House mouse colonization patterns on the sub-Antarctic Kerguelen Archipelago suggest singular primary invasions and resilience against re-invasion

Starting from Western Europe, the house mouse (Mus musculus domesticus) has spread across the globe in historic times. However, most oceanic islands were colonized by mice only within the past 300 years. This makes them an excellent model for studying the evolutionary processes during early stages of new colonization. We have focused here on the Kerguelen Archipelago, located within the sub-Antarctic area and compare the patterns with samples from other Southern Ocean islands

3D models related to the publication: “Molar wear in house mice: insight into diet preferences at an ecological time scale?”

This contribution contains 3D models of upper molar rows of house mice (Mus musculus domesticus) belonging to Western European commensal and Sub-Antarctic feral populations. These two groups are characterized by different patterns of wear and alignment of the three molars along the row, related to contrasted masticatory demand in relation with their diet. These models are analyzed in the following publication: Renaud et al 2023, “Molar wear in house mice, insight into diet preferences at an ecological time scale?”, https://doi.org/10.1093/biolinnean/blad09

The importance of urban areas in supporting vulnerable and endangered mammals

The fragmentation of habitats associated with urbanisation poses a significant threat to already vulnerable and endangered mammal species. While the county of Dorset has been identified as one of the UK’s biodiversity hotspots, it is characterised by large-scale urbanisation and intensive agriculture. Focusing on the largest urban area of Dorset—the conurbation of Bournemouth, Christchurch, and Poole—this study aims to investigate the importance of urban areas in supporting vulnerable and endangered mammals by comparing it to four other major land cover categories in the county: arable & horticulture, grassland, woodland, and heathland. The study utilises data collected by the county’s environmental records department through mainly volunteer-contributed ad-hoc sighting data of 10 872 georeferenced mammal records collected between 2000 and 2018. Our findings reveal that, despite having significantly different mammal communities to all other land covers, urban land cover was shown to host four out of five of the vulnerable and endangered species recorded in this study. These included the European rabbit (vulnerable on the IUCN red list), hazel dormouse (vulnerable on the UK red list), West European hedgehog (vulnerable on the UK red list) and European water vole (endangered on the UK red list). Our findings highlight the significance of urban areas as important habitats for mammal biodiversity, presenting an opportunity for the conservation of specific vulnerable and endangered species. Despite limitations in ad-hoc sighting data, our analysis indicates an overrepresentation of certain 'charismatic' species, like foxes and hedgehogs, in urban samples, likely due to their high intrinsic value to the population. While the recognition of urban habitats for 'red list' species is growing, it is also important to acknowledge the relative importance of charismatic species to urban human communities in conservation and management strategies

Environmental DNA reveals the temporal and spatial extent of spawning migrations of European shad in a highly fragmented river basin

1. Anthropogenic barriers on lowland rivers impede the spawning migrations of anadromous fishes, preventing access to historical spawning areas. In the cryptic European shads Alosa alosa and Alosa fallax (‘shad’ hereafter), this has resulted in population declines across their range. Conservation programmes aim to facilitate the passage of migrators over these barriers and so require baseline knowledge on spatial and temporal extent of current migrations. 2. Here, a shad-specific environmental DNA (eDNA) assay was used to quantify the spatial extent of shad spawning migrations in the River Severn basin, Western England. This basin is characterised by the presence of multiple anthropogenic barriers in the lower catchment. In 2017, the eDNA assay was piloted in the River Teme, an important shad spawning tributary, and then applied in 2018 and 2019 across the lower Severn basin. 3. In all years, shad DNA was detected between mid-May and mid-June, with the maximum spatial extent of shad distribution being in early June when shad eDNA was detected upstream of weirs that were generally considered as impassable. In 2018, this included the detection of shad above the most upstream weir on the main River Severn that required individual fish to have passed six weirs. 4. Although anthropogenic barriers inhibit the spawning migrations of shad, this eDNA assay revealed some highly vagile individuals might be able to ascend these barriers and migrate considerable distances upstream. This suggests that efforts to increase the permeability of these barriers could result in relatively high numbers of migrating shad reaching upstream spawning areas. These results demonstrate that this eDNA assay could be also utilised across their range, outside the study system, to further quantify the spatial extent of their spawning, including in highly fragmented rivers and those where shad are believed to only spawn occasionally and are rarely observed

