Hybridization between native and introduced species of deer in Eastern Europe

Can cryptic female choice prevent invasive hybridization in external fertilizing fish?

Polyandrous mating systems result in females mating with multiple males, generating opportunities for strong pre-mating and post-mating sexual selection. Polyandry also creates the potential for unintended matings and subsequent sperm competition with hybridizing species. Cryptic female choice allows females to bias paternity towards preferred males under sperm competition and may include conspecific sperm preference when under hybridization risk. The potential for hybridization becomes particularly important in context of invasive species that can novelly hybridize with natives, and by definition, have evolved allopatrically. We provide the first examination of conspecific sperm preference in a system of three species with the potential to hybridize: North American native Atlantic salmon (Salmo salar) and brook char (Salvelinus fontinalis), and invasive brown trout (Salmo trutta) from Europe. Using naturalized populations on the island of Newfoundland, we measured changes in sperm swimming performance, a known predictor of paternity, to determine the degree of modification in sperm swimming to female cues related to conspecific sperm preference. Compared to water alone, female ovarian fluid in general had a pronounced effect and changed sperm motility (by a mean of 53%) and swimming velocity (mean 30%), but not linearity (mean 6%). However, patterns in the degree of modification suggest there is no conspecific sperm preference in the North American populations. Furthermore, female cues from both native species tended to boost the sperm of invasive males more than their own. We conclude that cryptic female choice via ovarian fluid mediated sperm swimming modification is too weak in this system to prevent invasive hybridization and is likely insufficient to promote or maintain reproductive isolation between the native North American species.

European forests under global climate change: Review of tree growth processes, crises and management strategies

The ongoing global climate change is challenging all sectors, forestry notwithstanding. On the one hand, forest ecosystems are exposed to and threatened by climate change, but on the other hand, forests can influence the course of climate change by regulating the water regime, air quality, carbon sequestration, and even reduce climate extremes. Therefore, it is crucial to see climate change not only as a risk causing forest disturbances and economic consequences but also as an opportunity for innovative approaches to forest management, conservation, and silviculture based on the results of long-term research. We reviewed 365 studies evaluating the impact of climate change on European forest ecosystems, all published during the last 30 years (1993-2022). The most significant consequences of climate change include more frequent and destructive large-scale forest disturbances (wildfire, windstorm, drought, flood, bark beetle, root rot), and tree species migration. Species distribution shifts and changes in tree growth rate have substantial effects on ecosystem carbon storage. Diameter/volume increment changed from -1 to +99% in Central and Northern Europe, while it decreased from -12 to -49% in Southern Europe across tree species over the last ca. 50 years. However, it is important to sharply focus on the causes of climate change and subsequently, on adaptive strategies, which can successfully include the creation of species-diverse, spatially and age-wise structured stands (decrease drought stress and increase production), prolongation of the regenerative period, or the use of suitable introduced tree species (e.g., Douglas fir, black pine, and Mediterranean oaks). But the desired changes are based on increasing diversity and the mitigation of climate change, and will require significantly higher initial costs for silviculture practices. In conclusion, the scope and complexity of the topic require further comprehensive and long-term studies focusing on international cooperation. We see a critical gap in the transfer of research results into actual forest practice, which will be the key factor influencing afforestation of forest stands and forest growth in the following decades. What our forests will look like for future generations and what the resulting impact of climate change will be on forestry is in the hands of forest managers, depending on supportive forestry research and climate change policy, including adaptive and mitigation strategies.

Invasive and Alien Mammal Species in Poland—A Review

About 20 species of non-native mammals have been recorded in Poland. Some of them are already extinct or have been extirpated, while others are widely distributed and may affect the native biota in Poland. We review the literature on 15 non-native species found in this country, discussing their origin, distribution, and presence on lists of invasive species that pose a threat to wildlife in Poland and the EU. In addition, we discuss current knowledge on their impact on Polish ecosystems. However, on many of these species, there is little information, and the consequences of their presence remain unclear. Therefore, we emphasize the importance of this review for appropriate species management and suggest the introduction of monitoring, especially of species whose populations are increasing.

The effects of population management on wild ungulates: A systematic map of evidence for UK species

Introduction

Over recent decades, the abundance and geographic ranges of wild ungulate species have expanded in many parts of Europe, including the UK. Populations are managed to mitigate their ecological impacts using interventions, such as shooting, fencing and administering contraception. Predicting how target species will respond to interventions is critical for developing sustainable, effective and efficient management strategies. However, the quantity and quality of evidence of the effects of interventions on ungulate species is unclear. To address this, we systematically mapped research on the effects of population management on wild ungulate species resident in the UK.

