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Repeated climatic and vegetation changes during the Pleistocene have shaped biodiversity in Northern Europe including Denmark. The Northern Birch Mouse (Sicista betulina) was one of the first small rodent species to colonize Denmark after the Late Glacial Maximum. This study analyses complete mitochondrial genomes and two nuclear genes of the Northern Birch Mouse to investigate the phylogeographical pattern in North-western Europe and test whether the species colonized Denmark through several colonization events. The latter was prompt by (i) the present-day distinct northern and southern Danish distribution and (ii) the subfossil record of Northern Birch Mouse, supporting early Weichselian colonization. Samples from Denmark, Norway, Sweden, Russia, Latvia, Estonia, and Slovakia were included. Mitogenomes were obtained from 54 individuals, all representing unique mitogenomes supporting high genetic variation. Bayesian phylogenetic analysis identified two distinct evolutionary linages in Northern Europe diverging within the Elster glaciation period. The results of the two nuclear genomes showed lower genetic differentiation but supported the same evolutionary history. This suggests an allopatric origin of the clades followed by secondary contact. Individuals from southern Denmark were only found in one clade, while individuals from other areas, including northern Denmark, were represented in both clades. Nevertheless, we found no evidence for repeated colonization's explaining the observed fragmented distribution of the species today. The results indicated that the mitogenome pattern of the Northern Birch Mouse population in southern Denmark was either (i) due to the population being founded from northern Denmark, (ii) a result of climatic and anthropogenic effects reducing population size increasing genetic drift or (iii) caused by sampling bias.

In the past the European otter Lutra lutra was distributed throughout most of Europe but since the 1980s its distributional range has been reduced. Currently, the otter population is increasing. Conservation efforts have been implemented, however due to the natural elusiveness of the species it is difficult to monitor. Non-invasive sampling has proven to be the most effective method to derive population parameters such as presence/absence, genetic variability and population structure in European otters. The method to collect non-invasive samples is robust and provides reliable data. This study investigates the validity of the present state-of-The-Art method of identifying otter feces, and suggests modifications and improvements of the method. Results from the comparison of field collected data and data derived from a blind test show that the method is applicable in areas abundant with otters, however the method loses its power in the periphery of the distributional range. In these areas, it would be relevant to supplement traditional sampling with DNA analysis to verify the identification of the sample.

Conservation genetics is important in the management of endangered species, helping to understand their connectivity and long-term viability, thus identifying populations of importance for conservation. The pond bat (Myotis dasycneme) is a rare species classified as "Near Threatened" with a wide but patchy Palearctic distribution. A total of 277 samples representing populations in Denmark, Germany, Latvia, Hungary, and Russia were used in the genetic analyses; 224 samples representing Denmark, Germany, and Russia were analyzed at 10 microsatellite loci; 241 samples representing all areas were analyzed using mitochondrial D-loop and cytochrome B sequences. A Bayesian clustering approach revealed two poorly resolved clusters, one representing the Danish and German groups and the other the Russian group. However, significantly different pairwise FST and DEST estimates were observed between the Danish and German groups and between the Danish and Russian groups suggesting a recent population structure. These conflicting results might be attributed to the effect of migration or low resolution due to the number of microsatellite markers used. After concatenating the two mitochondrial sequences, analysis detected significant genetic differentiation between all populations, probably due to genetic drift combined with a founder event. The phylogenetic tree suggested a closer relationship between the Russian and Northern European populations compared to the Hungarian population, implying that the latter belongs to an older ancestral population. This was supported by the observed haplotype network and higher nucleotide diversity in this population. The genetic structuring observed in the Danish/German pond bat stresses the need for a cross-border management between the two countries. Further, the pronounced mtDNA structuring, together with the indicated migration between nearby populations suggest philopatric female behavior but male migration, emphasizes the importance of p