Reconciling the biogeography of an invader through recent and historic genetic patterns: the case of topmouth gudgeon Pseudorasbora parva

© 2018 The Author(s) The genetic variability and population structure of introduced species in their native range are potentially important determinants of their invasion success, yet data on native populations are often poorly represented in relevant studies. Consequently, to determine the contribution of genetic structuring in the native range of topmouth gudgeon Pseudorasbora parva to their high invasion success in Europe, we used a dataset comprising of 19 native and 11 non-native populations. A total of 666 samples were analysed at 9 polymorphic microsatellite loci and sequenced for 597 bp of mitochondrial DNA. The analysis revealed three distinct lineages in the native range, of which two haplogroups were prevalent in China (100%), with a general split around the Qinling Mountains. Dating of both haplogroups closely matched past geological events. More recently, its distribution has been influenced by fish movements in aquaculture, resulting in gene flow between previously separated populations in Northern and Southern China. Their phylogeography in Europe indicate as few as two introductions events and two dispersal routes. Microsatellite data revealed native populations had higher genetic diversity than those in the invasive range, a contrast to previous studies on P. parva. This study confirms the importance of extensive sampling in both the native and non-native range of invasive species in evaluating the influence of genetic variability on invasion success

Population genetics and demography of the endemic mouse species of Cyprus, Mus cypriacus

Mus cypriacus is one of three small palaeoendemic mammals that have survived the Mediterranean islands’ anthropization. This species, endemic to Cyprus, was described in 2006 and stands out as one of the last mammal species to have been discovered in Europe. Despite scarce data on its genetics, ecology, and life-history traits, Mus cypriacus is assessed as Least Concern LC in the IUCN Red List, partly due to its morphological similarity with the sympatric house mouse that prevented earlier identification. Our study uses mitochondrial and microsatellite markers to investigate this small rodent's population genetic structure and diversity. Our analysis did not identify any population genetic structure and suggested a high genetic diversity across Cyprus. When inferring habitat preference using sample locations, it appeared that M. cypriacus utilizes a diverse variety of habitats, covering more than 80% of the island. Although these results are encouraging for the conservation status of the species, they still need to be cautiously applied as potential threats may arise due to increasing habitat destruction and changes in land use. Consequently, our encouraging results should be applied judiciously. Additional ecological data are urgently needed to gain a more comprehensive understanding of this inconspicuous endemic species

Positive Selection in East Asians for an EDAR Allele that Enhances NF-κB Activation

Genome-wide scans for positive selection in humans provide a promising approach to establish links between genetic variants and adaptive phenotypes. From this approach, lists of hundreds of candidate genomic regions for positive selection have been assembled. These candidate regions are expected to contain variants that contribute to adaptive phenotypes, but few of these regions have been associated with phenotypic effects. Here we present evidence that a derived nonsynonymous substitution (370A) in EDAR, a gene involved in ectodermal development, was driven to high frequency in East Asia by positive selection prior to 10,000 years ago. With an in vitro transfection assay, we demonstrate that 370A enhances NF-κB activity. Our results suggest that 370A is a positively selected functional genetic variant that underlies an adaptive human phenotype

Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans

<p>Abstract</p> <p>Background</p> <p>The thrifty gene hypothesis posits that, in populations that experienced periods of feast and famine, natural selection favoured individuals carrying thrifty alleles that promote the storage of fat and energy. Polynesians likely experienced long periods of cold stress and starvation during their settlement of the Pacific and today have high rates of obesity and type 2 diabetes (T2DM), possibly due to past positive selection for thrifty alleles. Alternatively, T2DM risk alleles may simply have drifted to high frequency in Polynesians. To identify thrifty alleles in Polynesians, we previously examined evidence of positive selection on T2DM-associated SNPs and identified a T2DM risk allele at unusually high frequency in Polynesians. We suggested that the risk allele of the Gly482Ser variant in the <it>PPARGC1A </it>gene was driven to high frequency in Polynesians by positive selection and therefore possibly represented a thrifty allele in the Pacific.</p> <p>Methods</p> <p>Here we examine whether <it>PPARGC1A </it>is a thrifty gene in Pacific populations by testing for an association between Gly482Ser genotypes and BMI in two Pacific populations (Maori and Tongans) and by evaluating the frequency of the risk allele of the Gly482Ser variant in a sample of worldwide populations.</p> <p>Results</p> <p>We find that the Gly482Ser variant is associated with BMI in Tongans but not in Maori. In a sample of 58 populations worldwide, we also show that the 482Ser risk allele reaches its highest frequency in the Pacific.</p> <p>Conclusion</p> <p>The association between Gly482Ser genotypes and BMI in Tongans together with the worldwide frequency distribution of the Gly482Ser risk allele suggests that <it>PPARGC1A </it>remains a candidate thrifty gene in Pacific populations.</p

