The genetic legacy of multiple beaver reintroductions in Central Europe

Geo-evolutionary feedbacks: integrating rapid evolution and landscape change

We develop a conceptual framework for geo-evolutionary feedbacks which describes the mutual interplay between landscape change and the evolution of traits of organisms residing on the landscape, with an emphasis on contemporary timeframes. Geo-evolutionary feedbacks can be realized via the direct evolution of geomorphic engineering traits or can be mediated by the evolution of trait variation that affects the population size and distribution of the specific geomorphic engineering organisms involved. Organisms that modify their local environments provide the basis for patch-scale geo-evolutionary feedbacks, whereas spatial self-organization provides a mechanism for geo-evolutionary feedbacks at the landscape scale. Understanding these likely prevalent geo-evolutionary feedbacks, that occur at timescales similar to anthropogenic climate change, will be essential to better predict landscape adaptive capacity and change.

Corynebacterium ulcerans Infections in Eurasian Beavers (Castor fiber)

The Eurasian beaver (Castor fiber) has been reintroduced successfully in Germany since the 1990s. Since wildlife is an important source of zoonotic infectious diseases, monitoring of invasive and reintroduced species is crucial with respect to the One Health approach. Three Eurasian beavers were found dead in the German federal states of Bavaria, North Rhine-Westphalia and Baden-Wuerttemberg in 2015, 2021 and 2022, respectively. During post-mortem examinations, Corynebacterium (C.) ulcerans could be isolated from the abscesses of two beavers and from the lungs of one of the animals. Identification of the bacterial isolates at the species level was carried out by spectroscopic analysis using MALDI-TOF MS, FT-IR and biochemical profiles and were verified by molecular analysis based on 16-23S internal transcribed spacer (ITS) region sequencing. Molecular characterization of the C. ulcerans isolates using whole-genome sequencing (WGS) revealed a genome size of about 2.5 Mbp and a GC content of 53.4%. Multilocus sequence typing (MLST) analysis classified all three isolates as the sequence type ST-332. A minimum spanning tree (MST) based on cgMLST allelic profiles, including 1211 core genes of the sequenced C. ulcerans isolates, showed that the beaver-derived isolates clearly group on the branch of C. ulcerans with the closest relationship to each other, in close similarity to an isolate from a dog. Antibiotic susceptibility testing revealed resistance to clindamycin and, in one strain, to erythromycin according to EUCAST, while all isolates were susceptible to the other antimicrobials tested.

Genetic signature of blind reintroductions of Iberian ibex (Capra pyrenaica) in Catalonia, Northeast Spain

The Iberian ibex is one of the most singular species of the Iberian Peninsula. Throughout the years, this species suffered several threats which led the population to its decline. Many reintroductions and translocations were made, however, none of those actions took into account the genetic patterns of both reintroduced individuals and the target populations. In this paper, we explored the genetic traits of three populations of Iberian ibex in Catalonia, which experienced blind reintroductions in past years: The populations of Iberian ibex from Els Ports de Tortosa i Beseit National Game Reserve (TBNGR), Montserrat Natural Park (Monserrat) and Montgrí, les Illes Medes i el Baix Ter Natural Park (Montgrí) Based on the genetic patterns of the three populations coupled with the absence of genetic introgression with domestic goats–inferred using mitochondrial and nuclear markers–we propose that these should be regarded as two different management units: TBNGR coupled with Montserrat, and Montgrí. Montserrat population should be targeted as a population model for ecology and evolution studies. Although we did not detect evidences of recent bottleneck events, this population seems to be monomorphic for the mtDNA haplotype. Our results suggest that the blind reintroductions from TBNGR to Montserrat failed on maximizing the genetic diversity of the latter. We enhance the importance of genetic monitoring of both the source population and the selected individuals to be re-introduced. We conclude that the three studied population of Iberian ibex must be monitored to explore which strategy would be advantageous for maintaining the genetic diversity. On the other hand, TBNGR should be monitored to assess the existence of its singular genetic variation, where stochastic events could preserve this lost genetic variation.