Methods

We searched four bibliographic databases, Google Scholar and nine organisational websites using search terms tested with a library of 30 relevant articles. Worldwide published peer-reviewed articles were considered, supplemented by ‘grey’ literature from UK-based sources. Three reviewers identified and screened articles for eligibility at title, abstract and full-text levels, based on predefined criteria. Data and metadata were extracted and summarised in a narrative synthesis supported by structured graphical matrices.

Results

A total of 123 articles were included in the systematic map. Lethal interventions were better represented (85%, n = 105) than non-lethal interventions (25%, n = 25). Outcomes related to demography and behaviour were reported in 95% of articles (n = 117), whereas effects on health, physiology and morphology were studied in only 11% of articles (n = 14). Well-studied species included wild pigs (n = 58), red deer (n = 28) and roe deer (n = 23).

Conclusions

Evidence for the effects of population management on wild ungulate species is growing but currently limited and unevenly distributed across intervention types, outcomes and species. Priorities for primary research include: species responses to non-lethal interventions, the side-effects of shooting and studies on sika deer and Chinese muntjac. Shooting is the only intervention for which sufficient evidence exists for systematic review or meta-analysis.

Genomic divergence and a lack of recent introgression between commercial and wild bumblebees ( Bombus terrestris )

The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted gene complexes. However, neither the existence nor the extent of genomic introgression and evolutionary divergence between wild and commercial bumblebees is fully understood. We obtained whole‐genome sequencing data from wild and commercial Bombus terrestris collected from sites in Southern Sweden with and without long‐term use of commercially imported B. terrestris. We search for evidence of introgression, dispersal and genome‐wide differentiation in a comparative genomic analysis of wild and commercial bumblebees. Commercial B. terrestris were found in natural environments near sites where commercial bumblebees were used, as well as drifting wild B. terrestris in commercial bumblebee colonies. However, we found no evidence for widespread, recent genomic introgression of commercial B. terrestris into local wild conspecific populations. We found that wild B. terrestris had significantly higher nucleotide diversity (Nei's pi, π), while the number of segregating sites (Watterson's theta, θw) was higher in commercial B. terrestris. A highly divergent region on chromosome 11 was identified in commercial B. terrestris and found to be enriched with structural variants. The genes present in this region are involved in flight muscle contraction and structure and pathogen immune response, providing evidence for differing evolutionary processes operating in wild and commercial B. terrestris. We did not find evidence for recent introgression, suggesting that co‐occurring commercial B. terrestris have not disrupted evolutionary processes in wild B. terrestris populations.

Consequences of Hybridization in Mammals: A Systematic Review

Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.

A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic

Simple Summary

The sika deer is a very flexible invasive species, capable of living dynamically in both large forests and mixed environment characterized by a prevalence of agricultural land. The Japanese sika deer was introduced to the Czech Republic at the end of the 19th century. The success of an introduced alien species may consist in their hybridizing with closely related taxa. Where few barriers to gene flow exist, rapid introgression of genetic traits from one species into another frequently occurs. The current Czech sika populations embody the most abundant and expanding group in continental Europe. In western Bohemia, we confirmed the interspecific hybridization with the native red deer. In this context, the red deer gene pool is endangered. The animals proliferate steadily in all directions and will most probably spread all over the Czech Republic if no major, timely changes in game management are adopted.

Abstract

Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer–like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.

Locus-specific introgression in young hybrid swarms: Drift may dominate selection

Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These human-mediated hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44,997 SNPs to identify loci introgressing more or less when compared to the genome wide expectation in a human-mediated hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centres that were significantly different from the genome wide expectation, and 17.6% of all SNPs had excess rates of introgression. Based on simulations, we believe that many of these markers have diverged from the genome-wide average due to drift, rather than because of selection, and we suggest that these simulations can be useful as a null distribution for future studies of genomic clines. Future work on red deer and sika could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are responding to selection.

