Peter Wandeler

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2010-31 January 2011: PERMANENT GENETIC RESOURCES NOTE

This article documents the addition of 238 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alytes dickhilleni, Arapaima gigas, Austropotamobius italicus, Blumeria graminis f. sp. tritici, Cobitis lutheri, Dendroctonus ponderosae, Glossina morsitans morsitans, Haplophilus subterraneus, Kirengeshoma palmata, Lysimachia japonica, Macrolophus pygmaeus, Microtus cabrerae, Mytilus galloprovincialis, Pallisentis (Neosentis) celatus, Pulmonaria officinalis, Salminus franciscanus, Thais chocolata and Zootoca vivipara. These loci were cross‐tested on the following species: Acanthina monodon, Alytes cisternasii, Alytes maurus, Alytes muletensis, Alytes obstetricans almogavarii, Alytes obstetricans boscai, Alytes obstetricans obstetricans, Alytes obstetricans pertinax, Cambarellus montezumae, Cambarellus zempoalensis, Chorus giganteus, Cobitis tetralineata, Glossina fuscipes fuscipes, Glossina pallidipes, Lysimachia japonica var. japonica, Lysimachia japonica var. minutissima, Orconectes virilis, Pacifastacus leniusculus, Procambarus clarkii, Salminus brasiliensis and Salminus hilarii.

Development of SNP markers identifying European wildcats, domestic cats, and their admixed progeny

Introgression can be an important evolutionary force but it can also lead to species extinction and as such is a crucial issue for species conservation. However, introgression is difficult to detect, morphologically as well as genetically. Hybridization with domestic cats (Felis silvestris catus) is a major concern for the conservation of European wildcats (Felis s. silvestris). The available morphologic and genetic markers for the two Felis subspecies are not sufficient to reliably detect hybrids beyond first generation. Here we present a single nucleotide polymorphism (SNP) based approach that allows the identification of introgressed individuals. Using high‐throughput sequencing of reduced representation libraries we developed a diagnostic marker set containing 48 SNPs (Fst > 0.8) which allows the identification of wildcats, domestic cats, their hybrids and backcrosses. This allows assessing introgression rate in natural wildcat populations and is key for a better understanding of hybridization processes.

Microsatellite primers for the four Galápagos mockingbird species (Mimus parvulus, Mimus macdonaldi, Mimus melanotis and Mimus trifasciatus)

Nineteen di‐ and tetranucleotide and one trinucleotide microsatellite DNA markers were isolated from the Galápagos mockingbird (Mimus parvulus) and tested for cross‐species amplification in the other three mockingbird species in the Galápagos. In addition, primers for two microsatellite loci previously developed for Mimus polyglottos were redesigned to obtain shorter amplification fragments. The number of alleles per locus and species ranged from 1 to 8, and expected heterozygosity varied from 0.0 to 0.809. These microsatellite markers will be useful to study levels of inbreeding in different island populations.

Bigger is fitter? Quantitative genetic decomposition of selection reveals an adaptive evolutionary decline of body mass in a wild rodent population

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change.

Hybrid ancestry of an island subspecies of Galápagos mockingbird explains discordant gene trees

Introgression of genes through hybridization has been proposed to be an important driver of speciation, but in animals this has been shown only in relatively few cases until recently. Additionally, introgressive hybridization among non-sister species leads to a change in the gene tree topology of the concerned loci and thus complicates phylogenetic reconstruction. However, such cases of ancient introgression have been very difficult to demonstrate in birds. Here, we present such an example in an island bird subspecies, the Genovesa mockingbird (Mimus parvulus bauri). We assessed phylogenetic relationships and population structure among mockingbirds of the Galápagos archipelago using mitochondrial and nuclear DNA sequences, autosomal microsatellites, and morphological measurements. Mitochondrial haplotypes of Genovesa mockingbirds clustered closely with the haplotypes from two different species, San Cristóbal (M. melanotis) and Española (M. macdonaldi) mockingbirds. The same pattern was found for some haplotypes of two nuclear gene introns, while the majority of nuclear haplotypes of Genovesa mockingbirds were shared with other populations of the same species (M. parvulus). At 26 autosomal microsatellites, Genovesa mockingbirds grouped with other M. parvulus populations. This pattern shows that Genovesa mockingbirds contain mitochondria and some autosomal alleles that have most likely introgressed from M. melanotis into a largely M. parvulus background, making Genovesa mockingbirds a lineage of mixed ancestry, possibly undergoing speciation. Consistent with this hypothesis, mockingbirds on Genovesa are more clearly differentiated morphologically from other M. parvulus populations than M. melanotis is from M. parvulus.