Helminth fauna of the Eurasian beaver in the Czech Republic with remarks on the genetic diversity of specialist Stichorchis subtriquetrus (Digenea: Cladorchiidae)

Eurasian beaver (Castor fiber) is a well-established faunal element in the Czech Republic, even though, historically, its populations were almost eradicated in this region. Nowadays, its distribution and population density are well monitored; nonetheless, the beaver's parasites, as potential threats to the environment, are often neglected in wildlife management. Therefore, we investigated the endoparasitic helminth diversity of 15 beaver individuals from three collection sites in the Czech Republic. Three parasite species were collected: Stichorchis subtriquetrus (Digenea), Travassosius rufus, and Calodium hepaticum (Nematoda), of which the two nematode species were reported for the first time from C. fiber in the Czech Republic. The highest prevalence and intensity of infection were observed in S. subtriquetrus (P = 93%, I = 1-138), while the two other species were collected only from one beaver individual. Subsequent analysis of the genetic diversity of the specimens using highly variable genetic markers revealed a weak population structure among the individuals collected from different beaver hosts. There was only a weak association of COI haplotypes with geography, as the haplotypes from the Berounka basin formed homogeneous groups, and individuals from the Dyje basin and Morava partially shared a haplotype. Even though common population genetic markers (i.e., microsatellites) did not reveal any structure in the hosts, our results suggest that the genetic diversity of their parasites may shed more light on population partition and the historical migration routes of Eurasian beavers.

Genetic structure of Eurasian beaver in Romania: insights after two decades from the reintroduction

Once exploited for fur, meat, and extracting the yellowish exudate called castoreum, the Eurasian beaver disappeared from Romania during the eighteenth century. After, the reintroductions carried out two decades ago are currently thriving in the Danube River basin. Using nine nSSR markers, we analysed samples from 98 individuals, and we found no genetic substructure, suggesting high dispersal and gene flow capabilities. The stepwise mutation model (SMM) indicated the existence of a recent genetic bottleneck, though the Eurasian beaver retains high levels of genetic diversity and population growth facilitated variation in nSSR loci. A fine-scale spatial correlation in females was detected, contrasting with males’ dispersal on longer distances. While the movement and establishment of individuals’ new territories were made under natural predation pressure, the mix following natural expansion improved the fitness and could contribute to a higher genetic diversity than the source population. With any reintroduction, a focus on capturing individuals from various geographic origins, as well as securing many and suitable founding individuals (adults, subadults, and juveniles) with mixed origins, could secure the post-genetic bottleneck recovery and higher genetic diversity. Beyond this conservation success, future management strategies should consider building a National Action Plan (NAP) for the species, including a permanent genetic monitoring programme for Eurasian beaver.

Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient

Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.

Population genetics of the wolverine in Finland: the road to recovery?

After decades, even centuries of persecution, large carnivore populations are widely recovering in Europe. Considering the recent recovery of the wolverine (Gulo gulo) in Finland, our aim was to evaluate genetic variation using 14 microsatellites and mtDNA control region (579 bp) in order (1) to determine whether the species is represented by a single genetic population within Finland, (2) to quantify the genetic diversity, and (3) to estimate the effective population size. We found two major genetic clusters divided between eastern and northern Finland based on microsatellites (FST = 0.100) but also a significant pattern of isolation by distance. Wolverines in western Finland had a genetic signature similar to the northern cluster, which can be explained by former translocations of wolverines from northern to western Finland. For both main clusters, most estimates of the effective population size Ne were below 50. Nevertheless, the genetic diversity was higher in the eastern cluster (HE = 0.57, AR = 4.0, AP = 0.3) than in the northern cluster (HE = 0.49, AR = 3.7, AP = 0.1). Migration between the clusters was low. Two mtDNA haplotypes were found: one common and identical to Scandinavian wolverines; the other rare and not previously detected. The rare haplotype was more prominent in the eastern genetic cluster. Combining all available data, we infer that the genetic population structure within Finland is shaped by a recent bottleneck, isolation by distance, human-aided translocations and postglacial recolonization routes.

Low genetic polymorphism in the re-introduced Eurasian beaver (Castor fiber) population in Finland: implications for conservation

Background

Reduction of genetic diversity can lead to reduced fitness of species, such as the loss of adaptability to changing environments. The native Eurasian beaver (Castor fiber) was hunted to extinction from Finland and many other countries in Europe in the nineteenth century. In Finland, the species was re-introduced in the 1930s with only a few individuals from Norway. Re-introductions were performed also in other countries of northern Europe and as a result, Eurasian beaver populations have undergone population bottlenecks leading to low levels of genetic diversity.

Materials and Methods

Here, 200 Eurasian beaver samples from Finland, Estonia, Lithuania, and Russian Karelia were investigated using 12 microsatellite markers to examine the level of genetic diversity and relationship between the populations.

Results

While Russian and Estonian populations were genetically the closest, the Finnish population was clearly distinct from all others and had the lowest genetic variability among the study populations. This may be deleterious to the population especially in a changing environment.

