tool for testing hypotheses about the dawn song and can be used as a future bioassay of male vocalizations.

Download Full-text