Urmas Saarma

Institute of Ecology and Earth Sciences, University of Tartu · Department of Zoology

Native animal breeds constitute an invaluable pool of genetic resources in a changing environment. Discovering native breeds and safeguarding their genetic diversity through specific conservation programs is therefore of high importance. Endogenous retroviruses have proved to be a reliable genetic marker for studying the demographic history of shee...

Background Echinococcus tapeworms cause a severe helminthic zoonosis called echinococcosis. The genus comprises various species and genotypes, of which E. granulosus (sensu stricto) represents a significant global public health and socioeconomic burden. Mitochondrial (mt) genomes have provided useful genetic markers to explore the nature and extent...

By the beginning of the twentieth century, many brown bear populations in Europe were on the brink of extinction due to relentless hunting pressure and habitat loss. The situation was critical also in Estonia, where in the 1920s the population went through a severe demographic bottleneck. Thanks to the protective measures implemented in the 1930s,...

Cystic echinococcosis (CE), is one of the most important parasitic zoonotic diseases in the world and also represent an important public health and socio-economic concern. In the Mediterranean basin, CE is widespread and in Italy it is endemic, with a major prevalence in the south and islands. In the last few decades, the wild boar population in It...

For omnivorous brown bears, ants can seasonally constitute an important category of food with high nutritional value. A former dietary study conducted in Estonia revealed that the energy gained from animal and plant food was roughly equal, whereas the contribution of ants was almost 15%. Here, using the same dataset, we analyzed ant consumption by...

Cystic Echinococcosis (CE) caused by Echinococcus granulosus sensu lato (s.l.) is one of the most important parasitic zoonotic diseases in the world and it represents an important public health and socio-economic concern. In the Mediterranean basin, CE is widespread and it is endemic in Italy, with major prevalence in southern areas. Several studie...

The larval stage of the species complex Echinococcus granulosus sensu lato (s.l.) is the cause of a widespread zoonotic disease known as cystic echinococcosis (CE). The disease is highly prevalent in southern Italy and represents a serious public health issue. The main aim of this study was to characterize E. granulosus s.l. genotypes from wild boa...

The larval stages of tapeworms in the species complex Echinococcus granulosus sensu lato cause a zoonotic disease known as cystic echinococcosis (CE). Within this species complex, genotypes G6 and G7 are among the most common genotypes associated with human CE cases worldwide. However, our understanding of ecology, biology and epidemiology of G6 an...

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which co...

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus com...

Cystic echinococcosis (CE) is a zoonotic disease caused by the larval stage of the species complex Echinococcus granulosus sensu lato. Within this complex, genotypes G6 and G7 have been frequently associated with human CE worldwide. Previous studies exploring the genetic variability and phylogeography of genotypes G6 and G7 have been based on relat...

Cystic echinococcosis (CE), a zoonotic disease caused by tapeworms of the species complex Echinococcus granulosus sensu lato, represents a substantial global health and economic burden. Within this complex, E. granulosus sensu stricto (genotypes G1 and G3) is the most frequent causative agent of human CE. Currently, there is no fully reliable metho...

Tapeworms of the species complex of Echinococcus granulosus sensu lato ( s. l. ) are the cause of a severe zoonotic disease – cystic echinococcosis, which is listed among the most severe parasitic diseases in humans and is prioritized by the World Health Organization. A stable taxonomy of E. granulosus s. l. is essential to the medical and veterina...

Echinococcus granulosus sensu stricto (s.s.) is the major cause of human cystic echinococcosis worldwide and is listed among the most severe parasitic diseases of humans. To date, numerous studies have investigated the genetic diversity and population structure of E. granulosus s.s. in various geographic regions. However, there has been no global s...

Cystic echinococcosis (CE) is a severe parasitic disease caused by the species complex Echinococcus granulosus sensu lato. Human infections are most commonly associated with E. granulosus sensu stricto (s.s.), comprising genotypes G1 and G3. The objective of the current study was to provide first insight into the genetic diversity and phylogeograph...

Aim Climatic changes during the Late Pleistocene had major impacts on populations of plant and animal species. Brown bears and other large mammals are likely to have experienced analogous ecological pressures and phylogeographical processes. Here, we address several unresolved issues regarding the Late Pleistocene demography of brown bears: (1) the...

Protecting animal aggregation sites is intuitively an efficient conservation approach, particularly for threatened species in fragmented landscapes. However, the appropriate scale of protection depends on accompanying threats, such as predator attraction to the same aggregation sites, to which the target species may need to respond by moving to alt...

Large-scale pattern-oriented approaches are useful to understand the multi-level processes that shape the genetic structure of a population. Matching the scales of patterns and putative processes is both a key to success and a challenge. 2.We have developed a simple statistical approach, based on variogram analysis, that identifies multiple spatial...

Predation on livestock is a cause of serious and long-lasting conflict between farmers and wildlife, promoting negative public attitudes and endangering conservation of large carnivores. However, while large carnivores, especially the grey wolf (Canis lupus), are often blamed for killing sheep and other farm animals, free-ranging dogs may also act...

The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human–carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their number...

Capercaillie (Tetrao urogallus) and other grouse species represent conservation concerns across Europe due to their negative abundance trends. In addition to habitat deterioration, predation is considered a major factor contributing to population declines. While the role of generalist predators on grouse predation is relatively well known, the impa...

Morphological analysis of food items in wild boar faeces. FO % – percentage of frequency of occurrence; Volume % – percentage volume of different food categories. The smaller dataset (N = 52) includes wild boar faeces that gave a positive result with the molecular analysis, the larger dataset (N = 109) includes all samples that were collected and m...

Sarcoptic mange is a highly contagious zoonotic skin disease that can have severe effect on population dynamics of many wild mammals. However, very little is known about its effect on the activity and space use of infected animals. In this study we equipped two raccoon dogs (Nyctereutes procyonoides) in a mange outbreak area with radio-collars and...

1. Understanding how the diet of an ecologically important mesopredator varies throughout a large region can provide an insight into the trophic responses of generalist carnivores to global change. We review the diet of the red fox Vulpes vulpes in Europe. 2. The main aims of this study were: (1) to identify biogeographical patterns in red fox diet...

The survival of isolated small populations is threatened by both demographic and genetic factors. Large carnivores declined for centuries in most of Europe due to habitat changes, overhunting of their natural prey and direct persecution. However, the current rewilding trends are driving many carnivore populations to expand again, possibly reverting...

Distribution of the concatenated multifragment mtDNA haplotypes in wolves sampled all over the world. Country acronyms: IB = Iberian Peninsula; IT = Italy; HR = Croatia; SL = Slovenia; GR = Greece; BG = Bulgaria; PL = Poland; ES = Estonia; LA = Latvia; FI = Finland; UK = Ukraine; SW = Sweden; IR = Iran; OM = Oman; SA = Saudi Arabia; IS = Israel; IN...

ABC demographic scenarios and locations of the selected wolf populations. (PDF)

Delta K values [29] obtained in Structure analyses of dog and wolf samples assuming K values from 1 to 15. (PDF)

(A) NJ and (B) consensus ML mtDNA phylogenetic trees. Details of clade A are highlighted in the top -left figures. (PDF)

Phylogenetic tree of concatenated multi-fragment (control-region, ATP6, COIII and ND4) dog and wolf mtDNA haplotypes generated using a Bayesian procedure implemented in MrBayes [41]. A homologous concatenated sequence of Canis latrans (DQ480509) is used as an outgroup. Every node shows its posterior probability. Clade A, that includes the Italian w...

Model checking. Pre-evaluation of scenario-prior combinations; direct and logistic regression comparison methods of the estimated posterior probabilities among scenarios and fit of the selected best scenarios (Sc2 and Sc4) with the observed data. PCA I and II plotted using 10.000 data points. (PDF)

List of the wolf and dog samples analyzed in this study indicating: The country of origin, taxon, gender, mtDNA haplotypes at ATP6, COIII, ND4, CR and the concatenated multifragment sequences (MF). The individual Bayesian clustering assignments were computed using Structure with K = 3, assuming that genotypes could have ancestry in a dog cluster (q...

Haplotype composition. Detailed composition of the concatenated multifragment haplotypes. (PDF)

Results of Bayesian clustering analyses of dog and wolf samples obtained by Structure assuming K values from 1 to 15. Dog and wolf population samples are shown in the same sequence as in Fig 2: dogs (1), Italian wolves (2), Iberian wolves (3), Dinaric wolves (4), Balkanic wolves (5), Carpathian wolves (6), Baltic wolves (7). (PDF)

Prior (red) and posterior (green) density distributions of posterior probability for the selected ABC parameters from scenarios 2 and 4. (PDF)

Description of the genotyped autosomal (CFA) microsatellites (STR). (PDF)

List of mtDNA sequences downloaded from the GenBank. For every sample is shown: the accession number, country of origin of the sequenced sample (if available), taxon, dog breed (if available), and clade of memberships (BEAST analysis), and haplotypes at different genic regions. (PDF)

DIYABC prior distributions for demographic parameters and mutation rates. (PDF)

Model checking results for the best fitting scenario (SC2) based on 1,000 simulated datasets. (PDF)

(A) Description of laboratory methods with details on primers and PCR profiles for all the genotyped markers and (B) Details on MrBayes and BEAST models. (PDF)

Cystic echinococcosis, a zoonotic disease caused by Echinococcus granulosus sensu lato (s. l.), is a significant global public health concern. Echinococcus granulosus s. l. is currently divided into numerous genotypes (G1–G8 and G10) of which G1–G3 are the most frequently implicated genotypes in human infections. Although it has been suggested that...

