Predicting kill sites of an apex predator from GPS data in different multiprey systems.

Kill rates are a central parameter to assess the impact of predation on prey species. An accurate estimation of kill rates requires a correct identification of kill sites, often achieved by field-checking GPS location clusters (GLCs). However, there are potential sources of error included in kill-site identification, such as failing to detect GLCs that are kill sites, and misclassifying the generated GLCs (e.g., kill for nonkill) that were not field checked. Here, we address these two sources of error using a large GPS dataset of collared Eurasian lynx (Lynx lynx), an apex predator of conservation concern in Europe, in three multiprey systems, with different combinations of wild, semidomestic, and domestic prey. We first used a subsampling approach to investigate how different GPS-fix schedules affected the detection of GLC-indicated kill sites. Then, we evaluated the potential of the random forest algorithm to classify GLCs as nonkills, small prey kills, and ungulate kills. We show that the number of fixes can be reduced from seven to three fixes per night without missing more than 5% of the ungulate kills, in a system composed of wild prey. Reducing the number of fixes per 24 h decreased the probability of detecting GLCs connected with kill sites, particularly those of semidomestic or domestic prey, and small prey. Random forest successfully predicted between 73%-90% of ungulate kills, but failed to classify most small prey in all systems, with sensitivity (true positive rate) lower than 65%. Additionally, removing domestic prey improved the algorithm's overall accuracy. We provide a set of recommendations for studies focusing on kill-site detection that can be considered for other large carnivore species in addition to the Eurasian lynx. We recommend caution when working in systems including domestic prey, as the odds of underestimating kill rates are higher.

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts.

Disentangling the contribution of long-term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long-term isolation and/or more recent human-driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long-term isolation argue for the restoration of lost population connectivity.

Harvest models of small populations of a large carnivore using Bayesian forecasting.

Harvesting large carnivores can be a management tool for meeting politically set goals for their desired abundance. However, harvesting carnivores creates its own set of conflicts in both society and among conservation professionals, where one consequence is a need to demonstrate that management is sustainable, evidence-based, and guided by science. Furthermore, because large carnivores often also have high degrees of legal protection, harvest quotas have to be carefully justified and constantly adjusted to avoid damaging their conservation status. We developed a Bayesian state-space model to support adaptive management of Eurasian lynx harvesting in Scandinavia. The model uses data from the annual monitoring of lynx abundance and results from long-term field research on lynx biology, which has provided detailed estimates of key demographic parameters. We used the model to predict the probability that the forecasted population size will be below or above the management objectives when subjected to different harvest quotas. The model presented here informs decision makers about the policy risks of alternative harvest levels. Earlier versions of the model have been available for wildlife managers in both Sweden and Norway to guide lynx harvest quotas and the model predictions showed good agreement with observations. We combined monitoring data with data on vital rates and were able to estimate unobserved additional mortality rates, which are most probably due to poaching. In both countries, the past quota setting strategy suggests that there has been a de facto threshold strategy with increasing proportion, which means that there is no harvest below a certain population size, but above this threshold there is an increasing proportion of the population harvested as the population size increases. The annual assessment of the monitoring results, the use of forecasting models, and a threshold harvest approach to quota setting will all reduce the risk of lynx population sizes moving outside the desired goals. The approach we illustrate could be adapted to other populations of mammals worldwide.

Echinococcus multilocularis in a Eurasian lynx (Lynx lynx) in Turkey.

Echinococcus multilocularis is the causative agent of alveolar echinococcosis (AE), one of the most threatening zoonoses in Eurasia. Human AE is widespread in the Erzurum region of Turkey, but the situation of the disease in intermediate and definitive hosts is unknown. A Eurasian lynx (Lynx lynx) was killed in a traffic accident in the north of Erzurum, and was taken to our laboratory. Sedimentation and counting technique (SCT), DNA isolation and polymerase chain reaction (PCR) analysis were performed. The SCT results showed that the lynx was infected with E. multilocularis with a medium (745 worms) worm burden. The DNA of adult worms obtained from the lynx was analyzed with a species-specific PCR, and the worms were confirmed to be E. multilocularis by 12S rRNA gene sequence analysis. This is the first report of E. multilocularis from Eurasian lynx in Turkey.

Update of the helminth fauna in Eurasian lynx (Lynx lynx) in Poland.