Identification of populations and management units is an essential step in the study of natural systems. Still, there is limited consensus regarding how to define populations and management units, and whether genetic methods allow for inference at the relevant spatial and temporal scale. Here, we present a novel approach, integrating genetic, life-history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic structure in harbour seals. Second, we used harbour seal demographic and life-history data to conduct population viability analyses (PVAs) in the VORTEX simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (2010) "population viability criterion" for demographic independence. The genetic analyses revealed fine-scale population structuring in southern Scandinavian harbour seals and pointed to the existence of six genetic units. The PVAs indicated that the census population size of each of these genetic units was sufficiently large for long-term population viability, and hence that the six units could be classified as demographically independent management units. Our study suggests that population genetic inference can offer the same degree of temporal and spatial resolution as "non-genetic" methods, and that the combined use of genetic data and PVAs constitute a promising approach for delineating populations and management units. This article is protected by copyright. All rights reserved.

The impact of landscape structure and land management on the dispersal of populations of wild species inhabiting the agricultural landscape was investigated by determining the genetic diversity and gene flow of field vole (Microtus agrestis) in three different areas. The main hypotheses were: I) organic farms act as genetic sources and diversity reservoirs for species living in agricultural areas and II) gene flow and genetic structure in the agricultural landscape are influenced by the degree of landscape complexity and connectivity. A total of 443 individuals were sampled within two consecutive years from two agricultural areas and one relatively undisturbed grassland area. Fifteen polymorphic microsatellite loci and the central part of the cytochrome-b were analysed for all the samples. The results indicate that management (i.e. organic or conventional management) has an important effect in shaping the genetic structure across the landscape, but that landscape structure is the main factor shaping gene flow and genetic diversity. More importantly, the presence of organically managed areas does not act as a genetic reservoir for conventional areas and the most important predictor of effective population size is the amount of un-managed available habitat. Together with the findings that the relatively undisturbed natural area showed a completely different genetic structure and diversity levels as compared to the two agricultural areas, these results suggest that political decisions for supporting “wildlife friendly” land management should take into account both management and landscape structure factors.

The development of next-generation sequencing technologies enables rapid generation of large amounts of genome sequences. Next-generation sequencing was utilised to perform whole genome sequencing of two Phasianidae, common quail (Coturnix coturnix) and grey partridge (Perdix perdix). Sequence data corresponding to 8 to 9 fold coverage of the genomes of the two species were obtained. The amount of sequence data enabled generation of a rough de novo genome assembly suitable for either the identification of the sequence of specific genes or for use in comparative studies with other birds, such as chicken and turkey. Likewise, it was possible to identify numerous SNPs and microsatellites for use in other studies.

Several arthropods are known to be highly beneficial to agricultural production. Consequently it is of great relevance to study the importance of land management and land composition for the conservation of beneficial aphid-predator arthropod species in agricultural areas. Therefore our study focusing on the beneficial arthropod Bembidion lampros had two main purposes: I) identifying the physical barriers to the species’ dispersal in the agricultural landscape, and II) assessing the effect of different land management strategies (i.e. use of pesticides and intensiveness) on the dispersal patterns. The study was conducted using genetic analysis (microsatellite markers) applied to samples from two agricultural areas (in Denmark) with different agricultural intensity. Land management effects on dispersal patterns were investigated with particular focus on: physical barriers, use of pesticide and intensity of cultivation. The results showed that Bembidion lampros disperse preferably through hedges rather than fields, which act as physical barriers to gene flow. Moreover the results support the hypothesis that organic fields act as reservoirs for the re-colonization of conventional fields, but only when cultivation intensity is low. These results show the importance of non-cultivated areas and of low intensity organic managed areas within the agricultural landscape as corridors for dispersal (also for a species typically found within fields). Hence, the hypothesis that pesticide use cannot be used as the sole predictor of agriculture’s effect on wild species is supported as land structure and agricultural intensity can be just as important.

