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Here, we report on eDNA week, an international conference held online as a five-day series of webinars from January 17, 2022, to January 21, 2022. The conference was organized by the UK DNA working group, which has witnessed considerable growth and application of eDNA research since its founding and first conference in 2014. The 2022 event, held online due to the COVID-19 pandemic, provided an opportunity to invite international researchers who are leading the field, without the usual constraints of conference location. Compared with the previous UK-based in-person conferences, there was greater international participation amongst the 514 people who registered to attend the event. To emphasize the importance of collaboration between sectors in driving forward DNA monitoring, a session was devoted to presentations by participants from governmental agencies, and another to those from commercial companies developing and utilizing DNA tools. The industry and stakeholder sessions were accompanied by state-of-the-art presentations delivered by a global group of DNA/eDNA researchers from 11 countries. These sessions were complemented by an open forum session for reflection and discussion.

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

Environmental DNA (eDNA) metabarcoding can identify terrestrial taxa utilising aquatic habitats alongside aquatic communities, but terrestrial species' eDNA dynamics are understudied. We evaluated eDNA metabarcoding for monitoring semi-aquatic and terrestrial mammals, specifically nine species of conservation or management concern, and examined spatiotemporal variation in mammal eDNA signals. We hypothesised eDNA signals would be stronger for semi-aquatic than terrestrial mammals, and at sites where individuals exhibited behaviours. In captivity, we sampled waterbodies at points where behaviours were observed (‘directed’ sampling) and at equidistant intervals along the shoreline (‘stratified’ sampling). We surveyed natural ponds (N = 6) where focal species were present using stratified water sampling, camera traps, and field signs. eDNA samples were metabarcoded using vertebrate-specific primers. All focal species were detected in captivity. eDNA signal strength did not differ between directed and stratified samples across or within species, between semi-aquatic or terrestrial species, or according to behaviours. eDNA was evenly distributed in artificial waterbodies, but unevenly distributed in natural ponds. Survey methods deployed at natural ponds shared three species detections. Metabarcoding missed badger and red fox recorded by cameras and field signs, but detected small mammals these tools overlooked, e.g. water vole. Terrestrial mammal eDNA signals were weaker and detected less frequently than semi-aquatic mammal eDNA signals. eDNA metabarcoding could enhance mammal monitoring through large-scale, multi-species distribution assessment for priority and difficult to survey species, and provide early indication of range expansions or contractions. However, eDNA surveys need high spatiotemporal resolution and metabarcoding biases require further investigation before routine implementation.

Environmental DNA (eDNA) metabarcoding can identify terrestrial taxa utilising aquatic habitats alongside aquatic communities, but terrestrial species' eDNA dynamics are understudied. We evaluated eDNA metabarcoding for monitoring semi-aquatic and terrestrial mammals, specifically nine species of conservation or management concern, and examined spatiotemporal variation in mammal eDNA signals. We hypothesised eDNA signals would be stronger for semi-aquatic than terrestrial mammals, and at sites where individuals exhibited behaviours. In captivity, we sampled waterbodies at points where behaviours were observed (‘directed’ sampling) and at equidistant intervals along the shoreline (‘stratified’ sampling). We surveyed natural ponds (N = 6) where focal species were present using stratified water sampling, camera traps, and field signs. eDNA samples were metabarcoded using vertebrate-specific primers. All focal species were detected in captivity. eDNA signal strength did not differ between directed and stratified samples across or within species, between semi-aquatic or terrestrial species, or according to behaviours. eDNA was evenly distributed in artificial waterbodies, but unevenly distributed in natural ponds. Survey methods deployed at natural ponds shared three species detections. Metabarcoding missed badger and red fox recorded by cameras and field signs, but detected small mammals these tools overlooked, e.g. water vole. Terrestrial mammal eDNA signals were weaker and detected less frequently than semi-aquatic mammal eDNA signals. eDNA metabarcoding could enhance mammal monitoring through large-scale, multi-species distribution assessment for priority and difficult to survey species, and provide early indication of range expansions or contractions. However, eDNA surveys need high spatiotemporal resolution and metabarcoding biases require further investigation before routine implementation.

The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographical studies, although these have focussed on the more southerly part of its range. A substantial number of new samples, many of them from the periphery of the species' range, contribute to an exceptional dataset comprising 981 mitochondrial cytochrome b sequences. These new data provide sufficient resolution to transform our understanding of the survival of the species through the last glaciation and its subsequent re-colonization of the continent. The deepest genetic split that we found is in agreement with previous studies and runs from the Alps to central Ukraine, although we further distinguish two separate lineages in wood mice to the north and west of this line. It is likely that this part of Europe was colonized from two refugia, putatively located in the Iberian peninsula and the Dordogne or Carpathian region. The wood mouse therefore joins the growing number of species with extant populations that appear to have survived the Last Glacial Maximum in northern refugia, rather than solely in traditionally recognized refugial locations in the southern European peninsulas. Furthermore, the existence of a northern refugium for the species was predicted in a study of mitochondrial variation in a specific parasite of the wood mouse, demonstrating the potential value of data from parasites to phylogeographical studies. Lastly, the presence of related haplotypes in widely disparate locations, often on islands or separated by substantial bodies of water, demonstrates the propensity of the wood mouse for accidental human-mediated transport.

Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole ( Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA ( including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration., Funding Agencies|National Science Centre, Poland [N N304 058340]; European Union [245737]

Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole ( Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA ( including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration., Funding Agencies|National Science Centre, Poland [N N304 058340]; European Union [245737]

Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole ( Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA ( including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration., Funding Agencies|National Science Centre, Poland [N N304 058340]; European Union [245737]

Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole ( Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA ( including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration., Funding Agencies|National Science Centre, Poland [N N304 058340]; European Union [245737]

Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole ( Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA ( including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration., Funding Agencies|National Science Centre, Poland [N N304 058340]; European Union [245737]

Here, we report on eDNA week, an international conference held online as a five-day series of webinars from January 17, 2022, to January 21, 2022. The conference was organized by the UK DNA working group, which has witnessed considerable growth and application of eDNA research since its founding and first conference in 2014. The 2022 event, held online due to the COVID-19 pandemic, provided an opportunity to invite international researchers who are leading the field, without the usual constraints of conference location. Compared with the previous UK-based in-person conferences, there was greater international participation amongst the 514 people who registered to attend the event. To emphasize the importance of collaboration between sectors in driving forward DNA monitoring, a session was devoted to presentations by participants from governmental agencies, and another to those from commercial companies developing and utilizing DNA tools. The industry and stakeholder sessions were accompanied by state-of-the-art presentations delivered by a global group of DNA/eDNA researchers from 11 countries. These sessions were complemented by an open forum session for reflection and discussion.