Census Population Size Research Articles

Population Size in Evolutionary Biology Is More Than the Effective Size.

In population genetics idealized Wright-Fisher (WF) populations are generally considered equivalent to real populations with regard to the major evolutionary processes that influence genotype and allele frequencies. As a result we often model the response of populations by focusing on the effective size N e . The Diversity Partitioning Theorem (DPT) shows that you cannot model the behavior of a system solely on the basis of a diversity (accounting for unevenness among items) without taking richness into account. I show that the census population size (the number of adults, N c ) is equivalent to a richness, and that the effective size N e is equivalent to a true diversity. It follows logically from the DPT that we require both N e and N c to understand how drift, selection, mutation, and gene flow interact to shape the course of evolution of populations. Here I review evidence that both N c and N e affect evolutionary trajectories of populations for neutral and adaptive processes. This also influences how we should consider evolutionary potential and genetic criteria for conservation of populations. The effective size of a population is of huge importance in evolutionary biology, but it should not be the sole focus when population size is concerned. Applied evolutionary studies need to integrate N c in the equation more consistently when modeling the response to selection, mutation, migration, and drift.

Unraveling the Complexity of the N e/N c Ratio for Conservation of Large and Widespread Pelagic Fish Species: Current Status and Challenges.

Estimating and understanding the ratio between effective population size (N e) and census population size (N c) are pivotal in the conservation of large marine pelagic fish species, including bony fish such as tunas and cartilaginous fish such as sharks, given the challenges associated with obtaining accurate estimates of their abundance. The difficulties inherent in capturing and monitoring these species in vast and dynamic marine environments often make direct estimation of their population size challenging. By focusing on N e, it is conceivable in certain cases to approximate census size once the N e/N c ratio is known, although this ratio can vary and does not always increase linearly, as it is influenced by various ecological and evolutionary factors. Thus, this ratio presents challenges and complexities in the context of pelagic species conservation. To delve deeper into these challenges, firstly, we recall the diverse types of effective population sizes, including contemporary and historical sizes, and their implications in conservation biology. Secondly, we outline current knowledge about the influence of life history traits on the N e/N c ratio in the light of examples drawn from large and abundant pelagic fish species. Despite efforts to document an increasing number of marine species using recent technologies and statistical methods, establishing general rules to predict N e/N c remains elusive, necessitating further research and investment. Finally, we recall statistical challenges in relating N e and N c emphasizing the necessity of aligning temporal and spatial scales. This last part discusses the roles of generation and reproductive cycle effective population sizes to predict genetic erosion and guiding management strategies. Collectively, these sections underscore the multifaceted nature of effective population size estimation, crucial for preserving genetic diversity and ensuring the long-term viability of populations. By navigating statistical and theoretical complexities, and addressing methodological challenges, scientists should be able to advance our understanding of the N e/N c ratio.

How Big Is Big? The Effective Population Size of Marine Bacteria.

Genome-reduced bacteria constitute most of the cells in surface-ocean bacterioplankton communities. Their extremely large census population sizes (N c) have been unfoundedly translated to huge effective population sizes (N e)-the size of an ideal population carrying as much neutral genetic diversity as the actual population. As N e scales inversely with the strength of genetic drift, constraining the magnitude of N e is key to evaluating whether natural selection can overcome the power of genetic drift to drive evolutionary events. Determining the N e of extant species requires measuring the genomic mutation rate, a challenging step for most genome-reduced bacterioplankton lineages. Results for genome-reduced Prochlorococcus and CHUG are surprising-their N e values are an order of magnitude lower than those of less abundant lineages carrying large genomes, such as Ruegeria and Vibrio. As bacterioplankton genome reduction commonly occurred in the distant past, appreciating their population genetic mechanisms requires constraining their ancient N e values by other methods.

