Application of a SSR-GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics

Evidence for High Levels of Gene Flow in Hedgehogs (Erinaceus europaeus) Across South Wales, UK, Despite Potential Anthropogenic and Natural Barriers to Dispersal

Understanding how landscape connectivity affects gene flow can help to guide the management of animal species of conservation concern. One such species is the West European hedgehog (Erinaceus europaeus), which has seen significant declines across its distribution, with the highest rate of declines being reported in rural areas of the UK. The drivers of these declines are not well understood, but anthropogenic changes in the landscape such as modified agricultural practices and increased road traffic have been proposed to play a part. These impacts are likely to fragment populations into smaller sub-populations, leading to genetic differentiation and depletion. Here, we used genetic (microsatellite) and landscape data to investigate the impact of habitat resistance and landscape features (roads and waterways) on the genetic structure of hedgehogs across a 5800 km2 area of South Wales, UK. We found evidence of weak genetic structuring, with four genetic clusters present across the study area, but many individuals were admixed. We found no evidence that this genetic structure was related to roads, waterways, habitat resistance, or geographic distance, suggesting that hedgehogs may be able to disperse across these potential barriers frequently enough to minimise genetic fragmentation. This study demonstrates the importance of understanding the interactions between a species and the wider landscape to inform conservation management.

Oceanic islands act as drivers for the genetic diversity of marine species: Cardita calyculata (Linnaeus, 1758) in the NE Atlantic as a case-study

Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.

Population genetic structure and ecological differentiation in the bryozoan genus Reteporella across the Azores Archipelago (central North Atlantic)

The processes shaping population dynamics of benthic marine invertebrates with non-planktotrophic larvae are still poorly understood but have seen a renewed interest in applying integrative taxonomic approaches. We used mitochondrial and microsatellite (SSR-GBAS) data to estimate connectivity across islands and seamounts in the central North Atlantic Azores Archipelago in five species of the bryozoan genus Reteporella Busk, 1884. Discordant patterns were inferred between datasets, which might be due to methodological constraints related to the application of multilocus approaches based on amplification to multiple species or due to interspecific introgression in deep waters. A divergent cryptic ecotype of Reteporella atlantica (Busk, 1884) was found in shallow waters, likely resulting from ecologically-driven incipient speciation, posing new questions regarding the role of bathymetrical zonation as a promoter of differentiation. The occurrence of ecologically-driven differentiation and potential interspecific introgression in other bryozoans should be considered, both with potentially important evolutionary and biogeographical consequences. The discovery of incipient species, prompted by ecological factors, calls for the need to consider marine invertebrates when developing conservation strategies in oceanic insular ecosystems.

Small-scale metapopulation structure of a limnophilic fish species in a natural river system investigated using microsatellite genotyping by amplicon sequencing (SSR-GBAS)

Habitat niches of fish species can exert a strong influence on population structure, even on a small geographical scale. In this scope, Pelasgus thesproticus is a great model species to study connectivity in riverine environments owing to its naturally patchy habitat distribution. Furthermore, it is important to conduct such studies in near-natural systems to avoid the impact of human disturbances on the river, such as fragmentation, morphological changes and habitat degradation. In this sense, the Vjosa in Albania is an excellent study area. A total of 204 individuals were sampled from five locations in the lower Vjosa and two tributaries and genotyped with 33 newly designed microsatellites loci using high throughput sequencing. The application of microsatellite genotyping by sequencing revealed genetic structure and some differentiation, even at a small spatial scale (< 65 river km). A total of 500 alleles were found with an average of 0.93 private alleles among sites with rather low FST values (< 0.04). The extent of admixture observed in some populations indicate that the genetic structure is mainly influenced by upstream populations, either from the main river itself or from tributaries. In addition, the connection between a tributary and the other sites is disrupted by the flow regime, which is reflected in a high degree of divergence from the other populations. Our results indicate that hydrological conditions of the flowing river present strong barriers to gene flow, particularly in the upstream direction, but at the same time act as dispersal corridors in the downstream direction and exhibit source-sink dynamics in which upstream populations contribute disproportionately to downstream populations for this habitat specialist along the river. It is suggested that processes of colonization and reinforcement may play an important role in shaping the genetic structure of patchily distributed fish species in natural river systems. Future studies should increase the knowledge of dispersal factors, habitat heterogeneity, consequence of source-sink dynamics, and gene flow within the system, which will help to understand and maintain important processes related to metapopulation theory and the potential evolutionary consequences of habitat loss and fragmentation.

Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification

The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.

Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.

Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea

Developing new varieties in fruit and tea breeding programs is very costly and labor-intensive. Thus, establishing a variety discrimination system is important for protecting breeders’ rights and producers’ profits. Simple sequence repeat (SSR) databases that can be utilized for both next-generation sequencing (SSR-GBS) and polymerase chain reaction–capillary electrophoresis (PCR-CE) would be very useful in variety discrimination. In the present study, SSRs with tri-, tetra- and pentanucleotide repeats were examined in apple, pear and tea. Out of 37 SSRs that showed clear results in PCR-CE, 27 were suitable for SSR-GBS. Among the remaining markers, there was allele dropout for some markers that caused differences between the results of PCR-CE and SSR-GBS. For the selected 27 markers, the alleles detected by SSR-GBS were comparable to those detected by PCR-CE. Furthermore, we developed a computational pipeline for automated genotyping using SSR-GBS by setting a value “α” for each marker, a criterion whether a genotype is homozygous or heterozygous based on allele frequency. The set of 27 markers contains 10, 8 and 9 SSRs for apple, pear and tea, respectively, that are useful for both PCR-CE and SSR-GBS and suitable for automation. The databases help researchers discriminate varieties in various ways depending on sample size, markers and methods.

Informing conservation strategies with museum genomics: Long-term effects of past anthropogenic persecution on the elusive European wildcat

Like many carnivore species, European wildcats (Felis silvestris) have suffered severe anthropogenic population declines in the past, resulting in a strong population bottleneck at the beginning of the 20th century. In Germany, the species has managed to survive its near extinction in small isolated areas and is currently recolonizing former habitats owing to legal protection and concerted conservation efforts. Here, we SNP-genotyped and mtDNA-sequenced 56 historical and 650 contemporary samples to assess the impact of massive persecution on genetic diversity, population structure, and hybridization dynamics of wildcats. Spatiotemporal analyses suggest that the presumed postglacial differentiation between two genetically distinct metapopulations in Germany is in fact the result of the anthropogenic bottleneck followed by re-expansion from few secluded refugia. We found that, despite the bottleneck, populations experienced no severe genetic erosion, nor suffered from elevated inbreeding or showed signs of increased hybridization with domestic cats. Our findings have significant implications for current wildcat conservation strategies, as the data analyses show that the two presently recognized wildcat population clusters should be treated as a single conservation unit. Although current populations appear under no imminent threat from genetic factors, fostering connectivity through the implementation of forest corridors will facilitate the preservation of genetic diversity and promote long-term viability. The present study documents how museum collections can be used as essential resource for assessing long-term anthropogenic effects on natural populations, for example, regarding population structure and the delineation of appropriate conservation units, potentially informing todays' species conservation.

Molecular Evaluation and Identification of Some Barley Hybrids Tolerant to Salt Stress

