Historical DNA reveals the phylogenetic position of the extinct Alpine lynx

Insights into subspecies classification and conservation priorities of Central Asian lynx populations revealed by morphometric and genetic analyses

The Eurasian lynx (Lynx lynx) exhibits geographic variability and phylogenetic intraspecific relationships. Previous morphological studies have suggested the existence of multiple lynx subspecies, but recent genetic research has questioned this classification, particularly in Central Asia. In this study, we aimed to analyse the geographic and genetic variation in Central Asian lynx populations, particularly the Turkestan lynx and Altai lynx populations, using morphometric data and mtDNA sequences to contribute to their taxonomic classification. The comparative analysis of morphometric data revealed limited clinal variability between lynx samples from the Altai and Tien Shan regions. By examining mtDNA fragments (control region and cytochrome b) obtained from Kazakhstani lynx populations, two subspecies were identified: L. l. isabellinus (represented by a unique haplotype of the South clade, H46) and L. l. wrangeli (represented by haplotypes H36, H45, and H47 of the East clade). L. l. isabellinus was recognized only in Tien Shan Mountain, while Altai lynx was likely identical to L. l. wrangeli and found in northern Kazakhstan, Altai Mountain, Saur and Tarbagatai Mountains, and Tien Shan Mountain. The morphological and mtDNA evidence presented in this study, although limited in sample size and number of genetic markers, renders the differentiation of the two subspecies challenging. Further sampling and compilation of whole-genome sequencing data are necessary to confirm whether the proposed subspecies warrant taxonomic standing.

Diverging ecological traits between the Balkan lynx and neighbouring populations as a basis for planning its genetic rescue

Selecting appropriate candidates for genetic rescue mostly relies on previous genetic research and monitoring, while ecological and behavioural traits of the remnant and source populations are rarely considered for such conservation measures. Because of their slow recovery, Eurasian lynx Lynx lynx populations in Central and Western Europe have been a repeated target of genetic reinforcements and reintroductions in the past 50 years. Once inhabiting much of south-eastern Europe, the Balkan lynx L. l. balcanicus is now critically endangered and confined to a small population. Long-term isolation has caused loss of genetic diversity and has possibly led to inbreeding depression. Immediate actions need to consider genetic reinforcement to increase the genetic diversity and secure population viability. Here, we compared the Balkan lynx with two neighbouring populations: Dinaric population originating from the Carpathian subspecies (L.l. carpathicus) and Anatolian population of Caucasian subspecies (L.l. dinniki) to determine is better suited source from an ecological standpoint. Main findings suggest that the L.l. carpathicus is ecologically more similar to the L.l. balcanicus and therefore likely better suited for the environment of south-western Balkans on the basis of prey preference (roe deer being the main prey), local prey availability (lower lagomorph and higher ungulate availability) and habitat use (predominant use of the mixed and broadleaved forests). We discuss the contrasting results of genetic and ecological analyses from both the evolutionary and conservation perspective and provide potential solutions that would take into account both aspects to pave the road towards potential genetic rescue of the Balkan lynx.

Phylogenetic analyses of Eurasian lynx (Lynx lynx Linnaeus, 1758) including new mitochondrial DNA sequences from Iran

The Eurasian lynx (Lynx lynx) is one of the widespread felids in Eurasia; however, relatively little is known about the Asian subspecies, and especially the Iranian populations, which comprise the most southwestern part of its range. The current study aimed to assess the phylogenetic status of Iranian populations relative to other populations of Eurasia, by sequencing a 613 bp fragment of the mitochondrial control region. In total, 44 haplotypes were recorded from 83 sequences throughout Eurasia, two of which were found in Iran. The haplotype (H1) is dominant in all Iranian lynx populations and identical to specimens from SW Russia and central China. The second haplotype (H2) is unique and was recorded only from Ghazvin Province in the central Alborz Mountains. Both haplotypes occur in Ghazvin Province. The phylogenetic tree and a median-joining network identified four clades (i.e., East, West 1, West 2, and South). These results are congruent with previous studies and suggest that Eurasian lynx was restricted to the southern part of its range during the glacial maxima and expanded from there to East Asia and to Europe during several independent re-colonization events. The Caucasus region most like plays an important role as a refugium during glacial cycles.

Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx

Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.

The rise of a large carnivore population in Central Europe: genetic evaluation of lynx reintroduction in the Harz Mountains

Large carnivores have made a successful comeback across human-dominated landscapes in Central Europe. The Eurasian lynx, for instance, has been actively reintroduced in different regions. Genetic diversity is quickly eroding in these isolated, small populations, questioning the long-term success of lynx reintroductions. To track population development and genetic diversity in a reintroduced lynx population, we used microsatellite analysis and mtDNA haplotyping based on 379 samples collected during the initial 15 year period of lynx reintroduction in the Harz mountains National Park, Germany. The Harz lynx population shows higher genetic diversity relative to other lynx reintroductions, due to initial cross-breeding of divergent captive source lineages and a comparably high founder size. While the population shows significant population growth and spread into adjacent regions, genetic diversity is continiously declining. Expected heterozygosity values dropped from 0.63 after reintroduction (2006/2007) to 0.55 within a 10 year period. Despite this, the Harz lynx population is currently a viable component to an envisioned lynx metapopulation spanning across Central Europe. The ongoing genetic erosion in the Harz population along with a lack of geneflow from adjacent populations indicates that such connectivity is urgently needed to ensure long-term population persistence.

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.

Using questionnaire surveys and occupancy modelling to identify conservation priorities for the Critically Endangered Balkan lynx Lynx lynx balcanicus

With an estimated < 50 adult individuals remaining, the Critically Endangered Balkan lynx Lynx lynx balcanicus is one of the rarest, most threatened and least-studied large carnivores. To identify priority conservation areas and actions for the subspecies, during 2006–2014 we conducted 1,374 questionnaire surveys throughout the potential range of the Balkan lynx to (1) evaluate human–lynx interactions and identify potential threats, and (2) determine the probability of site use in 207 grid cells through occupancy modelling. Human–lynx interactions were related mainly to poaching of lynx, and damage to livestock by lynx. Poaching was intense throughout the potential range of the subspecies, apparently having affected 50–100% of the total estimated extant population. Damage to livestock was recorded only in relation to sheep, mainly in the southern part of the lynx's potential range. Occupancy modelling indicated 108 grid cells with high probability of site use, which was affected mainly by increased terrain ruggedness and reduced forest cover. Based on the combined results of our study we identified five priority areas for conservation, as well as in situ habitat protection, community participation in the conservation of the subspecies, and the improvement and implementation of the existing legal framework as the priority conservation actions for the Balkan lynx.

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 Çığlıkara Nature Reserve in Elmalı-Antalya and Allahuekber Mountains in Sarıkamış-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.

A European Concern? Genetic Structure and Expansion of Golden Jackals (Canis aureus) in Europe and the Caucasus

In the first continent-wide study of the golden jackal (Canis aureus), we characterised its population genetic structure and attempted to identify the origin of European populations. This provided a unique insight into genetic characteristics of a native carnivore population with rapid large-scale expansion. We analysed 15 microsatellite markers and a 406 base-pair fragment of the mitochondrial control region. Bayesian-based and principal components methods were applied to evaluate whether the geographical grouping of samples corresponded with genetic groups. Our analysis revealed low levels of genetic diversity, reflecting the unique history of the golden jackal among Europe’s native carnivores. The results suggest ongoing gene flow between south-eastern Europe and the Caucasus, with both contributing to the Baltic population, which appeared only recently. The population from the Peloponnese Peninsula in southern Greece forms a common genetic cluster with samples from south-eastern Europe (ΔK approach in STRUCTURE, Principal Components Analysis [PCA]), although the results based on BAPS and the estimated likelihood in STRUCTURE indicate that Peloponnesian jackals may represent a distinct population. Moreover, analyses of population structure also suggest either genetic distinctiveness of the island population from Samos near the coast of Asia Minor (BAPS, most STRUCTURE, PCA), or possibly its connection with the Caucasus population (one analysis in STRUCTURE). We speculate from our results that ancient Mediterranean jackal populations have persisted to the present day, and have merged with jackals colonising from Asia. These data also suggest that new populations of the golden jackal may be founded by long-distance dispersal, and thus should not be treated as an invasive alien species, i.e. an organism that is “non-native to an ecosystem, and which may cause economic or environmental harm or adversely affect human health”. These insights into the genetic structure and ancestry of Baltic jackals have important implications for management and conservation of jackals in Europe. The golden jackal is listed as an Annex V species in the EU Habitats Directive and as such, considering also the results presented here, should be legally protected in all EU member states.