The Eurasian lynx (Lynx lynx) is a strictly protected species of large carnivore in Poland. It inhabits forest complexes in north-eastern Poland and the Carpathian region in southern Poland. The status of the lynx within Poland requires special attention because its range decreased between 1980 and 2001 and has not yet recovered. One of the factors negatively affecting lynx populations is diseases, particularly parasites. The helminth fauna of the Eurasian lynx is not fully known in Poland. Previous coprological studies revealed that Polish lynx have been infected with seven species of nematodes, three species of cestodes, and one species of trematode. In this study, we present new data based on examination of opportunistically collected lynx carcasses. The aim of the study was to complement data on the helminth fauna of Eurasian lynx inhabiting Poland based on morphological and molecular analysis of parasites. Four species of cestodes-Taenia lynciscapreoli, Mesocestoides lineatus, Spirometra sp., and Taenia krabbei-were found for the first time in Eurasian lynx from Poland and three previously reported species of nematodes-Ancylostoma tubaeforme, Toxascaris leonina, and Toxocara cati-were confirmed. Larvae of Trichinella britovi were also detected in Eurasian lynx in Poland for the first time.

First identification of Cytauxzoon manul in Eurasian lynx (Lynx lynx) in northwestern China.

BACKGROUND: Multiple species of the genera Cytauxzoon and Hepatozoon can infect wild felines, but the diversity of these and other apicomplexan parasites in Eurasian lynx is scarcely known. The aim of this study was to detect Cytauxzoon and Hepatozoon species with molecular methods in Eurasian lynxes and their ticks in northwestern China. METHODS: DNA was extracted from the heart, liver, spleen, lung, and kidney samples of three Eurasian lynxes as well as from their five ixodid ticks. These DNA samples were screened with polymerase chain reactions (PCRs) for Cytauxzoon with the partial cytochrome b gene (CytB), cytochrome c oxidase subunit I gene (COI), and small subunit ribosomal RNA gene (18S rRNA), and Hepatozoon with three different fragments of small subunit ribosomal RNA gene (18S rRNA). PCR products were sequenced, aligned, and phylogenetically analyzed. RESULTS: One adult female of Eurasian lynx (#1, adult female) was co-infected with Cytauxzoon manul and Hepatozoon felis genotype I, while an adult male lynx (#2) was infected with C. manul. Interestingly, H. felis genotype I was both detected in a male cub (#3) and two out of five infesting Hyalomma asiaticum ticks. CONCLUSIONS: For the first time, Cytauxzoon manul is reported here from Eurasian lynx. In addition, H. felis has not been known to occur in this host species in China and Central Asia. Thus, the findings of this study extend our knowledge on the geographical distribution and host range of these haemoprotozoan parasites. Moreover, this is also the first evidence of C. manul and H. felis co-infection in Eurasian lynx.

Detection of Sarcocystis albifronsi, Eimeria alpacae, and Cystoisospora felis in Eurasian lynx (Lynx lynx) in northwestern China.

Eurasian lynx (Lynx lynx) is widely distributed in various habitats in Asia and Europe, and it may harbor multiple pathogens. Currently, the information on protozoan infection in Eurasian lynx is scarce. In this study, we performed nested polymerase chain reaction (nPCR) analysis to detect intestinal protozoan infection in three dead Eurasian lynxes, in northwestern China. Three dead Eurasian lynxes, an adult female (#1), an adult male (#2), and a cub male (#3), were sampled in West Junggar Mountain, the northwestern region of Xinjiang Uyghur Autonomous Region. The intestine samples were analyzed using nPCR. We used primers targeting the cytochrome C oxidase subunit I gene (COI) for detection of Sarcocystis and Eimeria species and targeting the small subunit 18 S ribosomal RNA gene (18S rRNA) for detection of Cystoisospora species. The nPCR-positive products were sequenced, aligned, and phylogenetically analyzed. Three intestinal protozoa, Sarcocystis albifronsi, Eimeria alpacae, and Cystoisospora felis, were found in three Eurasian lynxes. The intestine sample of Eurasian lynx #2 was detected with S. albifronsi and E. alpacae. In addition, C. felis was only found in the intestine sample of Eurasian lynx #3. To the best of our knowledge, S. albifronsi and E. alpacae were detected in Eurasian lynx for the first time. In addition, C. felis was firstly found in Eurasian lynx in China. These findings extend our knowledge of the geographical distribution and host range of intestinal protozoa.

Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivore Lynx lynx (Linnaeus, 1758).

Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north-western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre-adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate.

Shining a light on elusive lynx: Density estimation of three Eurasian lynx populations in Ukraine and Belarus.