Hurricane-induced dramatic decline and natural recovery of a vulnerable sportfish population: Shoal bass (Micropterus cataractae) in the Chipola River, Florida

Freshwater fishes are among the most biodiverse vertebrate groups and among the most threatened by anthropogenic activities. Many occur in small and geographically restricted populations that are increasingly subject to catastrophic events (hurricanes, wildfires, extreme floods and droughts), but it has rarely been possible to assess the impacts of such events. Here we document the decline and recovery of a regularly monitored, small shoal bass (Micropterus cataractae) population in the Chipola River, Florida following a catastrophic hurricane disturbance. The Chipola River population has the lowest level of interspecific hybridization (over 90 % non-introgressed shoal bass) within the species' range, a census population size of 2165 (95 % CI [1,383, 3,801]) in 2009 and a genetically effective population size Ne of 135 (95 % CI [70, 472]). In 2018, Hurricane Michael devastated the Chipola River and watershed. A survey conducted in 2019 indicated a severe decline (91 %) in relative population abundance and a very low Ne at 21 (95 % CI [16, 29]). However, the detection of young-of-year fish indicated that the depleted population had experienced successful reproduction. In fall 2021, the census population had recovered to 1039 fish (95 % CI [660, 1,814]) and Ne at 40 (95 % CI [31, 50]). While the population has shown considerable resilience in the face of hurricane disturbance, it remains vulnerable to future catastrophic events and may also suffer a long-term reduction in its adaptive potential due to a relatively low effective population size. To address these threats, continued monitoring is necessitated and targeted measures such as translocation of non-introgressed individuals from neighboring populations or establishment of a captive population of sufficient effective population size may be required to conserve the species in the long term.

The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder.

The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an 'effective population size' is often estimated from the amount of putatively neutral genetic diversity and is assumed to also capture a species' effectiveness of selection. A potentially more direct measure of the effectiveness of selection is the degree to which selection maintains preferred codons. However, past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here, we propose a new Codon Adaptation Index of Species (CAIS), based on Kullback-Leibler divergence, that corrects for both confounders. We demonstrate the use of CAIS correlations, as well as the Effective Number of Codons, to show that the protein domains of more highly adapted vertebrate species evolve higher intrinsic structural disorder.

Measuring changes in Plasmodium falciparum census population size in response to sequential malaria control interventions.

Here we introduce a new endpoint ″census population size″ to evaluate the epidemiology and control of Plasmodium falciparum infections, where the parasite, rather than the infected human host, is the unit of measurement. To calculate census population size, we rely on a definition of parasite variation known as multiplicity of infection (MOI var ), based on the hyper-diversity of the var multigene family. We present a Bayesian approach to estimate MOI var from sequencing and counting the number of unique DBLα tags (or DBLα types) of var genes, and derive from it census population size by summation of MOI var in the human population. We track changes in this parasite population size and structure through sequential malaria interventions by indoor residual spraying (IRS) and seasonal malaria chemoprevention (SMC) from 2012 to 2017 in an area of high-seasonal malaria transmission in northern Ghana. Following IRS, which reduced transmission intensity by > 90% and decreased parasite prevalence by ~40-50%, significant reductions in var diversity, MOI var , and population size were observed in ~2,000 humans across all ages. These changes, consistent with the loss of diverse parasite genomes, were short lived and 32-months after IRS was discontinued and SMC was introduced, var diversity and population size rebounded in all age groups except for the younger children (1-5 years) targeted by SMC. Despite major perturbations from IRS and SMC interventions, the parasite population remained very large and retained the var population genetic characteristics of a high-transmission system (high var diversity; low var repertoire similarity) demonstrating the resilience of P. falciparum to short-term interventions in high-burden countries of sub-Saharan Africa.

Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations.

Background selection describes the reduction in neutral diversity caused by selection against deleterious alleles at other loci. It is typically assumed that the purging of deleterious alleles affects linked neutral variants, and indeed simulations typically only treat a genomic window. However, background selection at unlinked loci also depresses neutral diversity. In agreement with previous analytical approximations, in our simulations of a human-like genome with a realistically high genome-wide deleterious mutation rate, the effects of unlinked background selection exceed those of linked background selection. Background selection reduces neutral genetic diversity by a factor that is independent of census population size. Outside of genic regions, the strength of background selection increases with the mean selection coefficient, contradicting the linked theory but in agreement with the unlinked theory. Neutral diversity within genic regions is fairly independent of the strength of selection. Deleterious genetic load among haploid individuals is underdispersed, indicating nonindependent evolution of deleterious mutations. Empirical evidence for underdispersion was previously interpreted as evidence for global epistasis, but we recover it from a non-epistatic model.