Long-range gene flow and the effects of climatic and ecological factors on genetic structuring in a large, solitary carnivore: the Eurasian lynx

Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers) was found in lynx from Norway and Białowieża Primeval Forest (BPF), which coincided with a recent demographic bottleneck (Norway) or high habitat fragmentation (BPF). The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum) on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus) in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and microsatellite population divergence patterns with climatic and ecological factors may suggest separate selective pressures acting on males and females in this solitary carnivore.

Large-scale genetic structuring of a widely distributed carnivore--the Eurasian lynx (Lynx lynx)

Over the last decades the phylogeography and genetic structure of a multitude of species inhabiting Europe and North America have been described. The flora and fauna of the vast landmasses of north-eastern Eurasia are still largely unexplored in this respect. The Eurasian lynx is a large felid that is relatively abundant over much of the Russian sub-continent and the adjoining countries. Analyzing 148 museum specimens collected throughout its range over the last 150 years we have described the large-scale genetic structuring in this highly mobile species. We have investigated the spatial genetic patterns using mitochondrial DNA sequences (D-loop and cytochrome b) and 11 microsatellite loci, and describe three phylogenetic clades and a clear structuring along an east-west gradient. The most likely scenario is that the contemporary Eurasian lynx populations originated in central Asia and that parts of Europe were inhabited by lynx during the Pleistocene. After the Last Glacial Maximum (LGM) range expansions lead to colonization of north-western Siberia and Scandinavia from the Caucasus and north-eastern Siberia from a refugium further east. No evidence of a Berinigan refugium could be detected in our data. We observed restricted gene flow and suggest that future studies of the Eurasian lynx explore to what extent the contemporary population structure may be explained by ecological variables.

Genetics at the verge of extinction: insights from the Iberian lynx

Population viability might become compromised by the loss of genetic diversity and the accumulation of inbreeding resulting from population decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a paradigmatic example of a species at the verge of extinction, and because of the well-documented and different demographic histories of the two remaining populations (Doñana and Andújar), it provides the opportunity to evaluate the performance of analytical methods commonly applied to recently declined populations. We used mitochondrial sequences and 36 microsatellite markers to evaluate the current genetic status of the species and to assess the genetic signatures of its past history. Mitochondrial diversity was extremely low with only two haplotypes, alternatively fixed in each population. Both remnant populations have low levels of genetic diversity at microsatellite markers, particularly the population from Doñana, and genetic differentiation between the two populations is high. Bayesian coalescent-based methods suggest an earlier decline starting hundreds of years ago, while heterozygosity excess and M-ratio tests did not provide conclusive and consistent evidence for recent bottlenecks. Also, a model of gene flow received overwhelming support over a model of pure drift. Results that are in conflict with the known recent demography of the species call for caution in the use of these methods, especially when no information on previous demographic history is available. Overall, our results suggest that current genetic patterns in the Iberian lynx are mainly the result of its recent decline and fragmentation and alerts on possible genetic risks for its persistence. Conservation strategies should explicitly consider this threat and incorporate an integrated genetic management of wild, captive and re-introduced populations, including genetic restoration through translocations.