The authors of the book present an informative updated graph in figure 4.1. on the development of genetic markers over time, and we can expect the sequencing of genomes playing an even more important ...role in the coming years. There is a new chapter on genetic monitoring (formerly included in the species identification and now expanded) and the book ends with a dedicated chapter on conservation genetics in practice (written by Helen Taylor). Genetic diversity is receiving more attention in management internationally and nationally, and this book gives a number of illustrative case studies.
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The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic ...variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.
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Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its ...evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve.
Efforts to understand the process of speciation have been central to the research of biologists since the origin of evolutionary biology as a discipline. While it is well established that geographic ...isolation has played a key role in many speciation events, particularly in birds, there is ongoing debate about how frequent speciation is in the partial or complete absence of geographical isolation. In the red crossbill Loxia curvirostra, good arguments do exist for sympatric speciation processes. In this species, several classes of calls are clustered in distinct groups, so‐called ‘call types', which mate assortatively. Often, several call types can be found at a single site, breeding and feeding next to each other. It has been hypothesized that red crossbill call types evolved by specialising in extracting seeds from cones of different conifer species. Alternatively, call types might have evolved in temporal geographic isolation. Within Europe, little is known about the distribution of the various call types and preferences for distinct food resources. In this study, we analysed the temporal and spatial occurrence of red crossbill call types in the Palearctic, investigated potential reasons for call‐type composition at a site, and compared the occurrence of call types with the fructification of conifers. Call‐type composition changed with site and season but hardly with conifer species. With our data, we could localise range areas of twelve different call types, which cannot be explained by conifer species occurrence. Therefore, we suggest that call types evolved in parapatry in most of the northern Palearctic region, and, although contradictory results exist from Iberia, we argue that differentiation might be driven by the same drivers there as well. Additionally, we discuss the potential influence of anthropogenic changes of forest composition and distribution on call types, which offers a unique possibility for future studies.
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Changing environmental conditions and human encroachment on natural habitats bring human populations closer to novel sources of parasites, which might then develop into new emerging diseases. ...Diseases transmitted by host generalist vectors are of special interest due to their capacity to move pathogens into novel hosts. We hypothesize that humans using forests for recreation are exposed to a broad range of parasites from wild animals and their vectors. A corollary of this is that new vector-host, parasite-host, and vector-parasite associations could eventually develop. Thus, we expect to observe atypical vector-host associations. Using molecular bloodmeal analysis via amplification of the mtDNA COI gene we identified the vertebrate hosts of Culicoides (Diptera: Ceratopogonidae) species in a sub-urban forest of Southwestern Germany. Bloodmeals were also checked for haemosporidian infections by amplifying a fragment of the mtDNA cyt b gene. We identified a total of 20 Culicoides species, thirteen of which fed on humans. From 105 screened bloodmeals we obtained high quality sequences for 77 samples, 73 (94.8%) originated from humans, two from livestock (Bos taurus and Equus caballus), and two from wild birds (Sylvia atricapilla and Turdus merula). We found that four Culicoides species previously assumed to feed exclusively on either birds (C. kibunensis) or domestic mammals (C. chiopterus, C. deltus, C. scoticus) fed also on humans. A total of six Culicoides abdomens were infected with avian haemosporidian parasites (Plasmodium or Haemoproteus), four of those abdomens contained blood derived from humans. Our results suggest that parasites of wild animals may be transferred to humans through infectious bites of Culicoides vectors. Further, we show that Culicoides vectors believed to be a specialist on specific vertebrate groups can have plastic feeding preferences, and that Culicoides are susceptible to infection by Plasmodium parasites, though vector viability must still be experimentally demonstrated.
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Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and ...used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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Airspace is a key but not well-understood habitat for many animal species. Enormous amounts of insects and birds use the airspace to forage, disperse, and migrate. Despite numerous studies on ...migration, the year-round flight activities of both birds and insects are still poorly studied. We used a 2 year dataset from a vertical-looking radar in Central Europe and developed an iterative hypothesis-testing algorithm to investigate the general temporal pattern of migratory and local movements. We estimated at least 3 million bird and 20 million insect passages over a 1 km transect annually. Most surprisingly, peak non-directional bird movement intensities during summer were of the same magnitude as seasonal directional movement peaks. Birds showed clear peaks in seasonally directional movements during day and night, coinciding well with the main migration period documented in this region. Directional insect movements occurred throughout the year, paralleling non-directional movements. In spring and summer, insect movements were non-directional; in autumn, their movements concentrated toward the southwest, similar to birds. Notably, the nocturnal movements of insects did not appear until April, while directional movements mainly occurred in autumn. This simple monitoring reveals how little we still know about the movement of biomass through airspace.
