DOI: 10.5061/dryad.msbcc2g7v
title: Data from: High-resolution analysis of red deer (<em>Cervus elaphus</em>) management units in a Central European region of high human population density reveals severe effects on genetic diversity and differentiation

description: The threat of isolation to red deer (Cervus elaphus) has been described in
 numerous European studies. The consequences range from reduced genetic
 diversity and increased inbreeding to inbreeding depression. It has been
 shown that the underlying factors cannot be generalised, but vary greatly
 in their effects depending on local conditions. The aim of this study was
 to analyse in detail the genetics of red deer in a large German federal
 state with a population density of 532 inhabitants per km2 and 23.8%
 settlement and traffic area, in order to generate data for future
 management of the region. 1199 individual samples of red deer were
 collected in all 21 Administrative Management Units (AMUs) and compared
 with existing results from the neighbouring state of Hesse (19 AMUs). All
 2400 individuals from both states were clustered using Bayesian methods
 and connectivity between neighbouring AMUs was quantified. Overall, 30% of
 the AMUs were found to be highly isolated, mostly with effective
 population sizes (Ne) &lt; 100. In contrast, 47.5% of the AMUs still
 had clear connectivity, allowing them to be merged into 4 larger red deer
 regions. For the small isolated areas, low genetic diversity was found in
 unit with high homozygosity and low Ne. With high sampling density and
 identical methodology, detailed information on AMUs can be obtained and
 the degree of vulnerability of individual AMUs as part of the overall
 population can be validated. These data will be available for future red
 deer management in the study area and beyond.
description: <strong>Study area, red deer populations and
 sampling</strong> The study area covers the
 entire region of the federal states of Hesse and North Rhine-Westphalia
 (NRW) in central and western Germany with a north-south extension of 350
 km, a west-east extension of 290 km and a total area of approximately
 55,213 km<sup>2</sup>. Compared to the
 German average of 237 persons per km<sup>2</sup>, the
 population density in 2023 was about 531.7 persons per
 km<sup>2</sup> in North Rhine-Westphalia and 302.6 persons per
 km<sup>2</sup> in Hesse (Statistisches Bundesamt 2024). Hesse
 consists of different types of land use, mainly forests (42.5%), pastures
 (13.4%) and agriculture (22.6%). Hesse is the German state with the
 largest forest area. The corresponding land use proportions for forest,
 pasture and agriculture in NRW were 26.9%, 12.1% and 31.1,
 respectively. The AMUs are scattered across the two
 states and vary considerably in size from 41.3 (RK) to 787.2
 km<sup>2</sup> (TAU) (Table 1). Forty AMUs were surveyed. The
 distances between AMUs ranged from 7.64 (DB-SIO) to 321.41 km (OD-RK)
 (centre to centre). They were separated by residential areas, fenced
 motorways, country roads or by larger contiguous agricultural areas. In
 the ‘red deer–free’ areas between AMUs, establishment of red deer
 populations should be prevented to protect vegetation from damage. Hunting
 in these areas could impede the migration of red deer between AMUs (Herzog
 et al. 2020). According to the local authorities and the red deer
 management associations legally responsible for the management of the
 respective AMUs, the estimated population size of the AMUs in spring
 ranged from 59 animals in Wattenberg-Weidelsburg to 3480 animals in
 Eifel-Zitterwald-Mürrel (Table 1). However, these figures are based on
 estimates, as exact numbers are not available. The estimates are based on
 calculations of hunting bag numbers according to the Oberste Jagdbehörde
 Hessen/HMUKLV (2023) in Hesse and according to Müller et al. (2020) in NRW
 (Forschungsstelle für Jagdkunde/LANUV 2022a, b).
 Samples were labelled with information on the animal (sex and age
 class) and the hunting area, and frozen until processed in the laboratory.
 A total of 1199 samples were collected in NRW during the 2020-2022 hunting
 seasons. No animals were killed specifically for the study. No live
 animals were sampled and no shed antlers were sought or collected for the
 study. Due to the impact of sample size on the accuracy of population
 genetic results (Reiner et al. 2019), the goal was to collect 60 samples
 per area. In the end, an average of 63.8 samples were collected per area
 (0.194 individuals per km<sup>2</sup>). The minimum sample
 size was 12 samples in Nutscheid (see Tables 1A and B for details). AMUs
 with close geographical/political links were grouped together to form
 ‘larger regions’, e.g. the Eifel (Point 1) with the individual AMUs 1.1
 (EHU), 1.2 (ENP), 1.3 (EZM) and 1.4 (EFW) (see Table 1A).
 No new samples were collected for Hesse. Rather, data from the
 already genotyped samples from 1291 individuals collected during the
 2018/2019 hunting season (Table 1B) (Reiner et al. 2021) were used and
 analysed together with the newly collected and genotyped samples from NRW.
 In total, samples from 2490 red deer individuals were analysed.
  <strong>DNA extraction and
 genotyping</strong> DNA was extracted using a
 commercially available kit (Instant Virus RNA Kit, Analytik Jena,
 Germany). For this purpose, 30 to 50 mg of tissue was processed according
 to the manufacturer's instructions. DNA concentration was determined
 photometrically and adjusted to 5 ng/μl with RNAse-free water. The
 presence of high molecular weight DNA was confirmed by agarose gel
 electrophoresis. Sixteen microsatellites were used to genotype red deer,
 as described in detail by Willems et al. (2016). Primers were combined in
 two multiplex PCRs (Reiner et al. 2021). PCR was performed in a volume of
 10 μl consisting of 5 μl 2× multiplex mastermix (Qiagen, Germany), 4 μl
 primer mix and 1 μl (5 ng) extracted DNA. After an initial denaturation
 step of 15 min, the DNA was amplified in 26 cycles of denaturation at 94
 °C for 30 s, annealing at 56 °C (multiplex PCR 4 at 50 °C) for 90 s and
 extension at 72 °C for 30 s. After a final step at 60 °C for 30 min, the
 PCR reactions were cooled to 4 °C.
 <strong>Capillary electrophoresis</strong>
 One microliter of fluorescently labelled PCR product and 0.375 µl
 DNA Size Standard 500 Orange (Nimagen, The Netherlands) were added to 12
 µl Hi-Di-formamide (Thermofisher Scientific, Germany) and electrophoresed
 on an ABI PRISM 310 automated sequencer. Allele sizes were determined
 using Peakscanner 2.0 software (Thermofisher Scientific,
 Germany). 
description: # Data from: High-resolution analysis of red deer (*Cervus elaphus*)
 management units in a Central European region of high human population
 density reveals severe effects on genetic diversity and differentiation
 [https://doi.org/10.5061/dryad.msbcc2g7v](https://doi.org/10.5061/dryad.msbcc2g7v) ## Description of the data and file structure A total of 2490 individual hunted red deer from two federal states in Germany were sampled and genotyped with 16 microsatellite markers to analyse population genetic parameters, genetic diversity, and isolation.  ### Files and variables #### File: Kopie_von_Genalex_basic_data.xlsx **Description:** Data are each two alleles of 16 microsatellite markers for 2490 red deer individuals from 40 red deer management units ##### Variables * Column A: ID including AMU (red deer administrative management unit) and individual number * Column B: AMU * Column C-AH: Pairwise illustration of microsatellite lengths. C: Allele 1 of microsatellite 1; D: Allele 2 of microsatellite 1; E: Allele 1 of microsatellite 2 and so on. * AI and AJ: Geographic coordinates of the AMUs No missing values, except null alleles (given as "0") ## Code/software The data can be read with Microsoft Excel or other free alternatives ## Access information not applicable