&lt;b&gt;Background and Objective:&lt;/b&gt; Barley is considering one of the most important cereal crops at the local and global levels. It is ranked second in terms of nutritional importance after wheat and its flour contributes significantly to bridging the large nutritional gap in the production of Egyptian bread. The aim of this study concentrated on knowing and testing the genetic behaviour responsible for salinity stress tolerance in barley as trying to improve barley crop and increase its ability for abiotic stress resistance under Egyptian conditions. &lt;b&gt;Materials and Methods:&lt;/b&gt; Twenty-one crosses and ten parents of barley with different responses to salinity tolerance were evaluated in this investigation under normal and salinity conditions. Yield and its components and some physiological traits related to salt stress tolerance were the most important studied attributes evaluated in this regard under both conditions. Moreover, SSR markers were used to evaluate and identified associated markers for salinity tolerance in selected hybrids and comparing among the ten barley parents. &lt;b&gt;Results:&lt;/b&gt; The final results confirmed that the three testers; Giza 123, Giza 126 and Giza 2000 besides; the crosses; Line 1XTester 1 (Giza 125XGiza 123), Line 2XTester 1 (Giza 133XGiza 123), Line 1XTester 2 (Giza 125XGiza 126), Line 2XTester 2 (Giza 133XGiza 126) and Line 1XTester 3 (Giza 125XGiza 2000) exhibited highly salinity tolerance under saline stress treatment compared with the control experiment. Among 15 analyzed barley entries, the chosen set of 11 markers amplified 20 alleles with an average of 1.81, with a range from 1-4 alleles. &lt;b&gt;Conclusion:&lt;/b&gt; The results of SSR analysis and the data on valued agricultural trait loci determined the genetic distance among parents and their hybrids, which is of an unlimited rate for breeders.

Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago

Background

In the marine realm, dispersal ability is among the major factors shaping the distribution of species. In the Northeast Atlantic Ocean, the Azores Archipelago is home to a multitude of marine invertebrates which, despite their dispersal limitations, maintain gene flow among distant populations, with complex evolutionary and biogeographic implications. The mechanisms and factors underlying the population dynamics and genetic structure of non-planktotrophic gastropods within the Azores Archipelago and related mainland populations are still poorly understood. The rissoid Cingula trifasciata is herewith studied to clarify its population structure in the Northeast Atlantic Ocean and factors shaping it, with a special focus in intra-archipelagic dynamics.

Results

Coupling microsatellite genotyping by amplicon sequencing (SSR-GBAS) and mitochondrial datasets, our results suggest the differentiation between insular and continental populations of Cingula trifasciata, supporting previously raised classification issues and detecting potential cryptic diversity. The finding of connectivity between widely separated populations was startling. In unique ways, dispersal ability, habitat type, and small-scale oceanographic currents appear to be the key drivers of C. trifasciata’s population structure in the remote Azores Archipelago. Dispersal as non-planktotrophic larvae is unlikely, but its small-size adults easily engage in rafting. Although the typical habitat of C. trifasciata, with low hydrodynamics, reduces the likelihood of rafting, individuals inhabiting algal mats are more prone to dispersal. Sea-surface circulation might create dispersal pathways for rafts, even between widely separated populations/islands.

Conclusions

Our results show that gene flow of a marine non-planktotrophic gastropod within a remote archipelago can reveal unanticipated patterns, such that the understanding of life in such areas is far from well-understood. We expect this work to be the starting of the application of SSR-GBAS in other non-model marine invertebrates, providing insights on their population dynamics at distinct geographical scales and on hidden diversity. How transversal is the role played by the complex interaction between functional traits, ecological features, and sea-surface circulation in the population structure of marine invertebrates can be further addressed by expanding this approach to more taxa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01862-1.

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

The use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

Genetic diversity of Nile tilapia (Oreochromis niloticus) populations in Ethiopia: insights from nuclear DNA microsatellites and implications for conservation

BACKGROUND

Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques.

RESULTS

The samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High FST values (Global FST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq.

CONCLUSIONS

The results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.

How Is Wildlife Affected by the COVID-19 Pandemic? Lockdown Effect on the Road Mortality of Hedgehogs

Globally, wildlife is affected by unprecedented changes related to the COVID-19 pandemic. In this paper, the lockdown effect on the traffic-related mortality in hedgehogs in an urban area was studied. Comparing the pre-pandemic (2018 and 2019) and pandemic (2020) years, we showed that hedgehog roadkill levels during the lockdown period were over 50% lower (which means a decrease greater than the decrease in road traffic in the same period measured by the number of accidents or the average number of vehicles per day). Based on literature data, we showed that this may mean at least tens of thousands of hedgehogs have survived on a national scale. We report the need to start intensive research on the possible demographic and genetic effects of this unique phenomenon. We also ask how stable the effect of the COVID-19 pandemic will be on wildlife and whether the lockdown (which is an anthropause) may reverse the negative trends in the decline in the number of wild species, including hedgehogs.