The Eurasian lynx is a large carnivore widely distributed across Eurasia. However, our understanding of population status is heterogeneous across their range, with some populations isolated that are at risk of reduced genetic variation and a complete lack of information about others. In many European countries, Eurasian lynx are monitored through demographic studies crucial for their conservation and management. Even so, there are only rough and fragmented population assessments from Ukraine and Belarus, despite strict protection in both countries and their importance for lynx connectivity across Europe. We monitored lynx from October 2020 to March 2021 and used camera trapping in combination with spatial capture-recapture (SCR) methods in a Bayesian framework to provide the first SCR density estimation of three lynx populations across Ukraine and Belarus, including the Ukrainian Chornobyl Exclusion Zone, southern Belarus and the Ukrainian Carpathians. Our density estimates varied within our study areas ranging from 0.45 to 1.54 individuals/100 km2. This work provides a substantial scientific component to the overall understanding of lynx conservation for a region where only broad information is available and opens the doors for further large-scale monitoring and trend assessments. The crucial information we provide can greatly enhance the range-wide assessments of the status of this protected species. We also discuss the implications for Eurasian lynx conservation, despite the geopolitical realities impacting species monitoring in the region. Our work serves as a baseline, not only for future conservation interventions but also to evaluate the effects of disturbance and threats to these protected populations.

High Toxocara cati prevalence in wild, free-ranging Eurasian lynx (Lynx lynx) in Finland, 1999-2015.

In Finland, free-ranging Eurasian lynx (Lynx lynx) population has grown from 30 to 40 individuals to 2800 individuals since the species became partly protected in 1962. Changes in host population size are known to have an impact on host-parasite dynamics, and the Eurasian lynx population in Finland provides a unique opportunity for studying the potential effects of dramatic population increase and expansion of a solitary apex predator on their parasite prevalence and abundance. Toxocara cati is a zoonotic gastrointestinal parasite infecting domestic cats and wild felids worldwide. We studied T. cati infection prevalence and worm burden in 2756 Eurasian lynx individuals from Finland, covering the years 1999-2015. Toxocara cati worms that had been collected from intestinal contents were identified based on morphology. We performed regression analyses to investigate possible associations of age, sex, and host population density with T. cati infection. We found T. cati from 2324 (84.3%, 95% confidence interval 82.9-86.0) of the examined lynx. Each year, the infection prevalence was higher than 75% and not density dependent. The parasites were strongly aggregated, with older individuals harboring fewer T. cati than younger ones did. Old females aged 9-15 years had higher T. cati abundance than males of the same age group. Our results indicate that T. cati was a common and abundant parasite of Eurasian lynx throughout the study period, regardless of the changing population size and density.

Description of a novel Babesia sp. genotype from a naturally infected Eurasian lynx (Lynx lynx) in Anatolia, Turkey, with remarks on its morphology and phylogenetic relation to other piroplasmid species.

There are very limited data on Babesia species infecting lynx species worldwide, and almost nothing is known about babesias in the Eurasian lynx, the most widely distributed wild feline species in the Palearctic geography. This study describes a novel Babesia sp. genotype in a free-living Eurasian lynx in Turkey, named tentatively as 'Babesia sp. lynx', and its integrated genetic and morphological features. Phylogenetic analyses of piroplasmids with the novel Babesia sp. genotype in the current study indicated that this genotype falls into the 'carnivore clade A' of Babesia sensu stricto (true babesias), at the level of different genes (mainly 18S rRNA, ITS1, ITS2, and cyt b) and is monophyletic with the Babesia sp. Ankara genotype, previously observed in Turkey. Additionally, the constructed phylogenetic trees showed that the Babesia sp. lynx genotype infecting the Eurasian lynx is closely related to certain domestic and wild carnivore babesias, mainly Babesia rossi, Babesia presentii, and Babesia pisicii, at the level of different genes. This study also genetically barcoded the lynx infected with the Babesia sp. lynx and Haemaphysalis erinacei, and specimens collected from the animal revealed significant genetic variations between the sample Ha. erinacei and Babesia sp. Ankara-related Ha. erinacei that persists with sympatric populations in Central Anatolia. The lynx infected with the Babesia sp. lynx genotype was also found to be coinfected with Hepatozoon felis, an adeleorinid tick-borne protozoan parasite infecting wild and domestic felids, confirming for the first time its presence in a lynx species. Therefore, this study is the first to describe a potential novel Babesia sp. using its both morphological and phylogenetic characteristics in a lynx species. Adding the Babesia sp. lynx genotype to the phylogeny of feline piroplasmids significantly expands our knowledge of feline babesias in the Palearctic geography and their putative coevolution with their vertebrate hosts.

Long-term changes in habitat selection and prey spectrum in a reintroduced Eurasian lynx (Lynx lynx) population in Switzerland.

