Global assessment of effective population sizes: Consistent taxonomic differences in meeting the 50/500 rule.

Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal and amphibian populations had a <54% probability of reaching N ̂ e $$ {\hat{N}}_e $$ = 50 and a <9% probability of reaching N ̂ e $$ {\hat{N}}_e $$ = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median N ̂ e $$ {\hat{N}}_e $$ than unlisted populations, and this was consistent across all taxonomic groups. N ̂ e $$ {\hat{N}}_e $$ was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of N ̂ e $$ {\hat{N}}_e $$ in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritise assessment of populations from taxa most at risk of failing to meet conservation thresholds.

Ex situ conservation of two rare oak species using microsatellite and SNP markers.

Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.

Phylogeographic Reconstruction to Trace the Source Population of Asian Giant Hornet Caught in Nanaimo in Canada and Blaine in the USA.

The Asian giant hornet, Vespa mandarinia, is an invasive species that could potentially destroy the local honeybee industry in North America. It has been observed to nest in the coastal regions of British Columbia in Canada and Washington State in the USA. What is the source population of the immigrant hornets? The identification of the source population can shed light not only on the route of immigration but also on the similarity between the native habitat and the potential new habitat in the Pacific Northwest. We analyzed mitochondrial COX1 sequences of specimens sampled from multiple populations in China, the Republic of Korea, Japan, and the Russian Far East. V. mandarinia exhibits phylogeographic patterns, forming monophyletic clades for 16 specimens from China, six specimens from the Republic of Korea, and two specimens from Japan. The two mitochondrial COX1 sequences from Nanaimo, British Columbia, are identical to the two sequences from Japan. The COX1 sequence from Blaine, Washington State, clustered with those from the Republic of Korea and is identical to one sequence from the Republic of Korea. Our geophylogeny, which allows visualization of genetic variation over time and space, provides evolutionary insights on the evolution and speciation of three closely related vespine species (V. tropica, V. soror, and V. mandarinia), with the speciation events associated with the expansion of the distribution to the north.

Revealing population demographics with environmental RNA.

The analyses of environmental DNA (eDNA) and environmental RNA (eRNA) released by organisms into their surrounding environment (water, soil and air) have emerged as powerful tools for monitoring biodiversity. While eDNA has been widely adopted for the non-invasive detection of species and characterization of community composition, the utilization of eRNA is still in its infancy. Due to its functional nature, eRNA holds intriguing potential for biodiversity monitoring offering new avenues of research beyond species detection. For example, conspecifics that are almost genetically identical can exhibit distinct transcriptomic differences depending on their life stage. In this issue of Molecular Ecology Resources, Parsley and Goldberg (2024) demonstrate, through a lab-validated field study, that eRNA can be used to detect distinct life stages of amphibians. This study elegantly demonstrates that eRNA can be used not only to detect invasive or endangered species but also to reveal population demographic information important for guiding effective conservation strategies.

The burden of anthropogenic changes and mutation load in a critically endangered harrier from the Reunion biodiversity hotspot, Circus maillardi.

Anthropogenic impact is causing the decline of a large proportion of species worldwide and reduces their genetic diversity. Island species typically have smaller ranges than continental species. As a consequence, island species are particularly liable to undergo population bottlenecks, giving rise to conservation challenges such as inbreeding and unmasking of deleterious genetic load. Such challenges call for more detailed assessments of the genetic make-up of threatened island populations. The Mascarene islands (Indian Ocean) present many prime examples, being unusual in having been pristine until first human arrival ~400 years ago, following which anthropogenic pressure was unusually intense. A threatened harrier (Circus maillardi) endemic to the westernmost island of the archipelago is a good example of the challenges faced by species that have declined to small population size following intense anthropogenic pressure. In this study, we use an extensive set of population genomic tools to quantify variation at near-neutral and coding loci, in order to test the historical impact of human activity on this species, and evaluate the species' (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from ~3000 to 300 individuals in the past 1000 years, with a more recent drop ~100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants but is unlikely to have allowed the purging of mildly deleterious variants. Our study shows how using relatively affordable methods can reveal the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.

Ecological restoration and rewilding: two approaches with complementary goals?

As we enter the UN Decade on Ecosystem Restoration (2021-2030) and address the urgent need to protect and restore ecosystems and their ecological functions at large scales, rewilding has been brought into the limelight. Interest in this discipline is thus increasing, with a large number of conceptual scientific papers published in recent years. Increasing enthusiasm has led to discussions and debates in the scientific community about the differences between ecological restoration and rewilding. The main goal of this review is to compare and clarify the position of each field. Our results show that despite some differences (e.g. top-down versus bottom-up and functional versus taxonomic approaches) and notably with distinct goals - recovery of a defined historically determined target ecosystem versus recovery of natural processes with often no target endpoint - ecological restoration and rewilding have a common scope: the recovery of ecosystems following anthropogenic degradation. The goals of ecological restoration and rewilding have expanded with the progress of each field. However, it is unclear whether there is a paradigm shift with ecological restoration moving towards rewilding or vice versa. We underline the complementarity in time and in space of ecological restoration and rewilding. To conclude, we argue that reconciliation of these two fields of nature conservation to ensure complementarity could create a synergy to achieve their common scope.