Microsatellite DNA markers for the snow vole (Chionomys nivalis).

A total of 14 dinucleotide microsatellite loci were characterized in the snow vole (Chionomys nivalis). Allelic polymorphism across all loci and 28 individuals representing a single population in the Swiss Alps was high (mean = 10.1 alleles). No significant linkage disequilibrium between pairs of loci and no departure from Hardy–Weinberg equilibrium were found. These loci will be useful for describing mating systems and population structure and to investigate the genetic consequences of a species living in a highly fragmented habitat.

Identifying Y-chromosomal diversity by long-template PCR

Comparing Y‐chromosomal and mitochondrial haplotype variation is a promising approach to independently investigate paternal and maternal evolutionary histories in wild mammal populations. However, the difficulty of developing male‐specific genetic markers, because of its distinctive genetic architecture and the general low level of polymorphisms observed on the Y chromosome, hampers usually an effective application of this approach. Here, we present a further method of the established Y chromosome conserved anchored tagged sequences strategy to develop Y‐chromosomal markers by screening introns of male‐specific region (MSY) genes for sequence polymorphisms. By applying long‐template PCR using target species‐specific primers, adequate sequence information of several kb in size can be obtained. We applied this method in the snow vole (Chionomys nivalis) and obtained 12.4 kb of male‐specific sequence data for nine males representing four populations in the Swiss Alps. A total of 28 single nucleotide polymorphisms, four indels (>1 bp) and one polymorphic microsatellite were identified in introns of the SMCY and DBY genes. Based on this information, we developed a Y‐chromosomal genotyping assay and identified four different paternal lineages within one local snow vole population. The method we present is straightforward and as such will probably be suitable to detect adequate Y‐chromosomal diversity in a wide range of mammalian species.

Development of microsatellite loci in the European Dipper, Cinclus cinclus

Eighteen polymorphic microsatellite DNA loci were isolated in the Central European subspecies of the European Dipper (Cinclus cinclus aquaticus). The loci were tested for polymorphism using a test panel of 24 breeding birds. Numbers of alleles ranged from 2 to 21 per locus and expected heterozygosities varied between 0.47 and 0.83. Two loci (Cici10 and Cici12) proved to be Z-linked. Some pairs of loci exhibited significant linkage disequilibrium but not the two loci that are located on the Z-chromosome. This pattern suggests that demographic effects rather than physical linkage are likely responsible for the observed levels of linkage disequilibrium. These loci will be useful for applied conservation projects and for investigations of the dispersal and mating patterns of European and other dippers.

Noninvasive molecular and morphological evidences for an undiscovered population of snow vole in Southern Spain.

Capturing wild animals can be time consuming and difficult or even impractical. Noninvasive sampling is potentially a cost-effective and efficient means to monitor wild animals, thereby avoiding the need of capture and disturb species in the wild. On the basis of the morphological and genetic analyses of owl pellet contents, a so far undetected European snow vole (Chionomys nivalis) population was discovered in the Sierra Segura mountain range (Southern Spain). The mtDNA sequence from the newly discovered haplotype was compared with sequences from vole populations of the Sierra Nevada and Sierra Peñalara mountain ranges (Spain) and from Churwalden (Switzerland). The nine recovered haplotypes clustered in four distinct lineages according to their geographical origin. The vole sequence from the Sierra Segura owl pellet belonged to a new haplotype, constituting a new lineage. The evolutionary divergence between sequences from the Sierra Segura and other Spanish populations was higher than that among other Spanish haplotypes. The new snow vole haplotype from this new locality duplicates the number of occurrence sites of this critically endangered species in Southern Spain, which is of great interest for further conservation and management plans of the European snow vole in the most southwestern area of its entire distribution range.