50/500 rule and minimum viable populations: response to Jamieson and Allendorf

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.

Diversity and genetic structure of freshwater shark Wallago attu: an emerging species of commercial interest

Pakistan has natural freshwater resources acting as a hotspot for diverse fish fauna. However, this aquatic fauna is declining at an alarming rate due to over-exploitation, habitat degradation, water pollution, climate change, and certain anthropogenic activities. The freshwater shark, Wallago attu, is a popular edible catfish inhabiting these freshwater ecosystems. Habitat degradation, overfishing, and human activities are heavily impacting the natural population of this species. So, sound knowledge about its population structure is necessary for its proper management in natural waters. The current study involves utilizing two mtDNA markers (COI, Cytb) to assess the genetic structure and differentiation among W. attu populations of Pakistani Rivers. Genetic variability analysis indicated a high haplotype (0.343 ± 0.046-0.870 ± 0.023) and low nucleotide diversity (0.0024 ± 0.012-0.0038 ± 0.018) among single and combined gene sequences, respectively. Overall, River Indus was populated with more diverse fauna of Wallago attu as compared to River Chenab and River Ravi. Population pairwise, Fst values (0.40-0.61) were found to be significantly different (p < 0.01) among three Riverine populations based upon combined gene sequences. The gene flow for the combined gene (COI + Cytb) dataset among three populations was less than 1.0. The transition/transversion bias value R (0.58) was calculated for testing of neutral evolution, and it declared low genetic polymorphism among natural riverine populations of Wallago attu. The current study's findings would be meaningful in planning the management and conservation of this economically important catfish in future.

Evolving spatial conservation prioritization with intraspecific genetic data

Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change.

Carnivore Contact: A Species Fracture Zone Delineated Amongst Genetically Structured North American Marten Populations (Martes americana and Martes caurina)

North American martens are forest dependent, influenced by human activity, and climate vulnerable. They have long been managed and harvested throughout their range as the American marten (Martes americana). Recent work has expanded evidence for the original description of two species in North America — M. americana and the Pacific Coast marten, M. caurina — but the geographic boundary between these groups has not been described in detail. From 2010 to 2016 we deployed 734 multi-taxa winter bait stations across a 53,474 km² study area spanning seven mountain ranges within the anticipated contact zone along the border of Canada and the United States. We collected marten hair samples and developed genotypes for 15 polymorphic microsatellite loci for 235 individuals, and 493 base-pair sequences of the mtDNA gene COI for 175 of those individuals. Both nuclear and mitochondrial genetic structure identified a sharp break across the Clark Fork Valley, United States with M. americana and M. caurina occurring north and south of the break, respectively. We estimated global effective population size (N_e) for each mountain range, clinal genetic neighborhood sizes (NS), calculated observed (H_o) and expected (H_e) heterozygosity, fixation index (F_ST), and clinal measures of allelic richness (Ar), H_o, and inbreeding coefficient (F_IS). Despite substantial genetic structure, we detected hybridization along the fracture zone with both contemporary (nuclear DNA) and historic (mtDNA) gene flow. Marten populations in our study area are highly structured and the break across the fracture zone being the largest documented in North America (F_ST range 0.21–0.34, mean = 0.27). With the exception of the Coeur d’Alene Mountains, marten were well distributed across higher elevation portions of our sampling area. Clinal NS values were variable suggesting substantial heterogeneity in marten density and movement. For both M. americana and M. caurina, elevationaly dependent gene flow and high genetic population structure suggest that connectivity corridors will be important to ensuring long-term population persistence. Our study is an example of how a combination of global and clinal molecular data analyses can provide important information for natural resource management.

Evidences for genetic differentiation within the highly endemic and endangered annual fish Austrolebias nigrofasciatus (Cyprinodontiformes: Rivulidae)

Samples of Austrolebias nigrofasciatus (n = 103), an endangered species of annual fish endemic to a small area of the Patos-Mirim lagoon system encompassing the São Gonçalo Channel lowlands, were collected from eight isolated temporary ponds, four located at the known distribution range of the species and four located along the Piratini River lowlands, where morphologically different individuals were found. In the laboratory, fragments of the mitochondrial cytochrome c oxidase I (coI), cytochrome b (cytb) and nuclear rhodopsin (rho) genes were amplified, purified and sequenced for 100, 99 and 58 of these individuals, respectively. Samples were further analysed using phylogenetic and phylogeographic methods to evaluate the patterns of genetic diversity and differentiation presented within and between populations, while assessing their evolutionary history, in order to guide the application of further conservation strategies. We found that the four new populations from the Piratini River lowlands encompass a different lineage of A. nigrofasciatus that diverged from that encountered in the São Gonçalo Channel at approximately 0.165 M years before present, during a population expansion and did not yet attain reciprocal monophyly. This divergence was associated with a glacial event that was preceded by an interglacial period putatively associated with the dispersal. Moreover, significant levels of genetic differentiation and a high number of exclusive haplotypes could be encountered even in micro-geographical scales, as in the comparisons between populations located within the same major lineage, indicating each of them may encompass independent management units. Conservation actions are certainly urgent, especially in the face of signs of a recent bottleneck.