When wild-caught Eurasian lynx (Lynx lynx) from the Slovak Carpathian Mountains were reintroduced to Central Switzerland in the early 1970s and spread through the north-western Swiss Alps (NWA), they faced a largely unfamiliar landscape with strongly fragmented forests, high elevations, and intense human land use. For more than 30 years, radio-collared lynx have been monitored during three different project periods (in the 1980s, 1990s, and 2010s). Our study explored, how lynx over generations have learned to adjust to the alpine environment. We predicted that (1) lynx nowadays select more strongly for open habitats, higher elevations, and steep slopes compared to the early stages of recolonization and that (2) consequently, there were significant changes in the Eurasian lynx' prey spectrum. To test our predictions, we analyzed telemetry data (VHF, GPS) of 13 adult resident lynx in the NWA over 35 years, using Resource Selection Functions. Furthermore, we compared kills recorded from different individuals inhabiting the same region during three project periods. In general, lynx preferred forested areas, but over the years, they avoided open habitat less. Compared to the early stage of the recolonization, lynx in the most recent project period selected for higher elevations and the proportion of chamois in their prey spectrum surmounted that of roe deer. Potential driving factors for the observed changes could be increasing tolerance to human presence, intraspecific competition, or fitness benefits through exploitation of new resources. Long-term studies like ours provide important insight into how animals can respond to sudden environmental changes, e.g., in the course of translocations into new areas or anthropogenic alterations of their habitats.

Lead and Other Trace Element Levels in Brains of Croatian Large Terrestrial Carnivores: Influence of Biological and Ecological Factors.

Trace element pollution can adversely affect the brains of individuals and thus impact the entire population of apex predators, such as large European carnivores. We assessed exposure to prominent neurotoxicants As, Cd, Hg and Pb by measuring their brain stem levels in brown bears (n = 114), grey wolves (n = 8), Eurasian lynx (n = 3), and golden jackals (n = 2) sampled in 2015-2022 in Croatia. The highest of the non-essential elements was the Pb level in the bears' brains (median, Q1-Q3; 11.1, 7.13-24.1 µg/kg wet mass), with 4% of animals, all subadults, exceeding the established normal bovine levels (100 µg/kg wet mass). Species-specific differences were noted for Ca, Cd, Cu, Fe, Pb and Se brain levels. Female brown bears had higher As brain levels than males. Cubs and yearlings had lower brain Cd, but higher Zn, while subadults had higher Cu than adult bears. Hepatic As, Cd, Cu and Hg levels were shown to be a moderate proxy for estimating brain levels in bears (rS = 0.30-0.69). Multiple associations of As, Cd, Hg and Pb with essential elements pointed to a possible interaction and disturbance of brain Ca, Cu, Fe, Se and Zn homeostasis. Non-essential element levels in the brains of four studied species were lower than reported earlier for terrestrial meso-carnivores and humans. The age and sex of animals were highlighted as essential factors in interpreting brain element levels in ecotoxicological studies of large carnivores.

New Insights into Gastrointestinal and Pulmonary Parasitofauna of Wild Eurasian lynx (Lynx lynx) in the Harz Mountains of Germany.

The Eurasian lynx (Lynx lynx) represents an endangered wild felid species. In Germany, it currently occurs in three isolated populations in and around the Harz Mountains, the Palatinate Forest and the Bavarian Forest. Lynx parasitic infections affect animal health and might have an influence on population performance. Therefore, we investigated the protozoan and helminth fauna of free-ranging Eurasian lynx of the Harz population with emphasis on zoonotic parasites. Individual scat samples (n = 24) were collected from wild animals between 2019 and 2021 in the Harz National Park and surrounding areas. In total, 15 taxa of endoparasites were detected, including seven nematodes (i.e., Aelurostrongylus abstrusus, Angiostrongylus spp., Uncinaria stenocephala, Toxascaris leonina, Toxocara cati, Cylicospirura spp. and Capillaria spp.), one cestode (Diphyllobothriidae) and one trematode (Heterophylidae) as well as six protozoans (i.e., Cystoisospora rivolta, Cystoisospora felis, Toxoplasma gondii/Hammondia spp., Sarcocystis spp., Giardia intestinalis and Cryptosporidium spp.). Moreover, first-stage larvae (L1) of spurious lungworm, Protostrongylus pulmonalis, originating from lagomorph preys were identified. This work represents the first report on patent A. abstrusus and Angiostrongylus spp. infections in wild German Eurasian lynxes. Some of the identified parasites represent relevant pathogens for lynxes, circulating between these carnivorous definitive hosts and a variety of mammalian and invertebrate intermediate hosts, e.g., Sarcocystis spp., T. gondii/Hammondia spp., T. cati, T. leonina, A. abstrusus and Angiostrongylus spp., while others are considered exclusively pathogenic for wild felids (e.g., Cylicospirura spp., C. rivolta, C. felis). This study provides insights in the occurrence of zooanthroponotically relevant metazoan (i.e., T. cati and U. stenocephala) and protozoan (i.e., G. intestinalis) species in free-ranging lynx. The present work should be considered as a baseline study for future monitoring surveys on endoparasites circulating in wild Eurasian lynx for appropriate management practices in lynx conservation strategies in Europe.