Conclusions

Genetic rescue could be the best solution to increase the genetic diversity and improve the future prospects of the population, although more studies are required to resolve the optimal source population.

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado 'Hass' draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan × Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community.

Streptococcus castoreus, an uncommon group A Streptococcus in beavers

Streptococcus castoreus is a rarely encountered beta-haemolytic group A Streptococcus with high tropism for the beaver as host. Based on 27 field isolates under study, evidence strongly suggests that S. castoreus behaves as an opportunistic pathogen in beavers. Although it belongs to the resident mucosal microbiota, this Streptococcus species is associated with purulent lesions in diseased animals. With few exceptions, isolates proved to be highly similar in a panel of phenotypic (including biochemistry, resistance pattern, MALDI-TOF mass spectrometry and Fourier transform-infrared spectroscopy) and classic molecular (16S rRNA and sodA gene) analyses, and thus did not show any specific pattern according to host species or spatio-temporal origin. Conversely, S. castoreus isolates were differentiated into a multitude of pulsed-field gel electrophoresis 'pulsotypes' that did not seem to reflect true epidemiologic lineages. In contrast, single reactions of genomic fingerprinting using BOX-, (GTG)₅- and RAPD-PCRs revealed at least subclusters with respect to host species, geographic origin or year, and confirmed the co-colonization of individuals with more than one isolate. In addition to isolates from free-ranging Eurasian beavers (Castor fiber), this study includes S. castoreus from captive North American beavers (Castor canadensis) for the first time.

De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.)

Our pioneering data provide the first comprehensive view of placental transcriptome of the beaver during single and multiple gestation. RNA-Seq and a de novo approach allowed global pattern identification of C. fiber placental transcriptome. Non-redundant beaver transcriptome comprised 211,802,336 nt of placental transcripts, grouped into 128,459 contigs and clustered into 83,951 unigenes. An Ensembl database search revealed 14,487, 14,994, 15,004, 15,267 and 15,892 non-redundant homologs for Ictidomys tridecemlineatus, Rattus norvegicus, Mus musculus, Homo sapiens and Castor canadensis, respectively. Due to expression levels, the identified transcripts were divided into two sets: non-redundant and highly expressed (FPKM > 2 in at least three examined samples), analysed simultaneously. Among 17,009 highly expressed transcripts, 12,147 had BLASTx hits. GO annotations (175,882) were found for 4301 transcripts that were assigned to biological process (16,386), cellular component (9149) and molecular function (8338) categories; 666 unigenes were also classified into 122 KEGG pathways. Comprehensive analyses were performed for 411 and 3078 highly expressed transcripts annotated with a list of processes linked to ‘placenta’ (31 GO terms) or ‘embryo’ (324 GO terms), respectively. Among transcripts with entire CDS annotation, 281 (placenta) and 34 (embryo) alternative splicing events were identified. A total of 8499 putative SNVs (~ 6.2 SNV/transcript and 1.7 SNV/1 kb) were predicted with 0.1 minimum frequency and maximum variant quality (p value 10e⁻⁹). Our results provide a broad-based characterization of the global expression pattern of the beaver placental transcriptome. Enhancement of transcriptomic resources for C. fiber should improve understanding of crucial pathways relevant to proper placenta development and successful reproduction.

Hotspots of recent hybridization between pigs and wild boars in Europe

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.

Fatal leptospirosis in free-ranging Eurasian beavers (Castor fiber L.), Switzerland

Leptospirosis was first diagnosed in free-ranging Eurasian beavers (Castor fiber L.) in Switzerland in 2010. Pathologic, serologic, molecular and epidemiologic analyses were carried out on 13 animals submitted for necropsy from 2010 through 2014. Typical lesions included alveolar haemorrhages in the lungs, tubular degeneration and interstitial nephritis in the kidneys. Microscopic agglutination test results were positive for serogroups Icterohaemorrhagiae, Australis, Autumnalis and Sejroe. Molecular analysis identified four distinct profiles belonging to serovar Icterohaemorrhagiae or Copenhageni. The severity and features of the lesions were consistent with a fatal disease associated with leptospires similarly to what has been reported in other animals and humans. The spatiotemporal occurrence of leptospirosis in beavers suggested an upstream spread of the bacteria and coincided with an increased incidence of leptospirosis in dogs and a case cluster in humans. However, an epidemiologic link among beaver cases and among species was not supported neither by the serologic nor molecular data.

Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA

Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.

The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative.

Nuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487-489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction.