Genetic spatial structure of European common hamsters (Cricetus cricetus)--a result of repeated range expansion and demographic bottlenecks

DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians

The region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.

Morphometric parameters predict body fat proportions in common hamsters

Common hamsters (Cricetus cricetus) are hibernators that rely both on body fat reserves and food stores for the winter period. They face an ongoing population decline in most parts of their distribution and recently were classified as critically endangered. Knowledge on individual body fat proportions in this species is of particular interest for conservation, because it could contribute to better understand the high plasticity in overwintering strategies, overwinter mortality rates, individual variations in reproductive output, and give information on the animals’ health state. To calculate body fat proportions, we validated a method that can be applied in the field without the use of anesthesia. To develop this method, we first analyzed the body fat in carcasses of common hamsters using Soxhlet extractions and measured four morphometric parameters (body mass, head length, tibia length, foot length). The morphometric measurements were then integrated in a linear regression model to predict body fat proportions based on the measured values. The morphometric variables yielded an explained variance (adjusted R²) of 96.42% and body fat proportions were predicted with a mean absolute error of 1.27 ± 0.11% from measured values. We applied the model to predict body fat for available field data, which consistently produced reliable values. By measuring the four morphometric parameters and following the provided instructions, body fat proportions can be reliably and noninvasively estimated in captive or free-ranging common hamsters. Furthermore, the method could be applicable to other rodents after species-specific validation.

Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes

We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene.

Successful post-glacial colonization of Europe by single lineage of freshwater amphipod from its Pannonian Plio-Pleistocene diversification hotspot

Gammarus roeselii Gervais, 1835 is a morphospecies with a wide distribution range in Europe. The Balkan Peninsula is known as an area of pre-Pleistocene cryptic diversification within this taxon, resulting in at least 13 Molecular Operational Taxonomic Units (MOTUs). The morphospecies diversified there during Neogene and has probably invaded other parts of the continent very recently, in postglacial or even historical times. Thus, the detailed goals of our study were to (1) identify which lineage(s) colonized Central-Western Europe (CWE), (2) determine their possible geographical origin, (3) verify, whether the colonisation was associated with demographic changes. In total, 663 individuals were sequenced for the cytochrome oxidase I (COI) barcoding fragment and 137 individuals for the internal transcribed spacer II (ITS2). We identified two MOTUs in the study area with contrasting Barcode Index Number and haplotype diversities. The Pannonian Basin (PB) appeared to be a potential ice age refugium for the species, while CWE was colonised by a single lineage (also present in PB), displaying low genetic diversity. Our results suggest that G. roeselii is a relatively recent coloniser in CWE, starting demographic expansion around 10 kya.

The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians

The Western Carpathians are a particularly interesting part of the Carpathian Arc. According to recent molecular data upon aquatic and terrestrial taxa, this mountain area is an important biodiversity hotspot of Europe. Moreover, the W Carpathians include rich systems of karst springs inhabited by specific fauna, where molecular diversity and phylogeographic patterns are yet to be fully explored. Our study aims to compare population genetic structure and molecular diversity of two related and commonly co-occurring riffle beetles, Elmis aenea (PWJ Müller, 1806) and Limnius perrisi (Dufour, 1843) in the springs and streams of the W Carpathians using the mitochondrial DNA barcoding fragment of the cytochrome c oxidase subunit I gene (COI). The relatively stable thermal and chemical conditions of springs throughout unfavourable climatic settings make these highly specific lotic systems potentially ideal for a long-term survival of some aquatic biota. Populations of both elmid species were relatively homogeneous genetically, with a single dominant haplotype. However, we revealed that E. aenea significantly dominated in the springs, while L. perrisi preferred streams. Relative isolation of the springs and their stable conditions were reflected in significantly higher molecular diversity of the E. aenea population in comparison to L. perrisi. The results of Bayesian Skyline Plot analysis also indicated the exceptional position of springs regarding maintaining the population size of E. aenea. On the other hand, it seems that streams in the W Carpathians provide more effective dispersal channels for L. perrisi, whose population expanded much earlier compared to E. aenea. Present study points out that different demographic histories of these two closely related elmid species are manifested by their different habitat preference and molecular diversity.

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae)

Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).

Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae)

The Eurasian steppes occupy a significant portion of the worldwide land surface and their biota have been affected by specific past range dynamics driven by ice ages-related climatic fluctuations. The dynamic alterations in conditions during the Pleistocene often triggered reticulate evolution and whole genome duplication events. Employing genomic, genetic and cytogenetic tools as well as morphometry we investigate the intricate evolution of Astragalus onobrychis, a widespread Eurasian steppe plant with diploid, tetraploid and octoploid cytotypes. To analyse the heteroploid RADseq dataset we employ both genotype-based and genotype-free methods that result in highly consistent results, and complement our inference with information from the plastid ycf1 region. We uncover a complex and reticulate evolutionary history, including at least one auto-tetraploidization event and two allo-octoploidization events; one of them involved also genetic contributions from other species, most likely A. goktschaicus. The present genetic structure points to the existence of four main clades within A. onobrychis, which only partly correspond to different ploidies. Time-calibrated diffusion models suggest that diversification within A. onobrychis was associated with ice age-related climatic fluctuations during the last million years. We finally argue for the usefulness of uniparentally inherited plastid markers, even in the genomic era, especially when investigating heteroploid systems.

Reconstructed historical distribution and phylogeography unravels non-steppic origin of Caucasotachea vindobonensis (Gastropoda: Helicidae)

Existing data on the phylogeography of European taxa of steppic provenance suggests that species were widely distributed during glacial periods but underwent range contraction and fragmentation during interglacials into "warm-stage refugia." Among the steppe-related invertebrates that have been examined, the majority has been insects, but data on the phylogeography of snails is wholly missing. To begin to fill this gap, phylogeographic and niche modeling studies on the presumed steppic snail Caucasotachea vindobonensis were conducted. Surprisingly, reconstruction of ancestral areas suggests that extant C. vindobonensis probably originated in the Balkans and survived there during the Late Pleistocene glaciations, with a more recent colonization of the Carpatho-Pannonian and the Ponto-Caspian regions. In the Holocene, C. vindobonensis colonized between the Sudetes and the Carpathians to the north, where its recent and current distribution may have been facilitated by anthropogenic translocations. Together, these data suggest a possible non-steppic origin of C. vindobonensis. Further investigation may reveal the extent to which the steppic snail assemblages consist partly of Holocene newcomers.

Phylogeographic structure of the Common hamster (Cricetus cricetus L.): Late Pleistocene connections between Caucasus and Western European populations

The Common hamster (Cricetus cricetus) is one of the most endangered mammals in Western and Central Europe. Its genetic diversity in Russia and Kazakhstan was investigated for the first time. The analysis of sequences of an mtDNA control region and cytochrome b gene revealed at least three phylogenetic lineages. Most of the species range (approximately 3 million km²), including central Russia, Crimea, the Ural region, and northern Kazakhstan), is inhabited by a single, well-supported phylogroup, E0. Phylogroup E1, previously reported from southeastern Poland and western Ukraine, was first described from Russia (Bryansk Province). E0 and E1 are sister lineages but both are monophyletic and separated by considerable genetic distance. Hamsters inhabiting Ciscaucasia represent a separate, distant phylogenetic lineage, named “Caucasus”. It is sister to the North phylogroup from Western Europe and the contemporary phylogeography for this species is discussed considering new data. These data enabled us to develop a new hypothesis to propose that in the Late Pleistocene, the continuous range of the Common hamster in the northern Mediterranean extended from the central and southern parts of modern France to the Caucasus; however, its distribution was subsequently interrupted, likely because of climate change.

The complete mitochondrial genome of Allocricetulus eversmanni (Rodentia: Cricetidae)

Allocricetulus eversmanni is a unique species in the Allocricetulus, belonging to the Cricetinae group. Its complete mitochondrial genome was first obtained and the total length was 16,282 bp. Protein-coding genes approximately accounted for 69.6% of the complete genome. The heavy strand contained 30% A, 14.4% G, 27.9% C, 27.7% T. Compared with most other mammals, it had the same arrangement and similar length of vary genes or regions. The complete mitochondrial genome of A. eversmanni was conducive to more accurately locate its taxonomic status in Cricetinae and its evolutionary history. At the same time, it provided significant information about consummation of A. eversmanni gene pool.

All things considered? Alternative reasons for hamster extinction

In 2002 a pest biologist (LEIRS 2002) calculated the survival chances of the European hamster (Cricetus cricetus) according to data provided by participants of the meeting of the International Hamster Workgroup in Tongeren. His model was based predominantly on demographic data as birth rates and predicted that the European hamster will be extinct in Western Europe within the next 50 years. Since then, the mean number of litters females raise in a year has diminished from 2-3 to 1-2. It is thus to be feared that the remaining time is only half as long as predicted and extinction might occur around 2030. However, since then hamster protection measures have improved considerably and two major milestones have been reached: (1) we are able to breed captive hamsters in a sufficient number and (2) most released hamsters survive long enough to reproduce once. Thus, at the present state we can claim that the hamster won.t go extinct as long as such breeding and releasing programs are in place. However, we haven.t achieved a state yet at which it is clear that the hamster will survive with its own means when such programs are stopped. To work on this will be the task of the coming years. This review might be a starting point for that. It reflects on which other factors possibly impair the survival of European hamster populations besides some aspects of modern agriculture, thus it searches for parameters which are not yet considered in conservation programs. Historical data as well as observations and research data from other species are reviewed. Additionally, new insights from the subterranean life of European hamsters in outdoor terrariums are presented, which suggest that the soil as habitat might need more attention in conservation. However, this conjecture can provide only new ideas, which still have to be confirmed by research. The intention is to spark a lively discussion on such potential alternative reasons for the decline of European hamsters, whether some of them are worth being investigated and whether we overlooked something. There is not much time left.

Extra-Mediterranean refugia: The rule and not the exception?

Some decades ago, biogeographers distinguished three major faunal types of high importance for Europe: (i) Mediterranean elements with exclusive glacial survival in the Mediterranean refugia, (ii) Siberian elements with glacial refugia in the eastern Palearctic and only postglacial expansion to Europe and (iii) arctic and/or alpine elements with large zonal distributions in the periglacial areas and postglacial retreat to the North and/or into the high mountain systems. Genetic analyses have unravelled numerous additional refugia both of continental and Mediterranean species, thus strongly modifying the biogeographical view of Europe. This modified notion is particularly true for the so-called Siberian species, which in many cases have not immigrated into Europe during the postglacial period, but most likely have survived the last, or even several glacial phases, in extra-Mediterranean refugia in some climatically favourable but geographically limited areas of southern Central and Eastern Europe. Recently, genetic analyses revealed that typical Mediterranean species have also survived the Last Glacial Maximum in cryptic northern refugia (e.g. in the Carpathians or even north of the Alps) in addition to their Mediterranean refuge areas.

Identification of the barrier to gene flow between phylogeographic lineages of the common hamster Cricetus cricetus

In anthropogenically disturbed habitats, natural barriers still exist and have to be recognized, as they are important for conservation measures. Areas of phylogeographic breaks within a species are often stabilized in inhospitable regions which act as natural barriers. An area of contact between phylogeographic lineages of the common hamster (Cricetus cricetus) was found in the Małopolska Upland in Poland. A total of 142 common hamsters were captured between 2005 and 2009. All hamsters were genotyped at 17 microsatellite loci and partial sequences of the mitochondrial (mtDNA) control region were obtained. No mixed populations with mtDNA haplotypes of both lineages were found. The distance between marginal populations was about 20 km; no hamsters were found in the area between. A principal components analysis (PCA) was performed on microsatellite data and the greatest change in PC1 scores was found between marginal samples. To define the habitat components responsible for the phylogeographic break, we compared the habitat composition of sites occupied by hamsters with those from which hamsters were absent. We found that hamsters avoided forested areas and sandy soils. The area of the potential barrier was characterized by a high proportion of woodland and unfavorable soils in comparison with neighboring areas inhabited by hamsters. They cannot settle in this area due to their high winter mortality in shallow burrows and high predation in the fields adjacent to forests.

Mitochondrial phylogeography of the European ground squirrel, Spermophilus citellus, yields evidence on refugia for steppic taxa in the southern Balkans

The spatial genetic structure of the European ground squirrel, a species characteristic of the short-grass steppe, was investigated on the basis of a 1140-bp cyt b gene sequence. The phylogeographical architecture of this species is expected to shed light on the putative long-term presence of the steppic ecosystem in south-eastern Europe and the evolutionary consequences of glacial cycles as forcing factors in speciation. Among 31 haplotypes, three highly divergent phylogenetic lineages (Southern, Northern and Jakupica) were recognized. This result suggests the past existence of an allopatric fragmentation event caused by effective biogeographical barriers. The Southern lineage consisted of the southernmost populations, those from Greece, Macedonia and European Turkey, and showed the highest divergence from all other samples. Haplotypes of the Northern lineage showed little geographical structure, with dispersal on both sides of the Danube River and in both of the two main geographical fragments of the species. The Jakupica lineage is a geographical isolate on a high plateau in central Macedonia. The estimated time for divergence of the Southern lineage (ca. 0.58 Mya) suggests the long-term persistence of a short-grass steppic refugium in the southern Balkans. Although the divergence between the Northern and Jakupica lineages occurred more recently (ca. 0.3 Mya), it still putatively predates two glacial cycles. The three phylogeographical lineages of the European ground squirrel should be regarded as independent units for conservation management purposes.

Morphometric Differences Between the Phylogeographic Lineages of the Common Hamster Cricetus Cricetus in Poland

As the common hamster is endangered in the European part of its range, it is necessary to define the conservation units for successful management of natural populations. Here we describe the case of clear morphometric differentiation between phylogeographic lineages of the common hamster. The standard external measurements were taken from 209 common hamsters collected during the period 2005-2007 from the present species range in Poland. The studied populations belong to different phylogeographic lineages P3 (Polish Pannonia) and E1, and the hamsters of P3 lineage are smaller with longer feet and tails than the hamsters of E1 lineage. The phylogeographic lineages of the common hamster can be defined as evolutionary significant units (ESU) due to the significant genetic differentiation and as management units (MU) with the evidence for ecological differentiation.

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Despite some popularity of hamsters as pets and laboratory animals there is no reliable phylogeny of the subfamily Cricetinae available so far. Contradicting views exist not only about the actual number of species but also concerning the validity of several genera. We used partial DNA sequences of two mitochondrial (cytochrome b, 12S rRNA) and one partial nuclear gene (von Willebrand Factor exon 28) to provide a first gene tree of the Cricetinae based on 15 taxa comprising six genera. According to our data, Palaearctic hamsters fall into three distinct phylogenetic groups: Phodopus, Mesocricetus, and Cricetus-related species which evolved during the late Miocene about 7-12MY ago. Surprisingly, the genus Phodopus, which was previously thought to have appeared during the Pleistocene, forms the oldest clade. The largest number of extant hamster genera is found in a group of Cricetus-related hamsters. The genus Cricetulus itself proved to be not truly monophyletic with Cricetulus migratorius appearing more closely related to Tscherskia, Cricetus, and Allocricetulus. We propose to place the species within a new monotypic genus. Molecular clock calculations are not always in line with the dating of fossil records. DNA based divergence time estimates as well as taxonomic relationships demand a reevaluation of morphological characters previously used to identify fossils and extant hamsters.