Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

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 reachingN ̂ e = 50 and a <9% probability of reachingN ̂ e = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller medianN ̂ e than unlisted populations, and this was consistent across all taxonomic groups.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 ofN ̂ 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.

Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets

Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.

Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data

Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.

Effects of subpopulation extinction on effective size (Ne) of metapopulations

Population extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis.

Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

Evaluation of proposed genetic goals and targets for the Convention on Biological Diversity

In the current negotiations regarding revision of the Convention on Biological Diversity (CBD) proposals have been made to strengthen the genetic goals, indicators, and targets for wild species in natural habitats by specifying “tolerable” losses of genetic diversity. However, they have not been subjected to evaluations of their continued use over 100 years, a common conservation time frame. I evaluated six scenarios (3, 5 or 10% loss of genetic diversity [heterozygosity] over 8 or 32 years) proposed as targets for revision of genetic indicators in CBD by predicting their consequences on genetic diversity, inbreeding, fitness, and evolutionary potential when applied at the same rate for 100 years. All proposals lead to substantial genetic harm to species when continued for 100 years that will compromise species persistence, especially in the context of environmental change. Consequently, none of the proposals are suitable for inclusion in the CBD. However, alternative indicators are proposed that would reflect improvements in the genetic status of populations and species, namely (1) the number of species and their populations being maintained at sizes sufficient to retain evolutionary potential in perpetuity, and (2) the number of species for which population genetic connectivity has been improved.

Demographic and Evolutionary History of Pallid and Shovelnose Sturgeon in the Upper Missouri River

Natural-origin pallid sturgeon Scaphirhynchus albus in the upper Missouri River are predicted to become extirpated as early as 2024.  To aid in recovery efforts for this endangered species, we used genetic data from 17 microsatellite loci to infer demographic and evolutionary history of pallid sturgeon and a sympatric shovelnose sturgeon S. platorynchus .  A recent sundering of geneflow between these species was indicated by overlapping allele size distributions at all loci and low level of genetic divergence ( F ST = 0.10).  Tests for recent bottlenecks, using heterozygosity excess or allele frequency mode-shift tests indicated demographic stability for both species while the M-Ratio identified historic bottlenecks had occurred in both species. Estimates of historical effective population size ( N e ), based on coalescent modeling of allele size distribution, suggested the geographic expansion of these species into the upper Missouri River during the late Pleistocene was associated with 10 to 19 fold reductions in N e .  In contrast estimates of contemporary estimates of N e based on linkage disequilibrium revealed that shovelnose sturgeon ( N e  = 2983) had approximately 10 times greater N e  than pallid sturgeon ( N e  = 254).  Our results are consistent with the recent collapse of pallid sturgeon being caused by dam construction which occurred between 1930 and 1965.  Fortunately, genetic diversity remaining in this long-lived species has provided an opportunity to conserve pre-dam pallid sturgeon genetic diversity via a successful captive breeding program. We provide recommendations to address key conservation needs including how to incorporate our estimate of N e / adult census size of 0.26 (95% CI: 0.16 – 0.47) into setting demographic recovery goals for pallid sturgeon.