Kolonisierung und Anpassung der Hausmaus (Mus musculus domesticus) auf der Kerguelen Archipel

Starting from Western Europe, the house mouse (Mus musculus domesticus) has spread across the globe in historic times. However, most of the southern oceanic islands were colonized by mice only within the past 300 years. This makes them an excellent model for studying the evolutionary processes during early stages of new colonization and for understanding mechanisms of early adaptation. Twenty-four microsatellite loci and the mitochondrial D-loop sequence were typed in a total of 534 mice mainly from the Kerguelen Archipelago but also from Falkland Islands, Marion Island, Amsterdam Island, Antipodes Island, Macquarie Island, Auckland Islands, and one sample from South Georgia. Although there was heavy ship traffic for over a hundred years to the Kerguelen Archipelago, it appears that only the mice that have arrived first have colonized the main island (Grande Terre) and most of the associated small islands indeed mice shared the same D-loop haplotype as well as the same Y chromosomal haplotype. The second mice invasion has occurred on islands that are detached from Grande Terre (Cimetière Island and Cochons Island) and were likely to have had no resident mice prior to their arrival. They displayed a different mitochondrial D-loop haplotype and were genetically distinct in the autosomes. However, the Y chromosome haplotype was related to the one found in Grande Terre, suggesting that they came from a related source population. These data suggest that an area colonized by mice is refractory to further introgression, possibly due to fast adaptations of the resident mice to local conditions. Interestingly, single step mutational derivatives of one of the major mitochondrial haplotypes were found several times in different southern hemisphere islands, suggesting an unusually high mutation rate or the putative presence of a selective sweep in the mitochondrial genome. In order to investigate further the genetic basis of adaptation on southern hemisphere islands a genome-wide microsatellite screen for selective sweeps was performed. 737 markers dispersed around the entire genome were typed in pooled samples from Kerguelen Archipelago populations and compared to European populations in order to pre-selected candidate loci for selective sweeps. A total of 38 pre-selected candidates loci were then individually typed from five different islands (Kerguelen Archipelago, Marion Island, Auckland Island, Marion Island, Antipodes Island) representing six mouse populations in order to identify genomic regions displaying similar patterns and to decrease the impact of the demographic history of the island on the hitchhiking mapping approach used. Five microsatellite candidate loci, all of them associated with a gene, were identified. Interestingly, one of the candidates has a known function during parasite infection. Another candidate gene is a sub-unit of a K+ channel and, surprisingly, the second sub-unit of this K+ channel was picked up during the less stringent pre-selection of the 38 loci, pointing to the importance of this channel for mouse adaptation to their new environment. Additional experiments are required in order to confirm these five candidate genes, but nevertheless this study demonstrates that a genome-wide microsatellite locus screen is a valuable approach to identify genes which are implicated in recent adaptations.Die Hausmaus (Mus musculus domesticus) hat sich im Laufe der Geschichte, von Westeuropa ausgehend, kontinuierlich über die gesamte Welt ausgebreitet. Die Besiedlung eines Großteils der ozeanischen Inseln der südliche Hemisphäre hingegen, geschah innerhalb des vergleichsweise kurzen Zeitraumes der letzten 300 Jahre. Letzteres macht diese Inseln zu einem hervorragenden Modellsystem, um evolutionäre Prozesse in frühen Stadien einer Neubesiedlung zu analysieren und Mechanismen rezenter Anpassung zu verstehen. Für die vorliegende Untersuchung