The analysis of the haplotype diversity represented by the sequences of the control region in the mitochondria in Danish partridges identified signals of population expansion as was the case in other European grey partridges. Based on this genetic analysis of the Danish recent and historical grey partridges together with previously analysed grey partridges from Germany, Poland, Hungary, France and Italy, it is hypothesized that the timing of the Grey partridge population expansions up through western Europe and the following dispersal of the grey partridge from the last LGM refugium in the French Pyrenees might be explained by the origin and spread of agriculture through Europe i.e. “following the plough”.

Non-local population stocking can have adverse genetic effects through loss of genetic diversity and introgressive hybridisation in wild populations exploited by man. The grey partridge (Perdix perdix) has been an important European game species for centuries, widely subject to translocation and stocking. After ca 80 years releasing reared grey partridges into Danish wild partridge areas, this study investigated whether an indigenous Danish grey partridge still existed. We predicted that (i) an indigenous Danish partridge would belong to the western European clade (W1) and (ii) would be more closely related to the historical, indigenous grey partridges than to farm bred partridges. These predictions were tested analysing the variation in the mitochondrial control region (CR1) and microsatellite markers in museum samples representing the ancestral indigenous Danish grey partridge, contemporary (recent) wild grey partridges and farmed grey partridges from the five largest farms in Denmark. Phylogeography- and population structure analyses showed traces of the indigenous Danish grey partridges amongst recent wild partridges in certain areas and significant genetic differences between reared, farmed partridges and historical- and recent partridges. The results also showed that the indigenous Danish grey partridges belonged to the western European clade (W1 haplotype). A foreign stocking effect was detected on the remote island of Bornholm, where the current population originated from introduced Danish and Bohemian grey partridges. The loss of haplotype diversity over time in certain geographical areas probably results from serious declines in wild Danish grey partridge numbers in recent decades. This combined with the 2 observation that hybridisation between released stocked and wild partridges can occur may complicate recovery of partridge populations.

Sufficient sequence data to initiate genome sequencing of quail and grey partridge has been obtained. The difference in assembly quality between species is a consequence of the difference in length of the sequence reads (54 cycles versus 101 cycles). Additional data will be required before sequence assembly are being performed. Specifically longer sequence reads (especially in quail) will be necessary to generate assemblies of a reasonable quality.

The impact of landscape structure and land management on the dispersal of populations of wild species inhabiting the agricultural landscape was investigated by determining the genetic diversity and gene flow of field vole (Microtus agrestis) in three different areas. The main hypotheses were: I) organic farms act as genetic sources and diversity reservoirs for species living in agricultural areas and II) gene flow and genetic structure in the agricultural landscape are influenced by the degree of landscape complexity and connectivity. A total of 443 individuals were sampled within two consecutive years from two agricultural areas and one relatively undisturbed grassland area. Fifteen polymorphic microsatellite loci and the central part of the cytochrome-b were analysed for all the samples. The results indicate that management (i.e. organic or conventional management) has an important effect in shaping the genetic structure across the landscape, but that landscape structure is the main factor shaping gene flow and genetic diversity. More importantly, the presence of organically managed areas does not act as a genetic reservoir for conventional areas and the most important predictor of effective population size is the amount of un-managed available habitat. Together with the findings that the relatively undisturbed natural area showed a completely different genetic structure and diversity levels as compared to the two agricultural areas, these results suggest that political decisions for supporting “wildlife friendly” land management should take into account both management and landscape structure factors.

• Økologiske marker har mere ukrudtsbiomasse end konventionelle. • Der er flere blomstrende arter i økologiske hegn end konventionelle forudsat, at der er kontinuitet i den økologiske drift. • Der er flere små pattedyr i små økologiske biotoper end konventionelle. • Fjernmålinger fra fly eller satellit, kaldet remote sensing, kan skelne hvilken afgrødetype der dyrkes, samt forekomsten af småbiotoper. • Uanset driftformen er det vigtigt at inddrage naturhensyn i driften, dvs., at der findes ekstensivt drevne arealer (græsmarker, overdrev, enge) til natur og direkte afsatte arealer til natur.

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