Knowledge of space use is central to understand animals’ role in ecosystems. The raccoon dog Nyctereutes procyonoides is considered as one of the most influential alien mesopredator species in Europe, having the potential to cause loss of local biodiversity and act as a vector for zoonotic diseases. We collared 12 animals to study their home range...

Table A Coordinates of location points used for data analysis. Table B Seasonal home range sizes of raccoon dogs in different areas in Europe. Home range sizes correspond either to average values or to the range from minimum to maximum if two values are given. (DOCX)

Differences and insights from survery and genomic data in the identification and interpretation of hybridization levels in European Suids

Although sheep (Ovis aries) have been one of the most exploited domestic animals in Esto-nia since the Late Bronze Age, relatively little is known about their genetic history. Here, we explore temporal changes in Estonian sheep populations and their mitochondrial genetic diversity over the last 3000 years. We target a 558 base pair fragment of the...

Median-joining network of ancient and modern samples from this study and Finland. (PDF)

Sampling and DNA extraction protocol. (PDF)

List of primers. (PDF)

Population pairwise FST of four temporal cohorts of Estonian ancient and modern Kihnu native sheep. (PDF)

Sample data. (PDF)

Haplotype data for ancient and modern samples of this study, and for comparative samples from Finland. (PDF)

Success rate of ancient samples. (PDF)

Haplotype data for ancient and modern samples of this study. (PDF)

Radiocarbon dating. (PDF)

Echinococcus granulosus is a taeniid cestode and the etiological agent of an infectious zoonotic disease known as cystic echinococcosis (CE) or hydatid disease. CE is a serious public health concern in many parts of the world, including the Americas, where it is highly endemic in many regions. Echinococcus granulosus displays high intraspecific gen...

lthough sheep (Ovis aries) have been one of the most exploited domestic animals in Estonia since the Late Bronze Age, relatively little is known about their genetic history. Here, we explore temporal changes in Estonian sheep populations and their mitochondrial genetic diversity over the last 3000 years. We target a 558 base pair fragment of the mi...

Introgression of domestic genes into wild populations is considered to be a threat to biodiversity leading to loss of local adaptation and spread of human selected gene variants. Additionally, the contact between wild and domestic stocks can result in the transmission of infectious diseases. Thus, a better understanding of hybridization patterns in...

Echinococcus granulosus is the causative agent of cystic echinococcosis. The disease is a significant global public health concern and human infections are most commonly associated with E. granulosus sensu stricto (s. s.) genotype G1. The objectives of this study were to: (i) analyse the genetic variation and phylogeography of E. granulosus s. s. G...

Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genom...

After a long and deliberate persecution, the grey wolf (Canis lupus) is slowly recolonizing its former areas in Europe, and the genetic consequences of this process are of particular interest. Wolves, though present in mainland Estonia for a long time, have only recently started to recolonize the country's two largest islands, Saaremaa and Hiiumaa....

Comparison of pairwise FST values below the diagonal between four genetic groups identified with ARLEQUIN. * p < 0.05. (DOCX)

Rate of change in log-likelihood values (ΔK) for the number of clusters (a) estimated by STRUCTURE (n = 168) and the mean log-likelihood of K (b). The maximal value of ΔK indicates the most likely number of clusters according to Evanno et al. [28]. (TIFF)

The average estimated membership coefficients of Estonian wolves (n = 168) belonging into four genetic groups identified with STRUCTURE. (DOCX)

Spatial distribution of core areas of the genetic groups G1–G4. Based on the posterior probabilities from STRUCTURE, statistically interpolated across the study area using procedure of universal kriging. The full colored area represents statistically significant high probability; p ≤ 0.05 according to 199 bootstrap iterations. The dots represent sa...

The microsatellite data and additional information of 168 analysed wolf samples. (XLSX)

The overall genetic diversity in Estonian wolf population and among G1, G2, G3 and G4 genetic groups during hunting seasons 2011–2012 and 2014–2015. Number of alleles (NA), allelic richness (AR), expected (HE) and observed heterozygosity (HO) and inbreeding estimator (FIS). * p < 0.05. (XLSX)

Red fox (Vulpes vulpes) is the most widely distributed canid in the world and an important source of multiple zoonotic pathogens capable of causing life-threatening diseases, such as rabies and alveolar echinococcosis. Informing general public of potential risks related to foxes is becoming more important since the fox densities have increased in m...