wurden 24 Mikrosatelliten-Marker, sowie D-loop-Sequenzen von insgesamt 534 Mäusen typisiert. Die Tiere stammten hauptsächlich von den Kerguelen Inseln, zusätzlich aber auch von den Falkland-Inseln, Marion Insel, Amsterdam Insel, Antipodes Insel, Macquarie Insel, Auckland Insel und eine Probe kam aus Süd-Georgien. Trotz des starken Schiffverkehrs über die letzten 100 Jahre zeigen die Ergebnisse, dass ausschließlich die Mäuse die zuerst auf den Kerguelen ankamen, die Hauptinsel (Grande Terre) und den Großteil der kleinen, zugehörigen Inseln besiedelten. Diese Tiere haben sowohl den gleichen D-loop Haplotyp, als auch den gleichen Y chromosomalen Haplotyp. Eine zweite Besiedlung durch Mäuse fand auf den Inseln statt, die weniger eng mit Grande Terre assoziiert sind und wahrscheinlich keine bereits etablierten Mauspopulationen hatten, wie Cimetière Insel und Cochons Insel. Die dortigen Mäuse haben einen anderen mitochondrialen D-loop Haplotypen und unterschieden sich auch in den Autosomen von den Tieren der Hauptinsel. Der Y Haplotyp jedoch entspricht dem der Populationen auf Grand Terre und den assoziierten Inseln, was darauf schließen lässt, dass beide Besiedlungswellen aus verwandten Ursprungspopulationen kamen. Diese Daten deuten daraufhin, dass bereits besiedelte Habitate weiterer Zuwanderung verschlossen sind, möglicherweise durch schnelle Anpassung der Erstbesiedler an die lokalen Bedingungen. Bemerkenswerter Weise wurden auf mehreren untersuchten Inseln mitochondriale Haplotypen gefunden, die durch eine einzelne Mutation aus dem Haupthaplotypen hervorgegangen waren. Dies weist auf eine ungewöhnlich hohe Mutationsrate oder einen „selective sweep“ im mitochondrialen Genom hin. Um die genetische Grundlage der Anpassungsprozesse auf den betrachteten Inseln eingehender zu untersuchen, wurde ein genomweiter Mikrosatellitenscreen zur Identifizierung selektiert Loci („selective sweeps“) durchgeführt. Zur Vorauswahl von Kandidaten-Loci wurden zunächst 737 genomweit verteilte Mikrosatelliten in gepoolten Proben von den Kerguelen typisiert und mit europäischen Populationen verglichen. Dann wurden insgesamt 38 ausgewählte Kandidaten-Loci für fünf unterschiedliche Inseln (Kerguelen Inseln, Marion Insel, Auckland Insel, Marion Insel, Antipodes Insel) und sechs Populationen individuell typisiert. So sollten genomische Regionen mit ähnlichen Mustern identifiziert und historisch bedingte Effekte auf diesen „hitchhiking mapping“-Ansatz reduziert werden. Auf diese Weise konnten fünf Mikrosatelliten-Kandidatenloci bestimmt werden, die alle mit jeweils einem Gen assoziiert waren. Einer der Kandidaten hat bekanntermaßen eine Funktion bei Parasiteninfektionen. Ein anderes Kandidatengen kodiert für Kcne1, die Untereinheit eines K+-Kanals, wobei das Gen für Kcnq1, eine weitere Untereinheit desselben K+-Kanals, ebenfalls unter den 38 zuvor weniger stringent ausgewählten Kandidatenloci war. Dies deutet darauf hin, dass dieser Kanal für die Mäuse eine Bedeutung für die Adaptation an die neue Umwelt hat. Zusätzliche Experimente sind erforderlich, um die fünf Kandidatengene weiter zu charakterisieren. Dennoch zeigt die vorliegende Studie, dass ein genomweiter Mikrosatellitenscreen ein geeigneter Ansatz zur Identifizierung von Genen darstellt, die an rezenten Anpassungsprozessen beteiligt sind

3D models related to the publication: Molar wear in house mice: insight into diet preferences at an ecological time scale?

This contribution contains 3D models of upper molar rows of house mice (Mus musculus domesticus) belonging to Western European commensal and Sub-Antarctic feral populations. These two groups are characterized by different patterns of wear and alignment of the three molars along the row, related to contrasted masticatory demand in relation with their diet. These models are analyzed in the following publication: Renaud et al 2023, "Molar wear in house mice, insight into diet preferences at an ecological time scale?", https://doi.org/10.1093/biolinnean/blad091