The phylogeography of the house mouse (Mus musculus L.), an emblematic species for genetic and biomedical studies, is only partly understood, essentially because of a sampling bias towards its most peripheral populations in Europe, Asia and the Americas. Moreover, the present-day phylogeographic hypotheses stem mostly from the study of mitochondrial lineages. In this article, we complement the mtDNA studies with a comprehensive survey of nuclear markers (19 microsatellite loci) typed in 963 individuals from 47 population samples, with an emphasis on the putative Middle-Eastern centre of dispersal of the species. Based on correspondence analysis, distance and allele-sharing trees, we find a good coherence between geographical origin and genetic make-up of the populations. We thus confirm the clear distinction of the three best described peripheral subspecies, M. m. musculus, M. m. domesticus and M. m. castaneus. A large diversity was found in the Iranian populations, which have had an unclear taxonomic status to date. In addition to samples with clear affiliation to M. m. musculus and M. m. domesticus, we find two genetic groups in Central and South East Iran, which are as distinct from each other as they are from the south-east Asian M. m. castaneus. These groups were previously also found to harbor distinct mitochondrial haplotypes. We propose that the Iranian plateau is home to two more taxonomic units displaying complex primary and secondary relationships with their long recognized neighbours. This central region emerges as the area with the highest known diversity of mouse lineages within a restricted geographical area, designating it as the focal place to study the mechanisms of speciation and diversification of this species.

Aim: In this study, we conduct a quantitative meta‐analysis to investigate broad patterns of genetic variation throughout large geographical regions in order to elucidate concordant geographical patterns across species and identify common historical processes to better inform the “cryptic refugia” versus the traditional “southern refugia” hypothesis debate.Location: Europe.Time period: Late Pleistocene to present day.Major taxa studied: Small mammals (Rodentia, Eulipotyphla).Methods: A meta‐analysis was performed on large‐scale patterns of genetic diversity for 19 species from 59 papers. For each species, haplotype and nucleotide diversity were calculated using the mitochondrial D‐loop and compared to the species’ range.Results: No consistent patterns were observed between mitochondrial DNA (mtDNA) diversity indices (nucleotide and haplotype diversity) and any of the indicators of distribution examined [latitude and longitude (max, min, centre, range)]. The patterns of genetic diversity observed in all the 19 species studied appear to be species‐specific.Main conclusions: In contrast to the traditional southern refugial hypotheses, we found no evidence for a consistent south–north post‐glacial expansion. Instead individual species appear to respond to climate oscillations in niche‐specific ways. This individual nature of each species’ phylogeographical history indicates a complex web of post‐glacial recolonization dynamics across Europe.

Assessments of fish communities tend to rely on capture‐based methods that, due to sampling biases, can underestimate actual species richness. Alternatively, environmental DNA (eDNA) based metabarcoding is a noncapture approach that infers species richness and distribution by collecting and sequencing DNA present in the ecosystem. Here, eDNA metabarcoding was applied to the lower River Severn, a highly modified and impounded river, to identify the species present in the fish assemblage. Using a universal primer for fish (12S mtDNA region), comparisons were made between the species identified as present by eDNA metabarcoding versus long‐term data available from fisheries monitoring data based on capture methods. Depending on the stringency of detection thresholds applied, the two methods detected between 15 and 25 fish species present in the river, with the eDNA metabarcoding detecting most species previously reported in the capture surveys, although with differences in the relative abundance of species between the methods. Notably, eDNA metabarcoding detected species of high conservation importance that were never sampled by capture techniques, including native European shads (Alosa spp.). Differences in the similarity indices of species detection were greater between the sampling methods than between sampling sites on each river. These results highlight the high potential of eDNA metabarcoding to provide an effective monitoring tool for biodiversity and conservation in rivers, but also indicate the need for complementary multi‐method sampling for robust estimates of fish species richness.

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.

Artificial 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 information on the spatial and temporal extent of current migrations. 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 characterized by the presence of multiple 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. 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. Although barriers inhibit the spawning migrations of shad, this eDNA assay showed that 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 also be used across their range, to further quantify the spatial extent of their spawning, including in highly fragmented rivers and those where shad are believed to spawn only occasionally and are rarely observed.

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.