The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)

Simple Summary

The gut microbiota (all microbes in the intestine) of fishes is known to play an essential role in diverse aspects of their life. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. This study characterised the microbial composition in gut samples of Nile Tilapia collected from Lake Tana and the Bahir Dar aquaculture facility centre applying modern molecular techniques. The results show clear differences in the gut microbiota in fish from the Lake Tana and the ones from aquaculture. Further, also significant differences were observed on the composition of the gut microbiota across sampling months. Samples from the aquaculture centre displayed a higher diversity than the wild catch Nile tilapia from Lake Tana even though there is also an overlapping of the detected microbial groups. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work will help to precisely explain the causes of these changes and their influence of the health and growth of Nile tilapia in Ethiopian lakes as well as under aquaculture conditions.

Abstract

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.

Evidence for multiple introductions of an invasive wild bee species currently under rapid range expansion in Europe

BACKGROUND

Invasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee species Megachile sculpturalis (Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts.

RESULT

To track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east-west differentiations in Middle-Europe.

CONCLUSION

We hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.

Genetic diversity and structure of the hedgehogs Erinaceus europaeus and Erinaceus roumanicus: evidence for ongoing hybridization in Eastern Europe

Secondary contact zones between related species are key to understanding speciation mechanisms. The Central European sympatry zone of West European (Erinaceus europaeus) and northern white-breasted (Erinaceus roumanicus) hedgehogs is well studied, whereas data on the Eastern European sympatry zone are scarce. We examined the genetic variation in Russian populations using the mitochondrial Cytb gene, TTR intron 1 and 11 microsatellites to assess genetic variability and distribution patterns. In contrast to the Central European sympatry zone, we found evidence of ongoing hybridization between the two species in the sympatry zone of European Russia, where the proportion of individuals with mixed ancestry was c. 20%. Our data indicate bi-directional mtDNA introgression, but with a higher frequency of E. europaeus haplotypes in hybrids. The proportion of pure specimens with introgressed mitotypes is higher in E. roumanicus than in E. europaeus. Nuclear data showed the prevalence of the genetic contribution from E. roumanicus in admixed individuals. Demographic analyses indicated recent population growth in E. europaeus and little change in E. roumanicus, suggesting that E. europaeus colonized East Europe later than E. roumanicus.

3D Geometric Morphometrics Reveals Convergent Character Displacement in the Central European Contact Zone between Two Species of Hedgehogs (Genus Erinaceus)

Simple Summary

Hedgehogs, being insectivores with slow metabolisms, are quite sensitive to temperature and food availability. As a consequence, their ranges have oscillated in relation to past climate changes. Species that have evolved in different regions, but their ranges have shifted and overlapped subsequently, often represent intense competitors as a result of ecological similarities. The present study focuses on this phenomenon in the contact zone in central Europe and adjacent regions, using genetic determination of species and description of size and shape of skull, the morphological structure mirroring many selection pressures related to ecology. While animals living outside of the contact zone show marked differences between the two species, individuals within the contact zone are more alike with a smaller skull size and a convergent jawbone shape. Changes in skull size can be related to inter-species competition and also facilitated by selection pressure, mediated by overpopulated medium-sized predators such as foxes or badgers. Since the function of the lower jaw is mainly connected to feeding, we hypothesize that this pattern is due to the selection to size and shape related to competition for food resources. The present study helps to describe general patterns related to species formation, as well as species responses to anthropogenic environmental changes.