DnaDot - fixing ecology and evolution’s blind spot, population size

To understand and manage any ecosystem, one of the most critical indicators is census population size (‘Nc’) for each component species. This is why the International Union for Conservation of Nature (IUCN) stipulates that it is ideal to know census size to an accuracy of ±10 % for each managed, endangered or exploited population. Knowledge of population size is also critical for: ecological studies in general; allowing biodiversity measures with low error margins; and assessing potential for evolutionary adaptation in long-term management. Unfortunately, despite their importance, all existing methods for estimating Nc have many difficulties, especially requiring independent knowledge or assumptions about demography, including: immigration, emigration, family size and its variance. As a result, even in the IUCN red list, many species are listed despite having unknown population size or trends. Therefore, we need an improved approach. This article introduces ‘DnaDot’, a strong new addition to our armory of census population size estimates, because it is an accurate estimate, with few assumptions. DnaDot is based on mark-release-recapture, but instead of marking, uses pre-existing polymorphisms to divide the population into separate groups. The method uses one sample, minimizing effort, uses no demographic assumptions or data, and does not require genotyping to be accurate enough to identify individuals and kin, which is problematic for other genetic methods especially when degraded field samples are used. DnaDot applies to any kind of variants, from tissue samples, or from noninvasive samples such as hair provided that the researcher can identify species-identity and variants within the species. DnaDot outperformed close competitors on minimal assumptions, and good detectability of marks. Also, in simulations of a wide range of scenarios, DnaDot had superior accuracy and precision, usually meeting the IUCN criterion of ±10 %, which competing methods rarely achieved. Finally, one other method is said to need smaller sample sizes than DnaDot, but only if that method is not required to meet the performance criteria of DnaDot.

Testing methods to estimate population size for wastewater treatment plants using census data: Implications for wastewater-based epidemiology

In wastewater-based epidemiology (WBE), wastewater loads are commonly reported as a per capita value. Census population counts are often used to obtain a population size to normalise wastewater loads. However, the methods used to calculate the population size of wastewater treatment plants (WWTPs) from census data are rarely reported in the WBE literature. This is problematic because the geographical extents of wastewater catchments and census area units rarely align perfectly with each other and exist at different spatial scales. This complicates efforts to estimate the number of people serviced by WWTPs in these census area units. This study compared four geospatial methods to combine wastewater catchment areas and census area units to calculate the census population size of wastewater treatment plants. These methods were applied nationally to WWTPs across New Zealand. Population estimates varied by up to 73 % between the methods, which could skew comparisons of per capita wastewater loads between sites. Variability in population estimates (relative standard deviation, RSD) was significantly higher in smaller catchments (rs = −0.727, P < .001), highlighting the importance of method selection in smaller sites. Census population estimates were broadly similar to those provided by wastewater operators, but significant variation was observed for some sites (ranging from 42 % lower to 78 % higher, RSD = 262 %). We present a widely applicable method to calculate population size from census, which involves disaggregating census area units by individual properties. The results reinforce the need for transparent reporting to maintain confidence in the comparison of WBE across sites and studies.

High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator.

Lewontin's paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π and Nc are found for highly abundant marine invertebrates. Yet, the influences of new mutations on π relative to extrinsic processes such as Nc fluctuations are unknown. Here, we provide the first germline mutation rate (μ) estimate for a marine invertebrate in corallivorous crown-of-thorns sea stars (Acanthaster cf. solaris). We use high-coverage whole-genome sequencing of 14 parent-offspring trios alongside empirical estimates of Nc in Australia's Great Barrier Reef to jointly examine the determinants of π in populations undergoing extreme Nc fluctuations. The A. cf. solaris mean μ was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08), exceeding estimates for other invertebrates and showing greater concordance with vertebrate mutation rates. Lower-than-expected Ne (~70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated weak influences of population outbreaks on long-term π. Our findings are consistent with elevated μ evolving in response to reduced Ne and generation time length, with important implications for explaining high mutational loads and the determinants of genetic diversity in marine invertebrate taxa.