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Effective management of both endangered native and invasive alien crayfishes requires knowledge about distribution, monitoring of existing and early detection of newly established populations. ...Complementary to traditional survey methods, eDNA sampling has recently emerged as a highly sensitive non-invasive detection method to monitor crayfish populations. To advance the use of eDNA as detection tool for crayfish we used a twofold approach: 1) we designed a novel set of specific eDNA-assays for all native (
Austropotamobius torrentium, Austropotamobius pallipes, Astacus astacus
) and the most relevant invasive crayfish species (
Pacifastacus leniusculus, Faxonius limosus, Faxonius immunis
) in Central Europe. To ensure specificity each primer pair was tested
in silico
,
in vitro,
and
in situ
; 2) we assessed the influence of spatio-temporal variables (distance to upstream population, season, stream size) on eDNA detection in seven streams using two different detection methods (qualitative endpoint PCR and quantitative droplet digital PCR, ddPCR). The newly developed eDNA assays successfully detected all crayfish species across different lotic and lentic habitats. eDNA detection rate (endpoint PCR) and eDNA-concentration (ddPCR) were significantly influenced by distance and season. eDNA detection was successful up to 7 km downstream of the source population and across all seasons, although detectability was lowest in winter. eDNA detection rate further decreased with increasing stream size. Finally, eDNA-concentration correlated positively with estimated upstream population size. Overall, we provide near operational eDNA assays for six crayfish species, enabling year-round detection, which represents a clear benefit over conventional methods. Due to its high sensitivity, eDNA detection is also suitable for the targeted search of as-yet unrecorded or newly emerging populations. Using quantitative ddPCR might further allow for a rough estimation of population size, provided that the identified spatio-temporal factors are accounted for. We therefore recommend implementing eDNA-detection as a complementary survey tool, particularly for a large-scale screening of data-deficient catchments or a year-round monitoring.
In tropical montane cloud forests, climate change can cause upslope shifts in the distribution ranges of species, leading to reductions in distributional range. Endemic species with small ranges are ...particularly vulnerable to such decreases in range size, as the population size may be reduced significantly. To ensure the survival of cloud forest species in the long term, it is crucial to quantify potential future shifts in their distribution ranges and the related changes in habitat availability in order to assure the long-term effectiveness of conservation measures. In this study, we assessed the influence of climate change on the availability of forested habitat for the endemic El Oro parakeet. We investigated the future range shift by modelling the climatic niche of the El Oro parakeets and projecting it to four different climate change scenarios. Depending on the intensity of climate change, the El Oro parakeets shift their range between 500 and 1700 m uphill by the year 2100. On average, the shift is accompanied by a reduction in range size to 15% and a reduction in forested habitat to only 10% of the original extent. Additionally, the connectivity between populations in different areas is decreasing in higher altitudes. To prevent a population decline due to habitat loss following an upslope range shift, it will be necessary to restore habitat across a large elevational span in order to allow for movement of El Oro parakeets into higher altitudes.
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The zebra finch (Taeniopygia guttata) is a small Australian grassland songbird that has been domesticated over the past two centuries. Because it is easy to breed in captivity, it has become a widely ...used study organism, especially in behavioural research. Most work has been conducted on domesticated populations maintained at numerous laboratories in Europe and North America. However, little is known about the extent to which, during the process of domestication, captive populations have gone through bottlenecks in population size, leading to inbred and potentially genetically differentiated study populations. This is an important issue, because (i) behavioural studies on captive populations might suffer from artefacts arising from high levels of inbreeding or lack of genetic variation in such populations, and (ii) it may hamper the comparability of research findings. To address this issue, we genotyped 1000 zebra finches from 18 captive and two wild populations at 10 highly variable microsatellite loci. We found that all captive populations have lost some of the genetic variability present in the wild, but there is no evidence that they have gone through a severe bottleneck, as the average captive population still showed a mean of 11.7 alleles per locus, compared to a mean of 19.3 alleles/locus for wild zebra finches. We found significant differentiation between the captive populations (FST = 0.062). Patterns of genetic similarity closely match geographical relationships, so the most pronounced differences occur between the three continents: Australia, North America, and Europe. By providing a tree of the genetic similarity of the different captive populations, we hope to contribute to a better understanding of variation in research findings obtained by different laboratories.
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