Abstract

Hedgehogs, as medium-sized plantigrade insectivores with low basal metabolic rates and related defensive anti-predator strategies, are quite sensitive to temperature and ecosystem productivity. Their ranges therefore changed dramatically due to Pleistocene climate oscillations, resulting in allopatric speciation and the subsequent formation of secondary contact zones. Such interactions between closely related species are known to generate strong evolutionary forces responsible for niche differentiation. In this connection, here, we detail the results of research on the phenotypic evolution in the two species of hedgehog present in central Europe, as based on genetics and geometric morphometrics in samples along a longitudinal transect that includes the contact zone between the species. While in allopatry, Erinaceus europaeus is found to have a larger skull than E. roumanicus and distinct cranial and mandibular shapes; the members of the two species in sympatry are smaller and more similar to each other, with a convergent shape of the mandible. The relevant data fail to reveal any major role for either hybridisation or clinal variation. We, therefore, hypothesise that competitive pressure exerted on the studied species does not generate divergent selection sufficient for divergent character displacement to evolve, instead giving rise to convergent selection in the face of resource limitation in the direction of smaller skull size. Considering the multi-factorial constraints present in the relevant adaptive landscape, reduction in size could also be facilitated by predator pressure in ecosystems characterised by mesopredator release and other anthropogenic factors. As the function of the animals’ lower jaw is mainly connected with feeding (in contrast to the cranium whose functions are obviously more complex), we interpret the similarity in shape as reflecting local adaptations to overlapping dietary resources in the two species and hence as convergent character displacement.

Impacts and Potential Mitigation of Road Mortality for Hedgehogs in Europe

Transport infrastructure is a pervasive element in modern landscapes and continues to expand to meet the demands of a growing human population and its associated resource consumption. Road-induced mortality is often thought to be a major contributor to the marked declines of European hedgehog populations. This review synthesizes available evidence on the population-level impacts of road mortality and the threat to population viability for the five hedgehog species in Europe. Local and national studies suggest that road mortality can cause significant depletions in population sizes, predominantly removing adult males. Traffic collisions are a probable cause of fragmentation effects, subsequently undermining ecological processes such as dispersal, as well as the genetic variance and fitness of isolated populations. Further studies are necessary to improve population estimates and explicitly examine the consequences of sex- and age-specific mortality rates. Hedgehogs have been reported to use crossing structures, such as road tunnels, yet evaluations of mitigation measures for population survival probability are largely absent. This highlights the need for robust studies that consider population dynamics and genetics in response to mitigation. In light of ongoing declines of hedgehog populations, it is paramount that applied research is prioritised and integrated into a holistic spatial planning process.

Evaluating the Impact of Wildlife Shelter Management on the Genetic Diversity of Erinaceus europaeus and E. roumanicus in Their Contact Zone

Simple Summary

Hedgehogs are regularly brought to wildlife shelters. Depending on the area from where animals are accepted, translocation can occur between different regions or populations. In this study, the genetic diversity of wild hedgehog populations was compared with “shelter populations” within central Europe focusing on the western contact zone between both European hedgehog species. Some shelters were hosting both species at the same time, in one this could be shown genetically. Generally, no difference in genetic diversity between shelter individuals and wild populations was found. Two shelters from Innsbruck hosted individuals that probably belong to two subpopulations. This indicates that shelter management-related translocations could facilitate gene flow across a dispersal barrier.

Abstract

Hedgehogs are among the most abundant species to be found within wildlife shelters and after successful rehabilitation they are frequently translocated. The effects and potential impact of these translocations on gene flow within wild populations are largely unknown. In this study, different wild hedgehog populations were compared with artificially created “shelter populations”, with regard to their genetic diversity, in order to establish basic data for future inferences on the genetic impact of hedgehog translocations. Observed populations are located within central Europe, including the species Erinaceus europaeus and E. roumanicus. Shelters were mainly hosting one species; in one case, both species were present syntopically. Apart from one exception, the results did not show a higher genetic diversity within shelter populations, indicating that individuals did not originate from a wider geographical area than individuals grouped into one of the wild populations. Two shelters from Innsbruck hosted individuals that belonged to two potential clusters, as indicated in a distance analysis. When such a structure stems from the effects of landscape elements like large rivers, the shelter management-related translocations might lead to homogenization across the dispersal barrier.

The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.)

The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.

Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.

Species assignment in forensics and the challenge of hybrids

Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.

Fast sequence-based microsatellite genotyping development workflow

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

BACKGROUND

The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations.

RESULTS

All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities.

CONCLUSIONS

The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.