Temporal genetic variation mediated by climate change-induced salinity decline, a study on Artemia (Crustacea: Anostraca) from Kyêbxang Co, a high altitude salt lake on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau is one of the areas the richest in salt lakes and Artemia sites. As a result of climate warming and wetting, the areas of salt lakes on the plateau have been increasing, and the salinities have decreased considerably since 1990s. However, the impact of salinity change on the genetic diversity of Artemia is still unknown. Kyêbxang Co is the highest (4620 m above sea level) salt lake currently with commercial harvesting of Artemia resting eggs in the world, and harbors the largest Artemia population on the plateau. Its salinity had dropped from ∼67 ppt in 1998 to ∼39 ppt in 2019. Using 13 microsatellite markers and the mitochondrial cytochrome oxidase submit I (COI) gene, we analyzed the temporal changes of genetic diversity, effective population size and genetic structure of this Artemia population based on samples collected in 1998, 2007 and 2019. Our results revealed a steady decline of genetic diversity and significant genetic differentiation among the sampling years, which may be a consequence of genetic drift and the selection of decreased salinity. A decline of effective population size was also detected, which may be relative to the fluctuation in census population size, skewed sex ratio, and selection of the declined salinity. In 2007 and 2019, the Artemia population showed an excess of heterozygosity and significant deviation from Hardy-Weinberg Equilibrium (p < 0.001), which may be associated with the heterozygote advantage under low salinity. To comprehensively understand the impact of climate warming and wetting on Artemia populations on the plateau, further investigation with broad and intensive sampling are needed.

Genetic monitoring for effective plant conservation: An example using the threatened Saxifraga hirculus L. in Scotland

Societal Impact StatementMany mountain plants persist in small, isolated patches on the verge of extinction. Observational methods of monitoring these populations, such as recording the number of flowering stems, do not indicate the number of genetically distinct individuals, which is crucial information for conserving small populations. Here, the rate of clonal reproduction and number of genetic individuals were measured in the threatened Saxifraga hirculus in Scotland. These methods showed that population size is a poor proxy for genotype diversity and identified highly diverse small populations that may otherwise have been overlooked. This highlights the necessity of using genetic data to ensure the successful conservation of threatened plants.Summary Habitat fragmentation and loss increase the isolation of plant populations, increasing the occurrence of within population reproduction, and the potential for negative genetic effects, such as inbreeding depression and loss of genetic diversity. We use the European protected Marsh Saxifrage (Saxifraga hirculus) in Scotland as an example for declining perennial plants and the genetic resources they encapsulate. S. hirculus has declined due to agricultural intensification, drainage, industrial afforestation and grazing. The species can spread by seed or vegetatively through the production of rhizomes. Flowering is rare though due to grazing, which limits sexual reproduction and gene flow. An almost complete genetic inventory of Scottish populations was done using 11 microsatellite markers. Furthermore, archived DNA samples were used to document temporal genetic changes. We showed that clonal growth is predominant in some populations and genetic diversity (HS and allelic richness) is relatively high. However, the number of genetically distinct individuals (genets) per population is extremely low (3–34). Archived DNA samples showed that some populations consist of the same few genets with no evidence for turnover. Thus, while clonal growth may have helped the species to persist, there is limited creation of new gene combinations. Our findings highlight that reducing grazing pressure and increasing gene flow will be essential to rescue this species from its evolutionary dead end. We demonstrate the benefits of genetic monitoring for determining census population sizes and thus effective plant management and conservation. This work further sets out a strategy for moving this species towards demographic and genetic sustainability.

Using pedigree relations to inform capture‐recapture data for the estimation of census population size

AbstractSeveral methods exist to estimate the census population size such as capture‐recapture (CR) methods, which require the direct or indirect capture and recapture of numerous animals across a large area. These methods are difficult to apply to small and medium‐sized carnivorous mammals because of their elusive nature, and also do not work if the sampling method is lethal at first physical capture, a problem relevant when analyzing data from exploited populations. We present a method that uses dead recoveries from hunting bags and other sources of mortality to estimate population size. Each individual is physically trapped once at the end of its capture history (dead recovery), and is considered recaptured on previous trapping occasions if it is genetically identified as the parent of one or several young. We used this parentage information to build capture histories of aged and sexed individuals, and then applied classic CR models for closed populations. We applied this method to the stone marten (Martes foina), an elusive medium‐sized carnivorous mammal in the Bresse Region of France (911 km2) and for which reliably estimating population size remains challenging but important for efficient management. To estimate the robustness of our approach, we also simulated population pedigrees with known population size and determined its accuracy, precision, and sensitivity to the true population size and sampling intensity. Stone marten population size was estimated at = 1,748 ± 341 (SD) individuals leading to a population density of = 1.92 ± 0.37 individuals/km2, which is within the range of the few previous density estimations of the species in rural or urban areas. Our method was not affected by population size, and reached the required levels of accuracy and precision to be effective in wildlife management for a given range of sampling intensity. It therefore demonstrated its widespread use in improving estimates of population size from age‐ and sex‐structured pedigree data coming from multi‐year dead recoveries.