Asia and Europe: So Distant So Close? The Case of Lipoptena fortisetosa in Italy

In Europe, 5 Lipoptena species have been recorded, including Lipoptena fortisetosa. This species, native to Asian countries, was described as a parasite of sika deer and its appearance in Europe dates back to more than 50 years ago. Lipoptena fortisetosa has been recently reported in Italy, sharing its hosts with Lipoptena cervi. A morpho-molecular approach was developed to determine the phylogenetic interrelationship of Italian and Asian CO1 haplotypes sequenced from Lipoptena fly individuals collected in Italy, and their DNA sequences were compared with conspecifics available in GenBank; morphological key-characters (terminalia) of L. fortisetosa were compared with the original description. Two haplotypes were recorded from Italy and assigned to L. cervi and L. fortisetosa, respectively. The latter was part of the monophyletic clade L. fortisetosa, along with 2 Central European and 2 Korean haplotypes (100% identical to one of the Korean haplotypes); moreover, Italian L. fortisetosa female terminalia were consistent with the original description of Asian individuals. Pending more in-depth investigations, this study provides a first answer to the hypothesis of the recent colonization of Italy by L. fortisetosa from Asia as we did not detect any obvious and stable morphological and molecular differences in specimens from the 2 geographical areas. The presence of the sika deer in Europe was retraced and the possible route traveled by the parasite from Asia and the eco-biological factors that may have enhanced its settlement are discussed.

Effects of Bark Stripping on Timber Production and Structure of Norway Spruce Forests in Relation to Climatic Factors

The aim of this study was to assess the effects of bark stripping caused by sika deer (Cervus nippon [Temminck]) on the production and structure of young Norway spruce (Picea abies L. Karst) forest stands (41–43 years). Production parameters, structure, diversity, and the dynamics of radial growth in selected forest stands in relation to climatic conditions were evaluated. Similar to other production parameters, stand volumes showed lower values on research plots heavily damaged by bark stripping (290 m3 ha−1) compared to stands with lower tree stem damages (441 m3 ha−1). A significant decrease in stem volume was recorded for trees with stem circumference damage higher than 1/3 of the stem circumference. In most cases, the trees were damaged between the ages of 10–23 years, specifically the radial growth was significantly lowered in this period. The diameter increment of damaged trees dropped to 64% of the healthy counterparts in this period. Bark stripping damages reached up to 93% of the stem circumference with a mean damage of 31%. Stem rot was found on 62% of damaged trees. In our study area, with respect to the terms of climatic conditions, precipitation had a higher effect on radial growth of the Norway spruce compared to temperature. The main limiting climatic factor of tree growth was the lack of precipitation within a growing season, particularly in June of the current year.

Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history

The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations.

Genetic diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France

In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years. In addition, we reconstructed the feeding habits and the habitat of red deer since the beginning of agriculture applying isotopic analyses in order to establish a basis for current environmental management strategies. We show that past and present red deer in the Vosges Mountains belong to mtDNA haplogroup A, suggesting that they originated from the Iberian refugium after the last glacial maximum (LGM). Palaeogenetic analysis of ancient bone material revealed the presence of two distinct haplotypes with different temporal distributions. Individuals belonging to the two haplotype groups apparently occupied two different habitats over at least 7'000 years. AM6 correlates with an ecological type that feeds in densely forested mountain landscapes, while AM235 correlates with feeding in lowland landscapes, composed of a mixture of meadows and riverine, herb-rich woodlands. Our results suggest that red deer of north-eastern France was able to adapt, over the long term, to these different habitat types, possibly due to efficient ethological barriers. Modern haplotype patterns support the historical record that red deer has been exposed to strong anthropogenic influences as a major game species.

The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes

We present here the de novo genome assembly CerEla1.0 for the red deer, Cervus elaphus, an emblematic member of the natural megafauna of the Northern Hemisphere. Humans spread the species in the South. Today, the red deer is also a farm-bred animal and is becoming a model animal in biomedical and population studies. Stag DNA was sequenced at 74× coverage by Illumina technology. The ALLPATHS-LG assembly of the reads resulted in 34.7 × 10³ scaffolds, 26.1 × 10³ of which were utilized in Cer.Ela1.0. The assembly spans 3.4 Gbp. For building the red deer pseudochromosomes, a pre-established genetic map was used for main anchor points. A nearly complete co-linearity was found between the mapmarker sequences of the deer genetic map and the order and orientation of the orthologous sequences in the syntenic bovine regions. Syntenies were also conserved at the in-scaffold level. The cM distances corresponded to 1.34 Mbp uniformly along the deer genome. Chromosomal rearrangements between deer and cattle were demonstrated. 2.8 × 10⁶ SNPs, 365 × 10³ indels and 19368 protein-coding genes were identified in CerEla1.0, along with positions for centromerons. CerEla1.0 demonstrates the utilization of dual references, i.e., when a target genome (here C. elaphus) already has a pre-established genetic map, and is combined with the well-established whole genome sequence of a closely related species (here Bos taurus). Genome-wide association studies (GWAS) that CerEla1.0 (NCBI, MKHE00000000) could serve for are discussed.