Testing theoretical metapopulation conditions with genotypic data from Boreal Chorus Frogs (Pseudacris maculata)

The metapopulation concept has far-reaching implications in ecology and conservation biology. Hanski’s criteria operationally define metapopulations, yet testing them is hindered by logistical and financial constraints inherent to the collection of long-term demographic data. Hence, ecologists and conservationists often assume metapopulation existence for dispersal-limited species that occupy patchy habitats. To advance understanding of metapopulation theory and improve conservation of metapopulations, we used population and landscape genetic tools to develop a methodological framework for evaluating Hanski’s criteria. We used genotypic data (11 microsatellite loci) from a purported metapopulation of Boreal Chorus Frogs (Pseudacris maculata (Agassiz, 1850)) in Colorado, U.S.A., to test Hanski’s four criteria. We found support for each criterion: (1) significant genetic differentiation between wetlands, suggesting distinct breeding populations; (2) wetlands had small effective population sizes and recent bottlenecks, suggesting populations do not experience long-term persistence; (3) population graphs provided evidence of gene flow between patches, indicating potential for recolonization; and (4) multiscale bottleneck analyses suggest asynchrony, indicating that simultaneous extinction of all populations was unlikely. Our methodological framework provides a logistically and financially feasible alternative to long-term demographic data for identifying amphibian metapopulations.

Do We Know Enough to Save European Riverine Fish?—A Systematic Review on Autecological Requirements During Critical Life Stages of 10 Rheophilic Species at Risk

Modeling of fish population developments in the context of hydropower impacts and restoration planning requires autecological information on critical life stages (especially on juvenile stages and reproduction). We compiled and examined the current data availability in peer-reviewed and grey literature on autecological requirements of ten rheophilic fish species at risk, belonging to the salmonid, cyprinid, and cottid families. In total, 1725 data points from 223 sources were included. Economically important salmonids and the common nase were the most studied species. Grey and peer-reviewed data showed similar dispersion and variance and contributed nearly equally to the data pool of the specific species. An in-depth analysis on seven ecological parameters revealed no significant differences between both sources in terms of data availability and quality. We found substantial deficits in the data for about a quarter of the reviewed ecological parameters, in particular on individual densities in the habitats, egg development and information about juvenile stages despite the necessity of such data for more advanced population analyses. To secure fish populations in the long term, more data on basic autecological parameters is needed and grey literature might add valuable information, particularly if it relies on standardized methodologies.

A multidisciplinary approach to inform assisted migration of the restricted rainforest tree, Fontainea rostrata

Assisted migration can aid in the conservation of narrowly endemic species affected by habitat loss, fragmentation and climate change. Here, we employ a multidisciplinary approach by examining the population genetic structure of a threatened, dioecious rainforest tree of the subtropical notophyll vine forests of eastern Australia, Fontainea rostrata, and its potential requirements for population enhancement and translocation to withstand the effects of anthropogenic fragmentation and climate change. We used microsatellite markers to gain an understanding of the way genetic diversity is partitioned within and among the nine extant populations of F. rostrata identified in this study. We combined the results with species distribution modelling to identify populations vulnerable to possible future range shifts based on climate change projections. We found regional differences between the species’ main distribution in the south and a disjunct northern population cluster (F_RT = 0.074, F_SR = 0.088, F_ST = 0.155), in mean allelic richness (A_R = 2.77 vs 2.33, p < 0.05), expected heterozygosity (H_E = 0.376 vs 0.328), and inbreeding (F = 0.116 vs 0.219). Species distribution models predicted that while southern populations of F. rostrata are likely to persist for the next 50 years under the RCP6.0 climate change scenario, with potential for a small-scale expansion to the south-east, the more highly inbred and less genetically diverse northern populations will come under increasing pressure to expand southwards as habitat suitability declines. Given the species’ genetic structure and with the aim to enhance genetic diversity and maximise the likelihood of reproductive success, we recommend that plant reintroductions to supplement existing populations should be prioritised over translocation of the species to new sites. However, future conservation efforts should be directed at translocation to establish new sites to increase population connectivity, focussing particularly on habitat areas identified as persisting under conditions of climate change.

Past, present, and future of a freshwater fish metapopulation in a threatened landscape

It is well documented that hydropower plants can affect the dynamics of fish populations through landscape alterations and the creation of new barriers. Less emphasis has been placed on the examination of the genetic consequences for fish populations of the construction of dams. The relatively few studies that focus on genetics often do not consider colonization history and even fewer tend to use this information for conservation purposes. As a case study, we used a 3-pronged approach to study the influence of historical processes, contemporary landscape features, and potential future anthropogenic changes in landscape on the genetic diversity of a fish metapopulation. Our goal was to identify the metapopulation's main attributes, detect priority areas for conservation, and assess the consequences of the construction of hydropower plants for the persistence of the metapopulation. We used microsatellite markers and coalescent approaches to examine historical colonization processes, traditional population genetics, and simulations of future populations under alternate scenarios of population size reduction and gene flow. Historical gene flow appeared to have declined relatively recently and contemporary populations appeared highly susceptible to changes in landscape. Gene flow is critical for population persistence. We found that hydropower plants could lead to a rapid reduction in number of alleles and to population extirpation 50-80 years after their construction. More generally, our 3-pronged approach for the analyses of empirical genetic data can provide policy makers with information on the potential impacts of landscape changes and thus lead to more robust conservation efforts.

Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area

The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival and reproduction, and the model predicted stable median population growth and a 15% probability of extinction over 50 years in the absence of inbreeding depression. However, our model also predicted the population will lose 40-57% of its heterozygosity in 50 years. When we reduced demographic parameters proportional to reductions documented in another wild population of mountain lions that experienced inbreeding depression, extinction probability rose to 99.7%. Simulating greater landscape connectivity by increasing immigration to greater than or equal to one migrant per generation appears sufficient to largely maintain genetic diversity and reduce extinction probability. We provide empirical support for the central tenet of the extinction vortex as interactions between genetics and demography greatly increased extinction probability relative to the risk from demographic and environmental stochasticity alone. Our modelling approach realistically integrates demographic and genetic data to provide a comprehensive assessment of factors threatening small populations.

Are heritability and selection related to population size in nature? Meta-analysis and conservation implications

It is widely thought that small populations should have less additive genetic variance and respond less efficiently to natural selection than large populations. Across taxa, we meta-analytically quantified the relationship between adult census population size (N) and additive genetic variance (proxy: h (2)) and found no reduction in h (2) with decreasing N; surveyed populations ranged from four to one million individuals (1735 h (2) estimates, 146 populations, 83 species). In terms of adaptation, ecological conditions may systematically differ between populations of varying N; the magnitude of selection these populations experience may therefore also differ. We thus also meta-analytically tested whether selection changes with N and found little evidence for systematic differences in the strength, direction or form of selection with N across different trait types and taxa (7344 selection estimates, 172 populations, 80 species). Collectively, our results (i) indirectly suggest that genetic drift neither overwhelms selection more in small than in large natural populations, nor weakens adaptive potential/h (2) in small populations, and (ii) imply that natural populations of varying sizes experience a variety of environmental conditions, without consistently differing habitat quality at small N. However, we caution that the data are currently insufficient to determine whether some small populations may retain adaptive potential definitively. Further study is required into (i) selection and genetic variation in completely isolated populations of known N, under-represented taxonomic groups, and nongeneralist species, (ii) adaptive potential using multidimensional approaches and (iii) the nature of selective pressures for specific traits.

Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations?

In salmonids, the release of hatchery-reared fish has been shown to cause irreversible genetic impacts on wild populations. However, although responsible practices for producing and releasing genetically diverse, hatchery-reared juveniles have been published widely, they are rarely implemented. Here, we investigated genetic differences between wild and early-generation hatchery-reared populations of the purple sea urchin Paracentrotus lividus (a commercially important species in Europe) to assess whether hatcheries were able to maintain natural levels of genetic diversity. To test the hypothesis that hatchery rearing would cause bottleneck effects (that is, a substantial reduction in genetic diversity and differentiation from wild populations), we compared the levels and patterns of genetic variation between two hatcheries and four nearby wild populations, using samples from both Spain and Ireland. We found that hatchery-reared populations were less diverse and had diverged significantly from the wild populations, with a very small effective population size and a high degree of relatedness between individuals. These results raise a number of concerns about the genetic impacts of their release into wild populations, particularly when such a degree of differentiation can occur in a single generation of hatchery rearing. Consequently, we suggest that caution should be taken when using hatchery-reared individuals to augment fisheries, even for marine species with high dispersal capacity, and we provide some recommendations to improve hatchery rearing and release practices. Our results further highlight the need to consider the genetic risks of releasing hatchery-reared juveniles into the wild during the establishment of restocking, stock enhancement and sea ranching programs.

Population size and the rate of evolution

Does evolution proceed faster in larger or smaller populations? The relationship between effective population size (Ne) and the rate of evolution has consequences for our ability to understand and interpret genomic variation, and is central to many aspects of evolution and ecology. Many factors affect the relationship between Ne and the rate of evolution, and recent theoretical and empirical studies have shown some surprising and sometimes counterintuitive results. Some mechanisms tend to make the relationship positive, others negative, and they can act simultaneously. The relationship also depends on whether one is interested in the rate of neutral, adaptive, or deleterious evolution. Here, we synthesize theoretical and empirical approaches to understanding the relationship and highlight areas that remain poorly understood.

Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii)

We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci to compare genetic variation among Kapiti LSK and the populations of Red Mercury, Tiritiri Matangi and Long Islands that were founded with birds from Kapiti. Two LSK native to D'Urville Island were also placed on Long Island. We found extremely low genetic variation and signatures of acute and recent genetic bottleneck effects in all four populations, indicating that LSK have survived multiple genetic bottlenecks. The Long Island population appears to have arisen from a single mating pair from Kapiti, suggesting there is no genetic contribution from D'Urville birds among extant LSK. The Ne/NC ratio of Kapiti Island LSK (0.03) is exceptionally low for terrestrial vertebrates and suggests that genetic diversity might still be eroding in this population, despite its large census size.