First Report of Joyeuxiella spp. Infection in Eurasian Lynx and Its Histopathology Study from Iran: A Case Report.

According to the last information of IUCN Red List, Eurasian lynx has been endangered since 2010. The population of this animal is heavily affected by infectious parasites. Two adult Eurasian lynx (one male and one female) were illegally hunted and found dead in Parvar National Park, Semnan Province, Iran. After the autopsy, the tissue and parasite samples were collected from gastrointestinal tract and transferred to 70% alcohol. Samples were recovered and identified as Joyeuxiella spp. Sonsino, 1889. Tissue samples were taken from the place of sticking of parasites on the intestinal wall, for histopathological examination, and were transferred to 10% buffered formalin. Following routine processes and H&E staining, the slides were examined microscopically. Main histopathological observations were epithelial hyperplasia and destruction, inflammatory cell infiltration in mucosa and submucosa of jejunum. To the best of the author's knowledge, this is the first report and histopathological study of Joyeuxiella spp. in the world in Eurasian lynx.

The morphological and molecular identification of the tapeworm, Taenia lynciscapreoli, in intermediate and definitive hosts in Poland.

The tapeworm Taenia lynciscapreoli is a new species of the genus Taenia described in 2016, and which remains poorly understood. The aim of the present study is to extend current knowledge regarding its, morphology and genome. Biological material was analysed from three species of wild animals: Eurasian lynx (Lynx lynx), roe deer (Capreolus capreolus) and moose (Alces alces). Twenty-four adult tapeworms and four larvae were obtained from Eurasian lynx and roe deer respectively; none were detected in the studied moose. On the basis of morphometric (hooks measurements) and molecular analysis (partial 780 bp cox 1 gene sequences), the analysed tapeworm was identified as Taenia lynciscapreoli species. The phylogenetic analysis of the obtained sequences identified two haplotypes. The obtained findings can be used to supplement the species description. To our knowledge this is the first morphological and molecular identification of T. lynciscapreoli in roe deer, intermediate host, in Poland.

The missing lynx of Eurasia at its Southern edge: a connection to the critically endangered Balkan lynx.

The populations of Eurasian lynx in Anatolia are as fragmented as the European populations. Although the origins of and the connections between the European lynx populations have been elucidated, there have been no genetic studies on the lynx populations in Turkey. The lack of genetic and evolutionary information about lynx in Anatolia, which is considered to be a biodiversity hotspot, makes it difficult to track the migration routes during the Quaternary. In this study, we present the genetic characteristics of two isolated lynx populations in Southwest Taurus Mountains and the Turkish Caucasus as well as two individuals from Erzincan area. DNA purified from the ecological scat samples collected from Çiglikara Nature Reserve in Elmali-Antalya and Allahuekber Mountains in Sarikamis-Kars, as well as two roadkill samples from Erzincan, has been analysed for phylogenetic markers such as the mitochondrial DNA control region and cytochrome b. The DNA sequences were compared with haplotypes previously detected in populations from Europe and the Caucasus in order to determine the evolutionary relationships of the populations. This study compares the current genetic structure of some of the Turkish lynx populations to the other lynx genetic data, mostly carried out with museum samples around the world. Three haplotypes were found in three different regions of Anatolia. The Northeast and Southwest populations harbour genetically distinct haplotypes, the latter one, a new haplotype: H13-TR is the only phylogenetic connection to the critically endangered Balkan lynx yet to be described.

Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species.

Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.

Phylogenetic relationship of Eurasian lynx (Lynx lynx) revealed by complete mitochondrial genome.

The Eurasian lynx (Lynx lynx) is an Endangered species in northeast China. We first obtained muscle sample, extracted the sample DNA and sequenced the whole mtDNA genome of lynx from northeast China. We reconstructed the phylogenetic tree of Eurasian lynx and 10 other most closely related Felidae species. This lynx's complete mitogenome is 17 054bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. The phylogenetic tree confirmed previous research results.