A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs.

Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).

Post-glacial colonization of the Fennoscandian coast by a plant parasitic insect with an unusual life history.

Species that exhibit very peculiar ecological traits combined with limited dispersal ability pose a challenge to our understanding of ecological and evolutionary mechanisms. This is especially true when they have managed to spread over long distances, overcome physical barriers, and colonize large areas. Climate and landscape changes, trophic web relations, as well as life history all interact to shape migration routes and present-day species distributions and their population genetic structures. Here we analyzed the post-glacial colonization of northern Europe by the gall midge Contarinia vincetoxici, which is a monophagous parasite on the perennial herb White swallowwort (Vincetoxicum hirundinaria). This insect not only has a narrow feeding niche but also limited dispersal ability and an exceptionally long dormancy. Gall midge larvae (n = 329) were collected from 16 sites along its distribution range in Denmark, Sweden, and Finland. Using microsatellite loci and knowledge of the species and the regions' history, we investigated the role of landscape change, host plant distribution, insect population dynamics, and life history in shaping the population genetic structure of the insect. We devoted particular interest to the role of the insect's presumed poor dispersal capacity in combination with its exceptionally extended diapause. We found significant levels of local inbreeding (95% highest posterior density interval = 0.42-0.47), low-level within-population heterozygosity (mean H E = 0.45, range 0.20-0.61) with private alleles in all populations except two. We also found significant (p < .001) regional isolation-by-distance patterns, suggesting regularly recurring mainly short-distance dispersal. According to approximate Bayesian computations, C. vincetoxici appears to have colonized the study area via wind-aided flights from remote areas approximately 4600-700 years before present when the land has gradually risen above the sea level. Extremely long dormancy periods have allowed the species to "disperse in time", thereby aiding population persistence despite generally low census population sizes.

Comparing estimates of census and effective population size in an endangered amphibian

AbstractThe field of conservation has seen a shift in focus from monitoring trends in census population size to trends in ‘effective’ population size. Numerous genetic methods exist for estimating effective population size, resulting in uncertainty among conservation practitioners as to which methods are most appropriate when conducting population assessments or evaluating recovery efforts. Demographic approaches offer a promising avenue to provide a link between census and effective population size using life‐history information, but rarely do studies have all three sources of data (genetic, demographic, life history) necessary to perform an explicit evaluation of their performance. Using data from a long‐term study of reticulated flatwoods salamanders (Ambystoma bishopi) in western Florida, USA, we assessed the magnitude of temporal variation in census population sizes and the effective number of breeders of two breeding populations to (1) document changes in the number of breeding adults over the 9‐year study duration, (2) determine whether and provide similar information about population size and trends and (3) compare alternative demographic and genetic approaches for estimating . We found that genetic estimates of , particularly if averaged across multiple estimation methods, closely tracked spatiotemporal variation in . Demographic estimates of also closely tracked but were sensitive to the assumed variance in reproductive success. In the absence of genetic information, detailed knowledge of mating systems and the environmental factors that skew reproductive contributions appear necessary for demographic to reliably inform management decisions. In these populations, appears too small (&lt;40 individuals) to confer long‐term genetic resilience, highlighting the importance of restoring landscape connectivity and indicating that caution must be taken when sourcing animals for reintroduction efforts. More generally, our study reveals insights into the utility of alternative estimation methods in guiding recovery efforts of threatened and endangered species.

Novel insights into the reproductive strategies of wild Chinese sturgeon (Acipenser sinensis) populations based on the kinship analysis