Intensive Management and Natural Genetic Variation in Red Deer (Cervus elaphus)

The current magnitude of big-game hunting has outpaced the natural growth of populations, making artificial breeding necessary to rapidly boost hunted populations. In this study, we evaluated if the rapid increase of red deer (Cervus elaphus) abundance, caused by the growing popularity of big-game hunting, has impacted the natural genetic diversity of the species. We compared several genetic diversity metrics between 37 fenced populations subject to intensive management and 21 wild free-ranging populations. We also included a historically protected population from a national park as a baseline for comparisons. Contrary to expectations, our results showed no significant differences in genetic diversity between wild and fenced populations. Relatively lower genetic diversity was observed in the protected population, although differences were not significant in most cases. Bottlenecks were detected in both wild and fenced populations, as well as in the protected population. Assignment tests identified individuals that did not belong to their population of origin, indicating anthropogenic movement. We discuss the most likely processes, which could have led to the observed high levels of genetic variability and lack of differentiation between wild and fenced populations and suggest cautionary points for future conservation. We illustrate our comparative approach in red deer. However, our results and interpretations can be largely applicable to most ungulates subject to big-game hunting as most of them share a common exploitation-recovery history as well as many ecological traits.

Metazoan parasite communities: support for the biological invasion of Barbus barbus and its hybridization with the endemic Barbus meridionalis

Background

Recently, human intervention enabled the introduction of Barbus barbus from the Rhône River basin into the Barbus meridionalis habitats of the Argens River. After an introduction event, parasite loss and lower infection can be expected in non-native hosts in contrast to native species. Still, native species might be endangered by hybridization with the incomer and the introduction of novel parasite species. In our study, we aimed to examine metazoan parasite communities in Barbus spp. populations in France, with a special emphasis on the potential threat posed by the introduction of novel parasite species by invasive B. barbus to local B. meridionalis.

Methods

Metazoan parasite communities were examined in B. barbus, B. meridionalis and their hybrids in three river basins in France. Microsatellites were used for the species identification of individual fish. Parasite abundance, prevalence, and species richness were compared. Effects of different factors on parasite infection levels and species richness were tested using GLM.

Results

Metazoan parasites followed the expansion range of B. barbus and confirmed its introduction into the Argens River. Here, the significantly lower parasite number and lower levels of infection found in B. barbus in contrast to B. barbus from the Rhône River supports the enemy release hypothesis. Barbus barbus × B. meridionalis hybridization in the Argens River basin was confirmed using both microsatellites and metazoan parasites, as hybrids were infected by parasites of both parental taxa. Trend towards higher parasite diversity in hybrids when compared to parental taxa, and similarity between parasite communities from the Barbus hybrid zone suggest that hybrids might represent “bridges” for parasite infection between B. barbus and B. meridionalis. Risk of parasite transmission from less parasitized B. barbus to more parasitized B. meridionalis indicated from our study in the Argens River might be enhanced in time as higher infection levels in B. barbus from the Rhône River were revealed. Hybrid susceptibility to metazoan parasites varied among the populations and is probably driven by host-parasite interactions and environmental forces.

Conclusions

Scientific attention should be paid to the threatened status of the endemic B. meridionalis, which is endangered by hybridization with the invasive B. barbus, i.e. by genetic introgression and parasite transmission.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1867-9) contains supplementary material, which is available to authorized users.

Female Sexual Preferences Toward Conspecific and Hybrid Male Mating Calls in Two Species of Polygynous Deer, Cervus elaphus and C. nippon

The behavioral processes at the basis of hybridization and introgression are understudied in terrestrial mammals. We use a unique model to test the role of sexual signals as a reproductive barrier to introgression by investigating behavioral responses to male sexual calls in estrous females of two naturally allopatric but reproductively compatible deer species, red deer and sika deer. Previous studies demonstrated asymmetries in acoustic species discrimination between these species: most but not all female red deer prefer conspecific over sika deer male calls while female sika deer exhibit no preference differences. Here, we extend this examination of acoustic species discrimination to the role of male sexual calls in introgression between parent species and hybrids. Using two-speaker playback experiments, we compared the preference responses of estrous female red and sika deer to male sexual calls from conspecifics versus red × sika hybrids. These playbacks simulate early secondary contact between previously allopatric species after hybridization has occurred. Based on previous conspecific versus heterospecific playbacks, we predicted that most female red deer would prefer conspecific calls while female sika deer would show no difference in their preference behaviors toward conspecific and hybrid calls. However, results show that previous asymmetries did not persist as neither species exhibited more preferences for conspecific over hybrid calls. Thus, vocal behavior is not likely to deter introgression between these species during the early stages of sympatry. On a wider scale, weak discrimination against hybrid sexual signals could substantially contribute to this important evolutionary process in mammals and other taxa.