Understanding the reproductive strategy of an organism is important in conservation ecology as it directly affects the population performance under changing environmental conditions. Chinese sturgeon (Acipenser sinensis) are the largest anadromous fish in the Yangtze River, China. Currently, the species has only one spawning ground and has failed to spawn in recent years, leading it to the brink of extinction. To develop effective conservation measures, a further understanding of its reproductive strategy is needed. In our study, we conducted kinship analyses by using mitochondrial and microsatellite DNA data from 216 wild juveniles collected over nine years (2006−2013, 2015) to understand the mating system, breeding interval, effective number of breeding adults, and reproductive success. The results from these analyses suggested polygynandry, with some parents contributing up to eight half-sibling juvenile genotypes. Although the spawning ground was restricted to a limited area, genetic diversity was maintained at a relatively high level (observed heterozygosity from 0.698 to 0.787 and expected heterozygosity from 0.763 to 0.787) and inbreeding coefficients in each year-class ranged from −1% to 9% (low to modest detrimental effects on offspring). A parental inference analysis revealed that Chinese sturgeon have a breeding interval of 2–6 years, indicating that it has the potential to feed, accumulate nutrition in the ocean, and then migrate back to the Yangtze River for iteroparous reproduction. The annual effective number of breeders in the Yangtze River ranged from 14 to 161 during the study period, and it decreased by 62.1% from the 2011−2014 year-classes. This sharp population decline likely contributes to the reproduction failure. However, the ratios of effective to census population size (Ne/Nc) were all larger than 0.20 after the 2010 year-class, indicating relatively even reproductive success. Based on these results, a suggested approach to protect this species is to restock parent fish to increase the reproductive stock size and optimize the discharge of the Three Gorges Dam to reduce the unsuitable hydrological conditions and rehabilitate spawning ground habitats.

Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid.

Ethiopian wolves, a canid species endemic to the Ethiopian Highlands, have been steadily declining in numbers for decades. Currently, out of 35 extant species, it is now one of the world's most endangered canids. Most conservation efforts have focused on preventing disease, monitoring movements and behavior, and assessing the geographic ranges of sub-populations. Here, we add an essential layer by determining the Ethiopian wolf's demographic and evolutionary history using high-coverage (∼40×) whole-genome sequencing from 10 Ethiopian wolves from the Bale Mountains. We observe exceptionally low diversity and enrichment of weakly deleterious variants in the Ethiopian wolves in comparison with two North American gray wolf populations and four dog breeds. These patterns are consequences of long-term small population size, rather than recent inbreeding. We infer the demographic history of the Ethiopian wolf and find it to be concordant with historic records and previous genetic analyses, suggesting Ethiopian wolves experienced a series of both ancient and recent bottlenecks, resulting in a census population size of fewer than 500 individuals and an estimated effective population size of approximately 100 individuals. Additionally, long-term small population size may have limited the accumulation of strongly deleterious recessive mutations. Finally, as the Ethiopian wolves have inhabited high-altitude areas for thousands of years, we searched for evidence of high-altitude adaptation, finding evidence of positive selection at a transcription factor in a hypoxia-response pathway [CREB-binding protein (CREBBP)]. Our findings are pertinent to continuing conservation efforts and understanding how demography influences the persistence of deleterious variation in small populations.

Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes.

Close-kin mark-recapture (CKMR) methods have recently been used to infer demographic parameters such as census population size and survival for fish of interest to fisheries and conservation. These methods have advantages over traditional mark-recapture methods as the mark is genetic, removing the need for physical marking and recapturing that may interfere with parameter estimation. For mosquitoes, the spatial distribution of close-kin pairs has been used to estimate mean dispersal distance, of relevance to vector-borne disease transmission and novel biocontrol strategies. Here, we extend CKMR methods to the life history of mosquitoes and comparable insects. We derive kinship probabilities for mother-offspring, father-offspring, full-sibling and half-sibling pairs, where an individual in each pair may be a larva, pupa or adult. A pseudo-likelihood approach is used to combine the marginal probabilities of all kinship pairs. To test the effectiveness of this approach at estimating mosquito demographic parameters, we develop an individual-based model of mosquito life history incorporating egg, larva, pupa and adult life stages. The simulation labels each individual with a unique identification number, enabling close-kin relationships to be inferred for sampled individuals. Using the dengue vector Aedes aegypti as a case study, we find the CKMR approach provides unbiased estimates of adult census population size, adult and larval mortality rates, and larval life stage duration for logistically feasible sampling schemes. Considering a simulated population of 3,000 adult mosquitoes, estimation of adult parameters is accurate when ca. 40 adult females are sampled biweekly over a three month period. Estimation of larval parameters is accurate when adult sampling is supplemented with ca. 120 larvae sampled biweekly over the same period. The methods are also effective at detecting intervention-induced increases in adult mortality and decreases in population size. As the cost of genome sequencing declines, CKMR holds great promise for characterizing the demography of mosquitoes and comparable insects of epidemiological and agricultural significance.

Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples.

Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.